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Sample records for accurate genetic information

  1. Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX

    PubMed Central

    Brotherton, Paul; Sanchez, Juan J.; Cooper, Alan; Endicott, Phillip

    2010-01-01

    The analysis of targeted genetic loci from ancient, forensic and clinical samples is usually built upon polymerase chain reaction (PCR)-generated sequence data. However, many studies have shown that PCR amplification from poor-quality DNA templates can create sequence artefacts at significant levels. With hominin (human and other hominid) samples, the pervasive presence of highly PCR-amplifiable human DNA contaminants in the vast majority of samples can lead to the creation of recombinant hybrids and other non-authentic artefacts. The resulting PCR-generated sequences can then be difficult, if not impossible, to authenticate. In contrast, single primer extension (SPEX)-based approaches can genotype single nucleotide polymorphisms from ancient fragments of DNA as accurately as modern DNA. A single SPEX-type assay can amplify just one of the duplex DNA strands at target loci and generate a multi-fold depth-of-coverage, with non-authentic recombinant hybrids reduced to undetectable levels. Crucially, SPEX-type approaches can preferentially access genetic information from damaged and degraded endogenous ancient DNA templates over modern human DNA contaminants. The development of SPEX-type assays offers the potential for highly accurate, quantitative genotyping from ancient hominin samples. PMID:19864251

  2. Polyallelic structural variants can provide accurate, highly informative genetic markers focused on diagnosis and therapeutic targets: Accuracy vs. Precision.

    PubMed

    Roses, A D

    2016-02-01

    Structural variants (SVs) include all insertions, deletions, and rearrangements in the genome, with several common types of nucleotide repeats including single sequence repeats, short tandem repeats, and insertion-deletion length variants. Polyallelic SVs provide highly informative markers for association studies with well-phenotyped cohorts. SVs can influence gene regulation by affecting epigenetics, transcription, splicing, and/or translation. Accurate assays of polyallelic SV loci are required to define the range and allele frequency of variable length alleles. PMID:26517180

  3. Approaching system equilibrium with accurate or not accurate feedback information in a two-route system

    NASA Astrophysics Data System (ADS)

    Zhao, Xiao-mei; Xie, Dong-fan; Li, Qi

    2015-02-01

    With the development of intelligent transport system, advanced information feedback strategies have been developed to reduce traffic congestion and enhance the capacity. However, previous strategies provide accurate information to travelers and our simulation results show that accurate information brings negative effects, especially in delay case. Because travelers prefer to the best condition route with accurate information, and delayed information cannot reflect current traffic condition but past. Then travelers make wrong routing decisions, causing the decrease of the capacity and the increase of oscillations and the system deviating from the equilibrium. To avoid the negative effect, bounded rationality is taken into account by introducing a boundedly rational threshold BR. When difference between two routes is less than the BR, routes have equal probability to be chosen. The bounded rationality is helpful to improve the efficiency in terms of capacity, oscillation and the gap deviating from the system equilibrium.

  4. 78 FR 34604 - Submitting Complete and Accurate Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-10

    ... COMMISSION 10 CFR Part 50 Submitting Complete and Accurate Information AGENCY: Nuclear Regulatory Commission... accurate information as would a licensee or an applicant for a license.'' DATES: Submit comments by August... may submit comments by any of the following methods (unless this document describes a different...

  5. Accurate measurements of dynamics and reproducibility in small genetic networks

    PubMed Central

    Dubuis, Julien O; Samanta, Reba; Gregor, Thomas

    2013-01-01

    Quantification of gene expression has become a central tool for understanding genetic networks. In many systems, the only viable way to measure protein levels is by immunofluorescence, which is notorious for its limited accuracy. Using the early Drosophila embryo as an example, we show that careful identification and control of experimental error allows for highly accurate gene expression measurements. We generated antibodies in different host species, allowing for simultaneous staining of four Drosophila gap genes in individual embryos. Careful error analysis of hundreds of expression profiles reveals that less than ∼20% of the observed embryo-to-embryo fluctuations stem from experimental error. These measurements make it possible to extract not only very accurate mean gene expression profiles but also their naturally occurring fluctuations of biological origin and corresponding cross-correlations. We use this analysis to extract gap gene profile dynamics with ∼1 min accuracy. The combination of these new measurements and analysis techniques reveals a twofold increase in profile reproducibility owing to a collective network dynamics that relays positional accuracy from the maternal gradients to the pair-rule genes. PMID:23340845

  6. Legal aspects of genetic information.

    PubMed Central

    Andrews, L. B.

    1991-01-01

    The federally funded Human Genome Initiative will lead to the development of new capabilities to learn about an individual's genetic status. Legal issues are raised concerning patients' and other parties' access to that information. This article discusses the effect of existing statutes and case law on three pivotal questions: To what sort of information are people entitled? What control should people have over their genetic information? Do people have a right to refuse genetic information? The article emphasizes that the law protects a patient's right to obtain or refuse genetic information about oneself, as well as the right to control the dissemination of that information to others. PMID:1897258

  7. Legal aspects of genetic information.

    PubMed

    Andrews, L B

    1991-01-01

    The federally funded Human Genome Initiative will lead to the development of new capabilities to learn about an individual's genetic status. Legal issues are raised concerning patients' and other parties' access to that information. This article discusses the effect of existing statutes and case law on three pivotal questions: To what sort of information are people entitled? What control should people have over their genetic information? Do people have a right to refuse genetic information? The article emphasizes that the law protects a patient's right to obtain or refuse genetic information about oneself, as well as the right to control the dissemination of that information to others.

  8. [Protective management for genetic information].

    PubMed

    Niikawa, Norio

    2005-03-01

    With advances in genomic and genetic medicine, genomic information is being used for the management of disorders. In addition, personalized medicine will be in practice in the near future. Because genetic information, i.e., disease diagnosis, gene mutations, and/or nucleotide sequences, remains unchanged through an individual's life, there are important issues for discussion, such as informed consent at sampling, protection of an individual's genetic information from any social discrimination, handling of samples, and genetic counseling. In this review, how to protect and manage the genetic information at researching and at medical practice, together with several bioethical guidelines regarding such issues, are described. A triangle system in which sample donators, directing physicians/researchers and genetic counselors participate, to manage genetic information appropriately, is also proposed.

  9. Property rights in genetic information.

    PubMed

    Spinello, Richard A

    2004-01-01

    The primary theme of this paper is the normative case against ownership of one's genetic information along with the source of that information (usually human tissues samples). The argument presented here against such "upstream" property rights is based primarily on utilitarian grounds. This issue has new salience thanks to the Human Genome Project and "bio-prospecting" initiatives based on the aggregation of genetic information, such as the one being managed by deCODE Genetics in Iceland. The rationale for ownership is twofold: ownership will protect the basic human rights of privacy and autonomy and it will enable the data subjects to share in the tangible benefits of the genetic research. Proponents of this viewpoint often cite the principle of genetic exceptionalism, which asserts that genetic information needs a higher level of protection than other kinds of personal information such as financial data. We argue, however, that the recognition of such ownership rights would lead to inefficiency along with the disutility of genetic discoveries. Biomedical research will be hampered if property rights in genes and genetic material are too extensive. We contend that other mechanisms such as informed consent and strict confidentiality rules can accomplish the same result as a property right without the liabilities of an exclusive entitlement. PMID:16969959

  10. On the accurate construction of consensus genetic maps.

    PubMed

    Wu, Yonghui; Close, Timothy J; Lonardi, Stefano

    2008-01-01

    We study the problem of merging genetic maps, when the individual genetic maps are given as directed acyclic graphs. The problem is to build a consensus map, which includes and is consistent with all (or, the vast majority of) the markers in the individual maps. When markers in the input maps have ordering conflicts, the resulting consensus map will contain cycles. We formulate the problem of resolving cycles in a combinatorial optimization framework, which in turn is expressed as an integer linear program. A faster approximation algorithm is proposed, and an additional speed-up heuristic is developed. According to an extensive set of experimental results, our tool is consistently better than JOINMAP, both in terms of accuracy and running time. PMID:19642288

  11. Accurate construction of consensus genetic maps via integer linear programming.

    PubMed

    Wu, Yonghui; Close, Timothy J; Lonardi, Stefano

    2011-01-01

    We study the problem of merging genetic maps, when the individual genetic maps are given as directed acyclic graphs. The computational problem is to build a consensus map, which is a directed graph that includes and is consistent with all (or, the vast majority of) the markers in the input maps. However, when markers in the individual maps have ordering conflicts, the resulting consensus map will contain cycles. Here, we formulate the problem of resolving cycles in the context of a parsimonious paradigm that takes into account two types of errors that may be present in the input maps, namely, local reshuffles and global displacements. The resulting combinatorial optimization problem is, in turn, expressed as an integer linear program. A fast approximation algorithm is proposed, and an additional speedup heuristic is developed. Our algorithms were implemented in a software tool named MERGEMAP which is freely available for academic use. An extensive set of experiments shows that MERGEMAP consistently outperforms JOINMAP, which is the most popular tool currently available for this task, both in terms of accuracy and running time. MERGEMAP is available for download at http://www.cs.ucr.edu/~yonghui/mgmap.html. PMID:20479505

  12. Accurate construction of consensus genetic maps via integer linear programming.

    PubMed

    Wu, Yonghui; Close, Timothy J; Lonardi, Stefano

    2011-01-01

    We study the problem of merging genetic maps, when the individual genetic maps are given as directed acyclic graphs. The computational problem is to build a consensus map, which is a directed graph that includes and is consistent with all (or, the vast majority of) the markers in the input maps. However, when markers in the individual maps have ordering conflicts, the resulting consensus map will contain cycles. Here, we formulate the problem of resolving cycles in the context of a parsimonious paradigm that takes into account two types of errors that may be present in the input maps, namely, local reshuffles and global displacements. The resulting combinatorial optimization problem is, in turn, expressed as an integer linear program. A fast approximation algorithm is proposed, and an additional speedup heuristic is developed. Our algorithms were implemented in a software tool named MERGEMAP which is freely available for academic use. An extensive set of experiments shows that MERGEMAP consistently outperforms JOINMAP, which is the most popular tool currently available for this task, both in terms of accuracy and running time. MERGEMAP is available for download at http://www.cs.ucr.edu/~yonghui/mgmap.html.

  13. Ultra-accurate collaborative information filtering via directed user similarity

    NASA Astrophysics Data System (ADS)

    Guo, Q.; Song, W.-J.; Liu, J.-G.

    2014-07-01

    A key challenge of the collaborative filtering (CF) information filtering is how to obtain the reliable and accurate results with the help of peers' recommendation. Since the similarities from small-degree users to large-degree users would be larger than the ones in opposite direction, the large-degree users' selections are recommended extensively by the traditional second-order CF algorithms. By considering the users' similarity direction and the second-order correlations to depress the influence of mainstream preferences, we present the directed second-order CF (HDCF) algorithm specifically to address the challenge of accuracy and diversity of the CF algorithm. The numerical results for two benchmark data sets, MovieLens and Netflix, show that the accuracy of the new algorithm outperforms the state-of-the-art CF algorithms. Comparing with the CF algorithm based on random walks proposed by Liu et al. (Int. J. Mod. Phys. C, 20 (2009) 285) the average ranking score could reach 0.0767 and 0.0402, which is enhanced by 27.3% and 19.1% for MovieLens and Netflix, respectively. In addition, the diversity, precision and recall are also enhanced greatly. Without relying on any context-specific information, tuning the similarity direction of CF algorithms could obtain accurate and diverse recommendations. This work suggests that the user similarity direction is an important factor to improve the personalized recommendation performance.

  14. Genetic Information, Non-Discrimination, and Privacy Protections in Genetic Counseling Practice

    PubMed Central

    Prince, Anya E.R.; Roche, Myra I.

    2014-01-01

    The passage of the Genetic Information Non Discrimination Act (GINA) was hailed as a pivotal achievement that was expected to calm the fears of both patients and research participants about the potential misuse of genetic information. However, six years later, patient and provider awareness of legal protections at both the federal and state level remains discouragingly low, thereby, limiting their potential effectiveness. The increasing demand for genetic testing will expand the number of individuals and families who could benefit from obtaining accurate information about the privacy and anti-discriminatory protections that GINA and other laws extend. In this paper we describe legal protections that are applicable to individuals seeking genetic counseling, review the literature on patient and provider fears of genetic discrimination and examine their awareness and understandings of existing laws, and summarize how genetic counselors currently discuss genetic discrimination. We then present three genetic counseling cases to illustrate issues of genetic discrimination and provide relevant information on applicable legal protections. Genetic counselors have an unprecedented opportunity, as well as the professional responsibility, to disseminate accurate knowledge about existing legal protections to their patients. They can strengthen their effectiveness in this role by achieving a greater knowledge of current protections including being able to identify specific steps that can help protect genetic information. PMID:25063358

  15. Genetic information, non-discrimination, and privacy protections in genetic counseling practice.

    PubMed

    Prince, Anya E R; Roche, Myra I

    2014-12-01

    The passage of the Genetic Information Non Discrimination Act (GINA) was hailed as a pivotal achievement that was expected to calm the fears of both patients and research participants about the potential misuse of genetic information. However, 6 years later, patient and provider awareness of legal protections at both the federal and state level remains discouragingly low, thereby, limiting their potential effectiveness. The increasing demand for genetic testing will expand the number of individuals and families who could benefit from obtaining accurate information about the privacy and anti-discriminatory protections that GINA and other laws extend. In this paper we describe legal protections that are applicable to individuals seeking genetic counseling, review the literature on patient and provider fears of genetic discrimination and examine their awareness and understandings of existing laws, and summarize how genetic counselors currently discuss genetic discrimination. We then present three genetic counseling cases to illustrate issues of genetic discrimination and provide relevant information on applicable legal protections. Genetic counselors have an unprecedented opportunity, as well as the professional responsibility, to disseminate accurate knowledge about existing legal protections to their patients. They can strengthen their effectiveness in this role by achieving a greater knowledge of current protections including being able to identify specific steps that can help protect genetic information.

  16. Accessing Genetic Information with Liquid Biopsies.

    PubMed

    Cai, Xuyu; Janku, Filip; Zhan, Qimin; Fan, Jian-Bing

    2015-10-01

    Recent scientific advances in understanding circulating tumor cells, cell-free DNA/RNA, and exosomes in blood have laid a solid foundation for the development of routine molecular 'liquid biopsies'. This approach provides non-invasive access to genetic information--somatic mutations, epigenetic changes, and differential expression--about the physiological conditions of our body and diseases. It opens a valuable avenue for future genetic studies and human disease diagnosis, including prenatal and neurodegenerative disease diagnosis, as well as for cancer screening and monitoring. With the rapid development of highly sensitive and accurate technologies such as next-generation sequencing, molecular 'liquid biopsies' will quickly become a central piece in the future of precision medicine.

  17. Introducing Students to the Genetic Information Age.

    ERIC Educational Resources Information Center

    Trumbo, Steve

    2000-01-01

    Provides opinions on interpreting reports on genetic influences on human behavior, which sometimes attribute genetic versus environmental effects with decimal precision. Discusses the need for scientific information and objectivity. (SAH)

  18. Information theory and the ethylene genetic network

    PubMed Central

    González-García, José S

    2011-01-01

    The original aim of the Information Theory (IT) was to solve a purely technical problem: to increase the performance of communication systems, which are constantly affected by interferences that diminish the quality of the transmitted information. That is, the theory deals only with the problem of transmitting with the maximal precision the symbols constituting a message. In Shannon's theory messages are characterized only by their probabilities, regardless of their value or meaning. As for its present day status, it is generally acknowledged that Information Theory has solid mathematical foundations and has fruitful strong links with Physics in both theoretical and experimental areas. However, many applications of Information Theory to Biology are limited to using it as a technical tool to analyze biopolymers, such as DNA, RNA or protein sequences. The main point of discussion about the applicability of IT to explain the information flow in biological systems is that in a classic communication channel, the symbols that conform the coded message are transmitted one by one in an independent form through a noisy communication channel, and noise can alter each of the symbols, distorting the message; in contrast, in a genetic communication channel the coded messages are not transmitted in the form of symbols but signaling cascades transmit them. Consequently, the information flow from the emitter to the effector is due to a series of coupled physicochemical processes that must ensure the accurate transmission of the message. In this review we discussed a novel proposal to overcome this difficulty, which consists of the modeling of gene expression with a stochastic approach that allows Shannon entropy (H) to be directly used to measure the amount of uncertainty that the genetic machinery has in relation to the correct decoding of a message transmitted into the nucleus by a signaling pathway. From the value of H we can define a function I that measures the amount of

  19. Information theory and the ethylene genetic network.

    PubMed

    González-García, José S; Díaz, José

    2011-10-01

    The original aim of the Information Theory (IT) was to solve a purely technical problem: to increase the performance of communication systems, which are constantly affected by interferences that diminish the quality of the transmitted information. That is, the theory deals only with the problem of transmitting with the maximal precision the symbols constituting a message. In Shannon's theory messages are characterized only by their probabilities, regardless of their value or meaning. As for its present day status, it is generally acknowledged that Information Theory has solid mathematical foundations and has fruitful strong links with Physics in both theoretical and experimental areas. However, many applications of Information Theory to Biology are limited to using it as a technical tool to analyze biopolymers, such as DNA, RNA or protein sequences. The main point of discussion about the applicability of IT to explain the information flow in biological systems is that in a classic communication channel, the symbols that conform the coded message are transmitted one by one in an independent form through a noisy communication channel, and noise can alter each of the symbols, distorting the message; in contrast, in a genetic communication channel the coded messages are not transmitted in the form of symbols but signaling cascades transmit them. Consequently, the information flow from the emitter to the effector is due to a series of coupled physicochemical processes that must ensure the accurate transmission of the message. In this review we discussed a novel proposal to overcome this difficulty, which consists of the modeling of gene expression with a stochastic approach that allows Shannon entropy (H) to be directly used to measure the amount of uncertainty that the genetic machinery has in relation to the correct decoding of a message transmitted into the nucleus by a signaling pathway. From the value of H we can define a function I that measures the amount of

  20. Information theory and the ethylene genetic network.

    PubMed

    González-García, José S; Díaz, José

    2011-10-01

    The original aim of the Information Theory (IT) was to solve a purely technical problem: to increase the performance of communication systems, which are constantly affected by interferences that diminish the quality of the transmitted information. That is, the theory deals only with the problem of transmitting with the maximal precision the symbols constituting a message. In Shannon's theory messages are characterized only by their probabilities, regardless of their value or meaning. As for its present day status, it is generally acknowledged that Information Theory has solid mathematical foundations and has fruitful strong links with Physics in both theoretical and experimental areas. However, many applications of Information Theory to Biology are limited to using it as a technical tool to analyze biopolymers, such as DNA, RNA or protein sequences. The main point of discussion about the applicability of IT to explain the information flow in biological systems is that in a classic communication channel, the symbols that conform the coded message are transmitted one by one in an independent form through a noisy communication channel, and noise can alter each of the symbols, distorting the message; in contrast, in a genetic communication channel the coded messages are not transmitted in the form of symbols but signaling cascades transmit them. Consequently, the information flow from the emitter to the effector is due to a series of coupled physicochemical processes that must ensure the accurate transmission of the message. In this review we discussed a novel proposal to overcome this difficulty, which consists of the modeling of gene expression with a stochastic approach that allows Shannon entropy (H) to be directly used to measure the amount of uncertainty that the genetic machinery has in relation to the correct decoding of a message transmitted into the nucleus by a signaling pathway. From the value of H we can define a function I that measures the amount of

  1. Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph

    PubMed Central

    Wu, Yonghui; Bhat, Prasanna R.; Close, Timothy J.; Lonardi, Stefano

    2008-01-01

    Genetic linkage maps are cornerstones of a wide spectrum of biotechnology applications, including map-assisted breeding, association genetics, and map-assisted gene cloning. During the past several years, the adoption of high-throughput genotyping technologies has been paralleled by a substantial increase in the density and diversity of genetic markers. New genetic mapping algorithms are needed in order to efficiently process these large datasets and accurately construct high-density genetic maps. In this paper, we introduce a novel algorithm to order markers on a genetic linkage map. Our method is based on a simple yet fundamental mathematical property that we prove under rather general assumptions. The validity of this property allows one to determine efficiently the correct order of markers by computing the minimum spanning tree of an associated graph. Our empirical studies obtained on genotyping data for three mapping populations of barley (Hordeum vulgare), as well as extensive simulations on synthetic data, show that our algorithm consistently outperforms the best available methods in the literature, particularly when the input data are noisy or incomplete. The software implementing our algorithm is available in the public domain as a web tool under the name MSTmap. PMID:18846212

  2. Automatic and Accurate Shadow Detection Using Near-Infrared Information.

    PubMed

    Rüfenacht, Dominic; Fredembach, Clément; Süsstrunk, Sabine

    2014-08-01

    We present a method to automatically detect shadows in a fast and accurate manner by taking advantage of the inherent sensitivity of digital camera sensors to the near-infrared (NIR) part of the spectrum. Dark objects, which confound many shadow detection algorithms, often have much higher reflectance in the NIR. We can thus build an accurate shadow candidate map based on image pixels that are dark both in the visible and NIR representations. We further refine the shadow map by incorporating ratios of the visible to the NIR image, based on the observation that commonly encountered light sources have very distinct spectra in the NIR band. The results are validated on a new database, which contains visible/NIR images for a large variety of real-world shadow creating illuminant conditions, as well as manually labeled shadow ground truth. Both quantitative and qualitative evaluations show that our method outperforms current state-of-the-art shadow detection algorithms in terms of accuracy and computational efficiency.

  3. [Genetic information and future medicine].

    PubMed

    Sakurai, Akihiro

    2012-11-01

    Rapid technological advances in genetic analysis have revealed the genetic background of various diseases. Elucidation of the genes responsible for a disease enables better clinical management of the disease and helps to develop targeted drugs. Also, early diagnosis and management of at-risk family members can be made by identification of a genetic disease in the proband. On the other hand, genetic issues often cause psychological distress to the family. To perform genetic testing appropriately and to protect patients and family members from any harm, guidelines for genetic testing were released from the alliance of Japanese genetics-related academic societies in 2003. As genetic testing is becoming incorporated into clinical practice more broadly, the guideline was revised and released by the Japanese Society of Medical Sciences in 2011. All medical professionals in Japan are expected to follow this guideline.

  4. A new accurate pill recognition system using imprint information

    NASA Astrophysics Data System (ADS)

    Chen, Zhiyuan; Kamata, Sei-ichiro

    2013-12-01

    Great achievements in modern medicine benefit human beings. Also, it has brought about an explosive growth of pharmaceuticals that current in the market. In daily life, pharmaceuticals sometimes confuse people when they are found unlabeled. In this paper, we propose an automatic pill recognition technique to solve this problem. It functions mainly based on the imprint feature of the pills, which is extracted by proposed MSWT (modified stroke width transform) and described by WSC (weighted shape context). Experiments show that our proposed pill recognition method can reach an accurate rate up to 92.03% within top 5 ranks when trying to classify more than 10 thousand query pill images into around 2000 categories.

  5. 16 CFR 1101.32 - Reasonable steps to assure information is accurate.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Reasonable steps to assure information is... Reasonable Steps Commission Will Take To Assure Information It Discloses Is Accurate, and That Disclosure Is... Administers § 1101.32 Reasonable steps to assure information is accurate. (a) The Commission considers...

  6. 16 CFR 1101.32 - Reasonable steps to assure information is accurate.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Reasonable steps to assure information is... Reasonable Steps Commission Will Take To Assure Information It Discloses Is Accurate, and That Disclosure Is... Administers § 1101.32 Reasonable steps to assure information is accurate. (a) The Commission considers...

  7. Genetic information and insurance: some ethical issues.

    PubMed

    O'Neill, O

    1997-08-29

    Life is risky, and insurance provides one of the best developed ways of controlling risks. By pooling, and so transferring risks, those who turn out to suffer antecedently uncertain harms can be assured in advance that they will be helped if those harms arise; they can then plan their lives and activities with confidence that they are less at the mercy of ill fortune. Both publicly organized and commercial insurance can organize the pooling of risk in ways that are beneficial for all concerned. They provide standard ways of securing fundamental ethical values such as solidarity and mutuality. Although policy holders do not know or contract with one another, each benefits from the contribution of others to a shared scheme for pooling and so controlling risk. Although there is a limit to the degree to which commercially-based insurance, where premiums depend on risk level, can go beyond mutuality towards solidarity, in practice it too often achieves a measure of solidarity by taking a broad brush approach to pooling risk. However, the ordinary practices of insurance, and in particular of commercial insurance, also raise ethical questions. These may be put in simple terms by contrasting the way in which an insurance market discriminates between different people, on the basis of characteristics that (supposedly) determine their risk level, and our frequent abhorrence of discrimination, in particular on the basis on religious, racial and gender characteristics. Are the discriminations on which insurance practice relies upon as standard acceptable or not? The increasing availability of genetic information, which testing (of individuals) and screening (of populations) may provide, could lend urgency to these questions. Genetic information may provide a way of obtaining more accurate assessment of individual risks to health and life. This information could be used to discriminate more finely between the risk levels of different individuals, and then to alter the

  8. Accurate genetic switch in Escherichia coli: novel mechanism of regulation by co-repressor.

    PubMed

    Tabaka, Marcin; Cybulski, Olgierd; Hołyst, Robert

    2008-04-01

    Understanding a biological module involves recognition of its structure and the dynamics of its principal components. In this report we present an analysis of the dynamics of the repression module within the regulation of the trp operon in Escherichia coli. We combine biochemical data for reaction rate constants for the trp repressor binding to trp operator and in vivo data of a number of tryptophan repressors (TrpRs) that bind to the operator. The model of repression presented in this report greatly differs from previous mathematical models. One, two or three TrpRs can bind to the operator and repress the transcription. Moreover, reaction rates for detachment of TrpRs from the operator strongly depend on tryptophan (Trp) concentration, since Trp can also bind to the repressor-operator complex and stabilize it. From the mathematical modeling and analysis of reaction rates and equilibrium constants emerges a high-quality, accurate and effective module of trp repression. This genetic switch responds accurately to fast consumption of Trp from the interior of a cell. It switches with minimal dispersion when the concentration of Trp drops below a thousand molecules per cell. PMID:18313075

  9. Genetic Counselling: Information Given, Recall and Satisfaction.

    ERIC Educational Resources Information Center

    Michie, Susan; McDonald, Valerie; Marteau, Theresa M.

    1997-01-01

    A questionnaire was sent to counselors (N=32) to categorize the key points given in genetic counseling; to assess the amount and type of information recalled; and to examine the relationships between counselees' knowledge, satisfaction with information received, the meeting of expectations, concern, and anxiety. Results emphasize the importance of…

  10. Accurate and interpretable nanoSAR models from genetic programming-based decision tree construction approaches.

    PubMed

    Oksel, Ceyda; Winkler, David A; Ma, Cai Y; Wilkins, Terry; Wang, Xue Z

    2016-09-01

    The number of engineered nanomaterials (ENMs) being exploited commercially is growing rapidly, due to the novel properties they exhibit. Clearly, it is important to understand and minimize any risks to health or the environment posed by the presence of ENMs. Data-driven models that decode the relationships between the biological activities of ENMs and their physicochemical characteristics provide an attractive means of maximizing the value of scarce and expensive experimental data. Although such structure-activity relationship (SAR) methods have become very useful tools for modelling nanotoxicity endpoints (nanoSAR), they have limited robustness and predictivity and, most importantly, interpretation of the models they generate is often very difficult. New computational modelling tools or new ways of using existing tools are required to model the relatively sparse and sometimes lower quality data on the biological effects of ENMs. The most commonly used SAR modelling methods work best with large datasets, are not particularly good at feature selection, can be relatively opaque to interpretation, and may not account for nonlinearity in the structure-property relationships. To overcome these limitations, we describe the application of a novel algorithm, a genetic programming-based decision tree construction tool (GPTree) to nanoSAR modelling. We demonstrate the use of GPTree in the construction of accurate and interpretable nanoSAR models by applying it to four diverse literature datasets. We describe the algorithm and compare model results across the four studies. We show that GPTree generates models with accuracies equivalent to or superior to those of prior modelling studies on the same datasets. GPTree is a robust, automatic method for generation of accurate nanoSAR models with important advantages that it works with small datasets, automatically selects descriptors, and provides significantly improved interpretability of models.

  11. A simplified and accurate detection of the genetically modified wheat MON71800 with one calibrator plasmid.

    PubMed

    Kim, Jae-Hwan; Park, Saet-Byul; Roh, Hyo-Jeong; Park, Sunghoon; Shin, Min-Ki; Moon, Gui Im; Hong, Jin-Hwan; Kim, Hae-Yeong

    2015-06-01

    With the increasing number of genetically modified (GM) events, unauthorized GMO releases into the food market have increased dramatically, and many countries have developed detection tools for them. This study described the qualitative and quantitative detection methods of unauthorized the GM wheat MON71800 with a reference plasmid (pGEM-M71800). The wheat acetyl-CoA carboxylase (acc) gene was used as the endogenous gene. The plasmid pGEM-M71800, which contains both the acc gene and the event-specific target MON71800, was constructed as a positive control for the qualitative and quantitative analyses. The limit of detection in the qualitative PCR assay was approximately 10 copies. In the quantitative PCR assay, the standard deviation and relative standard deviation repeatability values ranged from 0.06 to 0.25 and from 0.23% to 1.12%, respectively. This study supplies a powerful and very simple but accurate detection strategy for unauthorized GM wheat MON71800 that utilizes a single calibrator plasmid.

  12. Human genetics information on the Web.

    PubMed

    Abu-Amero, Khaled

    2003-06-01

    The genetics revolution is in full swing, especially following the recent release of the complete human genome sequence which will change forever the world in which we live by providing potential for new drugs and therapies and the means of preventing inherited genetic diseases. As a result of establishing the whole human genome sequence and the associated media publicity, the general public have become familiar with and more eager to learn about the subject of genetics and its potential impact on both their own lives and those of their families. One of the main sources of information available to the public today is the World Wide Web. Vast amounts of information are contained in the numerous websites available through the Internet. However, finding the right information can be very tedious, especially with the huge number of websites currently available. This article guides the public to key websites and webpages that cover information on genetics. All sites listed here have been tested and proven to be beneficial and informative. PMID:12852194

  13. Accurate crop classification using hierarchical genetic fuzzy rule-based systems

    NASA Astrophysics Data System (ADS)

    Topaloglou, Charalampos A.; Mylonas, Stelios K.; Stavrakoudis, Dimitris G.; Mastorocostas, Paris A.; Theocharis, John B.

    2014-10-01

    This paper investigates the effectiveness of an advanced classification system for accurate crop classification using very high resolution (VHR) satellite imagery. Specifically, a recently proposed genetic fuzzy rule-based classification system (GFRBCS) is employed, namely, the Hierarchical Rule-based Linguistic Classifier (HiRLiC). HiRLiC's model comprises a small set of simple IF-THEN fuzzy rules, easily interpretable by humans. One of its most important attributes is that its learning algorithm requires minimum user interaction, since the most important learning parameters affecting the classification accuracy are determined by the learning algorithm automatically. HiRLiC is applied in a challenging crop classification task, using a SPOT5 satellite image over an intensively cultivated area in a lake-wetland ecosystem in northern Greece. A rich set of higher-order spectral and textural features is derived from the initial bands of the (pan-sharpened) image, resulting in an input space comprising 119 features. The experimental analysis proves that HiRLiC compares favorably to other interpretable classifiers of the literature, both in terms of structural complexity and classification accuracy. Its testing accuracy was very close to that obtained by complex state-of-the-art classification systems, such as the support vector machines (SVM) and random forest (RF) classifiers. Nevertheless, visual inspection of the derived classification maps shows that HiRLiC is characterized by higher generalization properties, providing more homogeneous classifications that the competitors. Moreover, the runtime requirements for producing the thematic map was orders of magnitude lower than the respective for the competitors.

  14. Measuring informed choice in population-based reproductive genetic screening: a systematic review

    PubMed Central

    Ames, Alice Grace; Metcalfe, Sylvia Ann; Archibald, Alison Dalton; Duncan, Rony Emily; Emery, Jon

    2015-01-01

    Genetic screening and health-care guidelines recommend that programmes should facilitate informed choice. It is therefore important that accurate measures of informed choice are available to evaluate such programmes. This review synthesises and appraises measures used to evaluate informed choice in population-based genetic screening programmes for reproductive risk. Databases were searched for studies offering genetic screening for the purpose of establishing reproductive risk to an adult population sample, in which aspects of informed choice were measured. Studies were included if, at a minimum, measures of uptake of screening and knowledge were used. Searches identified 1462 citations and 76 studies were reviewed in full text; 34 studies met the inclusion criteria. Over 20 different measures of informed choice were used. Many measures lacked adequate validity and reliability data. This systematic review will inform future evaluation of informed choice in population genetic screening programmes. PMID:24848746

  15. Genetic Information Nondiscrimination Act. Final rule.

    PubMed

    2016-05-17

    The Equal Employment Opportunity Commission (EEOC or Commission) is issuing a final rule to amend the regulations implementing Title II of the Genetic Information Nondiscrimination Act of 2008 as they relate to employer-sponsored wellness programs. This rule addresses the extent to which an employer may offer an inducement to an employee for the employee's spouse to provide information about the spouse's manifestation of disease or disorder as part of a health risk assessment (HRA) administered in connection with an employer-sponsored wellness program. Several technical changes to the existing regulations are included. Published elsewhere in this issue of the Federal Register, the EEOC also issued a final rule to amend the regulations and interpretive guidance implementing Title I of the Americans with Disabilities Act (ADA) that addresses the extent to which employers may use incentives to encourage employees to participate in wellness programs that ask them to respond to disability-related inquiries and/or undergo medical examinations.

  16. Genetic information and life insurance: a 'real' risk?

    PubMed

    Joly, Yann; Knoppers, Bartha M; Godard, Béatrice

    2003-08-01

    Public concern about genetic discrimination, particularly access to insurance following genetic testing, has been reported in the literature. This paper aims to separate myths from realities regarding genetic discrimination in life insurance and to underline the positive aspects of allowing insurers access to relevant genetic information for underwriting purposes. We present a review of the literature pertinent to discrimination in life insurance and a comparative analysis of industries guidelines. There are few reported cases in the literature of validated genetic discrimination. However, the benefits to be gained by allowing insurers access to relevant genetic data could justify fostering a more active role in the use of genetic information by insurance companies.

  17. 29 CFR 1635.12 - Medical information that is not genetic information.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...)), and regulations at 29 CFR 1630.13, 1630.14, and 1630.16. (b) Genetic information related to a... 29 Labor 4 2014-07-01 2014-07-01 false Medical information that is not genetic information. 1635... COMMISSION GENETIC INFORMATION NONDISCRIMINATION ACT OF 2008 § 1635.12 Medical information that is...

  18. 29 CFR 1635.12 - Medical information that is not genetic information.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...)), and regulations at 29 CFR 1630.13, 1630.14, and 1630.16. (b) Genetic information related to a... 29 Labor 4 2013-07-01 2013-07-01 false Medical information that is not genetic information. 1635... COMMISSION GENETIC INFORMATION NONDISCRIMINATION ACT OF 2008 § 1635.12 Medical information that is...

  19. 29 CFR 1635.12 - Medical information that is not genetic information.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...)), and regulations at 29 CFR 1630.13, 1630.14, and 1630.16. (b) Genetic information related to a... 29 Labor 4 2011-07-01 2011-07-01 false Medical information that is not genetic information. 1635... COMMISSION GENETIC INFORMATION NONDISCRIMINATION ACT OF 2008 § 1635.12 Medical information that is...

  20. 29 CFR 1635.12 - Medical information that is not genetic information.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...)), and regulations at 29 CFR 1630.13, 1630.14, and 1630.16. (b) Genetic information related to a... 29 Labor 4 2012-07-01 2012-07-01 false Medical information that is not genetic information. 1635... COMMISSION GENETIC INFORMATION NONDISCRIMINATION ACT OF 2008 § 1635.12 Medical information that is...

  1. Fast and accurate nonenzymatic copying of an RNA-like synthetic genetic polymer.

    PubMed

    Zhang, Shenglong; Blain, J Craig; Zielinska, Daria; Gryaznov, Sergei M; Szostak, Jack W

    2013-10-29

    Recent advances suggest that it may be possible to construct simple artificial cells from two subsystems: a self-replicating cell membrane and a self-replicating genetic polymer. Although multiple pathways for the growth and division of model protocell membranes have been characterized, no self-replicating genetic material is yet available. Nonenzymatic template-directed synthesis of RNA with activated ribonucleotide monomers has led to the copying of short RNA templates; however, these reactions are generally slow (taking days to weeks) and highly error prone. N3'-P5'-linked phosphoramidate DNA (3'-NP-DNA) is similar to RNA in its overall duplex structure, and is attractive as an alternative to RNA because the high reactivity of its corresponding monomers allows rapid and efficient copying of all four nucleobases on homopolymeric RNA and DNA templates. Here we show that both homopolymeric and mixed-sequence 3'-NP-DNA templates can be copied into complementary 3'-NP-DNA sequences. G:T and A:C wobble pairing leads to a high error rate, but the modified nucleoside 2-thiothymidine suppresses wobble pairing. We show that the 2-thiothymidine modification increases both polymerization rate and fidelity in the copying of a 3'-NP-DNA template into a complementary strand of 3'-NP-DNA. Our results suggest that 3'-NP-DNA has the potential to serve as the genetic material of artificial biological systems. PMID:24101473

  2. Differential contribution of visual and auditory information to accurately predict the direction and rotational motion of a visual stimulus.

    PubMed

    Park, Seoung Hoon; Kim, Seonjin; Kwon, MinHyuk; Christou, Evangelos A

    2016-03-01

    Vision and auditory information are critical for perception and to enhance the ability of an individual to respond accurately to a stimulus. However, it is unknown whether visual and auditory information contribute differentially to identify the direction and rotational motion of the stimulus. The purpose of this study was to determine the ability of an individual to accurately predict the direction and rotational motion of the stimulus based on visual and auditory information. In this study, we recruited 9 expert table-tennis players and used table-tennis service as our experimental model. Participants watched recorded services with different levels of visual and auditory information. The goal was to anticipate the direction of the service (left or right) and the rotational motion of service (topspin, sidespin, or cut). We recorded their responses and quantified the following outcomes: (i) directional accuracy and (ii) rotational motion accuracy. The response accuracy was the accurate predictions relative to the total number of trials. The ability of the participants to predict the direction of the service accurately increased with additional visual information but not with auditory information. In contrast, the ability of the participants to predict the rotational motion of the service accurately increased with the addition of auditory information to visual information but not with additional visual information alone. In conclusion, this finding demonstrates that visual information enhances the ability of an individual to accurately predict the direction of the stimulus, whereas additional auditory information enhances the ability of an individual to accurately predict the rotational motion of stimulus.

  3. The utility of accurate mass and LC elution time information in the analysis of complex proteomes

    SciTech Connect

    Norbeck, Angela D.; Monroe, Matthew E.; Adkins, Joshua N.; Anderson, Kevin K.; Daly, Don S.; Smith, Richard D.

    2005-08-01

    Theoretical tryptic digests of all predicted proteins from the genomes of three organisms of varying complexity were evaluated for specificity and possible utility of combined peptide accurate mass and predicted LC normalized elution time (NET) information. The uniqueness of each peptide was evaluated using its combined mass (+/- 5 ppm and 1 ppm) and NET value (no constraint, +/- 0.05 and 0.01 on a 0-1 NET scale). The set of peptides both underestimates actual biological complexity due to the lack of specific modifications, and overestimates the expected complexity since many proteins will not be present in the sample or observable on the mass spectrometer because of dynamic range limitations. Once a peptide is identified from an LCMS/MS experiment, its mass and elution time is representative of a unique fingerprint for that peptide. The uniqueness of that fingerprint in comparison to that for the other peptides present is indicative of the ability to confidently identify that peptide based on accurate mass and NET measurements. These measurements can be made using HPLC coupled with high resolution MS in a high-throughput manner. Results show that for organisms with comparatively small proteomes, such as Deinococcus radiodurans, modest mass and elution time accuracies are generally adequate for peptide identifications. For more complex proteomes, increasingly accurate easurements are required. However, the majority of proteins should be uniquely identifiable by using LC-MS with mass accuracies within +/- 1 ppm and elution time easurements within +/- 0.01 NET.

  4. Information capacity of genetic regulatory elements

    PubMed Central

    Tkačik, Gašper; Callan, Curtis G.; Bialek, William

    2010-01-01

    Changes in a cell’s external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need to perform nontrivial computations that integrate several inputs and affect multiple genes. At the same time, the activities of the regulated genes would fluctuate even if the inputs were held fixed, as a consequence of the intrinsic noise in the system, and such noise must fundamentally limit the reliability of any genetic computation. Here we use information theory to formalize the notion of information transmission in simple genetic regulatory elements in the presence of physically realistic noise sources. The dependence of this “channel capacity” on noise parameters, cooperativity and cost of making signaling molecules is explored systematically. We find that, in the range of parameters probed by recent in vivo measurements, capacities higher than one bit should be achievable. It is of course generally accepted that gene regulatory elements must, in order to function properly, have a capacity of at least one bit. The central point of our analysis is the demonstration that simple physical models of noisy gene transcription, with realistic parameters, can indeed achieve this capacity: it was not self-evident that this should be so. We also demonstrate that capacities significantly greater than one bit are possible, so that transcriptional regulation need not be limited to simple “on-off” components. The question whether real systems actually exploit this richer possibility is beyond the scope of this investigation. PMID:18763985

  5. Genetic Information Nondiscrimination Act. Final rule.

    PubMed

    2016-05-17

    The Equal Employment Opportunity Commission (EEOC or Commission) is issuing a final rule to amend the regulations implementing Title II of the Genetic Information Nondiscrimination Act of 2008 as they relate to employer-sponsored wellness programs. This rule addresses the extent to which an employer may offer an inducement to an employee for the employee's spouse to provide information about the spouse's manifestation of disease or disorder as part of a health risk assessment (HRA) administered in connection with an employer-sponsored wellness program. Several technical changes to the existing regulations are included. Published elsewhere in this issue of the Federal Register, the EEOC also issued a final rule to amend the regulations and interpretive guidance implementing Title I of the Americans with Disabilities Act (ADA) that addresses the extent to which employers may use incentives to encourage employees to participate in wellness programs that ask them to respond to disability-related inquiries and/or undergo medical examinations. PMID:27192741

  6. A hybrid genetic algorithm-extreme learning machine approach for accurate significant wave height reconstruction

    NASA Astrophysics Data System (ADS)

    Alexandre, E.; Cuadra, L.; Nieto-Borge, J. C.; Candil-García, G.; del Pino, M.; Salcedo-Sanz, S.

    2015-08-01

    Wave parameters computed from time series measured by buoys (significant wave height Hs, mean wave period, etc.) play a key role in coastal engineering and in the design and operation of wave energy converters. Storms or navigation accidents can make measuring buoys break down, leading to missing data gaps. In this paper we tackle the problem of locally reconstructing Hs at out-of-operation buoys by using wave parameters from nearby buoys, based on the spatial correlation among values at neighboring buoy locations. The novelty of our approach for its potential application to problems in coastal engineering is twofold. On one hand, we propose a genetic algorithm hybridized with an extreme learning machine that selects, among the available wave parameters from the nearby buoys, a subset FnSP with nSP parameters that minimizes the Hs reconstruction error. On the other hand, we evaluate to what extent the selected parameters in subset FnSP are good enough in assisting other machine learning (ML) regressors (extreme learning machines, support vector machines and gaussian process regression) to reconstruct Hs. The results show that all the ML method explored achieve a good Hs reconstruction in the two different locations studied (Caribbean Sea and West Atlantic).

  7. Capturing Accurate and Useful Information on Medication-Related Telenursing Triage Calls.

    PubMed

    Lake, R; Li, L; Baysari, M; Byrne, M; Robinson, M; Westbrook, J I

    2016-01-01

    Registered nurses providing telenursing triage and advice services record information on the medication related calls they handle. However the quality and consistency of these data were rarely examined. Our aim was to examine medication related calls made to the healthdirect advice service in November 2014, to assess their basic characteristics and how the data entry format influenced information collected and data consistency. Registered nurses selected the patient question type from a range of categories, and entered the medications involved in a free text field. Medication names were manually extracted from the free text fields. We also compared the selected patient question type with the free text description of the call, in order to gauge data consistency. Results showed that nurses provided patients with advice on medication-related queries in a timely matter (the median call duration of 9 minutes). From 1835 calls, we were able to identify and classify 2156 medications into 384 generic names. However, in 204 cases (11.2% of calls) no medication name was entered. A further 308 (15.0%) of the medication names entered were not identifiable. When we compared the selected patient question with the free text description of calls, we found that these were consistent in 63.27% of cases. Telenursing and triage advice services provide a valuable resource to the public with quick and easily accessible advice. To support nurses provide quality services and record accurate information about the queries, appropriate data entry format and design would be beneficial. PMID:27440292

  8. Genetics

    MedlinePlus

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  9. Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks.

    PubMed

    Zhang, Xiujun; Zhao, Juan; Hao, Jin-Kao; Zhao, Xing-Ming; Chen, Luonan

    2015-03-11

    Mutual information (MI), a quantity describing the nonlinear dependence between two random variables, has been widely used to construct gene regulatory networks (GRNs). Despite its good performance, MI cannot separate the direct regulations from indirect ones among genes. Although the conditional mutual information (CMI) is able to identify the direct regulations, it generally underestimates the regulation strength, i.e. it may result in false negatives when inferring gene regulations. In this work, to overcome the problems, we propose a novel concept, namely conditional mutual inclusive information (CMI2), to describe the regulations between genes. Furthermore, with CMI2, we develop a new approach, namely CMI2NI (CMI2-based network inference), for reverse-engineering GRNs. In CMI2NI, CMI2 is used to quantify the mutual information between two genes given a third one through calculating the Kullback-Leibler divergence between the postulated distributions of including and excluding the edge between the two genes. The benchmark results on the GRNs from DREAM challenge as well as the SOS DNA repair network in Escherichia coli demonstrate the superior performance of CMI2NI. Specifically, even for gene expression data with small sample size, CMI2NI can not only infer the correct topology of the regulation networks but also accurately quantify the regulation strength between genes. As a case study, CMI2NI was also used to reconstruct cancer-specific GRNs using gene expression data from The Cancer Genome Atlas (TCGA). CMI2NI is freely accessible at http://www.comp-sysbio.org/cmi2ni.

  10. Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authentication.

    PubMed

    Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Bellato, Cláudia M; Motilal, Lambert; Zhang, Dapeng

    2014-01-15

    Cacao (Theobroma cacao L.), the source of cocoa, is an economically important tropical crop. One problem with the premium cacao market is contamination with off-types adulterating raw premium material. Accurate determination of the genetic identity of single cacao beans is essential for ensuring cocoa authentication. Using nanofluidic single nucleotide polymorphism (SNP) genotyping with 48 SNP markers, we generated SNP fingerprints for small quantities of DNA extracted from the seed coat of single cacao beans. On the basis of the SNP profiles, we identified an assumed adulterant variety, which was unambiguously distinguished from the authentic beans by multilocus matching. Assignment tests based on both Bayesian clustering analysis and allele frequency clearly separated all 30 authentic samples from the non-authentic samples. Distance-based principle coordinate analysis further supported these results. The nanofluidic SNP protocol, together with forensic statistical tools, is sufficiently robust to establish authentication and to verify gourmet cacao varieties. This method shows significant potential for practical application.

  11. The Genetic Information Nondiscrimination Act (GINA): A Civil Rights Victory

    ERIC Educational Resources Information Center

    Petruniak, Mark; Krokosky, Alyson; Terry, Sharon F.

    2011-01-01

    This article discusses the Genetic Information Nondiscrimination Act (GINA) which President George W. Bush officially signed in 2008. The law prohibits employers from making adverse employment decisions based on a person's genetic information, including family health history. It also forbids insurance companies from discriminating against…

  12. Fuzzy Information Retrieval Using Genetic Algorithms and Relevance Feedback.

    ERIC Educational Resources Information Center

    Petry, Frederick E.; And Others

    1993-01-01

    Describes an approach that combines concepts from information retrieval, fuzzy set theory, and genetic programing to improve weighted Boolean query formulation via relevance feedback. Highlights include background on information retrieval systems; genetic algorithms; subproblem formulation; and preliminary results based on a testbed. (Contains 12…

  13. Is genetic information relevantly different from other kinds of non-genetic information in the life insurance context?

    PubMed

    Malpas, P J

    2008-07-01

    Within the medical, legal and bioethical literature, there has been an increasing concern that the information derived from genetic tests may be used to unfairly discriminate against individuals seeking various kinds of insurance; particularly health and life insurance. Consumer groups, the general public and those with genetic conditions have also expressed these concerns, specifically in the context of life insurance. While it is true that all insurance companies may have an interest in the information obtained from genetic tests, life insurers potentially have a very strong incentive to (want to) use genetic information to rate applicants, as individuals generally purchase their own cover and may want to take out very large policies. This paper critically focuses on genetic information in the context of life insurance. We consider whether genetic information differs in any relevant way from other kinds of non-genetic information required by and disclosed to life insurance companies by potential clients. We will argue that genetic information should not be treated any differently from other types of health information already collected from those wishing to purchase life insurance cover.

  14. Genetic and Rare Diseases Information Center

    MedlinePlus

    ... and Students guides/pages/99/teachers-and-students Teaching Resources News 1 In The Spotlight News Archive ... about rare or genetic diseases in English or Spanish. text go Browse Diseases View diseases by alphabetical ...

  15. The nature and significance of behavioural genetic information.

    PubMed

    Newson, Ainsley

    2004-01-01

    In light of the human genome project, establishing the genetic aetiology of complex human diseases has become a research priority within Western medicine. However, in addition to the identification of disease genes, numerous research projects are also being undertaken to identify genes contributing to the development of human behavioural characteristics, such as cognitive ability and criminal tendency. The permissibility of this research is obviously controversial: will society benefit from this research, or will it adversely affect our conceptions of ourselves and each other? When assessing the permissibility of this research, it is important to consider the nature and deterministic significance of behavioural genetic information. Whilst to date there has been much discussion and debate about the properties of genetic information per se and genetic determinism, this has not been applied to behavioural genetic research and its ethical implications. Therefore, this paper elucidates how behavioural genetic information can be distinguished from other types of genetic and non-genetic information and also synthesizes the determinative significance of genetic factors for the development of human behavioural traits. Undertaking this analysis enables the ethical issues raised by this research to be debated in an appropriate context and indicates that separate policy considerations are warranted.

  16. Efforts to regulate the collection and use of genetic information.

    PubMed

    Reilly, P R

    1999-11-01

    Public fascination with and support for genetic medicine is complicated by a deeply held fear that genetic information will be used by third parties (eg, insurers, employers, school systems) in ways that will harm the individuals from whom it was derived. Since the mid-1990s there has been much state and some federal legislative activity to address 2 closely related issues: the maintenance of genetic privacy and the prevention of genetic discrimination. These laws have had to confront several challenging questions such as what constitutes a genetic test, is genetic information qualitatively different from other medical information, and is there a means to distinguish between the two. In general the state laws are not well crafted. I will argue that a far more preferable policy is to draft a global, comprehensive medical records privacy law and to develop a model statute that defines the role of predictive genetic information in insurance underwriting. Concerns over misuse of genetic information also pose major issues for the conduct of genomic research. Among those I discuss are ownership of the DNA sample, significant changes in the scope of consent that must precede the decision to volunteer as a subject in genomic research, the reuse of long-archived samples, the challenges to intellectual property rights that flow from research, and the rise of the doctrine of community consent.

  17. Highly Accurate Prediction of Protein-Protein Interactions via Incorporating Evolutionary Information and Physicochemical Characteristics

    PubMed Central

    Li, Zheng-Wei; You, Zhu-Hong; Chen, Xing; Gui, Jie; Nie, Ru

    2016-01-01

    Protein-protein interactions (PPIs) occur at almost all levels of cell functions and play crucial roles in various cellular processes. Thus, identification of PPIs is critical for deciphering the molecular mechanisms and further providing insight into biological processes. Although a variety of high-throughput experimental techniques have been developed to identify PPIs, existing PPI pairs by experimental approaches only cover a small fraction of the whole PPI networks, and further, those approaches hold inherent disadvantages, such as being time-consuming, expensive, and having high false positive rate. Therefore, it is urgent and imperative to develop automatic in silico approaches to predict PPIs efficiently and accurately. In this article, we propose a novel mixture of physicochemical and evolutionary-based feature extraction method for predicting PPIs using our newly developed discriminative vector machine (DVM) classifier. The improvements of the proposed method mainly consist in introducing an effective feature extraction method that can capture discriminative features from the evolutionary-based information and physicochemical characteristics, and then a powerful and robust DVM classifier is employed. To the best of our knowledge, it is the first time that DVM model is applied to the field of bioinformatics. When applying the proposed method to the Yeast and Helicobacter pylori (H. pylori) datasets, we obtain excellent prediction accuracies of 94.35% and 90.61%, respectively. The computational results indicate that our method is effective and robust for predicting PPIs, and can be taken as a useful supplementary tool to the traditional experimental methods for future proteomics research. PMID:27571061

  18. Highly Accurate Prediction of Protein-Protein Interactions via Incorporating Evolutionary Information and Physicochemical Characteristics.

    PubMed

    Li, Zheng-Wei; You, Zhu-Hong; Chen, Xing; Gui, Jie; Nie, Ru

    2016-01-01

    Protein-protein interactions (PPIs) occur at almost all levels of cell functions and play crucial roles in various cellular processes. Thus, identification of PPIs is critical for deciphering the molecular mechanisms and further providing insight into biological processes. Although a variety of high-throughput experimental techniques have been developed to identify PPIs, existing PPI pairs by experimental approaches only cover a small fraction of the whole PPI networks, and further, those approaches hold inherent disadvantages, such as being time-consuming, expensive, and having high false positive rate. Therefore, it is urgent and imperative to develop automatic in silico approaches to predict PPIs efficiently and accurately. In this article, we propose a novel mixture of physicochemical and evolutionary-based feature extraction method for predicting PPIs using our newly developed discriminative vector machine (DVM) classifier. The improvements of the proposed method mainly consist in introducing an effective feature extraction method that can capture discriminative features from the evolutionary-based information and physicochemical characteristics, and then a powerful and robust DVM classifier is employed. To the best of our knowledge, it is the first time that DVM model is applied to the field of bioinformatics. When applying the proposed method to the Yeast and Helicobacter pylori (H. pylori) datasets, we obtain excellent prediction accuracies of 94.35% and 90.61%, respectively. The computational results indicate that our method is effective and robust for predicting PPIs, and can be taken as a useful supplementary tool to the traditional experimental methods for future proteomics research. PMID:27571061

  19. Highly Accurate Prediction of Protein-Protein Interactions via Incorporating Evolutionary Information and Physicochemical Characteristics.

    PubMed

    Li, Zheng-Wei; You, Zhu-Hong; Chen, Xing; Gui, Jie; Nie, Ru

    2016-01-01

    Protein-protein interactions (PPIs) occur at almost all levels of cell functions and play crucial roles in various cellular processes. Thus, identification of PPIs is critical for deciphering the molecular mechanisms and further providing insight into biological processes. Although a variety of high-throughput experimental techniques have been developed to identify PPIs, existing PPI pairs by experimental approaches only cover a small fraction of the whole PPI networks, and further, those approaches hold inherent disadvantages, such as being time-consuming, expensive, and having high false positive rate. Therefore, it is urgent and imperative to develop automatic in silico approaches to predict PPIs efficiently and accurately. In this article, we propose a novel mixture of physicochemical and evolutionary-based feature extraction method for predicting PPIs using our newly developed discriminative vector machine (DVM) classifier. The improvements of the proposed method mainly consist in introducing an effective feature extraction method that can capture discriminative features from the evolutionary-based information and physicochemical characteristics, and then a powerful and robust DVM classifier is employed. To the best of our knowledge, it is the first time that DVM model is applied to the field of bioinformatics. When applying the proposed method to the Yeast and Helicobacter pylori (H. pylori) datasets, we obtain excellent prediction accuracies of 94.35% and 90.61%, respectively. The computational results indicate that our method is effective and robust for predicting PPIs, and can be taken as a useful supplementary tool to the traditional experimental methods for future proteomics research.

  20. Information transmission in genetic regulatory networks: a review.

    PubMed

    Tkačik, Gašper; Walczak, Aleksandra M

    2011-04-20

    Genetic regulatory networks enable cells to respond to changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits has deepened our understanding of what kinds of computations genetic regulatory networks can perform, and with what reliability. These advances have motivated researchers to look for connections between the architecture and function of genetic regulatory networks. Transmitting information between a network's inputs and outputs has been proposed as one such possible measure of function, relevant in certain biological contexts. Here we summarize recent developments in the application of information theory to gene regulatory networks. We first review basic concepts in information theory necessary for understanding recent work. We then discuss the functional complexity of gene regulation, which arises from the molecular nature of the regulatory interactions. We end by reviewing some experiments that support the view that genetic networks responsible for early development of multicellular organisms might be maximizing transmitted 'positional information'.

  1. [Personal genetic information and ethical consideration: from medical viewpoint].

    PubMed

    Morisaki, Takayuki

    2009-06-01

    Rapid progress in human genetic research has identified not only the entire DNA sequence of human genome DNA but the information on an individual risk to a hereditary disease or common diseases. Although individual genetic information will help to establish development of disease prevention method or better new therapeutic procedure, it will also raise quite a few ethical issues. Here, recent research progress on this field and corresponding regulatory procedures by professionals and governmental (Japan and other countries)/intergovernmental body are discussed.

  2. The impact of genetic information on policy and clinical practice.

    PubMed

    Abel, Elizabeth; Horner, Sharon D; Tyler, Diane; Innerarity, Sheryl A

    2005-02-01

    This article discusses genetics-related policy issues that have an impact on health care systems, health care providers, and their patients: privacy, mass screening, family screening, and knowledge dissemination. Access, cost, and ethical implications are important discussant points for each of these genetic-related policy issues. Embedded in the issue of privacy are concerns of insurability, confidentiality, and discrimination. The public health policy implications related to mass screening programs include efficacy of the screening tests, availability of primary and secondary interventions, access, costs, and program evaluation. Policy issues for family screening are similar to mass screening, with added concerns about privacy and availability of adequate resources, including health care providers and counselors trained in genetics. Knowledge dissemination is critical to maintaining currency of clinical information and applications of genetic technologies and treatments. As genetic information expands, the need for knowledge dissemination will increase. The importance of advanced practice nurses' involvement in these policy issues is discussed. PMID:16443953

  3. Reassessing insurers' access to genetic information: genetic privacy, ignorance, and injustice.

    PubMed

    Feiring, Eli

    2009-06-01

    Many countries have imposed strict regulations on the genetic information to which insurers have access. Commentators have warned against the emerging body of legislation for different reasons. This paper demonstrates that, when confronted with the argument that genetic information should be available to insurers for health insurance underwriting purposes, one should avoid appeals to rights of genetic privacy and genetic ignorance. The principle of equality of opportunity may nevertheless warrant restrictions. A choice-based account of this principle implies that it is unfair to hold people responsible for the consequences of the genetic lottery, since we have no choice in selecting our genotype or the expression of it. However appealing, this view does not take us all the way to an adequate justification of inaccessibility of genetic information. A contractarian account, suggesting that health is a condition of opportunity and that healthcare is an essential good, seems more promising. I conclude that if or when predictive medical tests (such as genetic tests) are developed with significant actuarial value, individuals have less reason to accept as fair institutions that limit access to healthcare on the grounds of risk status. Given the assumption that a division of risk pools in accordance with a rough estimate of people's level of (genetic) risk will occur, fairness and justice favour universal health insurance based on solidarity.

  4. Loss of genetic information in cancer.

    PubMed

    Cavenee, W K; Hansen, M F; Scrable, H J; James, C D

    1989-01-01

    The determination and comparison of genotypic combinations at genomic loci in normal and tumour tissues from patients with various types of cancer have defined the chromosomal locations of loci at which recessive mutations play a role in disease. The predisposing nature of some of these mutant alleles is exemplified in studies of retinoblastoma and osteogenic sarcoma. These two clinically associated diseases share a pathogenetically causal predisposition that maps to chromosome position 13q14. A similar mechanism at 11p15.5 is involved in the development of the embryonal variant of rhabdomyo-sarcoma, Wilms' tumour and hepatoblastoma. Finally, genomic alteration of chromosome 10 is apparent in glioblastomas and mixed tumours of glioblastoma/astrocytoma grade III but not in homogenous astrocytoma grades II or III, suggesting the definition of a locus involved in tumour progression and, perhaps, an approach to molecular genetic staging of tumours.

  5. State legislative approaches to regulating the use of genetic information.

    PubMed

    Neumann, P G; Brown, G L

    1995-11-01

    As genetic testing becomes more prevalent and the uses for genetic information multiply, we are likely to witness more demand for comprehensive state legislation on the order of the Oregon law regulating the procedures for obtaining and using genetic information. In addition, the United States Senate has expressed an interest in the subject. The Senate Labor and Human Resources Committee reportedly agreed on August 2, 1995 to include in a health insurance reform bill (S. 1028) language prohibiting health plans from using genetic information when determining eligibility, continuation, enrollment, or contribution requirements. 4 BNA's Health Law Rep. at 1218 (Aug. 10, 1995). Insurance companies continue to maintain that genetic test results are simply another factor that should rightfully be used during underwriting, much as age, medical history, and physical examinations are routinely used today. Right to privacy advocates argue that genetic testing provides employers and insurance companies with too much information and offers a great potential for discrimination. As more states wrestle with this issue, these competing interests are likely to be debated in public forums throughout the country.

  6. Ethical issues in the use of genetic information.

    PubMed

    Dinwiddie, Stephen H; Hoop, Jinger; Gershon, Elliot S

    2004-11-01

    Advances in molecular genetics promise to deepen our understanding of the biological basis of human behavior and shed light on the pathophysiology of mental illness. Genetic research is likely to improve our ability to develop somatic treatments for psychiatric syndromes as well as to identify targets for environmental intervention. However, population-screening tests for disorders with multifactorial inheritance may offer little clinical benefit to outweigh their potential for misuse. Relevant legal issues surrounding the use of genetic information in psychiatry include the perceived need for laws to prevent insurance and employment discrimination, and concerns about genetic status as a possible excuse for criminal behavior. Relevant ethical issues include threats to patient privacy and confidentiality and the importance of fairly distributing the benefits and burdens of genetic advances.

  7. Accurate refinement of docked protein complexes using evolutionary information and deep learning.

    PubMed

    Akbal-Delibas, Bahar; Farhoodi, Roshanak; Pomplun, Marc; Haspel, Nurit

    2016-06-01

    One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work, we introduced AccuRefiner, a machine learning based tool for refining protein-protein complexes. Given a docked complex, the refinement tool produces a small set of refined versions of the input complex, with lower root-mean-square-deviation (RMSD) of atomic positions with respect to the native structure. The method employs a unique ranking tool that accurately predicts the RMSD of docked complexes with respect to the native structure. In this work, we use a deep learning network with a similar set of features and five layers. We show that a properly trained deep learning network can accurately predict the RMSD of a docked complex with 1.40 Å error margin on average, by approximating the complex relationship between a wide set of scoring function terms and the RMSD of a docked structure. The network was trained on 35000 unbound docking complexes generated by RosettaDock. We tested our method on 25 different putative docked complexes produced also by RosettaDock for five proteins that were not included in the training data. The results demonstrate that the high accuracy of the ranking tool enables AccuRefiner to consistently choose the refinement candidates with lower RMSD values compared to the coarsely docked input structures. PMID:26846813

  8. Accurate refinement of docked protein complexes using evolutionary information and deep learning.

    PubMed

    Akbal-Delibas, Bahar; Farhoodi, Roshanak; Pomplun, Marc; Haspel, Nurit

    2016-06-01

    One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work, we introduced AccuRefiner, a machine learning based tool for refining protein-protein complexes. Given a docked complex, the refinement tool produces a small set of refined versions of the input complex, with lower root-mean-square-deviation (RMSD) of atomic positions with respect to the native structure. The method employs a unique ranking tool that accurately predicts the RMSD of docked complexes with respect to the native structure. In this work, we use a deep learning network with a similar set of features and five layers. We show that a properly trained deep learning network can accurately predict the RMSD of a docked complex with 1.40 Å error margin on average, by approximating the complex relationship between a wide set of scoring function terms and the RMSD of a docked structure. The network was trained on 35000 unbound docking complexes generated by RosettaDock. We tested our method on 25 different putative docked complexes produced also by RosettaDock for five proteins that were not included in the training data. The results demonstrate that the high accuracy of the ranking tool enables AccuRefiner to consistently choose the refinement candidates with lower RMSD values compared to the coarsely docked input structures.

  9. Can Raters with Reduced Job Descriptive Information Provide Accurate Position Analysis Questionnaire (PAQ) Ratings?

    ERIC Educational Resources Information Center

    Friedman, Lee; Harvey, Robert J.

    1986-01-01

    Job-naive raters provided with job descriptive information made Position Analysis Questionnaire (PAQ) ratings which were validated against ratings of job analysts who were also job content experts. None of the reduced job descriptive information conditions enabled job-naive raters to obtain either acceptable levels of convergent validity with…

  10. Molecular-genetic analysis is essential for accurate classification of renal carcinoma resembling Xp11.2 translocation carcinoma.

    PubMed

    Hayes, Malcolm; Peckova, Kvetoslava; Martinek, Petr; Hora, Milan; Kalusova, Kristyna; Straka, Lubomir; Daum, Ondrej; Kokoskova, Bohuslava; Rotterova, Pavla; Pivovarčikova, Kristyna; Branzovsky, Jindrich; Dubova, Magdalena; Vesela, Pavla; Michal, Michal; Hes, Ondrej

    2015-03-01

    tumours can only be sub-classified accurately by multi-parameter molecular-genetic analysis. PMID:25544614

  11. Laws Restricting Health Insurers' Use of Genetic Information: Impact on Genetic Discrimination

    PubMed Central

    Hall, Mark A.; Rich, Stephen S.

    2000-01-01

    Summary Since 1991, 28 states have enacted laws that prohibit insurers' use of genetic information in pricing, issuing, or structuring health insurance. This article evaluates whether these laws reduce the extent of genetic discrimination by health insurers. From the data collected at multiple sites, we find that there are almost no well-documented cases of health insurers either asking for or using presymptomatic genetic test results in their underwriting decisions, either (a) before or after these laws have been enacted or (b) in states with or without these laws. By using both in-person interviews with insurers and a direct market test, we found that a person with a serious genetic condition who is presymptomatic faces little or no difficulty in obtaining health insurance. Furthermore, there are few indications that the degree of difficulty varies according to whether a state regulates the use of genetic information. Nevertheless, these laws have made it less likely that insurers will use genetic information in the future. Although insurers and agents are only vaguely aware of these laws, the laws have shaped industry norms and attitudes about the legitimacy of using this information. PMID:10631158

  12. 16 CFR 1101.32 - Reasonable steps to assure information is accurate.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... to release to the public: (1) The Commission staff or a qualified person or entity outside the... will review the information in light of the comments. The degree of review by the Commission and...

  13. An examination of information quality as a moderator of accurate personality judgment.

    PubMed

    Letzring, Tera D; Human, Lauren J

    2014-10-01

    Information quality is an important moderator of the accuracy of personality judgment, and this article describes research focusing on how specific kinds of information are related to accuracy. In this study, 228 participants (159 female, 69 male; mean age = 23.43; 86.4% Caucasian) in unacquainted dyads were assigned to discuss thoughts and feelings, discuss behaviors, or engage in behaviors. Interactions lasted 25-30 min, and participants provided ratings of their partners and themselves following the interaction on the Big Five traits, ego-control, and ego-resiliency. Next, the amount of different types of information made available by each participant was objectively coded. The accuracy criterion, composed of self- and acquaintance ratings, was used to assess distinctive and normative accuracy using the Social Accuracy Model. Participants in the discussion conditions achieved higher distinctive accuracy than participants who engaged in behaviors, but normative accuracy did not differ across conditions. Information about specific behaviors and general behaviors were among the most consistent predictors of higher distinctive accuracy. Normative accuracy was more likely to decrease than increase when higher-quality information was available. Verbal information about behaviors is the most useful for learning about how people are unique.

  14. Using genetic research to inform imperiled and invasive species management

    USGS Publications Warehouse

    Hunter, Margaret E.; Pawlitz, Rachel J.

    2012-01-01

    The long-term viability of species and populations is related to their potential to migrate, reproduce, and adapt to environmental changes. In the southeast United States, U.S. Geological Survey (USGS) scientists are providing resource managers with genetic information to improve the long-term survival and sustainability of the Nation's aquatic species. Research focused on native and imperiled species can assess the genetic factors influencing their survival and recovery, while work on invasive species can provide information on their proliferation, dispersal, and impacts on native species.

  15. Hearing on the possible uses and misuses of genetic information.

    PubMed

    Healy, B

    1992-02-01

    In summary, I will reiterate the five points I would like to leave with you today: First, the biological revolution has extraordinary power to do good. As long as the use of our new genetic knowledge is guided by the traditional ideals of the healing professions--to help improve the human condition without doing harm--we can expect real benefits to come of it. Second, however, we need to prepare for the fact that, like all powerful tools, genetic information can be misused and abused. As I hope to have illustrated, NIH has the will and ability to work with the American public and the scientific community in preparing for the responsible use of genetic information for now and the future. To date, the best example of that will is the precedent-setting work being conducted in concert with the human genome program through our ELSI program. Third, as a part of that work, it will be imperative to continue to protect the voluntary nature of genetic services. The rights of people to determine for themselves whether or not to pursue genetic information about themselves must be defended, even from the forced choices that discriminatory social practices may create. Fourth, in order to allow those who choose to do so to benefit from our new genetic tools, discrimination based on genotype must be prohibited as a matter of basic civil rights. And finally, in the bright light of the Human Genome Project and its ELSI program, it is important not to let genetics eclipse the important ethical, legal and social issues that attend other biomedical advances. It is the purpose of NIH's new center for science policy studies to illuminate this broader view of the road ahead. Thank you. I will be happy to answer any questions you might have.

  16. Diffusion of information about genetic risk within families.

    PubMed

    Ayme, Ségolène; Macquart-Moulin, Geneviève; Julian-Reynier, Claire; Chabal, Françoise; Giraud, Francis

    1993-01-01

    Recent developments in genetics are likely to exacerbate the ethical issues in clinical practice, especially with regard to privacy and disclosure of genetic information. To evaluate the behaviour of patients with respect to transmitting carrier information, we undertook a survey of 283 families with a balanced chromosomal rearrangement as a model. In these families, 1816 relatives were considered at risk and 806 of them were karyotyped (44.4%). The percentage of karyotypes performed is significantly related to the number of living children of the index couple, the reason for referral, the nature of the anomaly, the training of the counsellor and the age of the index case. This study shows the limits of the screening of at risk individuals within families, based on the willingness of the patients, and addresses practical and ethical issues around family disclosure in medical genetics.

  17. Are Genetically Informed Designs Genetically Informative?: Comment on McGue, Elkins, Walden, and Iacono (2005) and Quantitative Behavioral Genetics

    ERIC Educational Resources Information Center

    Partridge, Ty

    2005-01-01

    M. McGue, I. Elkins, B. Walden, and W. G. Iacono (see record 2005-14938-011) presented the findings from a twin study examining the relative contributions of genetic and environmental factors to the developmental trajectories of parent-adolescent relationships. From a behavioral genetics perspective, this study is well conceptualized, is well…

  18. Exploratory Movement Generates Higher-Order Information That Is Sufficient for Accurate Perception of Scaled Egocentric Distance

    PubMed Central

    Mantel, Bruno; Stoffregen, Thomas A.; Campbell, Alain; Bardy, Benoît G.

    2015-01-01

    Body movement influences the structure of multiple forms of ambient energy, including optics and gravito-inertial force. Some researchers have argued that egocentric distance is derived from inferential integration of visual and non-visual stimulation. We suggest that accurate information about egocentric distance exists in perceptual stimulation as higher-order patterns that extend across optics and inertia. We formalize a pattern that specifies the egocentric distance of a stationary object across higher-order relations between optics and inertia. This higher-order parameter is created by self-generated movement of the perceiver in inertial space relative to the illuminated environment. For this reason, we placed minimal restrictions on the exploratory movements of our participants. We asked whether humans can detect and use the information available in this higher-order pattern. Participants judged whether a virtual object was within reach. We manipulated relations between body movement and the ambient structure of optics and inertia. Judgments were precise and accurate when the higher-order optical-inertial parameter was available. When only optic flow was available, judgments were poor. Our results reveal that participants perceived egocentric distance from the higher-order, optical-inertial consequences of their own exploratory activity. Analysis of participants’ movement trajectories revealed that self-selected movements were complex, and tended to optimize availability of the optical-inertial pattern that specifies egocentric distance. We argue that accurate information about egocentric distance exists in higher-order patterns of ambient energy, that self-generated movement can generate these higher-order patterns, and that these patterns can be detected and used to support perception of egocentric distance that is precise and accurate. PMID:25856410

  19. Does Childhood Anxiety Evoke Maternal Control? A Genetically Informed Study

    ERIC Educational Resources Information Center

    Eley, Thalia C.; Napolitano, Maria; Lau, Jennifer Y. F.; Gregory, Alice M.

    2010-01-01

    Background: Despite theoretical and empirical support for an association between maternal control and child anxiety, few studies have examined the origins of this association. Furthermore, none use observer-ratings of maternal control within a genetically informative design. This study addressed three questions: 1) do children who experience…

  20. Crossover Improvement for the Genetic Algorithm in Information Retrieval.

    ERIC Educational Resources Information Center

    Vrajitoru, Dana

    1998-01-01

    In information retrieval (IR), the aim of genetic algorithms (GA) is to help a system to find, in a huge documents collection, a good reply to a query expressed by the user. Analysis of phenomena seen during the implementation of a GA for IR has led to a new crossover operation, which is introduced and compared to other learning methods.…

  1. Information Business: Applying Infometry (Informational Geometry) in Cognitive Coordination and Genetic Programming for Electronic Information Packaging and Marketing.

    ERIC Educational Resources Information Center

    Tsai, Bor-sheng

    1994-01-01

    Describes the use of infometry, or informational geometry, to meet the challenges of information service businesses. Highlights include theoretical models for cognitive coordination and genetic programming; electronic information packaging; marketing electronic information products, including cost-benefit analyses; and recapitalization, including…

  2. Protecting genetic materials and genetic information: a case study of Guthrie Cards in Victoria.

    PubMed

    Lawson, C; Smith, R

    2001-11-01

    The authors are privileged to have been provided with correspondence about a dispute over the ongoing storage of genetic material (as Guthrie Cards) in Victoria. The correspondence details confusion over the roles of government and the private sector service provider in accounting for the storage, use and destruction of these stored genetic materials collected as part of a government public health program. The purpose in publishing this account is to highlight the present inadequacies in current practices and the ongoing potential for a crisis in the management of collected genetic materials through a lack of appropriate regulation, transparency and accountability. The article suggests measures to remedy some of the existing inadequacies in contractual arrangements and recommends that the government retain ownership and control of both the genetic materials and the derived information to ensure some accountability in the present legal environment.

  3. Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction.

    PubMed

    Braun, Tatjana; Koehler Leman, Julia; Lange, Oliver F

    2015-12-01

    Recent work has shown that the accuracy of ab initio structure prediction can be significantly improved by integrating evolutionary information in form of intra-protein residue-residue contacts. Following this seminal result, much effort is put into the improvement of contact predictions. However, there is also a substantial need to develop structure prediction protocols tailored to the type of restraints gained by contact predictions. Here, we present a structure prediction protocol that combines evolutionary information with the resolution-adapted structural recombination approach of Rosetta, called RASREC. Compared to the classic Rosetta ab initio protocol, RASREC achieves improved sampling, better convergence and higher robustness against incorrect distance restraints, making it the ideal sampling strategy for the stated problem. To demonstrate the accuracy of our protocol, we tested the approach on a diverse set of 28 globular proteins. Our method is able to converge for 26 out of the 28 targets and improves the average TM-score of the entire benchmark set from 0.55 to 0.72 when compared to the top ranked models obtained by the EVFold web server using identical contact predictions. Using a smaller benchmark, we furthermore show that the prediction accuracy of our method is only slightly reduced when the contact prediction accuracy is comparatively low. This observation is of special interest for protein sequences that only have a limited number of homologs.

  4. Honey bees can perform accurately directed waggle dances based solely on information from a homeward trip.

    PubMed

    Edrich, Wolfgang

    2015-10-01

    Honey bees were displaced several 100 m from their hive to an unfamiliar site and provisioned with honey. After feeding, almost two-thirds of the bees flew home to their hive within a 50 min observation time. About half of these returning, bees signalled the direction of the release site in waggle dances thus demonstrating that the dance can be guided entirely by information gathered on a single homeward trip. The likely reason for the bees' enthusiastic dancing on their initial return from this new site was the highly rewarding honeycomb that they were given there. The attractive nature of the site is confirmed by many of these bees revisiting the site and continuing to forage there.

  5. Accurately decoding visual information from fMRI data obtained in a realistic virtual environment

    PubMed Central

    Floren, Andrew; Naylor, Bruce; Miikkulainen, Risto; Ress, David

    2015-01-01

    Three-dimensional interactive virtual environments (VEs) are a powerful tool for brain-imaging based cognitive neuroscience that are presently under-utilized. This paper presents machine-learning based methods for identifying brain states induced by realistic VEs with improved accuracy as well as the capability for mapping their spatial topography on the neocortex. VEs provide the ability to study the brain under conditions closer to the environment in which humans evolved, and thus to probe deeper into the complexities of human cognition. As a test case, we designed a stimulus to reflect a military combat situation in the Middle East, motivated by the potential of using real-time functional magnetic resonance imaging (fMRI) in the treatment of post-traumatic stress disorder. Each subject experienced moving through the virtual town where they encountered 1–6 animated combatants at different locations, while fMRI data was collected. To analyze the data from what is, compared to most studies, more complex and less controlled stimuli, we employed statistical machine learning in the form of Multi-Voxel Pattern Analysis (MVPA) with special attention given to artificial Neural Networks (NN). Extensions to NN that exploit the block structure of the stimulus were developed to improve the accuracy of the classification, achieving performances from 58 to 93% (chance was 16.7%) with six subjects. This demonstrates that MVPA can decode a complex cognitive state, viewing a number of characters, in a dynamic virtual environment. To better understand the source of this information in the brain, a novel form of sensitivity analysis was developed to use NN to quantify the degree to which each voxel contributed to classification. Compared with maps produced by general linear models and the searchlight approach, these sensitivity maps revealed a more diverse pattern of information relevant to the classification of cognitive state. PMID:26106315

  6. An Integrated Korean Biodiversity and Genetic Information Retrieval System

    PubMed Central

    Lim, Jeongheui; Bhak, Jong; Oh, Hee-Mock; Kim, Chang-Bae; Park, Yong-Ha; Paek, Woon Kee

    2008-01-01

    Background On-line biodiversity information databases are growing quickly and being integrated into general bioinformatics systems due to the advances of fast gene sequencing technologies and the Internet. These can reduce the cost and effort of performing biodiversity surveys and genetic searches, which allows scientists to spend more time researching and less time collecting and maintaining data. This will cause an increased rate of knowledge build-up and improve conservations. The biodiversity databases in Korea have been scattered among several institutes and local natural history museums with incompatible data types. Therefore, a comprehensive database and a nation wide web portal for biodiversity information is necessary in order to integrate diverse information resources, including molecular and genomic databases. Results The Korean Natural History Research Information System (NARIS) was built and serviced as the central biodiversity information system to collect and integrate the biodiversity data of various institutes and natural history museums in Korea. This database aims to be an integrated resource that contains additional biological information, such as genome sequences and molecular level diversity. Currently, twelve institutes and museums in Korea are integrated by the DiGIR (Distributed Generic Information Retrieval) protocol, with Darwin Core2.0 format as its metadata standard for data exchange. Data quality control and statistical analysis functions have been implemented. In particular, integrating molecular and genetic information from the National Center for Biotechnology Information (NCBI) databases with NARIS was recently accomplished. NARIS can also be extended to accommodate other institutes abroad, and the whole system can be exported to establish local biodiversity management servers. Conclusion A Korean data portal, NARIS, has been developed to efficiently manage and utilize biodiversity data, which includes genetic resources. NARIS aims

  7. Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling.

    PubMed

    Bhaskara, Ramachandra M; Padhi, Amrita; Srinivasan, Narayanaswamy

    2014-07-01

    With the preponderance of multidomain proteins in eukaryotic genomes, it is essential to recognize the constituent domains and their functions. Often function involves communications across the domain interfaces, and the knowledge of the interacting sites is essential to our understanding of the structure-function relationship. Using evolutionary information extracted from homologous domains in at least two diverse domain architectures (single and multidomain), we predict the interface residues corresponding to domains from the two-domain proteins. We also use information from the three-dimensional structures of individual domains of two-domain proteins to train naïve Bayes classifier model to predict the interfacial residues. Our predictions are highly accurate (∼85%) and specific (∼95%) to the domain-domain interfaces. This method is specific to multidomain proteins which contain domains in at least more than one protein architectural context. Using predicted residues to constrain domain-domain interaction, rigid-body docking was able to provide us with accurate full-length protein structures with correct orientation of domains. We believe that these results can be of considerable interest toward rational protein and interaction design, apart from providing us with valuable information on the nature of interactions.

  8. 78 FR 13286 - Sharing Certain Business Information Regarding the Introduction of Genetically Engineered...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-27

    ... Certain Business Information Regarding the Introduction of Genetically Engineered Organisms With State and... rule. SUMMARY: We are proposing to amend our regulations regarding genetically engineered organisms... regulate certain genetically engineered organisms. DATES: We will consider all comments that we receive...

  9. Aging, genetics, and the environment: potential of errors introduced into genetic information transfer by metal ions.

    PubMed

    Eichhorn, G L

    1979-02-01

    Metal ions, which are introduced into living organisms from the environment, are required in every aspect of genetic information transfer. However, the "wrong" metal ion, or even the "right" metal ion in the wrong concentration, can produce deleterious information transfer effects. Metal ions react with nucleic acids in many different ways, and virtually all of these reactions effect major changes in the structure of the nucleic acids. Cellular metal ion concentrations change with age. The effects of such concentration changes on genetic information transfer suggest the possibility that metal ions can influence the aging process. A specific example of such influence is the accumulation in brain cells of aluminum ions, which may have a relationship to Alzheimer's disease.

  10. Sequencing Genetics Information: Integrating Data into Information Literacy for Undergraduate Biology Students

    ERIC Educational Resources Information Center

    MacMillan, Don

    2010-01-01

    This case study describes an information literacy lab for an undergraduate biology course that leads students through a range of resources to discover aspects of genetic information. The lab provides over 560 students per semester with the opportunity for hands-on exploration of resources in steps that simulate the pathways of higher-level…

  11. Comparison of participant information and informed consent forms of five European studies in genetic isolated populations.

    PubMed

    Mascalzoni, Deborah; Janssens, A Cecile J W; Stewart, Alison; Pramstaller, Peter; Gyllensten, Ulf; Rudan, Igor; van Duijn, Cornelia M; Wilson, James F; Campbell, Harry; Quillan, Ruth M C

    2010-03-01

    Family-based research in genetically isolated populations is an effective approach for identifying loci influencing variation in disease traits. In common with all studies in humans, those in genetically isolated populations need ethical approval; however, existing ethical frameworks may be inadequate to protect participant privacy and confidentiality and to address participants' information needs in such populations. Using the ethical-legal guidelines of the Council for International Organizations of Medical Sciences (CIOMS) as a template, we compared the participant information leaflets and consent forms of studies in five European genetically isolated populations to identify additional information that should be incorporated into information leaflets and consent forms to guarantee satisfactorily informed consent. We highlight the additional information that participants require on the research purpose and the reasons why their population was chosen; on the potential risks and benefits of participation; on the opportunities for benefit sharing; on privacy; on the withdrawal of consent and on the disclosure of genetic data. This research raises some important issues that should be addressed properly and identifies relevant types of information that should be incorporated into information leaflets for this type of study.

  12. Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.

    PubMed

    Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

    2016-01-01

    Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNA(Lys)(UUU) with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm(5)s(2)U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism. PMID:26791911

  13. Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code

    PubMed Central

    Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

    2016-01-01

    Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNALysUUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm5s2U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine–pyrimidine mismatches. We show that mnm5s2U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism. PMID:26791911

  14. Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code

    NASA Astrophysics Data System (ADS)

    Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

    2016-01-01

    Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNALysUUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm5s2U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm5s2U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.

  15. Panel-based Genetic Diagnostic Testing for Inherited Eye Diseases is Highly Accurate and Reproducible and More Sensitive for Variant Detection Than Exome Sequencing

    PubMed Central

    Bujakowska, Kinga M.; Sousa, Maria E.; Fonseca-Kelly, Zoë D.; Taub, Daniel G.; Janessian, Maria; Wang, Dan Yi; Au, Elizabeth D.; Sims, Katherine B.; Sweetser, David A.; Fulton, Anne B.; Liu, Qin; Wiggs, Janey L.; Gai, Xiaowu; Pierce, Eric A.

    2015-01-01

    Purpose Next-generation sequencing (NGS) based methods are being adopted broadly for genetic diagnostic testing, but the performance characteristics of these techniques have not been fully defined with regard to test accuracy and reproducibility. Methods We developed a targeted enrichment and NGS approach for genetic diagnostic testing of patients with inherited eye disorders, including inherited retinal degenerations, optic atrophy and glaucoma. In preparation for providing this Genetic Eye Disease (GEDi) test on a CLIA-certified basis, we performed experiments to measure the sensitivity, specificity, reproducibility as well as the clinical sensitivity of the test. Results The GEDi test is highly reproducible and accurate, with sensitivity and specificity for single nucleotide variant detection of 97.9% and 100%, respectively. The sensitivity for variant detection was notably better than the 88.3% achieved by whole exome sequencing (WES) using the same metrics, due to better coverage of targeted genes in the GEDi test compared to commercially available exome capture sets. Prospective testing of 192 patients with IRDs indicated that the clinical sensitivity of the GEDi test is high, with a diagnostic rate of 51%. Conclusion The data suggest that based on quantified performance metrics, selective targeted enrichment is preferable to WES for genetic diagnostic testing. PMID:25412400

  16. DNA extraction techniques compared for accurate detection of genetically modified organisms (GMOs) in maize food and feed products.

    PubMed

    Turkec, Aydin; Kazan, Hande; Karacanli, Burçin; Lucas, Stuart J

    2015-08-01

    In this paper, DNA extraction methods have been evaluated to detect the presence of genetically modified organisms (GMOs) in maize food and feed products commercialised in Turkey. All the extraction methods tested performed well for the majority of maize foods and feed products analysed. However, the highest DNA content was achieved by the Wizard, Genespin or the CTAB method, all of which produced optimal DNA yield and purity for different maize food and feed products. The samples were then screened for the presence of GM elements, along with certified reference materials. Of the food and feed samples, 8 % tested positive for the presence of one GM element (NOS terminator), of which half (4 % of the total) also contained a second element (the Cauliflower Mosaic Virus 35S promoter). The results obtained herein clearly demonstrate the presence of GM maize in the Turkish market, and that the Foodproof GMO Screening Kit provides reliable screening of maize food and feed products. PMID:26243938

  17. DNA extraction techniques compared for accurate detection of genetically modified organisms (GMOs) in maize food and feed products.

    PubMed

    Turkec, Aydin; Kazan, Hande; Karacanli, Burçin; Lucas, Stuart J

    2015-08-01

    In this paper, DNA extraction methods have been evaluated to detect the presence of genetically modified organisms (GMOs) in maize food and feed products commercialised in Turkey. All the extraction methods tested performed well for the majority of maize foods and feed products analysed. However, the highest DNA content was achieved by the Wizard, Genespin or the CTAB method, all of which produced optimal DNA yield and purity for different maize food and feed products. The samples were then screened for the presence of GM elements, along with certified reference materials. Of the food and feed samples, 8 % tested positive for the presence of one GM element (NOS terminator), of which half (4 % of the total) also contained a second element (the Cauliflower Mosaic Virus 35S promoter). The results obtained herein clearly demonstrate the presence of GM maize in the Turkish market, and that the Foodproof GMO Screening Kit provides reliable screening of maize food and feed products.

  18. Spatial assessment of Argentinean genetic admixture with geographical information systems.

    PubMed

    Diaz-Lacava, Amalia; Walier, Maja; Penacino, Gustavo; Wienker, Thomas F; Baur, Max P

    2011-08-01

    In recent years there has been much attention to Argentinean population stratification. We were interested in assessing population stratification from a geographical perspective and summarizing it in form of maps. We mapped the genetic admixture of the extant male population in central and northern Argentina on the basis of forensic Y-chromosomal haplotypes. We addressed the question which group of genetically similar individuals is predominant in this area. Haplotypes containing seven Y-chromosomal short tandem repeat polymorphisms (Y-STRs), also known as microsatellites - DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393 - were constructed for 145 individuals, recruited in 10 provinces. 97 distinct haplotypes were clustered into four clusters according to molecular distances. A genetic geostatistical analysis was conducted with the open-source geographical information system GRASS GIS. For each haplotype cluster, the according frequency was spatially interpolated over the total study area. Juxtaposing the interpolation surfaces, we screened point-wisely the maximal frequency as well as the label of the respective cluster. The screening results were combined in one summary map. We repeated this procedure for the second maximal frequencies. The resulting maps subdivide the study area into continuous regions comprising one predominant group of similar haplotypes. The first summary map divides the study area into three regions and the second summary map divides the area into four regions. The results of our analysis indicate that two groups of similar European haplotypes alternatively dominate the largest extension of the Argentinean territory. A third group, including South-American haplotypes, dominates the indigenous northwestern Argentinean area. The last group, including worldwide dispersed haplotypes, preponderates in frequency in second place in central Argentina. Our findings confirm a widespread European paternal ancestry, a substantial Amerindian

  19. Genetic Redundancies Enhance Information Transfer in Noisy Regulatory Circuits

    PubMed Central

    Rodrigo, Guillermo; Poyatos, Juan F.

    2016-01-01

    Cellular decision making is based on regulatory circuits that associate signal thresholds to specific physiological actions. This transmission of information is subjected to molecular noise what can decrease its fidelity. Here, we show instead how such intrinsic noise enhances information transfer in the presence of multiple circuit copies. The result is due to the contribution of noise to the generation of autonomous responses by each copy, which are altogether associated with a common decision. Moreover, factors that correlate the responses of the redundant units (extrinsic noise or regulatory cross-talk) contribute to reduce fidelity, while those that further uncouple them (heterogeneity within the copies) can lead to stronger information gain. Overall, our study emphasizes how the interplay of signal thresholding, redundancy, and noise influences the accuracy of cellular decision making. Understanding this interplay provides a basis to explain collective cell signaling mechanisms, and to engineer robust decisions with noisy genetic circuits. PMID:27741249

  20. Privacy, the individual and genetic information: a Buddhist perspective.

    PubMed

    Hongladarom, Soraj

    2009-09-01

    Bioinformatics is a new field of study whose ethical implications involve a combination of bioethics, computer ethics and information ethics. This paper is an attempt to view some of these implications from the perspective of Buddhism. Privacy is a central concern in both computer/information ethics and bioethics, and with information technology being increasingly utilized to process biological and genetic data, the issue has become even more pronounced. Traditionally, privacy presupposes the individual self but as Buddhism does away with the ultimate conception of an individual self, it has to find a way to analyse and justify privacy that does not presuppose such a self. It does this through a pragmatic conception that does not depend on a positing of the substantial self, which is then found to be unnecessary for an effective protection of privacy. As it may be possible one day to link genetic data to individuals, the Buddhist conception perhaps offers a more flexible approach, as what is considered to be integral to an individual person is not fixed in objectivity but depends on convention.

  1. Evaluation of Faecalibacterium 16S rDNA genetic markers for accurate identification of swine faecal waste by quantitative PCR.

    PubMed

    Duan, Chuanren; Cui, Yamin; Zhao, Yi; Zhai, Jun; Zhang, Baoyun; Zhang, Kun; Sun, Da; Chen, Hang

    2016-10-01

    A genetic marker within the 16S rRNA gene of Faecalibacterium was identified for use in a quantitative PCR (qPCR) assay to detect swine faecal contamination in water. A total of 146,038 bacterial sequences were obtained using 454 pyrosequencing. By comparative bioinformatics analysis of Faecalibacterium sequences with those of numerous swine and other animal species, swine-specific Faecalibacterium 16S rRNA gene sequences were identified and Polymerase Chain Okabe (PCR) primer sets designed and tested against faecal DNA samples from swine and non-swine sources. Two PCR primer sets, PFB-1 and PFB-2, showed the highest specificity to swine faecal waste and had no cross-reaction with other animal samples. PFB-1 and PFB-2 amplified 16S rRNA gene sequences from 50 samples of swine with positive ratios of 86 and 90%, respectively. We compared swine-specific Faecalibacterium qPCR assays for the purpose of quantifying the newly identified markers. The quantification limits (LOQs) of PFB-1 and PFB-2 markers in environmental water were 6.5 and 2.9 copies per 100 ml, respectively. Of the swine-associated assays tested, PFB-2 was more sensitive in detecting the swine faecal waste and quantifying the microbial load. Furthermore, the microbial abundance and diversity of the microbiomes of swine and other animal faeces were estimated using operational taxonomic units (OTUs). The species specificity was demonstrated for the microbial populations present in various animal faeces. PMID:27353369

  2. Current understanding of genetics and genetic testing and information needs and preferences of adults with inherited retinal disease.

    PubMed

    McKibbin, Martin; Ahmed, Mushtaq; Allsop, Matthew J; Downey, Louise; Gale, Richard; Grant, Hilary Louise; Potrata, Barbara; Willis, Thomas A; Hewison, Jenny

    2014-09-01

    Advances in sequencing technology and the movement of genetic testing into all areas of medicine will increase opportunities for molecular confirmation of a clinical diagnosis. For health-care professionals without formal genetics training, there is a need to know what patients understand about genetics and genetic testing and their information needs and preferences for the disclosure of genetic testing results. These topics were explored during face-to-face interviews with 50 adults with inherited retinal disease, selected in order to provide a diversity of opinions. Participants had variable understanding of genetics and genetic testing, including basic concepts such as inheritance patterns and the risk to dependents, and many did not understand the term 'genetic counselling'. Most were keen for extra information on the risk to others, the process for genetic testing and how to share the information with other family members. Participants were divided as to whether genetic testing should be offered at the time of the initial diagnosis or later. Many would prefer the results to be given by face-to-face consultation, supplemented by further information in a format accessible to those with visual impairment. Health-care professionals and either leaflets or websites of trusted agencies were the preferred sources of information. Permission should be sought for disclosure of genetic information to other family members. The information needs of many patients with inherited retinal disease appear to be unmet. An understanding of their information needs and preferences is required to help health-care professionals provide optimal services that meet patient expectations. PMID:24398793

  3. Individual olfactory perception reveals meaningful nonolfactory genetic information.

    PubMed

    Secundo, Lavi; Snitz, Kobi; Weissler, Kineret; Pinchover, Liron; Shoenfeld, Yehuda; Loewenthal, Ron; Agmon-Levin, Nancy; Frumin, Idan; Bar-Zvi, Dana; Shushan, Sagit; Sobel, Noam

    2015-07-14

    Each person expresses a potentially unique subset of ∼ 400 different olfactory receptor subtypes. Given that the receptors we express partially determine the odors we smell, it follows that each person may have a unique nose; to capture this, we devised a sensitive test of olfactory perception we termed the "olfactory fingerprint." Olfactory fingerprints relied on matrices of perceived odorant similarity derived from descriptors applied to the odorants. We initially fingerprinted 89 individuals using 28 odors and 54 descriptors. We found that each person had a unique olfactory fingerprint (P < 10(-10)), which was odor specific but descriptor independent. We could identify individuals from this pool using randomly selected sets of 7 odors and 11 descriptors alone. Extrapolating from this data, we determined that using 34 odors and 35 descriptors we could individually identify each of the 7 billion people on earth. Olfactory perception, however, fluctuates over time, calling into question our proposed perceptual readout of presumably stable genetic makeup. To test whether fingerprints remain informative despite this temporal fluctuation, building on the linkage between olfactory receptors and HLA, we hypothesized that olfactory perception may relate to HLA. We obtained olfactory fingerprints and HLA typing for 130 individuals, and found that olfactory fingerprint matching using only four odorants was significantly related to HLA matching (P < 10(-4)), such that olfactory fingerprints can save 32% of HLA tests in a population screen (P < 10(-6)). In conclusion, a precise measure of olfactory perception reveals meaningful nonolfactory genetic information.

  4. 78 FR 78462 - Open Government: Use of Genetic Information in Documenting and Evaluating Disability; Extension...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-26

    ... not purchase genetic testing to evaluate disability. However, we do consider all evidence in the record, including genetic testing and other genetic medical evidence, when we make a determination or... ADMINISTRATION Open Government: Use of Genetic Information in Documenting and Evaluating Disability; Extension...

  5. 78 FR 70617 - Open Government: Use of Genetic Information in Documenting and Evaluating Disability

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-26

    ... current, long-standing policy, we do not purchase genetic testing to evaluate disability. However, we do consider all evidence in the record, including genetic testing and other genetic medical evidence, when we... ADMINISTRATION Open Government: Use of Genetic Information in Documenting and Evaluating Disability...

  6. 76 FR 72424 - Submission for OMB Review; Comment Request Information Program on the Genetic Testing Registry

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-23

    ... Program on the Genetic Testing Registry AGENCY: National Institutes of Health (NIH), PHS, DHHS. ACTION... control number. Proposed Collection: Title: The Genetic Testing Registry; Type of Information Collection... developing a voluntary registry of genetic tests. The Genetic Testing Registry (GTR) will provide...

  7. How Can Psychological Science Inform Research About Genetic Counseling for Clinical Genomic Sequencing?

    PubMed Central

    Rini, Christine; Bernhardt, Barbara A.; Roberts, J. Scott; Christensen, Kurt D.; Evans, James P.; Brothers, Kyle B.; Roche, Myra I.; Berg, Jonathan S.; Henderson, Gail E.

    2016-01-01

    Next generation genomic sequencing technologies (including whole genome or whole exome sequencing) are being increasingly applied to clinical care. Yet, the breadth and complexity of sequencing information raise questions about how best to communicate and return sequencing information to patients and families in ways that facilitate comprehension and optimal health decisions. Obtaining answers to such questions will require multidisciplinary research. In this paper, we focus on how psychological science research can address questions related to clinical genomic sequencing by explaining emotional, cognitive, and behavioral processes in response to different types of genomic sequencing information (e.g., diagnostic results and incidental findings). We highlight examples of psychological science that can be applied to genetic counseling research to inform the following questions: (1) What factors influence patients' and providers' informational needs for developing an accurate understanding of what genomic sequencing results do and do not mean?; (2) How and by whom should genomic sequencing results be communicated to patients and their family members?; and (3) How do patients and their families respond to uncertainties related to genomic information? PMID:25488723

  8. What is genetic information, and why is it significant? A contextual, contrastive, approach.

    PubMed

    Manson, Neil C

    2006-01-01

    Is genetic information of special ethical significance? Does it require special regulation? There is considerable contemporary debate about this question (the 'genetic exceptionalism' debate). 'Genetic information' is an ambiguous term and, as an aid to avoiding conflation in the genetic exceptionalism debate, a detailed account is given of just how and why 'genetic information' is ambiguous. Whilst ambiguity is a ubiquitous problem of communication, it is suggested that 'genetic information' is ambiguous in a particular way, one that gives rise to the problem of 'significance creep' (i.e., where claims about the significance of certain kinds of genetic information in one context influence our thinking about the significance of other kinds of genetic information in other contexts). A contextual and contrastive methodology is proposed: evaluating the significance of genetic information requires us to be sensitive to the polysemy of 'genetic information' across contexts and then examine the contrast in significance (if any) of genetic, as opposed to nongenetic, information within contexts. This, in turn, suggests that a proper solution to the regulatory question requires us to pay more attention to how and why information, and its acquisition, possession and use, come to be of ethical significance.

  9. Patient autonomy and relatives' right to know genetic information.

    PubMed

    Gilbar, Roy

    2007-12-01

    One of the most difficult issues doctors face is a conflict between their professional duties. Such a conflict may arise when doctors know that information has implications not only for patients but also for family members but their duty of confidentiality prevents them from disclosing it. A comparative analysis of English and Israeli medical law reveals that the doctors' duty is based on two principles: a liberal perception of patient autonomy and an overriding utilitarian principle of prevention of harm. However, socio-medical research indicates that these principles do not entirely reflect the views of patients and doctors and are too narrow to deal with the complex situations in practice. Thus, it is argued that the doctor's legal duty of confidentiality should be reconsidered and qualified when it concerns the family. It is suggested that if medical law seeks to recognize the various interests family members have in genetic information then we should consider a different approach, founded on a relational interpretation of autonomy and communitarian notions of solidarity and moral responsibility. This approach perceives confidentiality and privacy as embracing the family unit, based on the view that close relatives are not entirely outside the private sphere of the individual but rather are integral to his or her identity. Thus, to the utilitarian mechanism available in medical law this approach adds a social criterion: The effect any decision (to disclose or not to disclose) will have on the familial relationship and on the dynamics of the particular family. This will provide a more flexible and workable alternative for doctors to resolve familial tensions over access to genetic information.

  10. Genetic information: Special or not? Responses from focus groups with members of a health maintenance organization.

    PubMed

    Diergaarde, Brenda; Bowen, Deborah J; Ludman, Evette J; Culver, Julie O; Press, Nancy; Burke, Wylie

    2007-03-15

    Genetic information is used increasingly in health care. Some experts have argued that genetic information is qualitatively different from other medical information and, therefore, raises unique social issues. This view, called "genetic exceptionalism," has importantly influenced recent policy efforts. Others have argued that genetic information is like other medical information and that treating it differently may actually result in unintended disparities. Little is known about how the general public views genetic information. To identify opinions about implications of genetic and other medical information among the general population, we conducted a series of focus groups in Seattle, WA. Participants were women and men between ages 18 and 74, living within 30 miles of Seattle and members of the Group Health Cooperative. A structured discussion guide was used to ensure coverage of all predetermined topics. Sessions lasted approximately 2 hr; were audio taped and transcribed. The transcripts formed the basis of the current analysis. Key findings included the theme that genetic information was much like other medical information and that all sensitive medical information should be well protected. Personal choice (i.e., the right to choose whether to know health risk information and to control who else knows) was reported to be of crucial importance. Participants had an understanding of the tensions involved in protecting privacy versus sharing medical information to help another person. These data may guide future research and policy concerning the use and protection of medical information, including genetic information.

  11. Understanding of genetic information in higher secondary students in northeast India and the implications for genetics education.

    PubMed

    Chattopadhyay, Ansuman

    2005-01-01

    Since the work of Watson and Crick in the mid-1950s, the science of genetics has become increasingly molecular. The development of recombinant DNA technologies by the agricultural and pharmaceutical industries led to the introduction of genetically modified organisms (GMOs). By the end of the twentieth century, reports of animal cloning and recent completion of the Human Genome Project (HGP), as well techniques developed for DNA fingerprinting, gene therapy and others, raised important ethical and social issues about the applications of such technologies. For citizens to understand these issues, appropriate genetics education is needed in schools. A good foundation in genetics also requires knowledge and understanding of topics such as structure and function of cells, cell division, and reproduction. Studies at the international level report poor understanding by students of genetics and genetic technologies, with widespread misconceptions at various levels. Similar studies were nearly absent in India. In this study, I examine Indian higher secondary students' understanding of genetic information related to cells and transmission of genetic information during reproduction. Although preliminary in nature, the results provide cause for concern over the status of genetics education in India. The nature of students' conceptual understandings and possible reasons for the observed lack of understanding are discussed.

  12. Consumer perception of genetically modified organisms and sources of information.

    PubMed

    Wunderlich, Shahla; Gatto, Kelsey A

    2015-11-01

    Genetically modified organisms (GMOs) have been available for commercial purchase since the 1990s, allowing producers to increase crop yields through bioengineering that creates herbicide-resistant and insect-resistant varieties. However, consumer knowledge about GMOs has not increased at the same rate as the adoption of GMO crops. Consumers worldwide are displaying limited understanding, misconceptions, and even unfamiliarity with GMO food products. Many consumers report that they receive information about GMO food products from the media, Internet, and other news sources. These sources may be less reliable than scientific experts whom consumers trust more to present the facts. Although many in the United States support mandatory GMO labeling (similar to current European standards), consumer awareness of current GMO labeling is low. A distinction must also be made between GMO familiarity and scientific understanding, because those who are more familiar with it tend to be more resistant to bioengineering, whereas those with higher scientific knowledge scores tend to have less negative attitudes toward GMOs. This brings to question the relation between scientific literacy, sources of information, and overall consumer knowledge and perception of GMO foods. PMID:26567205

  13. Consumer perception of genetically modified organisms and sources of information.

    PubMed

    Wunderlich, Shahla; Gatto, Kelsey A

    2015-11-01

    Genetically modified organisms (GMOs) have been available for commercial purchase since the 1990s, allowing producers to increase crop yields through bioengineering that creates herbicide-resistant and insect-resistant varieties. However, consumer knowledge about GMOs has not increased at the same rate as the adoption of GMO crops. Consumers worldwide are displaying limited understanding, misconceptions, and even unfamiliarity with GMO food products. Many consumers report that they receive information about GMO food products from the media, Internet, and other news sources. These sources may be less reliable than scientific experts whom consumers trust more to present the facts. Although many in the United States support mandatory GMO labeling (similar to current European standards), consumer awareness of current GMO labeling is low. A distinction must also be made between GMO familiarity and scientific understanding, because those who are more familiar with it tend to be more resistant to bioengineering, whereas those with higher scientific knowledge scores tend to have less negative attitudes toward GMOs. This brings to question the relation between scientific literacy, sources of information, and overall consumer knowledge and perception of GMO foods.

  14. Genetics and immunotherapy: using the genetic landscape of gliomas to inform management strategies.

    PubMed

    Wang, Joanna Y; Bettegowda, Chetan

    2015-07-01

    Recent work in genetics has identified essential driver mutations in gliomas and has profoundly changed our understanding of tumorigenesis. New insights into the molecular basis of glioma has informed the development of therapies demonstrating considerable potential, including immunotherapeutic approaches such as peptide and dendritic cell vaccines against EGFRvIII. However, the selective targeting of one component of a dysregulated pathway may be inadequate for a durable clinical response, given the intratumoral heterogeneity of glioblastoma (GBM) and hypermutated profiles displayed by tumor recurrences. Immune checkpoint blockade with anti-cytotoxic T lymphocyte antigen-4 (CTLA) and anti-programmed cell death 1 (PD-1) have demonstrated encouraging results in clinical trials with other solid tumors, and recent data suggest that this type of therapy may be particularly useful for tumors with high mutational burdens. Although the survival for patients with GBM has remains grim, the use of immunotherapy may finally change patient outcomes.

  15. Race, Genetics and Medicine: New Information, Enduring Questions

    SciTech Connect

    Beckwith, Jonathan R.

    2008-08-01

    Final Report on Conference held on April 9, 2005 and its Sequelae The Conference, “Race, Genetics and Medicine: New Information, Enduring Questions,” was held on Saturday, April 9, 2005 in the Science Center, Lecture Hall D at Harvard University, Cambridge, MA. Approximately 150 people attended. The audience was composed mainly of college and graduate school science students and postdoctoral fellows, some science and medical school faculty, science teachers at various levels, journalists and interested members of the public. The keynote speaker and the panelists reflected different academic disciplines (genetics, medicine, anthropology, sociology) and a CEO of a biotechnology company with background in medicine and law. They also presented different perspectives on the utility of race concepts in medicine and even on the use of the word “race.” While the talks often involved descriptions of genetic approaches that were not simple to explain, the speakers did an effective job of getting across the gist of studies that have been carried out on these issues. Although no consensus was reached, the conference gave the audience the opportunity to understand the issues and to have the tools to follow the debates in the future. Our strongest feedback was from attendees who had heard of the race and genetics issues through various media, but did not have a sense of what they were really about. They reported to us that they now felt they understood the basis of these discussions. Our post-conference activities have been successfully completed. While we had proposed to make available transcripts of the talks to the public through a Website, some of the speakers would not agree to have their presentations available in this way. Therefore, we asked permission from the DOE to use the funds to prepare classroom lesson plans for high school students to discuss the issues. These were prepared over a year-long period by the Genetic Screening Study Group Members with an

  16. Genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Capsicum represents one of several well characterized Solanaceous genera. A wealth of classical and molecular genetics research is available for the genus. Information gleaned from its cultivated relatives, tomato and potato, provide further insight for basic and applied studies. Early ...

  17. Evolutionary triangulation: informing genetic association studies with evolutionary evidence.

    PubMed

    Huang, Minjun; Graham, Britney E; Zhang, Ge; Harder, Reed; Kodaman, Nuri; Moore, Jason H; Muglia, Louis; Williams, Scott M

    2016-01-01

    Genetic studies of human diseases have identified many variants associated with pathogenesis and severity. However, most studies have used only statistical association to assess putative relationships to disease, and ignored other factors for evaluation. For example, evolution is a factor that has shaped disease risk, changing allele frequencies as human populations migrated into and inhabited new environments. Since many common variants differ among populations in frequency, as does disease prevalence, we hypothesized that patterns of disease and population structure, taken together, will inform association studies. Thus, the population distributions of allelic risk variants should reflect the distributions of their associated diseases. Evolutionary Triangulation (ET) exploits this evolutionary differentiation by comparing population structure among three populations with variable patterns of disease prevalence. By selecting populations based on patterns where two have similar rates of disease that differ substantially from a third, we performed a proof of principle analysis for this method. We examined three disease phenotypes, lactase persistence, melanoma, and Type 2 diabetes mellitus. We show that for lactase persistence, a phenotype with a simple genetic architecture, ET identifies the key gene, lactase. For melanoma, ET identifies several genes associated with this disease and/or phenotypes related to it, such as skin color genes. ET was less obviously successful for Type 2 diabetes mellitus, perhaps because of the small effect sizes in known risk loci and recent environmental changes that have altered disease risk. Alternatively, ET may have revealed new genes involved in conferring disease risk for diabetes that did not meet nominal GWAS significance thresholds. We also compared ET to another method used to filter for phenotype associated genes, population branch statistic (PBS), and show that ET performs better in identifying genes known to associate with

  18. The utility of immunohistochemistry for providing genetic information on tumors.

    PubMed

    Chan, John K C; Ip, Yiu-Tung; Cheuk, Wah

    2013-10-01

    With advances in immunohistochemical technology and growing knowledge of the molecular genetics of tumors, immunohistochemistry is playing an increasingly important role in providing genetic information for tumors. Specific chromosomal translocations can be demonstrated through detection of the protein product of one of the genes involved in gene fusion (such as BCL2, cyclin D, and ALK). Some mutations can be detected by (1) aberrant localization of the protein product (such as β-catenin and nucleophosmin), (2) abnormal accumulation of the protein product as a result of stabilization of the protein (such as p53), and (3) mutation-specific antibodies directed against the mutant protein (such as isocitrate dehydrogenase gene R132H mutation, epidermal growth factor receptor gene L858R and exon 19 deletion mutations, and BRAF gene V600E mutation). Gene deletion or loss of function can be demonstrated by the loss of immunostaining for the protein product (such as mismatch repair proteins in microsatellite-unstable tumors, E-cadherin in lobular carcinoma of the breast, and INI1 in rhabdoid tumors, atypical teratoid/rhabdoid tumors, and epithelioid sarcomas). Gene amplification can be demonstrated by overexpression of the protein product (such as HER2 in breast and gastric cancers, and MDM2 or CDK4 in well-differentiated/dedifferentiated liposarcomas). Viruses associated with tumors can be demonstrated directly (such as Epstein-Barr virus latent membrane protein-1 in Hodgkin lymphomas, human herpesvirus 8 in Kaposi sarcomas, and Merkel cell polyomavirus in Merkel cell carcinomas) or by a surrogate marker (such as p16 in human papillomavirus infection). In this review, examples are given to illustrate the principles and pitfalls of these applications. PMID:24065374

  19. Evolutionary triangulation: informing genetic association studies with evolutionary evidence.

    PubMed

    Huang, Minjun; Graham, Britney E; Zhang, Ge; Harder, Reed; Kodaman, Nuri; Moore, Jason H; Muglia, Louis; Williams, Scott M

    2016-01-01

    Genetic studies of human diseases have identified many variants associated with pathogenesis and severity. However, most studies have used only statistical association to assess putative relationships to disease, and ignored other factors for evaluation. For example, evolution is a factor that has shaped disease risk, changing allele frequencies as human populations migrated into and inhabited new environments. Since many common variants differ among populations in frequency, as does disease prevalence, we hypothesized that patterns of disease and population structure, taken together, will inform association studies. Thus, the population distributions of allelic risk variants should reflect the distributions of their associated diseases. Evolutionary Triangulation (ET) exploits this evolutionary differentiation by comparing population structure among three populations with variable patterns of disease prevalence. By selecting populations based on patterns where two have similar rates of disease that differ substantially from a third, we performed a proof of principle analysis for this method. We examined three disease phenotypes, lactase persistence, melanoma, and Type 2 diabetes mellitus. We show that for lactase persistence, a phenotype with a simple genetic architecture, ET identifies the key gene, lactase. For melanoma, ET identifies several genes associated with this disease and/or phenotypes related to it, such as skin color genes. ET was less obviously successful for Type 2 diabetes mellitus, perhaps because of the small effect sizes in known risk loci and recent environmental changes that have altered disease risk. Alternatively, ET may have revealed new genes involved in conferring disease risk for diabetes that did not meet nominal GWAS significance thresholds. We also compared ET to another method used to filter for phenotype associated genes, population branch statistic (PBS), and show that ET performs better in identifying genes known to associate with

  20. The impact of information order on intentions to undergo predictive genetic testing: an experimental study.

    PubMed

    Morrison, Val; Henderson, Bethan J; Taylor, Caroline; A'Ch Dafydd, Nonn; Unwin, Abbie

    2010-10-01

    As predictive genetic testing availability increases so does our need to understand factors associated with test uptake. This study tests whether the order positive and negative information about genetic testing for breast cancer is presented in affects intention to take a genetic test. Eighty-four women were randomly allocated into three groups: (1) positive then negative information; (2) negative then positive information; and (3) a control group. A significant effect was found in relation to perceived risk, attitudes towards genetic testing, perceived disadvantages of testing and intention. Our findings point to a primacy effect, whereby information presented first has the greatest effect.

  1. [The substance of genetic information--nucleic acids].

    PubMed

    Brdička, R

    2012-01-01

    If we look at the history of our knowledge of nucleic acids, we would see in the distant past of 140 years Friedrich Miescher who had identified the acidic substance within the cell nucleus, which he called nuclein. About 70 years after his initial observation, this substance was connected with genetic information. This very substantial finding happened during the World War II. This was the impulse that research of nucleic acids received to speed up continuously growing mountain of information, which is more and more difficult to understand. Another eruption of new information about our genome was the result of ten years of intensive cooperation of many manufacturers divided into two competitive blocks which offered us knowledge of nucleotide sequence of all 46 DNA molecules. The year 2000 became the landmark marking the start of the postgenomic era. It did not mean that human genome was totally explored, but the cornerstone has been settled. Since then, we could concentrate our efforts on variability; use of the project of 1,000 genomes brought many important findings, eg. copy number variability (CNV) exceeds the single nucleotide polymophisms (SNP). Also intergenomic relationships, studies on function and pathways began to be much more understandable by elucidation of the genome primary structure. NGS as a tool also accelerated the epigenetic research. All this improved molecular diagnostics by discovering many new markers playing their role in disease and treatment and allowed us to enter the field of multifactorial illnesses including cancer. The progress in diagnostic technologies which has happened during the last decade forced our research teams to include other professions - eg. bioinformatics.

  2. How communication of genetic information within the family is addressed in genetic counselling: a systematic review of research evidence.

    PubMed

    Mendes, Álvaro; Paneque, Milena; Sousa, Liliana; Clarke, Angus; Sequeiros, Jorge

    2016-03-01

    Supporting consultands to communicate risk information with their relatives is key to obtaining the full benefits of genetic health care. To understand how health-care professionals address this issue in clinical practice and what interventions are used specifically to assist consultands in their communication of genetic information to appropriate relatives, we conducted a systematic review. Four electronic databases and four subject-specific journals were searched for papers published, in English, between January 1997 and May 2014. Of 2926 papers identified initially, 14 papers met the inclusion criteria for the review and were heterogeneous in design, setting and methods. Thematic data analysis has shown that dissemination of information within families is actively encouraged and supported by professionals. Three overarching themes emerged: (1) direct contact from genetic services: sending letters to relatives of mutation carriers; (2) professionals' encouragement of initially reluctant consultands to share relevant information with at-risk relatives and (3) assisting consultands in communicating genetic information to their at-risk relatives, which included as subthemes (i) psychoeducational guidance and (ii) written information aids. Findings suggest that professionals' practice and interventions are predicated on the need to proactively encourage family communication. We discuss this in the context of what guidance of consultands by professionals might be appropriate, as best practices to facilitate family communication, and of the limits to non-directiveness in genetic counselling.

  3. Genetics of Post-Traumatic Stress Disorder: Informing Clinical Conceptualizations and Promoting Future Research

    PubMed Central

    Nugent, Nicole R.; Amstadter, Ananda B.; Koenen, Karestan C.

    2009-01-01

    The purpose of this article is to provide an overview of genetic research involving post-traumatic stress disorder (PTSD). First, we summarize evidence for genetic influences on PTSD from family investigations. Second, we discuss the distinct contributions to our understanding of the genetics of PTSD permitted by twin studies. Finally, we summarize findings from molecular genetic studies, which have the potential to inform our understanding of underlying biological mechanisms for the development of PTSD. PMID:18412098

  4. Biological Information Transfer Beyond the Genetic Code: The Sugar Code

    NASA Astrophysics Data System (ADS)

    Gabius, H.-J.

    In the era of genetic engineering, cloning, and genome sequencing the focus of research on the genetic code has received an even further accentuation in the public eye. In attempting, however, to understand intra- and intercellular recognition processes comprehensively, the two biochemical dimensions established by nucleic acids and proteins are not sufficient to satisfactorily explain all molecular events in, for example, cell adhesion or routing. The consideration of further code systems is essential to bridge this gap. A third biochemical alphabet forming code words with an information storage capacity second to no other substance class in rather small units (words, sentences) is established by monosaccharides (letters). As hardware oligosaccharides surpass peptides by more than seven orders of magnitude in the theoretical ability to build isomers, when the total of conceivable hexamers is calculated. In addition to the sequence complexity, the use of magnetic resonance spectroscopy and molecular modeling has been instrumental in discovering that even small glycans can often reside in not only one but several distinct low-energy conformations (keys). Intriguingly, conformers can display notably different capacities to fit snugly into the binding site of nonhomologous receptors (locks). This process, experimentally verified for two classes of lectins, is termed "differential conformer selection." It adds potential for shifts of the conformer equilibrium to modulate ligand properties dynamically and reversibly to the well-known changes in sequence (including anomeric positioning and linkage points) and in pattern of substitution, for example, by sulfation. In the intimate interplay with sugar receptors (lectins, enzymes, and antibodies) the message of coding units of the sugar code is deciphered. Their recognition will trigger postbinding signaling and the intended biological response. Knowledge about the driving forces for the molecular rendezvous, i

  5. Balancing autonomy and responsibility: the ethics of generating and disclosing genetic information.

    PubMed

    Hallowell, N; Foster, C; Eeles, R; Ardern-Jones, A; Murday, V; Watson, M

    2003-04-01

    Using data obtained during a retrospective interview study of 30 women who had undergone genetic testing-BRCA1/2 mutation searching-this paper describes how women, previously diagnosed with breast/ovarian cancer, perceive their role in generating genetic information about themselves and their families. It observes that when describing their motivations for undergoing DNA testing and their experiences of disclosing genetic information within the family these women provide care based ethical justifications for their actions. Finally, it argues that generating genetic information and disclosing this information to kin raise different types of ethical issues. The implications of these findings for ethical debates about informed choice in the context of genetic testing are discussed.

  6. A Theory of Information Genetics: How Four Subforces Generate Information and the Implications for Total Quality Knowledge Management.

    ERIC Educational Resources Information Center

    Tsai, Bor-sheng

    2002-01-01

    Proposes a model called information genetics to elaborate on the origin of information generating. Explains conceptual and data models; and describes a software program that was developed for citation data mining, infomapping, and information repackaging for total quality knowledge management in Web representation. (Contains 112 references.)…

  7. Ethical issues in genetic research: disclosure and informed consent.

    PubMed

    Reilly, P R; Boshar, M F; Holtzman, S H

    1997-01-01

    As research to correlate genetic status with predisposition to disease has accelerated, so has the concern that participation in such studies creates the risk of genetic discrimination and emotional distress. There is a need to broaden disclosure during the consent process to ensure that potential subjects understand these risks and other issues and to address them in the consent form. We describe the broad approach that we have taken in regard to disclosure and consent in gene mapping studies.

  8. The significance of content knowledge for informal reasoning regarding socioscientific issues: Applying genetics knowledge to genetic engineering issues

    NASA Astrophysics Data System (ADS)

    Sadler, Troy D.; Zeidler, Dana L.

    2005-01-01

    This study focused on informal reasoning regarding socioscientific issues. It sought to explore how content knowledge influenced the negotiation and resolution of contentious and complex scenarios based on genetic engineering. Two hundred and sixty-nine students drawn from undergraduate natural science and nonnatural science courses completed a quantitative test of genetics concepts. Two subsets (n = 15 for each group) of the original sample representing divergent levels of content knowledge participated in individual interviews, during which they articulated positions, rationales, counterpositions, and rebuttals in response to three gene therapy scenarios and three cloning scenarios. A mixed-methods approach was used to examine the effects of content knowledge on the use of informal reasoning patterns and the quality of informal reasoning. Participants from both groups employed the same general patterns of informal reasoning. Data did indicate that differences in content knowledge were related to variations in informal reasoning quality. Participants, with more advanced understandings of genetics, demonstrated fewer instances of reasoning flaws, as defined by a priori criteria, and were more likely to incorporate content knowledge in their reasoning patterns than participants with more naïve understandings of genetics. Implications for instruction and future research are discussed.

  9. Informed consent, participation in, and withdrawal from a population based cohort study involving genetic analysis

    PubMed Central

    Matsui, K; Kita, Y; Ueshima, H

    2005-01-01

    Design: Descriptive analyses. Setting and participants: The study evaluated two non-genetic subcohorts comprising 3166 people attending for a health checkup during 2002, and two genetic subcohorts comprising 2195 people who underwent a checkup during 2003. Main outcome measurements: Analysis endpoints were differences in participation rates between the non-genetic and genetic subcohorts, differences between providing non-extensive and extensive preliminary information, and changes in participation status between baseline and at 6 months. Results: Participation rates in the genetic subcohorts were 4·7–9·3% lower than those in the non-genetic subcohorts. The odds ratios (OR) of participation in genetic research were between 0·60 and 0·77, and the OR for withdrawal from the research was over 7·70; providing preliminary extensive information about genetic research reduced the withdrawal risks (OR 0·15 for all dependent variables) but worsened participation rates (OR 0·63–0·74). Conclusions: The general population responded sceptically towards genetic research. It is crucial that genetic researchers utilise an informative and educational consent process worthy of public trust. PMID:15994356

  10. Cancer Genetic Counselor Information Needs for Risk Communication: A Qualitative Evaluation of Interview Transcripts

    PubMed Central

    Overby, Casey Lynnette; Chung, Wendy K.; Hripcsak, George; Kukafka, Rita

    2013-01-01

    Personalized medicine is a model of healthcare that is predictive, personalized, preventive and participatory (“P4 Medicine”). Genetic counselors are an ideal group to study when designing tools to support cancer P4 Medicine activities more broadly. The goal for this work was to gain a better understanding of the information cancer genetic counselors seek from their patients to facilitate effective information exchange for discussing risk. This was an analysis of a qualitative data set from interviews of eight cancer genetic counselors, recruited from three institutions. Genetic counselors at each site were interviewed using a semi-structured, open-ended questionnaire. A selective coding approach was used to determine major themes associated with genetic counseling information needs for communicating risk. We generated a model for understanding categories of genetic counseling information needs to support risk communication activities. Common activities for risk communication included risk assessment and tailoring communication. Categories of information needs included: (a) clinical patient characteristics, (b) social and cognitive patient characteristics and (c) patient motivation and goals for the genetic counseling session. A logical next step is for this model to inform the design of software systems for pre-visit patient planning and delivering just-in-time educational information to facilitate cancer risk communication activities. PMID:24358447

  11. Admixture mapping of end stage kidney disease genetic susceptibility using estimated mutual information ancestry informative markers

    PubMed Central

    2010-01-01

    Background The question of a genetic contribution to the higher prevalence and incidence of end stage kidney disease (ESKD) among African Americans (AA) remained unresolved, until recent findings using admixture mapping pointed to the association of a genomic locus on chromosome 22 with this disease phenotype. In the current study we utilize this example to demonstrate the utility of applying a multi-step admixture mapping approach. Methods A multi-step case only admixture mapping study, consisted of the following steps was designed: 1) Assembly of the sample dataset (ESKD AA); 2) Design of the estimated mutual information ancestry informative markers (n = 2016) screening panel 3); Genotyping the sample set whose size was determined by a power analysis (n = 576) appropriate for the initial screening panel; 4) Inference of local ancestry for each individual and identification of regions with increased AA ancestry using two different ancestry inference statistical approaches; 5) Enrichment of the initial screening panel; 6) Power analysis of the enriched panel 7) Genotyping of additional samples. 8) Re-analysis of the genotyping results to identify a genetic risk locus. Results The initial screening phase yielded a significant peak using the ADMIXMAP ancestry inference program applying case only statistics. Subgroup analysis of 299 ESKD patients with no history of diabetes yielded peaks using both the ANCESTRYMAP and ADMIXMAP ancestry inference programs. The significant peak was found on chromosome 22. Genotyping of additional ancestry informative markers on chromosome 22 that took into account linkage disequilibrium in the ancestral populations, and the addition of samples increased the statistical significance of the finding. Conclusions A multi-step admixture mapping analysis of AA ESKD patients replicated the finding of a candidate risk locus on chromosome 22, contributing to the heightened susceptibility of African Americans to develop non-diabetic ESKD, and

  12. Simple genetics language as source of miscommunication between genetics researchers and potential research participants in informed consent documents.

    PubMed

    Morgenstern, Justin; Hegele, Robert A; Nisker, Jeff

    2015-08-01

    Informed consent is based on communication, requiring language to convey meanings and ensure understandings. The purpose of this study was to investigate the use of language in informed consent documents used in the genetics research funded by Canadian Institutes of Health Research and Genome Canada. Consent documents were requested from the principal investigators in a recent round of funding. A qualitative content analysis was performed, supported by NVivo7™. Potential barriers to informed consent were identified, including language that was vague and variable, words with both technical and common meanings, novel phrases without clear meaning, a lack of definitions, and common concepts that assume new definitions in genetics research. However, we noted that difficulties in comprehension were often obscured because the words used were generally simple and familiar. We conclude that language gaps between researcher and potential research participants may unintentionally impair comprehension and ultimately impair informed consent in genomics research. PMID:24751688

  13. Informed consent for human genetic and genomic studies: a systematic review.

    PubMed

    Khan, A; Capps, B J; Sum, M Y; Kuswanto, C N; Sim, K

    2014-09-01

    As genetic and genomic studies grow in scale, there are ethical concerns related to the collection and use of genetic information. The emergence of large public databases potentially redefine the terms of participation in genetic and genomic research, and suggests the changing application of traditional ethical principles such as privacy or consent. For this study, we wanted to see whether such developments are reflected in the informed consent processes in human genetic and genomic studies. Therefore, we performed a systematic review of the empirical studies that examined informed consent involving large genetic databases in human genetic and genomic studies, grouped the identified issues related to the different stakeholders (including subjects, researchers, and institutional review boards) and discussed the limitations and implications of these findings. Major themes related to the place of bioethical considerations, procured tissues, people involved, process of informed consent and study procedures. Frequently raised issues included confidentiality of participants, documentation of informed consent, public attitudes, future use of participant samples or data, and disclosure of results. Awareness and attention to these bioethical issues as well as assiduousness in managing these concerns in genetic/genomic research would further strengthen and safeguard the rights, safety and well-being of genetic research participants.

  14. The Significance of Content Knowledge for Informal Reasoning regarding Socioscientific Issues: Applying Genetics Knowledge to Genetic Engineering Issues

    ERIC Educational Resources Information Center

    Sadler, Troy D.; Zeidler, Dana L.

    2005-01-01

    This study focused on informal reasoning regarding socioscientific issues. It sought to explore how content knowledge influenced the negotiation and resolution of contentious and complex scenarios based on genetic engineering. Two hundred and sixty-nine students drawn from undergraduate natural science and nonnatural science courses completed a…

  15. Searching Online Mendelian Inheritance in Man (OMIM) for information on genetic loci involved in human disease.

    PubMed

    Baxevanis, Andreas D

    2012-04-01

    Online Mendelian Inheritance in Man (OMIM) is a comprehensive compendium of information on human genes and genetic disorders, with a particular emphasis on the interplay between observed phenotypes and underlying genotypes. This unit focuses on the basic methodology for formulating OMIM searches and illustrates the types of information that can be retrieved from OMIM, including descriptions of clinical manifestations resulting from genetic abnormalities. This unit also provides information on additional relevant medical and molecular biology databases. A basic knowledge of OMIM should be part of the armamentarium of physicians and scientists with an interest in research on the clinical aspects of genetic disorders.

  16. The need to be aware and beware of the genetic information nondiscrimination act.

    PubMed

    Steck, Mary Beth; Eggert, Julia A

    2011-06-01

    Genetic advancements have presented numerous discrimination predicaments to individuals, the healthcare community, and legislators at state and federal levels. Oncology nurses should be knowledgeable about the Genetic Information Nondiscrimination Act of 2008 (GINA) and its applications to clinical practice. GINA is the first federal law passed to protect U.S. citizens with inherited disorders from being treated unfairly because of their genetic makeup. Understanding the legislation known as GINA, including how it modifies existing federal laws governing health insurance coverage and employment discrimination, can assist oncology nurses in providing important education and advocating for patients and their extended families. Federal agencies that govern and enforce GINA's provisions are identified. Case situations are included to demonstrate how to apply information concerning GINA to patients with cancer and their families who are considering or have already completed genetic testing. Privacy of genetic information is a timely issue but difficult to understand; therefore, provisions of GINA should be addressed and evaluated carefully.

  17. The role of cognitive switching in head-up displays. [to determine pilot ability to accurately extract information from either of two sources

    NASA Technical Reports Server (NTRS)

    Fischer, E.

    1979-01-01

    The pilot's ability to accurately extract information from either one or both of two superimposed sources of information was determined. Static, aerial, color 35 mm slides of external runway environments and slides of corresponding static head-up display (HUD) symbology were used as the sources. A three channel tachistoscope was utilized to show either the HUD alone, the scene alone, or the two slides superimposed. Cognitive performance of the pilots was assessed by determining the percentage of correct answers given to two HUD related questions, two scene related questions, or one HUD and one scene related question.

  18. An Introduction to Genetic Algorithms and to Their Use in Information Retrieval.

    ERIC Educational Resources Information Center

    Jones, Gareth; And Others

    1994-01-01

    Genetic algorithms, a class of nondeterministic algorithms in which the role of chance makes the precise nature of a solution impossible to guarantee, seem to be well suited to combinatorial-optimization problems in information retrieval. Provides an introduction to techniques and characteristics of genetic algorithms and illustrates their…

  19. A Fuzzy Genetic Algorithm Approach to an Adaptive Information Retrieval Agent.

    ERIC Educational Resources Information Center

    Martin-Bautista, Maria J.; Vila, Maria-Amparo; Larsen, Henrik Legind

    1999-01-01

    Presents an approach to a Genetic Information Retrieval Agent Filter (GIRAF) that filters and ranks documents retrieved from the Internet according to users' preferences by using a Genetic Algorithm and fuzzy set theory to handle the imprecision of users' preferences and users' evaluation of the retrieved documents. (Author/LRW)

  20. On Using Genetic Algorithms for Multimodal Relevance Optimization in Information Retrieval.

    ERIC Educational Resources Information Center

    Boughanem, M.; Christment, C.; Tamine, L.

    2002-01-01

    Presents a genetic relevance optimization process performed in an information retrieval system that uses genetic techniques for solving multimodal problems (niching) and query reformulation techniques. Explains that the niching technique allows the process to reach different relevance regions of the document space, and that query reformulations…

  1. Genetically Informative Research on Adolescent Substance Use: Methods, Findings, and Challenges

    ERIC Educational Resources Information Center

    Lynskey, Michael T.; Agrawal, Arpana; Heath, Andrew C.

    2010-01-01

    Objective: To provide an overview of the genetic epidemiology of substance use and misuse in adolescents. Method: A selective review of genetically informative research strategies, their limitations, and key findings examining issues related to the heritability of substance use and substance use disorders in children and adolescents is presented.…

  2. A Genetically Informed Study of the Intergenerational Transmission of Marital Instability

    ERIC Educational Resources Information Center

    D'Onofrio, Brian M.; Turkheimer, Eric; Emery, Robert E.; Harden, K. Paige; Slutske, Wendy S.; Heath, Andrew C.; Madden, Pamela A. F.; Martin, Nicholas G.

    2007-01-01

    Environmental or genetic influences, or both could account for the increased risk of divorce among the offspring of separated parents. Previous studies have used covariates to statistically control for confounds, but the present research is the first genetically informed study of the topic. The investigation used the Children of Twins Design with…

  3. The Effect of Genetic Risk Information and Health Risk Assessment on Compliance with Preventive Behaviors.

    ERIC Educational Resources Information Center

    Bamberg, Richard; And Others

    1990-01-01

    Results from a study of 82 males provide no statistical support and limited encouragement that genetic risk information may motivate persons to make positive changes in preventive health behaviors. Health risk assessments were used to identify subjects at risk for coronary heart disease or lung cancer because of genetic factors. (IAH)

  4. Disclosing Genetic Information to Family Members About Inherited Cardiac Arrhythmias: An Obligation or a Choice?

    PubMed

    Vavolizza, Rick D; Kalia, Isha; Erskine Aaron, Kathleen; Silverstein, Louise B; Barlevy, Dorit; Wasserman, David; Walsh, Christine; Marion, Robert W; Dolan, Siobhan M

    2015-08-01

    Inherited cardiac arrhythmias such as long QT syndrome and Brugada syndrome, present clinical as well as ethical, legal, and social challenges. Many individuals who carry a deleterious mutation are largely asymptomatic and therefore may not be diagnosed until after the occurrence of a personal or family member's cardiac event. The familial nature of inherited genetic information raises numerous ethical, legal, and social issues regarding the sharing of genetic information, particularly when an individual found to carry a deleterious mutation refuses to disclose his or her results to at-risk family members who could benefit from life-saving treatments. This qualitative study sought to understand the experiences with genetic testing for individuals (n = 50) with a personal or family history of cardiac events or sudden death. Unstructured in-person focus groups or interviews were conducted for each participant in the study. The recordings of these interviews were transcribed verbatim and subsequently analyzed and coded. Participants' comments regarding sharing of genetic information centered around four main themes: (1) motivation to disclose; (2) extent of disclosure; (3) effect of disclosure on family dynamics; and (4) reasons for not sharing genetic information. The majority of individuals believed that affected individuals are obligated to disclose genetic information to family members. In the era of personalized medicine, the disclosure of genetic information provides individuals the opportunities to learn about the genetics, disease characteristics, and treatment options in order to reduce morbidity and mortality in themselves and their family members. Further research is necessary to identify and explore the barriers to sharing genetic information with at-risk family members. PMID:25400212

  5. Disclosing Genetic Information to Family Members about Inherited Cardiac Arrhythmias: An Obligation or a Choice?

    PubMed Central

    Vavolizza, Rick D.; Kalia, Isha; Aaron, Kathleen Erskine; Silverstein, Louise B.; Barlevy, Dorit; Wasserman, David; Walsh, Christine; Marion, Robert W.; Dolan, Siobhan M.

    2014-01-01

    Inherited cardiac arrhythmias such as long QT syndrome and Brugada syndrome, present clinical as well as ethical, legal, and social challenges. Many individuals who carry a deleterious mutation are largely asymptomatic and therefore may not be diagnosed until after the occurrence of a personal or family member’s cardiac event. The familial nature of inherited genetic information raises numerous ethical, legal, and social issues regarding the sharing of genetic information, particularly when an individual found to carry a deleterious mutation refuses to disclose his or her results to at-risk family members who could benefit from life-saving treatments. This qualitative study sought to understand the experiences with genetic testing for individuals (n= 50) with a personal or family history of cardiac events or sudden death. Unstructured in-person focus groups or interviews were conducted for each participant in the study. The recordings of these interviews were transcribed verbatim and subsequently analyzed and coded. Participants’ comments regarding sharing of genetic information centered around four main themes: (1) motivation to disclose; (2) extent of disclosure; (3) effect of disclosure on family dynamics; and (4) reasons for not sharing genetic information. The majority of individuals believed that affected individuals are obligated to disclose genetic information to family members. In the era of personalized medicine, the disclosure of genetic information provides individuals the opportunities to learn about the genetics, disease characteristics, and treatment options in order to reduce morbidity and mortality in themselves and their family members. Further research is necessary to identify and explore the barriers to sharing genetic information with at-risk family members. PMID:25400212

  6. Counsellee's experience of cancer genetic counselling with pedigrees that automatically incorporate genealogical and cancer database information.

    PubMed

    Stefansdottir, Vigdis; Johannsson, Oskar Th; Skirton, Heather; Jonsson, Jon J

    2016-07-01

    While pedigree drawing software is often utilised in genetic services, the use of genealogical databases in genetic counselling is unusual. This is mainly because of the unavailability of such databases in most countries. Electronically generated pedigrees used for cancer genetic counselling in Iceland create pedigrees that automatically incorporate information from a large, comprehensive genealogy database and nation-wide cancer registry. The aim of this descriptive qualitative study was to explore counsellees' experiences of genetic services, including family history taking, using these electronically generated pedigrees. Four online focus groups with 19 participants were formed, using an asynchronous posting method. Participants were encouraged to discuss their responses to questions posted on the website by the researcher. The main themes arising were motivation, information and trust, impact of testing and emotional responses. Most of the participants expressed trust in the method of using electronically generated pedigrees, although some voiced worries about information safety. Many experienced worry and anxiety while waiting for results of genetic testing, but limited survival guilt was noted. Family communication was either unchanged or improved following genetic counselling. The use of electronically generated pedigrees was well received by participants, and they trusted the information obtained via the databases. Age did not seem to influence responses. These results may be indicative of the particular culture in Iceland, where genealogical information is well known and freely shared. Further studies are needed to determine whether use of similar approaches to genealogical information gathering may be acceptable elsewhere. PMID:27372834

  7. Counsellee's experience of cancer genetic counselling with pedigrees that automatically incorporate genealogical and cancer database information.

    PubMed

    Stefansdottir, Vigdis; Johannsson, Oskar Th; Skirton, Heather; Jonsson, Jon J

    2016-07-01

    While pedigree drawing software is often utilised in genetic services, the use of genealogical databases in genetic counselling is unusual. This is mainly because of the unavailability of such databases in most countries. Electronically generated pedigrees used for cancer genetic counselling in Iceland create pedigrees that automatically incorporate information from a large, comprehensive genealogy database and nation-wide cancer registry. The aim of this descriptive qualitative study was to explore counsellees' experiences of genetic services, including family history taking, using these electronically generated pedigrees. Four online focus groups with 19 participants were formed, using an asynchronous posting method. Participants were encouraged to discuss their responses to questions posted on the website by the researcher. The main themes arising were motivation, information and trust, impact of testing and emotional responses. Most of the participants expressed trust in the method of using electronically generated pedigrees, although some voiced worries about information safety. Many experienced worry and anxiety while waiting for results of genetic testing, but limited survival guilt was noted. Family communication was either unchanged or improved following genetic counselling. The use of electronically generated pedigrees was well received by participants, and they trusted the information obtained via the databases. Age did not seem to influence responses. These results may be indicative of the particular culture in Iceland, where genealogical information is well known and freely shared. Further studies are needed to determine whether use of similar approaches to genealogical information gathering may be acceptable elsewhere.

  8. Assignment of Calibration Information to Deeper Phylogenetic Nodes is More Effective in Obtaining Precise and Accurate Divergence Time Estimates.

    PubMed

    Mello, Beatriz; Schrago, Carlos G

    2014-01-01

    Divergence time estimation has become an essential tool for understanding macroevolutionary events. Molecular dating aims to obtain reliable inferences, which, within a statistical framework, means jointly increasing the accuracy and precision of estimates. Bayesian dating methods exhibit the propriety of a linear relationship between uncertainty and estimated divergence dates. This relationship occurs even if the number of sites approaches infinity and places a limit on the maximum precision of node ages. However, how the placement of calibration information may affect the precision of divergence time estimates remains an open question. In this study, relying on simulated and empirical data, we investigated how the location of calibration within a phylogeny affects the accuracy and precision of time estimates. We found that calibration priors set at median and deep phylogenetic nodes were associated with higher precision values compared to analyses involving calibration at the shallowest node. The results were independent of the tree symmetry. An empirical mammalian dataset produced results that were consistent with those generated by the simulated sequences. Assigning time information to the deeper nodes of a tree is crucial to guarantee the accuracy and precision of divergence times. This finding highlights the importance of the appropriate choice of outgroups in molecular dating. PMID:24855333

  9. Privacy and confidentiality of genetic information: what rules for the new science?

    PubMed

    Anderlik, M R; Rothstein, M A

    2001-01-01

    This review covers the ethical, legal, and policy issues associated with the generation and dissemination of genetic information. First, conceptual issues, such as the definition of terms and the description of two modes of analysis, are addressed. Research findings on public attitudes toward privacy and genetics and other factors relevant to policy making are also reviewed. Second, the example of genetic research is used to highlight the importance of attention to the intrinsic harms associated with violations of genetic privacy. Subtopics include national databases and biobanks, gene brokers, and pharmacogenomics. Third, the example of insurer access to genetic information is used to highlight the importance of attention to discrimination and other instrumental harms associated with failures of regulation. Fourth, a summary of the preceding sections leads into an outline of a program for realizing the benefits of the new science in a manner that affirms rather than erodes privacy and other important values.

  10. Evaluating online direct-to-consumer marketing of genetic tests: informed choices or buyers beware?

    PubMed

    Geransar, Rose; Einsiedel, Edna

    2008-03-01

    Commercialization of genetic technologies is expanding the horizons for the marketing and sales of genetic tests direct-to-consumers (DTCs). This study assesses the information provision and access requirements that are in place for genetic tests that are being advertised DTC over the Internet. Sets of key words specific to DTC genetic testing were entered into popular Internet search engines to generate a list of 24 companies engaging in DTC advertising. Company requirements for physician mediation, genetic counseling arrangements, and information provision were coded to develop categories for quantitative analysis within each variable. Results showed that companies offering risk assessment and diagnostic testing were most likely to require that testing be mediated by a clinician, and to recommend physician-arranged counseling. Companies offering enhancement testing were less likely to require physician mediation of services and more likely to provide long-distance genetic counseling. DTC advertisements often provided information on disease etiology; this was most common in the case of multifactorial diseases. The majority of companies cited outside sources to support the validity of claims about clinical utility of the tests being advertised; companies offering risk assessment tests most frequently cited all information sources. DTC advertising for genetic tests that lack independent professional oversight raises troubling questions about appropriate use and interpretation of these tests by consumers and carries implications for the standards of patient care. These implications are discussed in the context of a public healthcare system.

  11. The information value of non-genetic inheritance in plants and animals.

    PubMed

    English, Sinead; Pen, Ido; Shea, Nicholas; Uller, Tobias

    2015-01-01

    Parents influence the development of their offspring in many ways beyond the transmission of DNA. This includes transfer of epigenetic states, nutrients, antibodies and hormones, and behavioural interactions after birth. While the evolutionary consequences of such non-genetic inheritance are increasingly well understood, less is known about how inheritance mechanisms evolve. Here, we present a simple but versatile model to explore the adaptive evolution of non-genetic inheritance. Our model is based on a switch mechanism that produces alternative phenotypes in response to different inputs, including genes and non-genetic factors transmitted from parents and the environment experienced during development. This framework shows how genetic and non-genetic inheritance mechanisms and environmental conditions can act as cues by carrying correlational information about future selective conditions. Differential use of these cues is manifested as different degrees of genetic, parental or environmental morph determination. We use this framework to evaluate the conditions favouring non-genetic inheritance, as opposed to genetic determination of phenotype or within-generation plasticity, by applying it to two putative examples of adaptive non-genetic inheritance: maternal effects on seed germination in plants and transgenerational phase shift in desert locusts. Our simulation models show how the adaptive value of non-genetic inheritance depends on its mechanism, the pace of environmental change, and life history characteristics. PMID:25603120

  12. The Information Value of Non-Genetic Inheritance in Plants and Animals

    PubMed Central

    English, Sinead; Pen, Ido; Shea, Nicholas; Uller, Tobias

    2015-01-01

    Parents influence the development of their offspring in many ways beyond the transmission of DNA. This includes transfer of epigenetic states, nutrients, antibodies and hormones, and behavioural interactions after birth. While the evolutionary consequences of such non-genetic inheritance are increasingly well understood, less is known about how inheritance mechanisms evolve. Here, we present a simple but versatile model to explore the adaptive evolution of non-genetic inheritance. Our model is based on a switch mechanism that produces alternative phenotypes in response to different inputs, including genes and non-genetic factors transmitted from parents and the environment experienced during development. This framework shows how genetic and non-genetic inheritance mechanisms and environmental conditions can act as cues by carrying correlational information about future selective conditions. Differential use of these cues is manifested as different degrees of genetic, parental or environmental morph determination. We use this framework to evaluate the conditions favouring non-genetic inheritance, as opposed to genetic determination of phenotype or within-generation plasticity, by applying it to two putative examples of adaptive non-genetic inheritance: maternal effects on seed germination in plants and transgenerational phase shift in desert locusts. Our simulation models show how the adaptive value of non-genetic inheritance depends on its mechanism, the pace of environmental change, and life history characteristics. PMID:25603120

  13. Imaging or imagining? A neuroethics challenge informed by genetics.

    PubMed

    Illes, Judy; Racine, Eric

    2005-01-01

    From a twenty-first century partnership between bioethics and neuroscience, the modern field of neuroethics is emerging, and technologies enabling functional neuroimaging with unprecedented sensitivity have brought new ethical, social and legal issues to the forefront. Some issues, akin to those surrounding modern genetics, raise critical questions regarding prediction of disease, privacy and identity. However, with new and still-evolving insights into our neurobiology and previously unquantifiable features of profoundly personal behaviors such as social attitude, value and moral agency, the difficulty of carefully and properly interpreting the relationship between brain findings and our own self-concept is unprecedented. Therefore, while the ethics of genetics provides a legitimate starting point--even a backbone--for tackling ethical issues in neuroimaging, they do not suffice. Drawing on recent neuroimaging findings and their plausible real-world applications, we argue that interpretation of neuroimaging data is a key epistemological and ethical challenge. This challenge is two-fold. First, at the scientific level, the sheer complexity of neuroscience research poses challenges for integration of knowledge and meaningful interpretation of data. Second, at the social and cultural level, we find that interpretations of imaging studies are bound by cultural and anthropological frameworks. In particular, the introduction of concepts of self and personhood in neuroimaging illustrates the interaction of interpretation levels and is a major reason why ethical reflection on genetics will only partially help settle neuroethical issues. Indeed, ethical interpretation of such findings will necessitate not only traditional bioethical input but also a wider perspective on the construction of scientific knowledge.

  14. Imaging or Imagining? A Neuroethics Challenge Informed by Genetics

    PubMed Central

    Illes, Judy; Racine, Eric

    2006-01-01

    From a twenty-first century partnership between bioethics and neuroscience, the modern field of neuroethics is emerging, and technologies enabling functional neuroimaging with unprecedented sensitivity have brought new ethical, social and legal issues to the forefront. Some issues, akin to those surrounding modern genetics, raise critical questions regarding prediction of disease, privacy and identity. However, with new and still-evolving insights into our neurobiology and previously unquantifiable features of profoundly personal behaviors such as social attitude, value and moral agency, the difficulty of carefully and properly interpreting the relationship between brain findings and our own self-concept is unprecedented. Therefore, while the ethics of genetics provides a legitimate starting point—even a backbone—for tackling ethical issues in neuroimaging, they do not suffice. Drawing on recent neuroimaging findings and their plausible real-world applications, we argue that interpretation of neuroimaging data is a key epistemological and ethical challenge. This challenge is two-fold. First, at the scientific level, the sheer complexity of neuroscience research poses challenges for integration of knowledge and meaningful interpretation of data. Second, at the social and cultural level, we find that interpretations of imaging studies are bound by cultural and anthropological frameworks. In particular, the introduction of concepts of self and personhood in neuroimaging illustrates the interaction of interpretation levels and is a major reason why ethical reflection on genetics will only partially help settle neuroethical issues. Indeed, ethical interpretation of such findings will necessitate not only traditional bioethical input but also a wider perspective on the construction of scientific knowledge. PMID:16036688

  15. Can genetic risk information enhance motivation for smoking cessation? An analogue study.

    PubMed

    Wright, Alison J; French, David P; Weinman, John; Marteau, Theresa M

    2006-11-01

    Protection motivation theory and the extended parallel processing model are used to predict the motivational impact of information regarding a genetic susceptibility to heart disease. One hundred ninety-eight smokers read 1 of 3 vignettes: gene positive, gene negative, or standard smoking risk information. Analyses examined whether the impact of type of risk information was moderated by smokers' self-efficacy (SE) levels. Key outcomes were intention to quit and intention to attend an information session about quitting. There were significant main effects of SE and of receiving gene-positive risk information on intentions to quit. There was a significant Risk x SE interaction on intentions to attend an information session. SE was not associated with intentions to attend the information session for smokers in the gene-positive group. Intentions to attend the session were negatively associated with SE for smokers in the lower risk groups. Implications for using genetic risk information to motivate smoking cessation are discussed.

  16. [The lack of information on genetically modified organisms in Brazil].

    PubMed

    Ribeiro, Isabelle Geoffroy; Marin, Victor Augustus

    2012-02-01

    This article presents a review about the labeling of products that have Genetically Modified Organisms (GMO), also called transgenic elements in their composition. It addresses the conventions, laws and regulations relating to such products currently governing the market, the adequacy of these existing standards and their acceptance by society. It also examines the importance of the cautionary principle when assessing the application of new technologies or technologies where little is known or where there is no relevant scientific knowledge about the potential risks to the environment, human health and society. PMID:22267031

  17. [The lack of information on genetically modified organisms in Brazil].

    PubMed

    Ribeiro, Isabelle Geoffroy; Marin, Victor Augustus

    2012-02-01

    This article presents a review about the labeling of products that have Genetically Modified Organisms (GMO), also called transgenic elements in their composition. It addresses the conventions, laws and regulations relating to such products currently governing the market, the adequacy of these existing standards and their acceptance by society. It also examines the importance of the cautionary principle when assessing the application of new technologies or technologies where little is known or where there is no relevant scientific knowledge about the potential risks to the environment, human health and society.

  18. State legislative efforts to regulate use and potential misuse of genetic information.

    PubMed

    McEwen, J E; Reilly, P R

    1992-09-01

    The purpose of this study was to review existing and proposed legislation specifically intended to regulate the collection, use, and potential misuse of genetic data. The study encompasses laws relating to confidentiality, informed consent, discrimination, and related issues. It excludes from consideration legislation relating to medical records generally that may bear indirectly on genetic information. It also excludes both legislation relating to the regulation of DNA data collection for law enforcement purposes and state laws relating to the confidentiality of data collected by newborn-screening programs. While relatively few laws that explicitly regulate the treatment of genetic information have been enacted to date, a considerable amount of activity is currently underway in the nation's legislatures. Although most of the bills under consideration are not comprehensive in scope, they reflect a growing societal awareness that the uncontrolled dissemination and use of genetic data entails significant risks.

  19. State legislative efforts to regulate use and potential misuse of genetic information.

    PubMed Central

    McEwen, J E; Reilly, P R

    1992-01-01

    The purpose of this study was to review existing and proposed legislation specifically intended to regulate the collection, use, and potential misuse of genetic data. The study encompasses laws relating to confidentiality, informed consent, discrimination, and related issues. It excludes from consideration legislation relating to medical records generally that may bear indirectly on genetic information. It also excludes both legislation relating to the regulation of DNA data collection for law enforcement purposes and state laws relating to the confidentiality of data collected by newborn-screening programs. While relatively few laws that explicitly regulate the treatment of genetic information have been enacted to date, a considerable amount of activity is currently underway in the nation's legislatures. Although most of the bills under consideration are not comprehensive in scope, they reflect a growing societal awareness that the uncontrolled dissemination and use of genetic data entails significant risks. PMID:1496992

  20. The Lunar Laser Ranging Experiment: Accurate ranges have given a large improvement in the lunar orbit and new selenophysical information.

    PubMed

    Bender, P L; Currie, D G; Poultney, S K; Alley, C O; Dicke, R H; Wilkinson, D T; Eckhardt, D H; Faller, J E; Kaula, W M; Mulholland, J D; Plotkin, H H; Silverberg, E C; Williams, J G

    1973-10-19

    The lunar ranging measurements now being made at the McDonald Observatory have an accuracy of 1 nsec in round-trip travel time. This corresponds to 15 cm in the one-way distance. The use of lasers with pulse-lengths of less than 1 nsec is expected to give an accuracy of 2 to 3 cm in the next few years. A new station is under construction in Hawaii, and additional stations in other countries are either in operation or under development. It is hoped that these stations will form the basis for a worldwide network to determine polar motion and earth rotation on a regular basis, and will assist in providing information about movement of the tectonic plates making up the earth's surface. Several mobile lunar ranging stations with telescopes having diameters of 1.0 m or less could, in the future, greatly extend the information obtainable about motions within and between the tectonic plates. The data obtained so far by the McDonald Observatory have been used to generate a new lunar ephemeris based on direct numerical integration of the equations of motion for the moon and planets. With this ephemeris, the range to the three Apollo retro-reflectors can be fit to an accuracy of 5 m by adjusting the differences in moments of inertia of the moon about its principal axes, the selenocentric coordinates of the reflectors, and the McDonald longitude. The accuracy of fitting the results is limited currently by errors of the order of an arc second in the angular orientation of the moon, as derived from the best available theory of how the moon rotates in response to the torques acting on it. Both a new calculation of the moon's orientation as a function of time based on direct numerical integration of the torque equations and a new analytic theory of the moon's orientation are expected to be available soon, and to improve considerably the accuracy of fitting the data. The accuracy already achieved routinely in lunar laser ranging represents a hundredfold improvement over any

  1. The Lunar Laser Ranging Experiment: Accurate ranges have given a large improvement in the lunar orbit and new selenophysical information.

    PubMed

    Bender, P L; Currie, D G; Poultney, S K; Alley, C O; Dicke, R H; Wilkinson, D T; Eckhardt, D H; Faller, J E; Kaula, W M; Mulholland, J D; Plotkin, H H; Silverberg, E C; Williams, J G

    1973-10-19

    The lunar ranging measurements now being made at the McDonald Observatory have an accuracy of 1 nsec in round-trip travel time. This corresponds to 15 cm in the one-way distance. The use of lasers with pulse-lengths of less than 1 nsec is expected to give an accuracy of 2 to 3 cm in the next few years. A new station is under construction in Hawaii, and additional stations in other countries are either in operation or under development. It is hoped that these stations will form the basis for a worldwide network to determine polar motion and earth rotation on a regular basis, and will assist in providing information about movement of the tectonic plates making up the earth's surface. Several mobile lunar ranging stations with telescopes having diameters of 1.0 m or less could, in the future, greatly extend the information obtainable about motions within and between the tectonic plates. The data obtained so far by the McDonald Observatory have been used to generate a new lunar ephemeris based on direct numerical integration of the equations of motion for the moon and planets. With this ephemeris, the range to the three Apollo retro-reflectors can be fit to an accuracy of 5 m by adjusting the differences in moments of inertia of the moon about its principal axes, the selenocentric coordinates of the reflectors, and the McDonald longitude. The accuracy of fitting the results is limited currently by errors of the order of an arc second in the angular orientation of the moon, as derived from the best available theory of how the moon rotates in response to the torques acting on it. Both a new calculation of the moon's orientation as a function of time based on direct numerical integration of the torque equations and a new analytic theory of the moon's orientation are expected to be available soon, and to improve considerably the accuracy of fitting the data. The accuracy already achieved routinely in lunar laser ranging represents a hundredfold improvement over any

  2. Pharmacogenetics: Using Genetic Information to Guide Drug Therapy

    PubMed Central

    CHANG, KU-LANG; WEITZEL, KRISTIN; SCHMIDT, SIEGFRIED

    2016-01-01

    Clinical pharmacogenetics, the use of genetic data to guide drug therapy decisions, is beginning to be used for medications commonly prescribed by family physicians. However, clinicians are largely unfamiliar with principles supporting clinical use of this type of data. For example, genetic variability in the cytochrome P450 2D6 drug metabolizing enzyme can alter the clinical effects of some opioid analgesics (e.g., codeine, tramadol), whereas variability in the CYP2C19 enzyme affects the antiplatelet agent clopidogrel. If testing is performed, patients who are ultrarapid or poor metabolizers of CYP2D6 should avoid codeine use (and possibly tramadol, hydrocodone, and oxycodone) because of the potential for increased toxicity or lack of effectiveness. Patients undergoing percutaneous coronary intervention for acute coronary syndromes who are known to be poor metabolizers of CYP2C19 should consider alternate antiplatelet therapy (e.g., ticagrelor, prasugrel). Some guidelines are available that address appropriate drug therapy changes, and others are in development. Additionally, a number of clinical resources are emerging to support family physicians in the use of pharmacogenetics. When used appropriately, pharmacogenetic testing can be a practical tool to optimize drug therapy and avoid medication adverse effects. PMID:26447442

  3. Pharmacogenetics: Using Genetic Information to Guide Drug Therapy.

    PubMed

    Chang, Ku-Lang; Weitzel, Kristin; Schmidt, Siegfried

    2015-10-01

    Clinical pharmacogenetics, the use of genetic data to guide drug therapy decisions, is beginning to be used for medications commonly prescribed by family physicians. However, clinicians are largely unfamiliar with principles supporting clinical use of this type of data. For example, genetic variability in the cytochrome P450 2D6 drug metabolizing enzyme can alter the clinical effects of some opioid analgesics (e.g., codeine, tramadol), whereas variability in the CYP2C19 enzyme affects the antiplatelet agent clopidogrel. If testing is performed, patients who are ultrarapid or poor metabolizers of CYP2D6 should avoid codeine use (and possibly tramadol, hydrocodone, and oxycodone) because of the potential for increased toxicity or lack of effectiveness. Patients undergoing percutaneous coronary intervention for acute coronary syndromes who are known to be poor metabolizers of CYP2C19 should consider alternate antiplatelet therapy (e.g., ticagrelor, prasugrel). Some guidelines are available that address appropriate drug therapy changes, and others are in development. Additionally, a number of clinical resources are emerging to support family physicians in the use of pharmacogenetics. When used appropriately, pharmacogenetic testing can be a practical tool to optimize drug therapy and avoid medication adverse effects.

  4. Pharmacogenetics: Using Genetic Information to Guide Drug Therapy.

    PubMed

    Chang, Ku-Lang; Weitzel, Kristin; Schmidt, Siegfried

    2015-10-01

    Clinical pharmacogenetics, the use of genetic data to guide drug therapy decisions, is beginning to be used for medications commonly prescribed by family physicians. However, clinicians are largely unfamiliar with principles supporting clinical use of this type of data. For example, genetic variability in the cytochrome P450 2D6 drug metabolizing enzyme can alter the clinical effects of some opioid analgesics (e.g., codeine, tramadol), whereas variability in the CYP2C19 enzyme affects the antiplatelet agent clopidogrel. If testing is performed, patients who are ultrarapid or poor metabolizers of CYP2D6 should avoid codeine use (and possibly tramadol, hydrocodone, and oxycodone) because of the potential for increased toxicity or lack of effectiveness. Patients undergoing percutaneous coronary intervention for acute coronary syndromes who are known to be poor metabolizers of CYP2C19 should consider alternate antiplatelet therapy (e.g., ticagrelor, prasugrel). Some guidelines are available that address appropriate drug therapy changes, and others are in development. Additionally, a number of clinical resources are emerging to support family physicians in the use of pharmacogenetics. When used appropriately, pharmacogenetic testing can be a practical tool to optimize drug therapy and avoid medication adverse effects. PMID:26447442

  5. Subjective sense of memory strength and the objective amount of information accurately remembered are related to distinct neural correlates at encoding.

    PubMed

    Qin, Shaozheng; van Marle, Hein J F; Hermans, Erno J; Fernández, Guillén

    2011-06-15

    Although commonly used, the term memory strength is not well defined in humans. Besides durability, it has been conceptualized by retrieval characteristics, such as subjective confidence associated with retrieval, or objectively, by the amount of information accurately retrieved. Behaviorally, these measures are not necessarily correlated, indicating that distinct neural processes may underlie them. Thus, we aimed at disentangling neural activity at encoding associated with either a subsequent subjective sense of memory strength or with a subsequent objective amount of information remembered. Using functional magnetic resonance imaging (fMRI), participants were scanned while incidentally encoding a series of photographs of complex scenes. The next day, they underwent two memory tests, quantifying memory strength either subjectively (confidence on remembering the gist of a scene) or objectively (the number of details accurately remembered within a scene). Correlations between these measurements were mutually partialed out in subsequent memory analyses of fMRI data. Results revealed that activation in left ventral lateral prefrontal cortex and temporoparietal junction predicted subsequent confidence ratings. In contrast, parahippocampal and hippocampal activity predicted the number of details remembered. Our findings suggest that memory strength may reflect a functionally heterogeneous set of (at least two) phenomena. One phenomenon appears related to prefrontal and temporoparietal top-down modulations, resulting in the subjective sense of memory strength that is potentially based on gist memory. The other phenomenon is likely related to medial-temporal binding processes, determining the amount of information accurately encoded into memory. Thus, our study dissociated two distinct phenomena that are usually described as memory strength.

  6. Genetically informative research on adolescent substance use: methods, findings and challenges

    PubMed Central

    Lynskey, Michael T.; Agrawal, Arpana; Heath, Andrew C.

    2010-01-01

    Objective To provide an overview of the genetic epidemiology of substance use and misuse in adolescents. Method We present a selective review of genetically informative research strategies, their limitations and key findings examining issues related to the heritability of substance use and substance use disorders in children and adolescents. Results Adoption, twin and extended family designs have established there is a strong heritable component to liability to nicotine, alcohol and illicit drug dependence in adults. However, shared environmental influences are relatively stronger in youth samples and at earlier stages of substance involvement (e.g., use). There is considerable overlap in the genetic influences associated with the abuse/ dependence across drug classes while shared genetic influences also contribute to the commonly observed associations between substance use disorders and both externalizing and, to a lesser extent, internalizing psychopathology. Rapid technological advances have made the identification of specific gene variants that influence risks for substance use disorders feasible and linkage and association (including genomewide association studies) have identified promising candidate genes implicated in the development of substance use disorders. Conclusions Studies using genetically informative research designs, including those that examine aggregate genetic factors and those examining specific gene variants, individually and in interaction with environmental influences, offer promising avenues not only for delineating genetic effects on substance use disorders but also for understanding the unfolding of risk across development and the interaction between environmental and genetic factors in the etiology of these disorders. PMID:21093770

  7. The use of genetic information in the insurance sector--a German perspective.

    PubMed

    Armbrüster, Christian; Obal, Monika

    2013-01-01

    The following paper offers an introduction to the legal framework concerning the use of genetic information in the insurance sector in Germany. The main contents and the controversial issues of the key regulation are examined. The aim of this rule being to secure human dignity by respecting the right to informational self-determination regarding genetic data, including the individual's right not to know about their genetic characteristics, there are a number of open issues which are being addressed. For instance, the influence of the prohibition to ask for genetic testing and to use the results of any such testing by the insurer is examined. This examination leads to some explicit results, such as the assumption that in addition to the ban on the use of genetic testing no questions about family medical history are admissible. The authors embark on the definition of genetic testing and the question to what extent the results of diagnostic genetic testing may still be made use of in the context of the insured person's obligation to display pre-existing conditions and diseases when the contract is concluded. In this respect distinctions between diagnostic and predictive genetic testing as well as between disease and disposition are drawn. Furthermore, the exceptions from the prohibition to use results of genetic testing are examined, and the scope of the prohibition of acceptance of results of genetic testing even if performed at the instigation of the insured is explored. Finally the consequences, encompassing criminal liability and private law ramifications, of the violation of the prohibition are presented. In this context, a narrow understanding of the aggravated criminal offence of using results of genetic testing with the intent to personal enrichment or in return for payments is developed. Finally the effects on the validity of the insurance contract and the question whether the insurer may be forced to conclude a contract are examined. PMID:24868956

  8. Toward a genetically-informed model of borderline personality disorder.

    PubMed

    Livesley, John

    2008-02-01

    This article describes a conceptual framework for describing borderline personality disorder (BPD) based on empirical studies of the phenotypic structure and genetic architecture of personality. The proposed phenotype has 2 components: (1) a description of core self and interpersonal pathology-the defining features of personality disorder-as these features are expressed in the disorder; and (2) a set of traits based on the anxious-dependent or emotional dysregulation factor of the four-factor model of PD. Four kinds of traits are described: emotional (anxiousness, emotional reactivity, emotional intensity, and pessimistic-anhedonia), interpersonal (submissiveness, insecure attachment, social apprehensiveness, and need for approval), cognitive (cognitive dysregulation), and self-harm (behaviors and ideas). Formulation of the phenotype was guided by the conceptualization of personality as a system of interrelated sub-systems. The psychopathology associated with BPD involves most components of the system. The trait structure of the disorder is assumed to reflect the genetic architecture of personality and individual traits are assumed to be based on adaptive mechanisms. It is suggested that borderline traits are organized around the trait of anxiousness and that an important feature of BPD is dysregulation of the threat management system leading to pervasive fearfulness and unstable emotions. The interpersonal traits are assumed to be heritable characteristics that evolved to deal with interpersonal threats that arose as a result of social living. The potential for unstable and conflicted interpersonal relationships that is inherent to the disorder is assumed to result from the interplay between the adaptive structure of personality and psychosocial adversity. The etiology of the disorder is discussed in terms of biological and environmental factors associated with each component of the phenotype.

  9. Assessing Website Quality in Context: Retrieving Information about Genetically Modified Food on the Web

    ERIC Educational Resources Information Center

    McInerney, Claire R.; Bird, Nora J.

    2005-01-01

    Introduction: Knowing the credibility of information about genetically modified food on the Internet is critical to the everyday life information seeking of consumers as they form opinions about this nascent agricultural technology. The Website Quality Evaluation Tool (WQET) is a valuable instrument that can be used to determine the credibility of…

  10. Information Recall in Genetic Counselling: A Pilot Study of Its Assessment.

    ERIC Educational Resources Information Center

    Michie, Susan; French, David; Allanson, Abi; Bobrow, Martin; Marteau, Theresa M.

    1997-01-01

    Validity of using genetic counselors' reports of information given in consultations as a measure of patient recall was studied. Counselors' reports were compared with tape recordings and patient follow-up calls. Measures include patient expectations, patient anxiety, demographics, patient recall, patient-defined important information, and…

  11. Journal Self-Citedness in "Journal Citation Reports" Library and Information Science and Genetics Journal Rankings.

    ERIC Educational Resources Information Center

    Nisonger, Thomas E.

    1998-01-01

    Investigates the effect of journal self-citedness on "Journal Citation Reports" (JCR) rankings of library and information science and genetics journals using data from 1994 on CD-ROM. Results for library and information science indicate that the effect of self-citedness on both JCR impact factor and total citation rankings was minimal. (Author/AEF)

  12. Optimizing information flow in small genetic networks. IV. Spatial coupling

    NASA Astrophysics Data System (ADS)

    Sokolowski, Thomas R.; Tkačik, Gašper

    2015-06-01

    We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the input) by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively different regulatory strategy emerges where individual cells respond to the input in a nearly steplike fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models.

  13. Spatio-temporal dynamics in the origin of genetic information

    NASA Astrophysics Data System (ADS)

    Kim, Pan-Jun; Jeong, Hawoong

    2005-04-01

    We study evolutionary processes induced by spatio-temporal dynamics in prebiotic evolution. Using numerical simulations, we demonstrate that hypercycles emerge from complex interaction structures in multispecies systems. In this work, we also find that ‘hypercycle hybrid’ protects the hypercycle from its environment during the growth process. There is little selective advantage for one hypercycle to maintain coexistence with others. This brings the possibility of the outcompetition between hypercycles resulting in the negative effect on information diversity. To enrich the information in hypercycles, symbiosis with parasites is suggested. It is shown that symbiosis with parasites can play an important role in the prebiotic immunology.

  14. Assessment of a decision aid to assist genetic testing research participants in the informed consent process.

    PubMed

    Sorenson, J R; Lakon, C; Spinney, T; Jennings-Grant, T

    2004-01-01

    Limited attention has been given to applying decision-making theories from psychology to the content and process of informed consent in genetic testing research. Data are presented from a study that developed and assessed a psychological theory-based decision aid as part of the informed consent process. This innovative approach assisted at-risk women in assessing the consequences of participating in a research project that offered them free hemophilia A genetic carrier testing. Results suggest: (1) the decision aid can be incorporated into the consent process with few problems; (2) women of varying educational backgrounds can complete the decision aid; (3) while women consider many consequences of genetic testing, their primary focus is on the implications for their family; and (4) this is in marked contrast to the typical benefit-harm statements prepared by researchers for genetic testing.

  15. Communicating genetic information in the family: enriching the debate through the notion of integrity.

    PubMed

    Boddington, Paula; Gregory, Maggie

    2008-12-01

    Genetic information about one individual often has medical and reproductive implications for that individual's relatives. There is a debate about whether policy on transmitting genetic information within the family should change to reflect this shared aspect of genetic information. Even if laws on medical confidentiality remain unchanged, there still remains the question of professional practice and whether, to what extent and by what means professionals should encourage disclosure within a family. The debate so far has tended to focus on who has a right to genetic information, or has a right to decline genetic information, frequently drawing on the notion of individual autonomy. There are significant divergences within this debate, and difficulties with the use of autonomy in this context have been noted. This paper draws on theoretical considerations as well as on qualitative empirical data to show that shifting from talk of autonomy to talk of integrity will greatly enrich and illuminate the issues. It becomes possible to gain deeper insights into the ethical significance of the timing and the manner of such communication, the character of recipients of knowledge, and the nuanced nature of communication and different levels of understanding within a family.

  16. Consumer reaction to information on the labels of genetically modified food

    PubMed Central

    Sebastian-Ponce, Miren Itxaso; Sanz-Valero, Javier; Wanden-Berghe, Carmina

    2014-01-01

    OBJECTIVE To analyze consumer opinion on genetically modified foods and the information included on the label. METHODS A systematic review of the scientific literature on genetically modified food labeling was conducted consulting bibliographic databases (Medline – via PubMed –, EMBASE, ISI-Web of knowledge, Cochrane Library Plus, FSTA, LILACS, CINAHL and AGRICOLA) using the descriptors “organisms, genetically modified” and “food labeling”. The search covered the first available date, up to June 2012, selecting relevant articles written in English, Portuguese or Spanish. RESULTS Forty articles were selected after applying the inclusion and exclusion criteria. All of them should have conducted a population-based intervention focused on consumer awareness of genetically modified foods and their need or not, to include this on the label. The consumers expressed a preference for non-genetically modified products, and added that they were prepared to pay more for this but, ultimately, the product bought was that with the best price, in a market which welcomes new technologies. In 18 of the articles, the population was in favor of obligatory labelling, and in six, in favor of this being voluntary; seven studies showed the consumer knew little about genetically modified food, and in three, the population underestimated the quantity they consumed. Price was an influencing factor in all cases. CONCLUSIONS Label should be homogeneous and clarify the degree of tolerance of genetically modified products in humans, in comparison with those non-genetically modified. Label should also present the content or not of genetically modified products and how these commodities are produced and should be accompanied by the certifying entity and contact information. Consumers express their preference for non-genetically modifiedproducts and they even notice that they are willing to pay more for it, but eventually they buy the item with the best price, in a market that welcomes

  17. Insurance companies' access to genetic information: why regulation alone is not enough.

    PubMed

    Juth, Niklas

    2003-01-01

    The background of this paper is the ongoing dismantling of the social insurance systems in favour of commercialisation and privatisation of insurances needed for illness, old age and premature death. This combined with the increased possibility of using genetic testing for differentiating personal insurance premiums has the potentiality of creating a 'genetic proletariat'--an uninsurable high-risk population. The common way of handling this problem in Sweden, and many other developed countries around the North Atlantic, has been to regulate insurance companies' right to ask for and use genetic information in various ways. There is a distinction between partial regulation (that allows insurance companies access to genetic information from genetic tests already made, sometimes only above a specified amount, but not to demand new tests) and total regulation (that forbids insurance companies to ask for or use any genetic information). I will argue that these forms of regulation probably will have adverse consequences given the dismantling of collective social insurance systems. If this is convincing, a better way to solve the problem of an uninsurable high-risk population (and other problems) is to resurrect the collective, obligatory insurance systems in which the individual risk profile does not constitute a basis for premium determination. Both arguments cast in terms of consequences and justice render support for this conclusion.

  18. Exosomes and microvesicles: extracellular vesicles for genetic information transfer and gene therapy.

    PubMed

    Lee, Yi; El Andaloussi, Samir; Wood, Matthew J A

    2012-10-15

    Exosomes and microvesicles are extracellular nanovesicles released by most but not all cells. They are specifically equipped to mediate intercellular communication via the transfer of genetic information, including the transfer of both coding and non-coding RNAs, to recipient cells. As a result, both exosomes and microvesicles play a fundamental biological role in the regulation of normal physiological as well as aberrant pathological processes, via altered gene regulatory networks and/or via epigenetic programming. For example, microvesicle-mediated genetic transfer can regulate the maintenance of stem cell plasticity and induce beneficial cell phenotype modulation. Alternatively, such vesicles play a role in tumor pathogenesis and the spread of neurodegenerative diseases via the transfer of specific microRNAs and pathogenic proteins. Given this natural property for genetic information transfer, the possibility of exploiting these vesicles for therapeutic purposes is now being investigated. Stem cell-derived microvesicles appear to be naturally equipped to mediate tissue regeneration under certain conditions, while recent evidence suggests that exosomes might be harnessed for the targeted delivery of human genetic therapies via the introduction of exogenous genetic cargoes such as siRNA. Thus, extracellular vesicles are emerging as potent genetic information transfer agents underpinning a range of biological processes and with therapeutic potential.

  19. Informational structure of genetic sequences and nature of gene splicing

    NASA Astrophysics Data System (ADS)

    Trifonov, E. N.

    1991-10-01

    Only about 1/20 of DNA of higher organisms codes for proteins, by means of classical triplet code. The rest of DNA sequences is largely silent, with unclear functions, if any. The triplet code is not the only code (message) carried by the sequences. There are three levels of molecular communication, where the same sequence ``talks'' to various bimolecules, while having, respectively, three different appearances: DNA, RNA and protein. Since the molecular structures and, hence, sequence specific preferences of these are substantially different, the original DNA sequence has to carry simultaneously three types of sequence patterns (codes, messages), thus, being a composite structure in which one had the same letter (nucleotide) is frequently involved in several overlapping codes of different nature. This multiplicity and overlapping of the codes is a unique feature of the Gnomic, language of genetic sequences. The coexisting codes have to be degenerate in various degrees to allow an optimal and concerted performance of all the encoded functions. There is an obvious conflict between the best possible performance of a given function and necessity to compromise the quality of a given sequence pattern in favor of other patterns. It appears that the major role of various changes in the sequences on their ``ontogenetic'' way from DNA to RNA to protein, like RNA editing and splicing, or protein post-translational modifications is to resolve such conflicts. New data are presented strongly indicating that the gene splicing is such a device to resolve the conflict between the code of DNA folding in chromatin and the triplet code for protein synthesis.

  20. Lethal autonomy: the malfunction of the informed consent mechanism within the context of prenatal diagnosis of genetic variants.

    PubMed

    Dunne, C; Warren, C

    1998-01-01

    In this article, Cara Dunne and Catherine Warren challenge the current role of genetic counselors in advising expectant mothers about potential genetic defects of their fetuses. They show that genetic counselors sometimes provide one-sided negative information to women undergoing prenatal diagnosis of genetic variants. This biased information promotes abortion of what are considered "defective" fetuses. The misleading information provided by the genetic counselors and the termination of the pregnancies is akin to the eugenics movement. The authors describe the early 20th century eugenics movement, explore the origin and development of the Human Genome Project, analyze the current role of genetic counseling, and explain the importance of the informed consent process to the exercise of autonomy. Dunne and Warren conclude by offering methods by which to restructure the informed consent mechanism to offer a more balanced assessment of the risks and benefits associated with genetic disability.

  1. Postmortem disclosure of genetic information to family members: active or passive?

    PubMed

    Boers, Sarah N; van Delden, Johannes J M; Knoers, Nine V; Bredenoord, Annelien L

    2015-03-01

    Advances in next-generation DNA sequencing (NGS) now make it possible, and affordable, to sequence the entire genome of an individual. Routine clinical application is on the horizon. There is a consensus that some subsets of genetic information should be disclosed to patients, but disclosure to their relatives is less consensual. This issue becomes especially salient after a patient's death, when permission can no longer be sought. There has however been little debate on postmortem disclosure. We identify and explain the arguments in favor of and against disclosure of genetic information to the relatives of a deceased patient. We conclude that there are valid reasons to communicate some subsets of genetic information to family members after death, and we propose a passive postmortem disclosure policy.

  2. Disclosing genetic information to at-risk relatives: new Australian privacy principles, but uniformity still elusive.

    PubMed

    Otlowski, Margaret F A

    2015-04-01

    There is growing understanding of the need for genetic information to be shared with genetic relatives in some circumstances. Since 2006, s 95AA of the Privacy Act 1988 (Cwlth) has permitted the disclosure of genetic information to genetic relatives without the patient's consent, provided that the health practitioner reasonably believes that disclosure is necessary to lessen or prevent a serious threat to the life, health or safety of the genetic relatives. Enabling guidelines were introduced in 2009. These were limited to the private sector, and excluded doctors working in the public sector at both Commonwealth and state and territory levels. Privacy legislation was amended in March 2014, and new Australian Privacy Principles, which replace the National Privacy Principles and Information Privacy Principles, now cover the collection and use of personal information. The Privacy Act and the Australian Privacy Principles now extend to practitioners employed by the Commonwealth but not to health practitioners working in state and territory public hospitals. In this article, I review these legislative developments and highlight the implications of the lack of uniformity and the consequent need for a collaborative, uniform approach by states and territories. PMID:25832164

  3. Disclosing genetic information to at-risk relatives: new Australian privacy principles, but uniformity still elusive.

    PubMed

    Otlowski, Margaret F A

    2015-04-01

    There is growing understanding of the need for genetic information to be shared with genetic relatives in some circumstances. Since 2006, s 95AA of the Privacy Act 1988 (Cwlth) has permitted the disclosure of genetic information to genetic relatives without the patient's consent, provided that the health practitioner reasonably believes that disclosure is necessary to lessen or prevent a serious threat to the life, health or safety of the genetic relatives. Enabling guidelines were introduced in 2009. These were limited to the private sector, and excluded doctors working in the public sector at both Commonwealth and state and territory levels. Privacy legislation was amended in March 2014, and new Australian Privacy Principles, which replace the National Privacy Principles and Information Privacy Principles, now cover the collection and use of personal information. The Privacy Act and the Australian Privacy Principles now extend to practitioners employed by the Commonwealth but not to health practitioners working in state and territory public hospitals. In this article, I review these legislative developments and highlight the implications of the lack of uniformity and the consequent need for a collaborative, uniform approach by states and territories.

  4. Genetic testing information standardization in HL7 CDA and ISO13606.

    PubMed

    Bosca, Diego; Marco, Luis; Burriel, Veronica; Jaijo, Teresa; Millán, Jose M; Levin, Ana; Pastor, Oscar; Robles, Montserrat; Maldonado, Jose Alberto

    2013-01-01

    Communicating genetic testing reports of a patient in a semantically interoperable way remains difficult. Most of the information is stored as non-communicable documents which cannot automatically be processed. The objective of the project was to obtain semantically interoperable genetic testing reports which could be used not only for communication purposes but also for secondary uses, for example clinical trials or clinical decision support. This work describes the first part of the project, the modeling of genetic information reports using EHR standards. We used the Implementation Guide for CDA R2 Genetic Testing Report (GTR) as a basis for modeling the archetypes for both HL7 CDA and CEN/ISO 13606. This approach was validated with the information included in Usher Syndrome reports available at ISS-La Fe. The result of this work were three archetypes following ISO13606 and three archetypes following HL7 CDA model which contained all the information available in both Usher syndrome genetic testing reports and the implementation guide significant parts. PMID:23920572

  5. Communicating Genetic Risk Information for Common Disorders in the Era of Genomic Medicine

    PubMed Central

    Lautenbach, Denise M.; Christensen, Kurt D.; Sparks, Jeffrey A.; Green, Robert C.

    2013-01-01

    Communicating genetic risk information in ways that maximize understanding and promote health is increasingly important given the rapidly expanding availability and capabilities of genomic technologies. A well-developed literature on risk communication in general provides guidance for best practices, including presentation of information in multiple formats, attention to framing effects, use of graphics, sensitivity to the way numbers are presented, parsimony of information, attentiveness to emotions, and interactivity as part of the communication process. Challenges to communicating genetic risk information include deciding how best to tailor it, streamlining the process, deciding what information to disclose, accepting that communications may have limited influence, and understanding the impact of context. Meeting these challenges has great potential for empowering individuals to adopt healthier lifestyles and improve public health, but will require multidisciplinary approaches and collaboration. PMID:24003856

  6. Eugenics and Mandatory Informed Prenatal Genetic Testing: A Unique Perspective from China.

    PubMed

    Zhang, Di; Ng, Vincent H; Wang, Zhaochen; Zhai, Xiaomei; Lie, Reidar K

    2016-08-01

    The application of genetic technologies in China, especially in the area of prenatal genetic testing, is rapidly increasing in China. In the wealthy regions of China, prenatal genetic testing is already very widely adopted. We argue that the government should actively promote prenatal genetic testing to the poor areas of the country. In fact, the government should prioritize resources first to make prenatal genetic testing a standard routine care with an opt-out model in these area. Healthcare professions would be required to inform pregnant women about the availability of genetic testing and provide free testing on a routine basis unless the parents choose not to do so. We argue that this proposal will allow parents to make a more informed decision about their reproductive choices. Secondarily, this proposal will attract more healthcare professionals and other healthcare resources to improve the healthcare infrastructures in the less-developed regions of the country. This will help to reduce the inequity of accessing healthcare services between in different regions of China. We further argue that this policy proposal is not practicing eugenics.

  7. Eugenics and Mandatory Informed Prenatal Genetic Testing: A Unique Perspective from China.

    PubMed

    Zhang, Di; Ng, Vincent H; Wang, Zhaochen; Zhai, Xiaomei; Lie, Reidar K

    2016-08-01

    The application of genetic technologies in China, especially in the area of prenatal genetic testing, is rapidly increasing in China. In the wealthy regions of China, prenatal genetic testing is already very widely adopted. We argue that the government should actively promote prenatal genetic testing to the poor areas of the country. In fact, the government should prioritize resources first to make prenatal genetic testing a standard routine care with an opt-out model in these area. Healthcare professions would be required to inform pregnant women about the availability of genetic testing and provide free testing on a routine basis unless the parents choose not to do so. We argue that this proposal will allow parents to make a more informed decision about their reproductive choices. Secondarily, this proposal will attract more healthcare professionals and other healthcare resources to improve the healthcare infrastructures in the less-developed regions of the country. This will help to reduce the inequity of accessing healthcare services between in different regions of China. We further argue that this policy proposal is not practicing eugenics. PMID:26222676

  8. Acquisition and disclosure of genetic information under alternative policy regimes: an economic analysis.

    PubMed

    Wilson, Deborah

    2006-07-01

    A current policy issue is whether, and if so under what circumstances, insurance companies should be given access to genetic test results. The insurance industry argues for mandatory disclosure in order to avoid problems of adverse selection; an alternative would be a moratorium or legislation preventing such disclosure; a third option a voluntary disclosure law. This paper investigates the impact of these policies on individuals' incentives to both acquire genetic information and to disclose it to providers of health and/or life insurance. The theoretical framework used to inform this analysis is provided by the 'games of persuasion' literature, in which one agent tries to influence another agent's decision by selectively withholding her private information regarding quality. The application of the theoretical framework to this policy context yields the following results. Individuals have the incentive to acquire genetic information and to disclose the test results if disclosure is voluntary. If, however, they are obliged to disclose the results of any genetic tests they have taken, their incentive may be not to acquire such information. I discuss the policy implications of these findings both from the point of view of the insurance industry and from a public health perspective.

  9. Argon Cluster Sputtering Source for ToF-SIMS Depth Profiling of Insulating Materials: High Sputter Rate and Accurate Interfacial Information.

    PubMed

    Wang, Zhaoying; Liu, Bingwen; Zhao, Evan W; Jin, Ke; Du, Yingge; Neeway, James J; Ryan, Joseph V; Hu, Dehong; Zhang, Kelvin H L; Hong, Mina; Le Guernic, Solenne; Thevuthasan, Suntharampilai; Wang, Fuyi; Zhu, Zihua

    2015-08-01

    The use of an argon cluster ion sputtering source has been demonstrated to perform superiorly relative to traditional oxygen and cesium ion sputtering sources for ToF-SIMS depth profiling of insulating materials. The superior performance has been attributed to effective alleviation of surface charging. A simulated nuclear waste glass (SON68) and layered hole-perovskite oxide thin films were selected as model systems because of their fundamental and practical significance. Our results show that high sputter rates and accurate interfacial information can be achieved simultaneously for argon cluster sputtering, whereas this is not the case for cesium and oxygen sputtering. Therefore, the implementation of an argon cluster sputtering source can significantly improve the analysis efficiency of insulating materials and, thus, can expand its applications to the study of glass corrosion, perovskite oxide thin film characterization, and many other systems of interest.

  10. Exploring dispositional tendencies to seek online information about direct-to-consumer genetic testing.

    PubMed

    Paquin, Ryan S; Richards, Adam S; Koehly, Laura M; McBride, Colleen M

    2012-12-01

    Varying perspectives exist regarding the implications of genetic susceptibility testing for common disease, with some anticipating adverse effects and others expecting positive outcomes; however, little is known about the characteristics of people who are most likely to be interested in direct-to-consumer genetic testing. To that end, this study examines the association of individual dispositional differences with health risk perceptions and online information seeking related to a free genetic susceptibility test. Healthy adults enrolled in a large health maintenance organization were surveyed by telephone. Eligible participants (N = 1,959) were given access to a secure website that provided risk and benefit information about a genetic susceptibility test and given the option to be tested. Neuroticism was associated with increased perceptions of disease risk but not with logging on. Those scoring high in conscientiousness were more likely to log on. We found no evidence that neuroticism, a dispositional characteristic commonly linked to adverse emotional response, was predictive of online genetic information seeking in this sample of healthy adults.

  11. Between personal and relational privacy: understanding the work of informed consent in cancer genetics in Brazil.

    PubMed

    Goldim, José Roberto; Gibbon, Sahra

    2015-07-01

    Drawing from perspectives of both bioethics and anthropology, this article explores how the boundaries between personal and relational privacy are negotiated by patients and practitioners in the context of an emerging domain of cancer genetics in Brazil. It reflects on the place of informed consent in the history of bioethics in North America in contrast to the development of bioethics in Brazil and the particular social cultural context in which consent is sought in Brazilian public health care. Making use of empirical research with families and individuals receiving genetic counselling related to increased genetic risk for cancer, in genetic clinics in southern Brazil, it examines how informed consent is linked to the necessary movement between personal and relational privacy. The paper illustrates the value of a particular tool known as a 'sociogram' to examine the complex interpersonal dynamics that arise in negotiating informed consent at the interface between the family and the individual in Brazil. The paper, therefore, points to the scope of further interdisciplinary exchanges between anthropology and bioethics, confronting the new challenges that arise in the context of medical genetics in developing country.

  12. Etiology and Measurement of Relational Aggression: A Multi-Informant Behavior Genetic Investigation

    PubMed Central

    Tackett, Jennifer L.; Waldman, Irwin D.; Lahey, Benjamin B.

    2013-01-01

    Although the study of relational aggression is gaining attention in the literature, little is known about the underlying causes of this behavior and the relative validity of various informants. These issues were addressed in a sample of 1981 6- to 18-year-old twin pairs (36% female, 34% male, 30% opposite-sex). Relational aggression was assessed via maternal- and self-report using a structured interview. Univariate models estimated genetic and environmental influences by informant and examined evidence for gender differences. A psychometric model combined data from both informants to estimate etiologic influences that were both common to the informants and informant-specific. In both sexes, the latent variable reflecting the mother’s and child’s shared perception of the child’s relational aggression was substantially influenced by both additive genetic (63%) and shared environmental (37%) influences, although this latent variable accounted for much greater variance in maternal report (66%) than it did in youth report (9%). In addition, informant specific additive genetic and shared environmental influences were found only for youth report, with all remaining variance in mother’s report attributed to nonshared environmental influences. Results are discussed in the context of measuring relational aggression and the importance of multiple informants. PMID:19899842

  13. Effects of information on young consumers' willingness to pay for genetically modified food: experimental auction analysis.

    PubMed

    Kajale, Dilip B; Becker, T C

    2014-01-01

    This study examines the effects of information on consumers' willingness to pay (WTP) for genetically modified food (GMF). We used Vickrey second price experimental auction method for elicitation of consumer WTP for GM potato chips and GM soya-chocolate bar. The sample used in this study was university students from Delhi, India. Four information formats (positive, negative, no information, and combined information about GM technology) were used for the examination. The results show that, when students received the combine information they were willing to pay around 17%-20% premium for GMF and when received the negative information they demanded around 22% discount for GMF. While the positive- and the no-information formats alone have no considerable effect on consumers' WTP for GMF. Overall, our findings suggest that while doing marketing of GMF in India, the best strategy is to provide combined information about GM technology.

  14. Effects of information on young consumers' willingness to pay for genetically modified food: experimental auction analysis.

    PubMed

    Kajale, Dilip B; Becker, T C

    2014-01-01

    This study examines the effects of information on consumers' willingness to pay (WTP) for genetically modified food (GMF). We used Vickrey second price experimental auction method for elicitation of consumer WTP for GM potato chips and GM soya-chocolate bar. The sample used in this study was university students from Delhi, India. Four information formats (positive, negative, no information, and combined information about GM technology) were used for the examination. The results show that, when students received the combine information they were willing to pay around 17%-20% premium for GMF and when received the negative information they demanded around 22% discount for GMF. While the positive- and the no-information formats alone have no considerable effect on consumers' WTP for GMF. Overall, our findings suggest that while doing marketing of GMF in India, the best strategy is to provide combined information about GM technology. PMID:24735210

  15. Genetic counseling practice in next generation sequencing research: implications for the ethical oversight of the informed consent process.

    PubMed

    Egalite, Nathalie; Groisman, Iris Jaitovich; Godard, Beatrice

    2014-08-01

    The potential for next generation sequencing research (NGS) to generate individual genetic results could have implications for the informed consent process and the provision of genetic counseling. We undertook a content analysis of informed consent templates and guidelines produced by Canadian institutional review boards, purposively sampling documents used by researchers to obtain consent from participants in genetics studies. Our goal was to examine the extent to which the informed consent documents addressed genetic counseling and the return of individual genetic results. Our analysis reveals that the majority of informed consent documents did not mention genetic counseling while several did not mention the return of results. We found differences in the ways in which documents addressed availability of counseling, eligibility criteria for referral to a genetic counselor, genetic counselor involvement, provision of services to family members of participants and incidental findings. From an ethical standpoint, consent documents should provide appropriate information so that participants may make an informed decision about their participation in research. The need to ensure adequate counseling for study populations in an NGS research context will necessarily involve adapting values that underlie care in genetic counseling practice. If the interests of research participants are to be truly promoted, the drafting and review of informed consent documents should give proper due to genetic counseling.

  16. Genetic counseling practice in next generation sequencing research: implications for the ethical oversight of the informed consent process.

    PubMed

    Egalite, Nathalie; Groisman, Iris Jaitovich; Godard, Beatrice

    2014-08-01

    The potential for next generation sequencing research (NGS) to generate individual genetic results could have implications for the informed consent process and the provision of genetic counseling. We undertook a content analysis of informed consent templates and guidelines produced by Canadian institutional review boards, purposively sampling documents used by researchers to obtain consent from participants in genetics studies. Our goal was to examine the extent to which the informed consent documents addressed genetic counseling and the return of individual genetic results. Our analysis reveals that the majority of informed consent documents did not mention genetic counseling while several did not mention the return of results. We found differences in the ways in which documents addressed availability of counseling, eligibility criteria for referral to a genetic counselor, genetic counselor involvement, provision of services to family members of participants and incidental findings. From an ethical standpoint, consent documents should provide appropriate information so that participants may make an informed decision about their participation in research. The need to ensure adequate counseling for study populations in an NGS research context will necessarily involve adapting values that underlie care in genetic counseling practice. If the interests of research participants are to be truly promoted, the drafting and review of informed consent documents should give proper due to genetic counseling. PMID:24664856

  17. Using the GRIN-Global System to Identify Useful Plant Genetic Resources & Information

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The GRIN-Global (GG) System has been developed to provide the world's crop genebanks and plant genetic resource (PGR) users with a powerful, flexible, easy-to-use PGR information management system. Developed jointly by the USDA Agricultural Research Service, Bioversity International and the Global C...

  18. Machine Learning for Information Retrieval: Neural Networks, Symbolic Learning, and Genetic Algorithms.

    ERIC Educational Resources Information Center

    Chen, Hsinchun

    1995-01-01

    Presents an overview of artificial-intelligence-based inductive learning techniques and their use in information science research. Three methods are discussed: the connectionist Hopfield network; the symbolic ID3/ID5R; evolution-based genetic algorithms. The knowledge representations and algorithms of these methods are examined in the context of…

  19. Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases

    PubMed Central

    Naz, Mufassra; Kodamullil, Alpha Tom

    2016-01-01

    The work we present here is based on the recent extension of the syntax of the Biological Expression Language (BEL), which now allows for the representation of genetic variation information in cause-and-effect models. In our article, we describe, how genetic variation information can be used to identify candidate disease mechanisms in diseases with complex aetiology such as Alzheimer’s disease and Parkinson’s disease. In those diseases, we have to assume that many genetic variants contribute moderately to the overall dysregulation that in the case of neurodegenerative diseases has such a long incubation time until the first clinical symptoms are detectable. Owing to the multilevel nature of dysregulation events, systems biomedicine modelling approaches need to combine mechanistic information from various levels, including gene expression, microRNA (miRNA) expression, protein–protein interaction, genetic variation and pathway. OpenBEL, the open source version of BEL, has recently been extended to match this requirement, and we demonstrate in our article, how candidate mechanisms for early dysregulation events in Alzheimer’s disease can be identified based on an integrative mining approach that identifies ‘chains of causation’ that include single nucleotide polymorphism information in BEL models. PMID:26249223

  20. The informed consent aftermath of the genetic revolution. An Italian example of implementation.

    PubMed

    Artizzu, Federica

    2008-06-01

    A great part of human genetics research is carried out collecting data and building large databases of biological samples that are in a non-anonymous format. These constitute a valuable resource for future research. The construction of such databases and tissue banks facilitates important scientific progress. However, biobanks have been recognized as ethically problematic because they contain thousands of data that could expose individuals and populations to discrimination, stigmatization and psychological stress if misused. Informed consent is regarded as a cornerstone in the protection of personal autonomy in research involving human subjects. Yet in recent years this fundamental concept has been overwhelmed by the genomic revolution. From a general overview of international literature, it seems evident that informed consent issues have come into sharp focus, in particular in relation to the twin issues of time extension (blanket versus specific/repeated consent) and personal extension (group consent). After an introduction on obtaining informed consent in the context of genetic research, this paper addresses the apparent lack of a single, universal model of obtaining informed consent among populations involved in genetic research and it argues for the need to develop an ethical framework tailored to the specific features of each project. In order to support this theory of contextualizing, the case of a private biotechnology company, SharDNA is presented. The present paper explores the management of its biobank, developed from a genetic research project carried out on isolated populations living on the Italian island of Sardinia. In particular, the paper highlights how the company is tackling the problem of informed consent and other ethical requirements for genetic research, such as the respect of individual privacy, the population approach and the existing Italian legal regulatory framework.

  1. IrisPlex: a sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information.

    PubMed

    Walsh, Susan; Liu, Fan; Ballantyne, Kaye N; van Oven, Mannis; Lao, Oscar; Kayser, Manfred

    2011-06-01

    A new era of 'DNA intelligence' is arriving in forensic biology, due to the impending ability to predict externally visible characteristics (EVCs) from biological material such as those found at crime scenes. EVC prediction from forensic samples, or from body parts, is expected to help concentrate police investigations towards finding unknown individuals, at times when conventional DNA profiling fails to provide informative leads. Here we present a robust and sensitive tool, termed IrisPlex, for the accurate prediction of blue and brown eye colour from DNA in future forensic applications. We used the six currently most eye colour-informative single nucleotide polymorphisms (SNPs) that previously revealed prevalence-adjusted prediction accuracies of over 90% for blue and brown eye colour in 6168 Dutch Europeans. The single multiplex assay, based on SNaPshot chemistry and capillary electrophoresis, both widely used in forensic laboratories, displays high levels of genotyping sensitivity with complete profiles generated from as little as 31pg of DNA, approximately six human diploid cell equivalents. We also present a prediction model to correctly classify an individual's eye colour, via probability estimation solely based on DNA data, and illustrate the accuracy of the developed prediction test on 40 individuals from various geographic origins. Moreover, we obtained insights into the worldwide allele distribution of these six SNPs using the HGDP-CEPH samples of 51 populations. Eye colour prediction analyses from HGDP-CEPH samples provide evidence that the test and model presented here perform reliably without prior ancestry information, although future worldwide genotype and phenotype data shall confirm this notion. As our IrisPlex eye colour prediction test is capable of immediate implementation in forensic casework, it represents one of the first steps forward in the creation of a fully individualised EVC prediction system for future use in forensic DNA intelligence.

  2. Neuroscientific and behavioral genetic information in criminal cases in the Netherlands

    PubMed Central

    de Kogel, C.H.; Westgeest, E.J.M.C.

    2015-01-01

    In this contribution an empirical approach is used to gain more insight into the relationship between neuroscience and criminal law. The focus is on case law in the Netherlands. Neuroscientific information and techniques have found their way into the courts of the Netherlands. Furthermore, following an Italian case in which a mentally ill offender received a penalty reduction in part because of a ‘genetic vulnerability for impulsive aggression’, the expectation was expressed that such ‘genetic defenses’ would appear in the Netherlands too. To assess how neuroscientific and behavioral genetic information are used in criminal justice practice in the Netherlands, we systematically collect Dutch criminal cases in which neuroscientific or behavioral genetic information is introduced. Data and case law examples are presented and discussed. Although cases are diverse, several themes appear, such as prefrontal brain damage in relation to criminal responsibility and recidivism risk, and divergent views of the implications of neurobiological knowledge about addiction for judging criminal responsibility. Whereas in the international ‘neurolaw literature’ the emphasis is often on imaging techniques, the Dutch findings also illustrate the role of neuropsychological methods in criminal cases. Finally, there appears to be a clear need of practice oriented instruments and guidelines. PMID:27774213

  3. The Australian joint inquiry into the Protection of Human Genetic Information.

    PubMed

    Weisbrot, David

    2003-04-01

    The Australian Law Reform Commission (ALRC) and the Australian Health Ethics Committee are currently engaged in an inquiry into the Protection of Human Genetic Information. In particular, the Attorney-General and the Minister for Health and Ageing have asked us to focus, in relation to human genetic information and tissue samples, on how best to ensure world's best practice in relation to: privacy protection; protection against unlawful discrimination; and the maintenance of high ethical standards in medical research and clinical practice. While initial concerns and controversies have related mainly to aspects of medical research (e.g. consent; re-use of samples) and access to private insurance coverage, relevant issues arise in a wide variety of contexts, including: employment; medical practice; tissue banks and genetic databases; health administration; superannuation; access to government services (e.g. schools, nursing homes); law enforcement; and use by government authorities (e.g. for immigration purposes) or other bodies (e.g. by sports associations). Under the Australian federal system, it is also the case that laws and practices may vary across states and territories. For example, neonatal genetic testing is standard, but storage and retention policies for the resulting 'Guthrie cards' differ markedly. Similarly, some states have developed highly linked health information systems (e.g. incorporating hospitals, doctors' offices and public records), while others discourage such linkages owing to concerns about privacy. The challenge for Australia is to develop policies, standards and practices that promote the intelligent use of genetic information, while providing a level of security with which the community feels comfortable. The inquiry is presently reviewing the adequacy of existing laws and regulatory mechanisms, but recognizes that it will be even more important to develop a broad mix of strategies, such as community and professional education, and the

  4. 75 FR 39699 - Request for Information (RFI) on the National Institutes of Health Plan to Develop the Genetic...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-12

    ... Health Plan to Develop the Genetic Testing Registry; Notice On June 11, 2010, the National Institutes of... Information (RFI) on its plan to develop a voluntary Genetic Testing Registry (GTR), a centralized public resource that will provide information about the availability, scientific basis, and usefulness of...

  5. Information Needs in the Precision Medicine Era: How Genetics Home Reference Can Help

    PubMed Central

    Calvo, Sherri; Greenberg, Kathleen; Forman Neall, Lisa; Morrison, Stephanie

    2016-01-01

    Precision medicine focuses on understanding individual variability in disease prevention, care, and treatment. The Precision Medicine Initiative, launched by President Obama in early 2015, aims to bring this approach to all areas of health care. However, few consumer-friendly resources exist for the public to learn about precision medicine and the conditions that could be affected by this approach to care. Genetics Home Reference, a website from the US National Library of Medicine, seeks to support precision medicine education by providing the public with summaries of genetic conditions and their associated genes, as well as information about issues related to precision medicine such as disease risk and pharmacogenomics. With the advance of precision medicine, consumer-focused resources like Genetics Home Reference can be foundational in providing context for public understanding of the increasing amount of data that will become available. PMID:27122232

  6. Information Needs in the Precision Medicine Era: How Genetics Home Reference Can Help.

    PubMed

    Collins, Heather; Calvo, Sherri; Greenberg, Kathleen; Forman Neall, Lisa; Morrison, Stephanie

    2016-01-01

    Precision medicine focuses on understanding individual variability in disease prevention, care, and treatment. The Precision Medicine Initiative, launched by President Obama in early 2015, aims to bring this approach to all areas of health care. However, few consumer-friendly resources exist for the public to learn about precision medicine and the conditions that could be affected by this approach to care. Genetics Home Reference, a website from the US National Library of Medicine, seeks to support precision medicine education by providing the public with summaries of genetic conditions and their associated genes, as well as information about issues related to precision medicine such as disease risk and pharmacogenomics. With the advance of precision medicine, consumer-focused resources like Genetics Home Reference can be foundational in providing context for public understanding of the increasing amount of data that will become available. PMID:27122232

  7. Genetic Counseling

    MedlinePlus

    ... Articles Genetic Counseling Information For... Media Policy Makers Genetic Counseling Language: English Español (Spanish) Recommend on Facebook ... informed decisions about testing and treatment. Reasons for Genetic Counseling There are many reasons that people go ...

  8. The new genetics and informed consent: differentiating choice to preserve autonomy.

    PubMed

    Bunnik, Eline M; de Jong, Antina; Nijsingh, Niels; de Wert, Guido M W R

    2013-07-01

    The advent of new genetic and genomic technologies may cause friction with the principle of respect for autonomy and demands a rethinking of traditional interpretations of the concept of informed consent. Technologies such as whole-genome sequencing and micro-array based analysis enable genome-wide testing for many heterogeneous abnormalities and predispositions simultaneously. This may challenge the feasibility of providing adequate pre-test information and achieving autonomous decision-making. At a symposium held at the 11th World Congress of Bioethics in June 2012 (Rotterdam), organized by the International Association of Bioethics, these challenges were presented for three different areas in which these so-called 'new genetics' technologies are increasingly being applied: newborn screening, prenatal screening strategies and commercial personal genome testing. In this article, we build upon the existing ethical framework for a responsible set-up of testing and screening offers and reinterpret some of its criteria in the light of the new genetics. As we will argue, the scope of a responsible testing or screening offer should align with the purpose(s) of testing and with the principle of respect for autonomy for all stakeholders involved, including (future) children. Informed consent is a prerequisite but requires a new approach. We present preliminary and general directions for an individualized or differentiated set-up of the testing offer and for the informed consent process. With this article we wish to contribute to the formation of new ideas on how to tackle the issues of autonomy and informed consent for (public) healthcare and direct-to-consumer applications of the new genetics. PMID:23718722

  9. The new genetics and informed consent: differentiating choice to preserve autonomy.

    PubMed

    Bunnik, Eline M; de Jong, Antina; Nijsingh, Niels; de Wert, Guido M W R

    2013-07-01

    The advent of new genetic and genomic technologies may cause friction with the principle of respect for autonomy and demands a rethinking of traditional interpretations of the concept of informed consent. Technologies such as whole-genome sequencing and micro-array based analysis enable genome-wide testing for many heterogeneous abnormalities and predispositions simultaneously. This may challenge the feasibility of providing adequate pre-test information and achieving autonomous decision-making. At a symposium held at the 11th World Congress of Bioethics in June 2012 (Rotterdam), organized by the International Association of Bioethics, these challenges were presented for three different areas in which these so-called 'new genetics' technologies are increasingly being applied: newborn screening, prenatal screening strategies and commercial personal genome testing. In this article, we build upon the existing ethical framework for a responsible set-up of testing and screening offers and reinterpret some of its criteria in the light of the new genetics. As we will argue, the scope of a responsible testing or screening offer should align with the purpose(s) of testing and with the principle of respect for autonomy for all stakeholders involved, including (future) children. Informed consent is a prerequisite but requires a new approach. We present preliminary and general directions for an individualized or differentiated set-up of the testing offer and for the informed consent process. With this article we wish to contribute to the formation of new ideas on how to tackle the issues of autonomy and informed consent for (public) healthcare and direct-to-consumer applications of the new genetics.

  10. Genetic Information-Seeking Behaviors and Knowledge among Family Members and Patients with Inherited Bone Marrow Failure Syndromes.

    PubMed

    Hamilton, Jada G; Hutson, Sadie P; Frohnmayer, Amy E; Han, Paul K J; Peters, June A; Carr, Ann G; Alter, Blanche P

    2015-10-01

    Inherited bone marrow failure syndromes (IBMFS) including Fanconi anemia, dyskeratosis congenita, Diamond-Blackfan anemia, and Shwachman-Diamond syndrome are rare genetic disorders characterized by hematologic complications and increased risk of cancer. Patients and their families likely experience obstacles in obtaining sufficient health information given their disorders' rarity. To investigate this possibility, we examined information-seeking behaviors and levels of general and disorder-specific genetic knowledge among 315 members of 174 families with an IBMFS, and how information-seeking behaviors and socio-demographic factors may be associated with their genetic knowledge. Cross-sectional survey data indicated that participants were most likely to have ever used the Internet or healthcare providers for genetic information. On average, participants correctly answered 57 % of items assessing general genetic knowledge and 49-59 % of disorder-specific knowledge items. Greater knowledge was associated with greater education and ever experiencing genetic counseling, attending a scientific meeting, and seeking information from the Internet and scientific literature. Among families with Fanconi anemia (whose family support organization has the longest history of providing information), greater disorder-specific genetic knowledge was also associated with seeking information from support groups and other affected families. Results suggest that families with IBMFS have uncertainty regarding genetic aspects of their disorder, and highlight potential channels for delivering educational resources.

  11. The dark side of friends: a genetically informed study of victimization within early adolescents' friendships.

    PubMed

    Brendgen, Mara; Girard, Alain; Vitaro, Frank; Dionne, Ginette; Boivin, Michel

    2015-01-01

    Using a genetically informed twin design, this study examined (a) whether, in line with gene-environment correlation (rGE), a genetic disposition for anxiety puts children at risk of being victimized by a close friend or by other peers, and (b) whether, in line with gene-environment interaction (GxE), victimization by a close friend or by other peers moderates the expression of a genetic disposition for anxiety. Participants were 268 monozygotic and dizygotic twin pairs (MZ males = 71, MZ females = 80, DZ males = 56, DZ females = 61; 87% of European descent) assessed via questionnaires in Grade 8 (M age = 14.06 years, SD = 3.60). Participants reported about their victimization by a close friend and by other peers and their anxiety level. Victimization by a close friend and victimization by other peers were uncorrelated. In line with rGE, genetic factors related to anxiety predicted victimization by other peers, whereas victimization by a close friend was not predicted by heritable characteristics. Moreover, in line with a suppression process of GxE, victimization by other peers reduced the role of genetic factors in explaining interindividual differences in anxiety. In contrast, in line with a diathesis-stress process of GxE, victimization by a close friend fostered the expression of a genetic disposition for anxiety. Victimization by a close friend seems to happen to adolescents regardless of their personal, heritable characteristics. If it does occur, however, it is a source of distress mostly for youth with a genetic vulnerability for anxiety.

  12. Fatalistic responses to different types of genetic risk information: exploring the role of self-malleability.

    PubMed

    Claassen, Liesbeth; Henneman, Lidewij; De Vet, Riekie; Knol, Dirk; Marteau, Theresa; Timmermans, Danielle

    2010-02-01

    Providing people with genetic risk information may induce a sense of fatalism, the belief that little can be done to reduce the risk. We postulated that fatalism is a function of health risk information and individual differences in self-perception. DNA-based risk information was hypothesised to generate more fatalism than risk information based on family history or non-genetic risk information. Moreover, people who view themselves as more rather than less able to change self-attributes were hypothesised to respond least fatalistically. Factor analyses in separate samples were used to construct a five-item 'Malleability of self' measure. Predictive validity of the measure was tested using a within-subjects analogue design. Participants responded to three scenario vignettes in which they were informed of an increased risk of cardiovascular disease (CVD). In Scenario 1, risk was ascertained by DNA testing, family history and cholesterol testing; in Scenario 2, it was ascertained by family history and cholesterol testing; in Scenario 3, risk was ascertained by cholesterol testing alone. Scenario 1 was associated with least perceived control over cholesterol level and CVD risk. People who viewed themselves as more able to change self-attributes experienced more control in all three scenarios.

  13. Tailoring the process of informed consent in genetic and genomic research.

    PubMed

    Rotimi, Charles N; Marshall, Patricia A

    2010-01-01

    Genomic science and associated technologies are facilitating an unprecedented rate of discovery of novel insights into the relationship between human genetic variation and health. The willingness of large numbers of individuals from different ethnic and cultural backgrounds to donate biological samples is one of the major factors behind the success of the ongoing genomic revolution. Although current informed consent documents and processes demonstrate a commitment to ensuring that study participants are well informed of the risks and benefits of participating in genomic studies, there continues to be a need to develop effective new approaches for adequately informing participants of the changing complexities of the scientific and ethical issues that arise in the conduct of genomics research. Examples of these complexities in genomic research include more widespread use of whole-genome sequencing technologies, broad sharing of individual-level data, evolving information technology, the growing demand for the return of genetic results to participants, and changing attitudes about privacy and the expansion of genomics studies to global populations representing diverse cultural, linguistic and socio-economic backgrounds. We highlight and briefly discuss the importance of ten core scientific, cultural and social factors that are particularly relevant to tailoring informed consent in genomic research, and we draw attention to the need for the informed consent document and process to be responsive to the evolving nature of genomic research.

  14. Skin Cancer Concerns and Genetic Risk Information-Seeking in Primary Care

    PubMed Central

    Hay, J.; Kaphingst, K.A.; Baser, R.; Li, Y.; Hensley-Alford, S.; McBride, C.M.

    2012-01-01

    Background Genomic testing for common genetic variants associated with skin cancer risk could enable personalized risk feedback to motivate skin cancer screening and sun protection. Methods In a cross-sectional study, we investigated whether skin cancer cognitions and behavioral factors, sociodemographics, family factors, and health information-seeking were related to perceived importance of learning about how (a) genes and (b) health habits affect personal health risks using classification and regression trees (CART). Results The sample (n = 1,772) was collected in a large health maintenance organization as part of the Multiplex Initiative, ranged in age from 25–40, was 53% female, 41% Caucasian, and 59% African-American. Most reported that they placed somewhat to very high importance on learning about how genes (79%) and health habits (88%) affect their health risks. Social influence actors were associated with information-seeking about genes and health habits. Awareness of family history was associated with importance of health habit, but not genetic, information-seeking. Conclusions The investment of family and friends in health promotion may be a primary motivator for prioritizing information-seeking about how genes and health habits affect personal health risks and may contribute to the personal value, or personal utility, of risk information. Individuals who seek such risk information may be receptive to interventions aimed to maximize the social implications of healthy lifestyle change to reduce their health risks. PMID:21921576

  15. Genetic code evolution reveals the neutral emergence of mutational robustness, and information as an evolutionary constraint.

    PubMed

    Massey, Steven E

    2015-01-01

    The standard genetic code (SGC) is central to molecular biology and its origin and evolution is a fundamental problem in evolutionary biology, the elucidation of which promises to reveal much about the origins of life. In addition, we propose that study of its origin can also reveal some fundamental and generalizable insights into mechanisms of molecular evolution, utilizing concepts from complexity theory. The first is that beneficial traits may arise by non-adaptive processes, via a process of "neutral emergence". The structure of the SGC is optimized for the property of error minimization, which reduces the deleterious impact of point mutations. Via simulation, it can be shown that genetic codes with error minimization superior to the SGC can emerge in a neutral fashion simply by a process of genetic code expansion via tRNA and aminoacyl-tRNA synthetase duplication, whereby similar amino acids are added to codons related to that of the parent amino acid. This process of neutral emergence has implications beyond that of the genetic code, as it suggests that not all beneficial traits have arisen by the direct action of natural selection; we term these "pseudaptations", and discuss a range of potential examples. Secondly, consideration of genetic code deviations (codon reassignments) reveals that these are mostly associated with a reduction in proteome size. This code malleability implies the existence of a proteomic constraint on the genetic code, proportional to the size of the proteome (P), and that its reduction in size leads to an "unfreezing" of the codon - amino acid mapping that defines the genetic code, consistent with Crick's Frozen Accident theory. The concept of a proteomic constraint may be extended to propose a general informational constraint on genetic fidelity, which may be used to explain variously, differences in mutation rates in genomes with differing proteome sizes, differences in DNA repair capacity and genome GC content between organisms, a

  16. Genetic Code Evolution Reveals the Neutral Emergence of Mutational Robustness, and Information as an Evolutionary Constraint

    PubMed Central

    Massey, Steven E.

    2015-01-01

    The standard genetic code (SGC) is central to molecular biology and its origin and evolution is a fundamental problem in evolutionary biology, the elucidation of which promises to reveal much about the origins of life. In addition, we propose that study of its origin can also reveal some fundamental and generalizable insights into mechanisms of molecular evolution, utilizing concepts from complexity theory. The first is that beneficial traits may arise by non-adaptive processes, via a process of “neutral emergence”. The structure of the SGC is optimized for the property of error minimization, which reduces the deleterious impact of point mutations. Via simulation, it can be shown that genetic codes with error minimization superior to the SGC can emerge in a neutral fashion simply by a process of genetic code expansion via tRNA and aminoacyl-tRNA synthetase duplication, whereby similar amino acids are added to codons related to that of the parent amino acid. This process of neutral emergence has implications beyond that of the genetic code, as it suggests that not all beneficial traits have arisen by the direct action of natural selection; we term these “pseudaptations”, and discuss a range of potential examples. Secondly, consideration of genetic code deviations (codon reassignments) reveals that these are mostly associated with a reduction in proteome size. This code malleability implies the existence of a proteomic constraint on the genetic code, proportional to the size of the proteome (P), and that its reduction in size leads to an “unfreezing” of the codon – amino acid mapping that defines the genetic code, consistent with Crick’s Frozen Accident theory. The concept of a proteomic constraint may be extended to propose a general informational constraint on genetic fidelity, which may be used to explain variously, differences in mutation rates in genomes with differing proteome sizes, differences in DNA repair capacity and genome GC content

  17. Scale-free properties of information flux networks in genetic algorithms

    NASA Astrophysics Data System (ADS)

    Wu, Jieyu; Shao, Xinyu; Li, Jinhang; Huang, Gang

    2012-02-01

    In this study, we present empirical analysis of statistical properties of mating networks in genetic algorithms (GAs). Under the framework of GAs, we study a class of interaction network model-information flux network (IFN), which describes the information flow among generations during evolution process. The IFNs are found to be scale-free when the selection operator uses a preferential strategy rather than a random. The topology structure of IFN is remarkably affected by operations used in genetic algorithms. The experimental results suggest that the scaling exponent of the power-law degree distribution is shown to decrease when crossover rate increases, but increase when mutation rate increases, and the reason may be that high crossover rate leads to more edges that are shared between nodes and high mutation rate leads to many individuals in a generation possessing low fitness. The magnitude of the out-degree exponent is always more than the in-degree exponent for the systems tested. These results may provide a new viewpoint with which to view GAs and guide the dissemination process of genetic information throughout a population.

  18. Filtering genetic variants and placing informative priors based on putative biological function.

    PubMed

    Friedrichs, Stefanie; Malzahn, Dörthe; Pugh, Elizabeth W; Almeida, Marcio; Liu, Xiao Qing; Bailey, Julia N

    2016-02-03

    High-density genetic marker data, especially sequence data, imply an immense multiple testing burden. This can be ameliorated by filtering genetic variants, exploiting or accounting for correlations between variants, jointly testing variants, and by incorporating informative priors. Priors can be based on biological knowledge or predicted variant function, or even be used to integrate gene expression or other omics data. Based on Genetic Analysis Workshop (GAW) 19 data, this article discusses diversity and usefulness of functional variant scores provided, for example, by PolyPhen2, SIFT, or RegulomeDB annotations. Incorporating functional scores into variant filters or weights and adjusting the significance level for correlations between variants yielded significant associations with blood pressure traits in a large family study of Mexican Americans (GAW19 data set). Marker rs218966 in gene PHF14 and rs9836027 in MAP4 significantly associated with hypertension; additionally, rare variants in SNUPN significantly associated with systolic blood pressure. Variant weights strongly influenced the power of kernel methods and burden tests. Apart from variant weights in test statistics, prior weights may also be used when combining test statistics or to informatively weight p values while controlling false discovery rate (FDR). Indeed, power improved when gene expression data for FDR-controlled informative weighting of association test p values of genes was used. Finally, approaches exploiting variant correlations included identity-by-descent mapping and the optimal strategy for joint testing rare and common variants, which was observed to depend on linkage disequilibrium structure.

  19. Is Information on Genetic Determinants of Obesity Helpful or Harmful for Obese People?—A Randomized Clinical Trial

    PubMed Central

    Conradt, Matthias; Dierk, Jan-Michael; Rauh, Elisabeth; Schlumberger, Pia; Hinney, Anke; Hebebrand, Johannes

    2007-01-01

    Background and Objectives Although more and more genetic information is available, it is unclear whether this information is helpful for patients. Therefore, we assessed the positive and negative effects of informing obese people about the genetic etiology of being overweight. Design, Participants Two hundred ninety-four obese people were randomized to 2 interventions (a 1-session consultation for obese people on how to manage obesity either including genetic information or not); their results were compared to a control group (116). Subjects were assessed before and after consultation and 6 months later. Measurements Weight, scales on feeling guilty for being overweight, self-control, negative mood (primary endpoint), body acceptance, restraint eating. Results Both types of consultations were considered helpful by the participants, and had comparable effects on body weight. The consultation with genetic information was rated superior in terms of leading to new insights (advantage for consultation with genetic information, even 6 months later; p = 0.046). No negative effects (e.g., loss of self-efficacy/self-control, increase of body weight; all p > 0.20 for interaction consultation × time) were observed for informing obese people about the genetic etiology of being overweight. The consultation resulted in long-term improvement of negative mood if it included genetic information in the case of participants with a family history of obesity and if it included no genetic information in the case of obese people without a family history of obesity (p = 0.03 for interaction of group, intervention, and time). Conclusions Consultations in obesity can be helpful in general. These consultations should include genetic information if people have a family history of obesity. PMID:17879121

  20. Family physicians' awareness and knowledge of the Genetic Information Non-Discrimination Act (GINA).

    PubMed

    Laedtke, Amanda L; O'Neill, Suzanne M; Rubinstein, Wendy S; Vogel, Kristen J

    2012-04-01

    Historically, physicians have expressed concern about their patients' risk of genetic discrimination, which has acted as a barrier to uptake of genetic services. The Genetic Information Nondiscrimination Act of 2008 (GINA) is intended to protect patients against employer and health insurance discrimination. Physicians' awareness and knowledge of GINA has yet to be evaluated. In 2009, we mailed surveys to 1500 randomly selected members of the American Academy of Family Physicians. Questions measured physicians' current knowledge of GINA and their level of concern for genetic discrimination. In total, 401 physicians completed the survey (response rate 26.9%). Approximately half (54.5%) of physicians had no awareness of GINA. Of physicians who reported basic knowledge of GINA, the majority were aware of the protections offered for group health insurance (92.7%), private health insurance (82.9%), and employment (70.7%). Fewer physicians were aware of GINA's limitations regarding life insurance (53.7%) and long-term care insurance (58.8%). Physicians demonstrated highest levels of concern for health insurance, life insurance, and long-term care insurance discrimination, with less concern for employer and family/social discrimination. Level of concern for the risk of genetic discrimination did not correlate significantly with awareness of GINA. Approximately 17 months after GINA was signed into federal law, physicians' knowledge remained limited regarding the existence of this legislation and relevant details. Physicians who are aware of GINA continue to have significant concerns regarding the risk of genetic discrimination. This study reveals the need to further educate physicians about the existence of GINA and the protections offered.

  1. Disclosure of Genetic Information and Change in Dietary Intake: A Randomized Controlled Trial

    PubMed Central

    Nielsen, Daiva E.; El-Sohemy, Ahmed

    2014-01-01

    Background Proponents of consumer genetic tests claim that the information can positively impact health behaviors and aid in chronic disease prevention. However, the effects of disclosing genetic information on dietary intake behavior are not clear. Methods A double-blinded, parallel group, 2∶1 online randomized controlled trial was conducted to determine the short- and long-term effects of disclosing nutrition-related genetic information for personalized nutrition on dietary intakes of caffeine, vitamin C, added sugars, and sodium. Participants were healthy men and women aged 20–35 years (n = 138). The intervention group (n = 92) received personalized DNA-based dietary advice for 12-months and the control group (n = 46) received general dietary recommendations with no genetic information for 12-months. Food frequency questionnaires were collected at baseline and 3- and 12-months after the intervention to assess dietary intakes. General linear models were used to compare changes in intakes between those receiving general dietary advice and those receiving DNA-based dietary advice. Results Compared to the control group, no significant changes to dietary intakes of the nutrients were observed at 3-months. At 12-months, participants in the intervention group who possessed a risk version of the ACE gene, and were advised to limit their sodium intake, significantly reduced their sodium intake (mg/day) compared to the control group (−287.3±114.1 vs. 129.8±118.2, p = 0.008). Those who had the non-risk version of ACE did not significantly change their sodium intake compared to the control group (12-months: −244.2±150.2, p = 0.11). Among those with the risk version of the ACE gene, the proportion who met the targeted recommendation of 1500 mg/day increased from 19% at baseline to 34% after 12 months (p = 0.06). Conclusions These findings demonstrate that disclosing genetic information for personalized nutrition results in greater changes

  2. Analysis of Informed Consent Document Utilization in a Minimal-Risk Genetic Study

    PubMed Central

    Desch, Karl; Li, Jun; Kim, Scott; Laventhal, Naomi; Metzger, Kristen; Siemieniak, David; Ginsburg, David

    2012-01-01

    Background The signed informed consent document certifies that the process of informed consent has taken place and provides research participants with comprehensive information about their role in the study. Despite efforts to optimize the informed consent document, only limited data are available about the actual use of consent documents by participants in biomedical research. Objective To examine the use of online consent documents in a minimal-risk genetic study. Design Prospective sibling cohort enrolled as part of a genetic study of hematologic and common human traits. Setting University of Michigan Campus, Ann Arbor, Michigan. Participants Volunteer sample of healthy persons with 1 or more eligible siblings aged 14 to 35 years. Enrollment was through targeted e-mail to student lists. A total of 1209 persons completed the study. Measurements Time taken by participants to review a 2833-word online consent document before indicating consent and identification of a masked hyperlink near the end of the document. Results The minimum predicted reading time was 566 seconds. The median time to consent was 53 seconds. A total of 23% of participants consented within 10 seconds, and 93% of participants consented in less than the minimum predicted reading time. A total of 2.5% of participants identified the masked hyperlink. Limitation The online consent process was not observed directly by study investigators, and some participants may have viewed the consent document more than once. Conclusion Few research participants thoroughly read the consent document before agreeing to participate in this genetic study. These data suggest that current informed consent documents, particularly for low-risk studies, may no longer serve the intended purpose of protecting human participants, and the role of these documents should be reassessed. Primary Funding Source National Institutes of Health. PMID:21893624

  3. Genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Maintaining genetic variation in wild populations of Arctic organisms is fundamental to the long-term persistence of high latitude biodiversity. Variability is important because it provides options for species to respond to changing environmental conditions and novel challenges such as emerging path...

  4. Human Variome Project country nodes: documenting genetic information within a country.

    PubMed

    Patrinos, George P; Smith, Timothy D; Howard, Heather; Al-Mulla, Fahd; Chouchane, Lotfi; Hadjisavvas, Andreas; Hamed, Sherifa A; Li, Xi-Tao; Marafie, Makia; Ramesar, Rajkumar S; Ramos, Feliciano J; de Ravel, Thomy; El-Ruby, Mona O; Shrestha, Tilak Ram; Sobrido, María-Jesús; Tadmouri, Ghazi; Witsch-Baumgartner, Martina; Zilfalil, Bin Alwi; Auerbach, Arleen D; Carpenter, Kevin; Cutting, Garry R; Dung, Vu Chi; Grody, Wayne; Hasler, Julia; Jorde, Lynn; Kaput, Jim; Macek, Milan; Matsubara, Yoichi; Padilla, Carmancita; Robinson, Helen; Rojas-Martinez, Augusto; Taylor, Graham R; Vihinen, Mauno; Weber, Tom; Burn, John; Qi, Ming; Cotton, Richard G H; Rimoin, David

    2012-11-01

    The Human Variome Project (http://www.humanvariomeproject.org) is an international effort aiming to systematically collect and share information on all human genetic variation. The two main pillars of this effort are gene/disease-specific databases and a network of Human Variome Project Country Nodes. The latter are nationwide efforts to document the genomic variation reported within a specific population. The development and successful operation of the Human Variome Project Country Nodes are of utmost importance to the success of Human Variome Project's aims and goals because they not only allow the genetic burden of disease to be quantified in different countries, but also provide diagnosticians and researchers access to an up-to-date resource that will assist them in their daily clinical practice and biomedical research, respectively. Here, we report the discussions and recommendations that resulted from the inaugural meeting of the International Confederation of Countries Advisory Council, held on 12th December 2011, during the 2011 Human Variome Project Beijing Meeting. We discuss the steps necessary to maximize the impact of the Country Node effort for developing regional and country-specific clinical genetics resources and summarize a few well-coordinated genetic data collection initiatives that would serve as paradigms for similar projects.

  5. Combining genetic and demographic information to prioritize conservation efforts for anadromous alewife and blueback herring

    PubMed Central

    Palkovacs, Eric P; Hasselman, Daniel J; Argo, Emily E; Gephard, Stephen R; Limburg, Karin E; Post, David M; Schultz, Thomas F; Willis, Theodore V

    2014-01-01

    A major challenge in conservation biology is the need to broadly prioritize conservation efforts when demographic data are limited. One method to address this challenge is to use population genetic data to define groups of populations linked by migration and then use demographic information from monitored populations to draw inferences about the status of unmonitored populations within those groups. We applied this method to anadromous alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis), species for which long-term demographic data are limited. Recent decades have seen dramatic declines in these species, which are an important ecological component of coastal ecosystems and once represented an important fishery resource. Results show that most populations comprise genetically distinguishable units, which are nested geographically within genetically distinct clusters or stocks. We identified three distinct stocks in alewife and four stocks in blueback herring. Analysis of available time series data for spawning adult abundance and body size indicate declines across the US ranges of both species, with the most severe declines having occurred for populations belonging to the Southern New England and the Mid-Atlantic Stocks. While all alewife and blueback herring populations deserve conservation attention, those belonging to these genetic stocks warrant the highest conservation prioritization. PMID:24567743

  6. Consumer awareness and attitudes about insurance discrimination post enactment of the Genetic Information Nondiscrimination Act.

    PubMed

    Allain, Dawn C; Friedman, Sue; Senter, Leigha

    2012-12-01

    To examine the awareness and attitudes about the Genetic Information Nondiscrimination Act in individuals who made contact with a Hereditary Breast and Ovarian Cancer Syndrome advocacy group. This is a descriptive study of individuals (n = 1,699) who were invited via email and advertisements to complete an online questionnaire available from August 2009 through December 2010. Response distributions of relevant subgroups were compared using cross tabulation and Chi-squared tests were used. The majority of respondents (69.2 %) had undergone genetic testing (n = 1,156) and 30.2 % had not. Of those who did not undergo genetic testing, the most common reason given for declining testing was cost (28.8 %), followed by concerns about insurance discrimination (19.5 %). More than half (60.5 %) were worried about health insurance discrimination when they first considered genetic testing and 28.6 % were worried about employment discrimination. Slightly more individuals were worried about health insurance discrimination if they had no prior knowledge of GINA. While "cost" was cited most frequently as the reason not to test, "fear of insurance discrimination" was the second most common reason. Knowledge of GINA among consumers is still limited and public education may help promote reduction in fear.

  7. The attitudes of people with sarcoma and their family towards genomics and incidental information arising from genetic research

    PubMed Central

    2013-01-01

    Purpose The study aimed to examine attitudes of individuals diagnosed with sarcoma and their family members towards genetics, genomic research and incidental information arising as a result of participating in genetic research. Methods A questionnaire was administered to 1200 individuals from the International Sarcoma Kindred Study (ISKS). Respondents were divided into three groups: individuals affected with sarcoma (probands), their spouses and family members. Results Approximately half of all research participants felt positively towards new discoveries in human genetics. Overall, more were positive in their attitudes towards genetic testing for inherited conditions (60%) but family members were less so. Older participants reported more highly positive attitudes more often than younger participants. Males were less likely to feel positive about new genetic discoveries and more likely to believe they could modify genetic risk by altering lifestyle factors. Almost all ISKS participants believed participants would like to be given ancillary information arising as a result of participating in genetic research. Conclusions The only difference between the study groups was the decreased likelihood of family members being highly positive about genetic testing. This may be important if predictive testing for sarcoma becomes available. Generally ISKS research participants supported the notion of returning incidental genetic information to research participants. PMID:23898988

  8. TANTAMOUNT TO FRAUD?: EXPLORING NON-DISCLOSURE OF GENETIC INFORMATION IN LIFE INSURANCE APPLICATIONS AS GROUNDS FOR POLICY RESCISSION.

    PubMed

    Prince, Anya E R

    2016-01-01

    Many genetic counselors recommend that individuals secure desired insurance policies, such as life insurance, prior to undergoing predictive genetic testing. It has been argued, however, that this practice is "tantamount to fraud" and that failure to disclose genetic test results, or conspiring to secure a policy before testing, opens an individual up to legal recourse. This debate traps affected individuals in a Catch-22. If they apply for life insurance and disclose a genetic test result, they may be denied. If they apply without disclosing the information, they may have committed fraud. The consequences of life insurance fraud are significant: If fraud is found on an application, a life insurer can rescind the policy, in some cases even after the individual has passed away. Such a rescission could leave family members or beneficiaries without the benefits of the life insurance policy payment after the individual's death and place them in in economic difficulty. Although it is clear that lying in response to a direct question about genetic testing would be tantamount to fraud, few, if any, life insurance applications currently include broad questions about genetic testing. This paper investigates whether non-disclosure of unasked for genetic information constitutes fraud and explores varying types of insurance questions that could conceivably be interpreted as seeking genetic information. Life insurance applicants generally have no duty to disclose unasked for information, including genetic information, on an application. However, given the complexities of genetic information, individuals may be exposed to fraud and rescission of their life insurance policy despite honest attempts to truthfully and completely answer all application questions. PMID:27263254

  9. TANTAMOUNT TO FRAUD?: EXPLORING NON-DISCLOSURE OF GENETIC INFORMATION IN LIFE INSURANCE APPLICATIONS AS GROUNDS FOR POLICY RESCISSION.

    PubMed

    Prince, Anya E R

    2016-01-01

    Many genetic counselors recommend that individuals secure desired insurance policies, such as life insurance, prior to undergoing predictive genetic testing. It has been argued, however, that this practice is "tantamount to fraud" and that failure to disclose genetic test results, or conspiring to secure a policy before testing, opens an individual up to legal recourse. This debate traps affected individuals in a Catch-22. If they apply for life insurance and disclose a genetic test result, they may be denied. If they apply without disclosing the information, they may have committed fraud. The consequences of life insurance fraud are significant: If fraud is found on an application, a life insurer can rescind the policy, in some cases even after the individual has passed away. Such a rescission could leave family members or beneficiaries without the benefits of the life insurance policy payment after the individual's death and place them in in economic difficulty. Although it is clear that lying in response to a direct question about genetic testing would be tantamount to fraud, few, if any, life insurance applications currently include broad questions about genetic testing. This paper investigates whether non-disclosure of unasked for genetic information constitutes fraud and explores varying types of insurance questions that could conceivably be interpreted as seeking genetic information. Life insurance applicants generally have no duty to disclose unasked for information, including genetic information, on an application. However, given the complexities of genetic information, individuals may be exposed to fraud and rescission of their life insurance policy despite honest attempts to truthfully and completely answer all application questions.

  10. Informativeness of minisatellite and microsatellite markers for genetic analysis in papaya.

    PubMed

    Oliveira, G A F; Dantas, J L L; Oliveira, E J

    2015-10-01

    The objective of this study was to evaluate information on minisatellite and microsatellite markers in papaya (Carica papaya L.). Forty minisatellites and 91 microsatellites were used for genotyping 24 papaya accessions. Estimates of genetic diversity, genetic linkage and analyses of population structure were compared. A lower average number of alleles per locus was observed in minisatellites (3.10) compared with microsatellites (3.57), although the minisatellites showed rarer alleles (18.54 %) compared with microsatellite (13.85 %). Greater expected (He = 0.52) and observed (Ho = 0.16) heterozygosity was observed in the microsatellites compared with minisatellites (He = 0.42 and Ho = 0.11), possibly due to the high number of hermaphroditic accessions, resulting in high rates of self-fertilization. The polymorphic information content and Shannon-Wiener diversity were also higher for microsatellites (from 0.47 to 1.10, respectively) compared with minisatellite (0.38 and 0.85, respectively). The probability of paternity exclusion was high for both markers (>0.999), and the combined probability of identity was from 1.65(-13) to 4.33(-38) for mini- and micro-satellites, respectively, which indicates that both types of markers are ideal for genetic analysis. The Bayesian analysis indicated the formation of two groups (K = 2) for both markers, although the minisatellites indicated a substructure (K = 4). A greater number of accessions with a low probability of assignment to specific groups were observed for microsatellites. Collectively, the results indicated higher informativeness of microsatellites. However, the lower informative power of minisatellites may be offset by the use of larger number of loci. Furthermore, minisatellites are subject to less error in genotyping because there is greater power to detect genotyping systems when larger motifs are used.

  11. MINT: Mutual Information Based Transductive Feature Selection for Genetic Trait Prediction.

    PubMed

    He, Dan; Rish, Irina; Haws, David; Parida, Laxmi

    2016-01-01

    Whole genome prediction of complex phenotypic traits using high-density genotyping arrays has attracted a lot of attention, as it is relevant to the fields of plant and animal breeding and genetic epidemiology. Since the number of genotypes is generally much bigger than the number of samples, predictive models suffer from the curse of dimensionality. The curse of dimensionality problem not only affects the computational efficiency of a particular genomic selection method, but can also lead to a poor performance, mainly due to possible overfitting, or un-informative features. In this work, we propose a novel transductive feature selection method, called MINT, which is based on the MRMR (Max-Relevance and Min-Redundancy) criterion. We apply MINT on genetic trait prediction problems and show that, in general, MINT is a better feature selection method than the state-of-the-art inductive method MRMR. PMID:27295642

  12. Synthetic biology with artificially expanded genetic information systems. From personalized medicine to extraterrestrial life.

    PubMed

    Benner, Steven A; Hutter, Daniel; Sismour, A Michael

    2003-01-01

    Over 15 years ago, the Benner group noticed that the DNA alphabet need not be limited to the four standard nucleotides known in natural DNA. Rather, twelve nucleobases forming six base pairs joined by mutually exclusive hydrogen bonding patterns are possible within the geometry of the Watson-Crick pair (Fig. 1). Synthesis and studies on these compounds have brought us to the threshold of a synthetic biology, an artificial chemical system that does basic processes needed for life (in particular, Darwinian evolution), but with unnatural chemical structures. At the same time, the artificial genetic information systems (AEGIS) that we have developed have been used in FDA-approved commercial tests for managing HIV and hepatitis C infections in individual patients, and in a tool that seeks the virus for severe acute respiratory syndrome (SARS). AEGIS also supports the next generation of robotic probes to search for genetic molecules on Mars, Europa, and elsewhere where NASA probes will travel.

  13. Using genetic information to test causal relationships in cross-sectional data

    PubMed Central

    Verhulst, Brad; Estabrook, Ryne

    2013-01-01

    Cross-sectional data from twins contain information that can be used to derive a test of causality between traits. This test of directionality is based upon the fact that genetic relationships between family members conform to an established structural pattern. In this paper we examine several common methods for empirically testing causality as well as several genetic models that we build on for the Direction of Causation (DoC) model. We then discuss the mathematical components of the DoC model and highlight limitations of the model and potential solutions to these limitations. We conclude by presenting an example from the personality and politics literature that has begun to explore the question whether or not personality traits cause people to hold specific political attitudes. PMID:23946557

  14. The non-power model of the genetic code: a paradigm for interpreting genomic information.

    PubMed

    Gonzalez, Diego Luis; Giannerini, Simone; Rosa, Rodolfo

    2016-03-13

    In this article, we present a mathematical framework based on redundant (non-power) representations of integer numbers as a paradigm for the interpretation of genomic information. The core of the approach relies on modelling the degeneracy of the genetic code. The model allows one to explain many features and symmetries of the genetic code and to uncover hidden symmetries. Also, it provides us with new tools for the analysis of genomic sequences. We review briefly three main areas: (i) the Euplotid nuclear code, (ii) the vertebrate mitochondrial code, and (iii) the main coding/decoding strategies used in the three domains of life. In every case, we show how the non-power model is a natural unified framework for describing degeneracy and deriving sound biological hypotheses on protein coding. The approach is rooted on number theory and group theory; nevertheless, we have kept the technical level to a minimum by focusing on key concepts and on the biological implications. PMID:26857679

  15. Parent involvement, sibling companionship, and adolescent substance use: A longitudinal, genetically informed design.

    PubMed

    Samek, Diana R; Rueter, Martha A; Keyes, Margaret A; McGue, Matt; Iacono, William G

    2015-08-01

    A large literature shows that parent and sibling relationship factors are associated with an increased likelihood of adolescent substance use. Less is known about the etiology of these associations. Using a genetically informed sibling design, we examined the prospective associations between parent involvement, sibling companionship, and adolescent substance use at 2 points in mid- and late-adolescence. Adolescents were adopted (n = 568) or the biological offspring of both parents (n = 412). Cross-lagged panel results showed that higher levels of parent involvement in early adolescence were associated with lower levels of substance use later in adolescence. Results did not significantly differ across adoption status, suggesting this association cannot be due to passive gene-environment correlation. Adolescent substance use at Time 1 was not significantly associated with parent involvement at Time 2, suggesting this association does not appear to be solely due to evocative (i.e., "child-driven") effects either. Together, results support a protective influence of parent involvement on subsequent adolescent substance use that is environmental in nature. The cross-paths between sibling companionship and adolescent substance use were significant and negative in direction (i.e., protective) for sisters, but positive for brothers (in line with a social contagion hypothesis). These effects were consistent across genetically related and unrelated pairs, and thus appear to be environmentally mediated. For mixed gender siblings, results were consistent with environmentally driven, protective influence hypothesis for genetically unrelated pairs, but in line with a genetically influenced, social contagion hypothesis for genetically related pairs. Implications are discussed. PMID:26030026

  16. Information avoidance tendencies, threat management resources, and interest in genetic sequencing feedback

    PubMed Central

    Taber, Jennifer M.; Klein, William M.P.; Ferrer, Rebecca A.; Lewis, Katie L.; Harris, Peter R.; Shepperd, James A.; Biesecker, Leslie G.

    2015-01-01

    Background Information avoidance is a defensive strategy that undermines receipt of potentially beneficial but threatening health information and may especially occur when threat management resources are unavailable. Purpose We examined whether individual differences in information avoidance predicted intentions to receive genetic sequencing results for preventable and unpreventable (i.e., more threatening) disease and, secondarily, whether threat management resources of self-affirmation or optimism mitigated any effects. Methods Participants (N=493) in an NIH study (ClinSeq®) piloting the use of genome sequencing reported intentions to receive (optional) sequencing results and completed individual difference measures of information avoidance, self-affirmation, and optimism. Results Information avoidance tendencies corresponded with lower intentions to learn results, particularly for unpreventable diseases. The association was weaker among individuals higher in self-affirmation or optimism, but only for results regarding preventable diseases. Conclusions Information avoidance tendencies may influence decisions to receive threatening health information; threat management resources hold promise for mitigating this association. PMID:25582989

  17. Smoking during pregnancy and ADHD risk: A genetically informed, multiple-rater approach.

    PubMed

    Knopik, Valerie S; Marceau, Kristine; Bidwell, L Cinnamon; Palmer, Rohan H C; Smith, Taylor F; Todorov, Alexandre; Evans, Allison Schettini; Heath, Andrew C

    2016-10-01

    Maternal smoking during pregnancy (SDP) is a significant public health concern with adverse consequences to the health and well-being of the developing child, including behavioral outcomes such as Attention-Deficit Hyperactivity Disorder (ADHD). There is substantial interest in understanding the nature of this reported association, particularly in light of more recent genetically informed studies that suggest that the SDP-ADHD link is less clear than once thought. In a sample of families (N = 173) specifically selected for sibling pairs discordant for prenatal smoking exposure, we use a sibling-comparison approach that controls for shared genetic and familial influences to assess the effects of SDP on ADHD symptom dimensions. ADHD was measured by both parent and teacher report on the Conners report forms and the Child Behavior Checklist/Teacher Report Form (CBCL/TRF). Results for the CBCL/TRF Total ADHD score are consistent with prior genetically informed approaches and suggest that previously reported associations between SDP and ADHD are largely due to familial confounding rather than causal teratogenic effects. However, results from the Conners parent report suggest a potentially causal effect of SDP on hyperactive/impulsive and, to a lesser extent, total ADHD symptoms; SDP results in increased parent-reported hyperactive/impulsive and total ADHD symptoms even after accounting for genetic and familial confounding factors. This suggests that the Conners assessment (parent-report) may provide a sensitive measure for use in studies examining child specific SDP effects on continuous and dimensional aspects of ADHD. © 2016 Wiley Periodicals, Inc.

  18. Genetic structure and differentiation analysis of a Eurasian Uyghur population by use of 27 continental ancestry-informative SNPs.

    PubMed

    Wei, Yi-Liang; Sun, Qi-Fan; Li, Qing; Yi, Jun-Ling; Zhao, Lei; Ou, Yuan; Jiang, Li; Zhang, Tao; Liu, Hai-Bo; Chen, Jian-Gang; Zhu, Bo-Feng; Ye, Jian; Hu, Lan; Li, Cai-Xia

    2016-07-01

    Previously, we developed and validated a multiplex assay of 27 ancestry-informative markers (AIMs) for analyzing African (AFR), European (EUR), and East Asian (EAS) ancestry components. In this study, we typed and collectively analyzed a large Uyghur sample of 979 individuals to estimate the genetic coefficients of the 27 AIMs and investigate differentiation parameters between Uyghur and Han. The Uyghur allele frequencies ranged from 0.243 to 0.952, and heterozygosities ranged from 0.091 to 0.500. Values of F st 3 and I n 3 for EUR, Uyghur, and EAS ranged from 0.028 to 0.550 and 0.0002 to 0.345, respectively. The Uyghur population displays a substantial ancestry contribution of 50.3:49.7 (EUR:EAS) and was efficiently discriminated from Han Chinese with an accuracy of 99.285 %. All populations were clustered into AFR, EUR, EAS, and admixture groups of these three ancestries. Central Asian was obviously stratified from the other admixture populations of South Asians, North Asians, and the Americans. The 27 SNPs yield a circle with an average distance of 0.936 from the center (0, 0) in PCA analysis. Using this set, Chinese Uyghur and Han populations achieved accurate differentiation, and our updated genotype database (by citing 1000 Genomes data) of 43 worldwide populations is a useful resource for forensic applications and disease association studies. PMID:26932865

  19. Reconstructing genetic mating systems in the absence of parental information in colonially breeding waterbirds

    PubMed Central

    2011-01-01

    Spoonbill. In fact, extra-pair paternity and conspecific brood parasitism were common in the latter two species, with a combined frequency of 7.5% and 11.3% in Roseate Spoonbill and Wood Stork, respectively. Although geographically co-distributed, differences among these species may be due to variation in their life histories. From a methodological standpoint, the approach implemented here, although not free from limitations, can have broad application for analyzing systems with limited genealogical information and/or in studying similarly challenging organisms in which obtaining genetic data on complete families is problematic. PMID:21740559

  20. Understanding of Genetic Information in Higher Secondary Students in Northeast India and the Implications for Genetics Education

    ERIC Educational Resources Information Center

    Chattopadhyay, Ansuman

    2005-01-01

    Since the work of Watson and Crick in the mid-1950s, the science of genetics has become increasingly molecular. The development of recombinant DNA technologies by the agricultural and pharmaceutical industries led to the introduction of genetically modified organisms (GMOs). By the end of the twentieth century, reports of animal cloning and recent…

  1. Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information

    PubMed Central

    2010-01-01

    Background The genetic contributions to human common disorders and mouse genetic models of disease are complex and often overlapping. In common human diseases, unlike classical Mendelian disorders, genetic factors generally have small effect sizes, are multifactorial, and are highly pleiotropic. Likewise, mouse genetic models of disease often have pleiotropic and overlapping phenotypes. Moreover, phenotypic descriptions in the literature in both human and mouse are often poorly characterized and difficult to compare directly. Methods In this report, human genetic association results from the literature are summarized with regard to replication, disease phenotype, and gene specific results; and organized in the context of a systematic disease ontology. Similarly summarized mouse genetic disease models are organized within the Mammalian Phenotype ontology. Human and mouse disease and phenotype based gene sets are identified. These disease gene sets are then compared individually and in large groups through dendrogram analysis and hierarchical clustering analysis. Results Human disease and mouse phenotype gene sets are shown to group into disease and phenotypically relevant groups at both a coarse and fine level based on gene sharing. Conclusion This analysis provides a systematic and global perspective on the genetics of common human disease as compared to itself and in the context of mouse genetic models of disease. PMID:20092628

  2. Extracting directed information flow networks: An application to genetics and semantics

    NASA Astrophysics Data System (ADS)

    Masucci, A. P.; Kalampokis, A.; Eguíluz, V. M.; Hernández-García, E.

    2011-02-01

    We introduce a general method to infer the directional information flow between populations whose elements are described by n-dimensional vectors of symbolic attributes. The method is based on the Jensen-Shannon divergence and on the Shannon entropy and has a wide range of application. We show here the results of two applications: first we extract the network of genetic flow between meadows of the seagrass Poseidonia oceanica, where the meadow elements are specified by sets of microsatellite markers, and then we extract the semantic flow network from a set of Wikipedia pages, showing the semantic channels between different areas of knowledge.

  3. LIMITING OCCUPATIONAL MEDICAL EVALUATIONS UNDER THE AMERICANS WITH DISABILITIES ACT AND THE GENETIC INFORMATION NONDISCRIMINATION ACT.

    PubMed

    Rothstein, Mark A; Roberts, Jessica; Guidotti, Tee L

    2015-01-01

    Although medical care delivery by one's personal physician is the paradigmatic American healthcare arrangement, in the workplace setting, many Americans undergo medical evaluations to assess their fitness for duty or degree of impairment. This Article explores the complex and evolving legal status of occupational medical evaluations. Beginning with the legal and ethical frameworks of occupational medical practice, the Article then examines the effects of increasingly detailed legal regulation under the Americans with Disabilities Act and the Genetic Information Nondiscrimination Act on employees, employers, and physicians. PMID:26863849

  4. Customized oligonucleotide microchips that convert multiple genetic information to simple patterns, are portable and reusable

    DOEpatents

    Mirzabekov, Andrei; Guschin, Dmitry Y.; Chik, Valentine; Drobyshev, Aleksei; Fotin, Alexander; Yershov, Gennadiy; Lysov, Yuri

    2002-01-01

    This invention relates to using customized oligonucleotide microchips as biosensors for the detection and identification of nucleic acids specific for different genes, organisms and/or individuals in the environment, in food and in biological samples. The microchips are designed to convert multiple bits of genetic information into simpler patterns of signals that are interpreted as a unit. Because of an improved method of hybridizing oligonucleotides from samples to microchips, microchips are reusable and transportable. For field study, portable laser or bar code scanners are suitable.

  5. Genetic Counseling

    MedlinePlus

    Genetic counseling provides information and support to people who have, or may be at risk for, genetic disorders. A ... meets with you to discuss genetic risks. The counseling may be for yourself or a family member. ...

  6. Maternal Smoking During Pregnancy and Offspring Birth Weight: A Genetically-Informed Approach Comparing Multiple Raters.

    PubMed

    Knopik, Valerie S; Marceau, Kristine; Palmer, Rohan H C; Smith, Taylor F; Heath, Andrew C

    2016-05-01

    Maternal smoking during pregnancy (SDP) is a significant public health concern with adverse consequences to the health and well-being of the fetus. There is considerable debate about the best method of assessing SDP, including birth/medical records, timeline follow-back approaches, multiple reporters, and biological verification (e.g., cotinine). This is particularly salient for genetically-informed approaches where it is not always possible or practical to do a prospective study starting during the prenatal period when concurrent biological specimen samples can be collected with ease. In a sample of families (N = 173) specifically selected for sibling pairs discordant for prenatal smoking exposure, we: (1) compare rates of agreement across different types of report-maternal report of SDP, paternal report of maternal SDP, and SDP contained on birth records from the Department of Vital Statistics; (2) examine whether SDP is predictive of birth weight outcomes using our best SDP report as identified via step (1); and (3) use a sibling-comparison approach that controls for genetic and familial influences that siblings share in order to assess the effects of SDP on birth weight. Results show high agreement between reporters and support the utility of retrospective report of SDP. Further, we replicate a causal association between SDP and birth weight, wherein SDP results in reduced birth weight even when accounting for genetic and familial confounding factors via a sibling comparison approach.

  7. Are Aquatic Viruses a Biological Archive of Genetic Information from Universe?

    NASA Astrophysics Data System (ADS)

    Toparceanu, F.; Negoita, Gh. T.; Nita, I. I.; Sava, D.

    2009-04-01

    After 1990, when the viruses were admited as the most abundant lifeforms from aquatic environments, it became obvious that viral lysis had an essential role on release and recycling of nutrients. Studies on cellular cultures and modeling suggest that this is an important quantitative process. The viruses from oceans represent the widest source of genetic diversity on the Earth, uncharacterized yet. The ancient lifeforms records stretching back a million years are locked in ice caps. The trend of glaciers melting as effect of actual climate change will promote the release of ancient viruses from ice caps. The increasing of the freshwater layer led to the replace of some algae species by others. Law-Racovitza Station (69o23'S 76o23'E) from East Antarctica (Larsemann Hills Oasis) offers opportunities to study the Antarctic marine ecosystem, as well as archaic aquatic ecosystems from this area ( 150 lakes and waterways resulted from ice and snow melting during the austral summer). According to Law-Racovitza Station Scientific Program, we are performing studies regarding the effect of climate changes on virus-algae host relationship in these aquatic ecosystems. Phycodnaviruses, that infect the eukaryote algae, are comprised of ancient genes and they are considered a "peek" of genetic diversity useful in biological studies and exobiology regarding the evolution of genetic sequencing. The latest discoveries of the giant aquatic viruses open the unexpected perspectives for understanding the role of viral infection in global ecosystem; beyond the old concept which considered that the viruses were only etiological agents of human, animals and plants illnesses. The aquatic viruses which infect microalgae contain similar genes of other viruses, bacteria, arhebacteria and eukaryotes, all of them being on the same genome. Which is the signification of enormous abundance of viruses and excessive diversity of genetic information encoded by viruses? There is the possibility that

  8. Genetic parameter estimates for carcass traits and visual scores including or not genomic information.

    PubMed

    Gordo, D G M; Espigolan, R; Tonussi, R L; Júnior, G A F; Bresolin, T; Magalhães, A F Braga; Feitosa, F L; Baldi, F; Carvalheiro, R; Tonhati, H; de Oliveira, H N; Chardulo, L A L; de Albuquerque, L G

    2016-05-01

    CS, FP, and MS could be used as selection criteria to improve HCW, BF, and LMA. The use of genomic information permitted the detection of greater additive genetic variability for LMA and BF. For HCW, the high magnitude of the genetic correlations with visual scores was probably sufficient to recover genetic variability. The methods provided similar breeding value accuracies, especially for the visual scores. PMID:27285679

  9. SOCIAL ADVERSITY, GENETIC VARIATION, STREET CODE, AND AGGRESSION: A GENETICLLY INFORMED MODEL OF VIOLENT BEHAVIOR

    PubMed Central

    Simons, Ronald L.; Lei, Man Kit; Stewart, Eric A.; Brody, Gene H.; Beach, Steven R. H.; Philibert, Robert A.; Gibbons, Frederick X.

    2011-01-01

    Elijah Anderson (1997, 1999) argues that exposure to extreme community disadvantage, residing in “street” families, and persistent discrimination encourage many African Americans to develop an oppositional culture that he labels the “code of the street.” Importantly, while the adverse conditions described by Anderson increase the probability of adopting the code of the street, most of those exposed to these adverse conditions do not do so. The present study examines the extent to which genetic variation accounts for these differences. Although the diathesis-stress model guides most genetically informed behavior science, the present study investigates hypotheses derived from the differential susceptibility perspective (Belsky & Pluess, 2009). This model posits that some people are genetically predisposed to be more susceptible to environmental influence than others. An important implication of the model is that those persons most vulnerable to adverse social environments are the same ones who reap the most benefit from environmental support. Using longitudinal data from a sample of several hundred African American males, we examined the manner in which variants in three genes - 5-HTT, DRD4, and MAOA - modulate the effect of community and family adversity on adoption of the street code and aggression. We found strong support for the differential susceptibility perspective. When the social environment was adverse, individuals with these genetic variants manifested more commitment to the street code and aggression than those with other genotypes, whereas when adversity was low they demonstrated less commitment to the street code and aggression than those with other genotypes. PMID:23785260

  10. Accounting for the physical and mental health benefits of entry into marriage: a genetically informed study of selection and causation.

    PubMed

    Horn, Erin E; Xu, Yishan; Beam, Christopher R; Turkheimer, Eric; Emery, Robert E

    2013-02-01

    Married adults show better psychological adjustment and physical health than their separated/divorced or never-married counterparts. However, this apparent "marriage benefit" may be due to social selection, social causation, or both processes. Genetically informed research designs offer critical advantages for helping to disentangle selection from causation by controlling for measured and unmeasured genetic and shared environmental selection. Using young-adult twin and sibling pairs from the National Longitudinal Study of Adolescent Health (Harris, 2009), we conducted genetically informed analyses of the association between entry into marriage, cohabitation, or singlehood and multiple indices of psychological and physical health. The relation between physical health and marriage was completely explained by nonrandom selection. For internalizing behaviors, selection did not fully explain the benefits of marriage or cohabitation relative to being single, whereas for externalizing symptoms, marriage predicted benefits over cohabitation. The genetically informed approach provides perhaps the strongest nonexperimental evidence that these observed effects are causal.

  11. Generating information-rich high-throughput experimental materials genomes using functional clustering via multitree genetic programming and information theory.

    PubMed

    Suram, Santosh K; Haber, Joel A; Jin, Jian; Gregoire, John M

    2015-04-13

    High-throughput experimental methodologies are capable of synthesizing, screening and characterizing vast arrays of combinatorial material libraries at a very rapid rate. These methodologies strategically employ tiered screening wherein the number of compositions screened decreases as the complexity, and very often the scientific information obtained from a screening experiment, increases. The algorithm used for down-selection of samples from higher throughput screening experiment to a lower throughput screening experiment is vital in achieving information-rich experimental materials genomes. The fundamental science of material discovery lies in the establishment of composition-structure-property relationships, motivating the development of advanced down-selection algorithms which consider the information value of the selected compositions, as opposed to simply selecting the best performing compositions from a high throughput experiment. Identification of property fields (composition regions with distinct composition-property relationships) in high throughput data enables down-selection algorithms to employ advanced selection strategies, such as the selection of representative compositions from each field or selection of compositions that span the composition space of the highest performing field. Such strategies would greatly enhance the generation of data-driven discoveries. We introduce an informatics-based clustering of composition-property functional relationships using a combination of information theory and multitree genetic programming concepts for identification of property fields in a composition library. We demonstrate our approach using a complex synthetic composition-property map for a 5 at. % step ternary library consisting of four distinct property fields and finally explore the application of this methodology for capturing relationships between composition and catalytic activity for the oxygen evolution reaction for 5429 catalyst compositions in a

  12. Genetic Diversity of Cryptosporidium in Children in an Urban Informal Settlement of Nairobi, Kenya

    PubMed Central

    Mbae, Cecilia; Mulinge, Erastus; Waruru, Anthony; Ngugi, Benjamin; Wainaina, James; Kariuki, Samuel

    2015-01-01

    Introduction Globally Cryptosporidium and Giardia species are the most common non-bacterial causes of diarrhoea in children and HIV infected individuals, yet data on their role in paediatric diarrhoea in Kenya remains scant. This study investigated the occurrence of Cryptosporidium species, genotypes and subtypes in children, both hospitalized and living in an informal settlement in Nairobi. Methods This was a prospective cross-sectional study in which faecal specimen positive for Cryptosporidium spp. by microscopy from HIV infected and uninfected children aged five years and below presenting with diarrhoea at selected outpatient clinics in Mukuru informal settlements, or admitted to the paediatric ward at the Mbagathi District Hospital were characterized. The analysis was done by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) of the 18srRNA gene for species identification and PCR-sequencing of the 60 kDa glycoprotein (GP60) gene for subtyping. Results C. hominis was the most common species of Cryptosporidium identified in125/151(82.8%) of the children. Other species identified were C. parvum 18/151(11.9%), while C. felis and C. meleagridis were identified in 4 and 2 children, respectively. Wide genetic variation was observed within C. hominis, with identification of 5 subtype families; Ia, Ib, Id, Ie and If and 21 subtypes. Only subtype family IIc was identified within C. parvum. There was no association between species and HIV status or patient type. Conclusion C. hominis is the most common species associated with diarrhoea in the study population. There was high genetic variability in the C. hominis isolates with 22 different subtypes identified, whereas genetic diversity was low within C. parvum with only one subtype family IIc identified. PMID:26691531

  13. Ancient dna from pleistocene fossils: Preservation, recovery, and utility of ancient genetic information for quaternary research

    NASA Astrophysics Data System (ADS)

    Yang, Hong

    Until recently, recovery and analysis of genetic information encoded in ancient DNA sequences from Pleistocene fossils were impossible. Recent advances in molecular biology offered technical tools to obtain ancient DNA sequences from well-preserved Quaternary fossils and opened the possibilities to directly study genetic changes in fossil species to address various biological and paleontological questions. Ancient DNA studies involving Pleistocene fossil material and ancient DNA degradation and preservation in Quaternary deposits are reviewed. The molecular technology applied to isolate, amplify, and sequence ancient DNA is also presented. Authentication of ancient DNA sequences and technical problems associated with modern and ancient DNA contamination are discussed. As illustrated in recent studies on ancient DNA from proboscideans, it is apparent that fossil DNA sequence data can shed light on many aspects of Quaternary research such as systematics and phylogeny. conservation biology, evolutionary theory, molecular taphonomy, and forensic sciences. Improvement of molecular techniques and a better understanding of DNA degradation during fossilization are likely to build on current strengths and to overcome existing problems, making fossil DNA data a unique source of information for Quaternary scientists.

  14. What’s at Stake? Genetic Information from the Perspective of People with Epilepsy and their Family Members

    PubMed Central

    Shostak, Sara; Zarhin, Dana; Ottman, Ruth

    2011-01-01

    Substantial progress has been made in identifying genes that raise risk for epilepsy, and genetic testing for some of these genes is increasingly being used in clinical practice. However, almost no empirical data are available from the perspective of people with epilepsy and their family members about the impact of genetic information and potential benefits and harms of genetic testing. To address this gap we conducted in-depth qualitative interviews with 40 individuals (22 with epilepsy, 18 unaffected) in the USA from families containing multiple affected individuals who had participated in epilepsy genetics research. The interviews were coded and analyzed using the principles of grounded theory. Several major themes emerged from these interviews. Participants expressed “personal theories of inheritance” that emphasized commonalities among relatives and the idea that disease risk is most shared by family members who share physical or personality traits. Most participants said they would have genetic testing if it were offered. They cited many potential benefits, including learning what caused epilepsy in their family, being better able to care and advocate for children at risk, reducing guilt and blame, providing an increased sense of control, and relieving anxiety in unaffected individuals who test negative. The influence of genetic information on reproduction was a particularly salient theme. Although respondents believed genetic testing would be useful for informing their reproductive choices, they also expressed fear that it could lead to external pressures to modify these choices. Other concerns about the potential negative impact of genetic information included increased blame and guilt, increased stigma and discrimination in employment and insurance, self-imposed limitations on life goals, and alterations in fundamental conceptions of “what epilepsy is.” Consideration of the perspectives of people with epilepsy and their family members is critical

  15. Difference and Choice: Exploring Prenatal Testing and the Use of Genetic Information with People with Learning Difficulties.

    ERIC Educational Resources Information Center

    Ward, Linda; Howarth, Joyce; Rodgers, Jackie

    2002-01-01

    This article describes two workshops that explained the use of prenatal testing and genetic information to inform choices in pregnancy to people with learning difficulties, explored the issues with them, and describe the contribution subsequently made by these people to a British national conference on this subject. (Contains references.)…

  16. The Genetic Information Nondiscrimination Act (GINA): public policy and medical practice in the age of personalized medicine.

    PubMed

    Feldman, Eric A

    2012-06-01

    Survey data suggest that many people fear genetic discrimination by health insurers or employers. In fact, such discrimination has not yet been a significant problem. This article examines the fear and reality of genetic discrimination in the United States, describes how Congress sought to prohibit such discrimination by passing the Genetic Information Nondiscrimination Act of 2008 (GINA), and explores the implications of GINA for general internists and their institutions. It concludes that medical providers and health care institutions must be familiar with the general intent and specific terms of GINA, and should continue to collect genetic information that can contribute to the high quality provision of medical treatment. Not doing so violates their medical mission and diminishes the quality of care patients deserve.

  17. "Obligated aliens": recognizing sperm donors' ethical obligation to disclose genetic information.

    PubMed

    Tamir, Sivan

    2013-03-01

    Sperm donors' obligations are typically constrained to the immediate circumstances surrounding the donation and to its time frame. This paper makes the case for recognizing an ongoing ethical obligation that binds sperm donors to disclose, in a timely manner, meaningful genetic information to recipients and donor-conceived children. The paper delineates and conceptualizes the suggested (potentially reciprocal) duty and argues that it is not the genetic link between the donor and the donor-conceived child that binds donors by said duty, but rather social responsibility. Accordingly, an original perception of the donor as an obligated alien is suggested and developed. The main thesis of the paper is supported inter alia by a comparison between transmitting infectious diseases and passing faulty genes on to donor-conceived children. The paper also provides an in-depth analysis of the conflicting interests of the parties generated by such an obligation and proposes a model for embedding this ethical duty in a (legal) contractual framework. PMID:23678628

  18. Genetic Pool Information Reflects Highly Suitable Areas: The Case of Two Parapatric Endangered Species of Tuco-tucos (Rodentia: Ctenomiydae)

    PubMed Central

    Galiano, Daniel; Bernardo-Silva, Jorge; de Freitas, Thales R. O.

    2014-01-01

    Conservation of small mammals requires knowledge of the genetically and ecologically meaningful spatial scales at which species respond to habitat modifications. Conservation strategies can be improved through the use of ecological niche models and genetic data to classify areas of high environmental suitability. In this study, we applied a Maxent model integrated with genetic information (nucleotide diversity, haplotype diversity and Fu's Fs neutrality tests) to evaluate potential genetic pool populations with highly suitable areas for two parapatric endangered species of tuco-tucos (Ctenomys minutus and C. lami). Our results demonstrated that both species were largely influenced by vegetation and soil variables at a landscape scale and inhabit a highly specific niche. Ctenomys minutus was also influenced by the variable altitude; the species was associated with low altitudes (sea level). Our model of genetic data associated with environmental suitability indicate that the genetic pool data were associated with highly suitable areas for C. minutus. This pattern was not evident for C. lami, but this outcome could be a consequence of the restricted range of the species. The preservation of species requires not only detailed knowledge of their natural history and genetic structure but also information on the availability of suitable areas where species can survive, and such knowledge can aid significantly in conservation planning. This finding reinforces the use of these two techniques for planning conservation actions. PMID:24819251

  19. Genetic pool information reflects highly suitable areas: the case of two parapatric endangered species of Tuco-tucos (Rodentia: Ctenomiydae).

    PubMed

    Galiano, Daniel; Bernardo-Silva, Jorge; Freitas, Thales R O de

    2014-01-01

    Conservation of small mammals requires knowledge of the genetically and ecologically meaningful spatial scales at which species respond to habitat modifications. Conservation strategies can be improved through the use of ecological niche models and genetic data to classify areas of high environmental suitability. In this study, we applied a Maxent model integrated with genetic information (nucleotide diversity, haplotype diversity and Fu's Fs neutrality tests) to evaluate potential genetic pool populations with highly suitable areas for two parapatric endangered species of tuco-tucos (Ctenomys minutus and C. lami). Our results demonstrated that both species were largely influenced by vegetation and soil variables at a landscape scale and inhabit a highly specific niche. Ctenomys minutus was also influenced by the variable altitude; the species was associated with low altitudes (sea level). Our model of genetic data associated with environmental suitability indicate that the genetic pool data were associated with highly suitable areas for C. minutus. This pattern was not evident for C. lami, but this outcome could be a consequence of the restricted range of the species. The preservation of species requires not only detailed knowledge of their natural history and genetic structure but also information on the availability of suitable areas where species can survive, and such knowledge can aid significantly in conservation planning. This finding reinforces the use of these two techniques for planning conservation actions.

  20. Mouse models of human AML accurately predict chemotherapy response

    PubMed Central

    Zuber, Johannes; Radtke, Ina; Pardee, Timothy S.; Zhao, Zhen; Rappaport, Amy R.; Luo, Weijun; McCurrach, Mila E.; Yang, Miao-Miao; Dolan, M. Eileen; Kogan, Scott C.; Downing, James R.; Lowe, Scott W.

    2009-01-01

    The genetic heterogeneity of cancer influences the trajectory of tumor progression and may underlie clinical variation in therapy response. To model such heterogeneity, we produced genetically and pathologically accurate mouse models of common forms of human acute myeloid leukemia (AML) and developed methods to mimic standard induction chemotherapy and efficiently monitor therapy response. We see that murine AMLs harboring two common human AML genotypes show remarkably diverse responses to conventional therapy that mirror clinical experience. Specifically, murine leukemias expressing the AML1/ETO fusion oncoprotein, associated with a favorable prognosis in patients, show a dramatic response to induction chemotherapy owing to robust activation of the p53 tumor suppressor network. Conversely, murine leukemias expressing MLL fusion proteins, associated with a dismal prognosis in patients, are drug-resistant due to an attenuated p53 response. Our studies highlight the importance of genetic information in guiding the treatment of human AML, functionally establish the p53 network as a central determinant of chemotherapy response in AML, and demonstrate that genetically engineered mouse models of human cancer can accurately predict therapy response in patients. PMID:19339691

  1. Incorporating Functional Genomic Information in Genetic Association Studies Using an Empirical Bayes Approach

    PubMed Central

    Spencer, Amy V.; Cox, Angela; Lin, Wei‐Yu; Easton, Douglas F.; Michailidou, Kyriaki

    2016-01-01

    ABSTRACT There is a large amount of functional genetic data available, which can be used to inform fine‐mapping association studies (in diseases with well‐characterised disease pathways). Single nucleotide polymorphism (SNP) prioritization via Bayes factors is attractive because prior information can inform the effect size or the prior probability of causal association. This approach requires the specification of the effect size. If the information needed to estimate a priori the probability density for the effect sizes for causal SNPs in a genomic region isn't consistent or isn't available, then specifying a prior variance for the effect sizes is challenging. We propose both an empirical method to estimate this prior variance, and a coherent approach to using SNP‐level functional data, to inform the prior probability of causal association. Through simulation we show that when ranking SNPs by our empirical Bayes factor in a fine‐mapping study, the causal SNP rank is generally as high or higher than the rank using Bayes factors with other plausible values of the prior variance. Importantly, we also show that assigning SNP‐specific prior probabilities of association based on expert prior functional knowledge of the disease mechanism can lead to improved causal SNPs ranks compared to ranking with identical prior probabilities of association. We demonstrate the use of our methods by applying the methods to the fine mapping of the CASP8 region of chromosome 2 using genotype data from the Collaborative Oncological Gene‐Environment Study (COGS) Consortium. The data we analysed included approximately 46,000 breast cancer case and 43,000 healthy control samples. PMID:26833494

  2. Incorporating Functional Genomic Information in Genetic Association Studies Using an Empirical Bayes Approach.

    PubMed

    Spencer, Amy V; Cox, Angela; Lin, Wei-Yu; Easton, Douglas F; Michailidou, Kyriaki; Walters, Kevin

    2016-04-01

    There is a large amount of functional genetic data available, which can be used to inform fine-mapping association studies (in diseases with well-characterised disease pathways). Single nucleotide polymorphism (SNP) prioritization via Bayes factors is attractive because prior information can inform the effect size or the prior probability of causal association. This approach requires the specification of the effect size. If the information needed to estimate a priori the probability density for the effect sizes for causal SNPs in a genomic region isn't consistent or isn't available, then specifying a prior variance for the effect sizes is challenging. We propose both an empirical method to estimate this prior variance, and a coherent approach to using SNP-level functional data, to inform the prior probability of causal association. Through simulation we show that when ranking SNPs by our empirical Bayes factor in a fine-mapping study, the causal SNP rank is generally as high or higher than the rank using Bayes factors with other plausible values of the prior variance. Importantly, we also show that assigning SNP-specific prior probabilities of association based on expert prior functional knowledge of the disease mechanism can lead to improved causal SNPs ranks compared to ranking with identical prior probabilities of association. We demonstrate the use of our methods by applying the methods to the fine mapping of the CASP8 region of chromosome 2 using genotype data from the Collaborative Oncological Gene-Environment Study (COGS) Consortium. The data we analysed included approximately 46,000 breast cancer case and 43,000 healthy control samples.

  3. Availability of birth defects and genetic disease information in public libraries -- implications for the Human Genome Project

    SciTech Connect

    Sell, S.; Gettig, E.; Mulvihill, J.J.

    1994-09-01

    In order to better educate the public about birth defects and genetic diseases/testing, access to information is critical. The public library system of the United States is extensive and serves as an invaluable resource to citizens. We surveyed reference librarians at each of 87 public libraries in Allegheny and Westmoreland Counties, Pennsylvania. The study design included a questionnaire to ascertain the genetic knowledge of reference librarians and cataloged current resources in print and via telecommunications available to the public. A high compliance rate was achieved due to the incentive of providing copies of the Alliance of Genetic Support Group Directory to those who responded to the survey along with complete sets of the forty-three March of Dimes Information Sheets currently available. Analysis of demographic data related to the age, gender, and educational background, in addition to the occurrence of personal experiences with genetic disease was ascertained. Reference librarians were chosen as the study group due to the common experience of families seeking further information from the public library after or prior to a genetic consultation. As the Human Genome Project identifies new genes for conditions, people will seek public information more frequently. The study shows that public libraries are an appropriate point of education to and for the public.

  4. Informed choice in direct-to-consumer genetic testing (DTCGT) websites: a content analysis of benefits, risks, and limitations

    PubMed Central

    Singleton, Amanda; Erby, Lori Hamby; Foisie, Kathryn V.; Kaphingst, Kimberly

    2012-01-01

    An informed choice about health-related direct-to-consumer genetic testing (DTCGT) requires knowledge of potential benefits, risks, and limitations. To understand the information that potential consumers of DTCGT services are exposed to on company websites, we conducted a content analysis of 23 health-related DTCGT websites. Results revealed that benefit statements outweighed risk and limitation statements 6 to 1. The most frequently described benefits were 1) disease prevention, 2) consumer education, 3) personalized medical recommendations, and 4) the ability to make health decisions. Thirty-five percent of websites also presented at least one risk of testing. Seventy-eight percent of websites mentioned at least one limitation of testing. Based on this information, potential consumers might get an inaccurate picture of genetic testing which could impact their ability to make an informed decision. Practices that enhance the presentation of balanced information on DTCGT company websites should be encouraged. PMID:22194036

  5. Student Information Systems Demystified: The Increasing Demand for Accurate, Timely Data Means Schools and Districts Are Relying Heavily on SIS Technologies

    ERIC Educational Resources Information Center

    McIntire, Todd

    2004-01-01

    Student information systems, one of the first applications of computer technology in education, are undergoing a significant transition yet again. The first major shift in SIS technologies occurred about 15 years ago when they evolved from mainframe programs to client-server solutions. Now, vendors across the board are offering centralized…

  6. Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis.

    PubMed

    Peng, Zhi-yu; Zhou, Xin; Li, Linchuan; Yu, Xiangchun; Li, Hongjiang; Jiang, Zhiqiang; Cao, Guangyu; Bai, Mingyi; Wang, Xingchun; Jiang, Caifu; Lu, Haibin; Hou, Xianhui; Qu, Lijia; Wang, Zhiyong; Zuo, Jianru; Fu, Xiangdong; Su, Zhen; Li, Songgang; Guo, Hongwei

    2009-01-01

    Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including auxin, gibberellin, cytokinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Here, we develop an Arabidopsis hormone database, which aims to provide a systematic and comprehensive view of genes participating in plant hormonal regulation, as well as morphological phenotypes controlled by plant hormones. Based on data from mutant studies, transgenic analysis and gene ontology (GO) annotation, we have identified a total of 1026 genes in the Arabidopsis genome that participate in plant hormone functions. Meanwhile, a phenotype ontology is developed to precisely describe myriad hormone-regulated morphological processes with standardized vocabularies. A web interface (http://ahd.cbi.pku.edu.cn) would allow users to quickly get access to information about these hormone-related genes, including sequences, functional category, mutant information, phenotypic description, microarray data and linked publications. Several applications of this database in studying plant hormonal regulation and hormone cross-talk will be presented and discussed.

  7. Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis.

    PubMed

    Peng, Zhi-yu; Zhou, Xin; Li, Linchuan; Yu, Xiangchun; Li, Hongjiang; Jiang, Zhiqiang; Cao, Guangyu; Bai, Mingyi; Wang, Xingchun; Jiang, Caifu; Lu, Haibin; Hou, Xianhui; Qu, Lijia; Wang, Zhiyong; Zuo, Jianru; Fu, Xiangdong; Su, Zhen; Li, Songgang; Guo, Hongwei

    2009-01-01

    Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including auxin, gibberellin, cytokinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Here, we develop an Arabidopsis hormone database, which aims to provide a systematic and comprehensive view of genes participating in plant hormonal regulation, as well as morphological phenotypes controlled by plant hormones. Based on data from mutant studies, transgenic analysis and gene ontology (GO) annotation, we have identified a total of 1026 genes in the Arabidopsis genome that participate in plant hormone functions. Meanwhile, a phenotype ontology is developed to precisely describe myriad hormone-regulated morphological processes with standardized vocabularies. A web interface (http://ahd.cbi.pku.edu.cn) would allow users to quickly get access to information about these hormone-related genes, including sequences, functional category, mutant information, phenotypic description, microarray data and linked publications. Several applications of this database in studying plant hormonal regulation and hormone cross-talk will be presented and discussed. PMID:19015126

  8. Consumer Perception of Genetically Modified Organisms and Sources of Information123

    PubMed Central

    Wunderlich, Shahla; Gatto, Kelsey A

    2015-01-01

    Genetically modified organisms (GMOs) have been available for commercial purchase since the 1990s, allowing producers to increase crop yields through bioengineering that creates herbicide-resistant and insect-resistant varieties. However, consumer knowledge about GMOs has not increased at the same rate as the adoption of GMO crops. Consumers worldwide are displaying limited understanding, misconceptions, and even unfamiliarity with GMO food products. Many consumers report that they receive information about GMO food products from the media, Internet, and other news sources. These sources may be less reliable than scientific experts whom consumers trust more to present the facts. Although many in the United States support mandatory GMO labeling (similar to current European standards), consumer awareness of current GMO labeling is low. A distinction must also be made between GMO familiarity and scientific understanding, because those who are more familiar with it tend to be more resistant to bioengineering, whereas those with higher scientific knowledge scores tend to have less negative attitudes toward GMOs. This brings to question the relation between scientific literacy, sources of information, and overall consumer knowledge and perception of GMO foods. PMID:26567205

  9. Genetic networks and the flow of positional information in embryonic development

    NASA Astrophysics Data System (ADS)

    Bialek, William

    When we study a biological system, we make inferences about the underlying mechanisms and dynamics. But biological systems themselves must also solve inference problems, as when our brains draw conclusions about the world given (often quite limited) data from our eyes and ears. My colleagues and I have been exploring both of these inference problems as they play out in the first hours of development in the fruit fly embryo. In this system, the concentrations of particular molecules encode the position of each cell in the embryo, and these concentrations are the outputs of a genetic network. Putting ourselves in the place of the cells, we have been able to read the code, building a dictionary that maps gene expression levels back into estimates of position. If our dictionary really is the one used by the embryo, then mutants should build predictably distorted body plans, and preliminary results show quantitative agreement with these predictions. Independent of their role as carriers of information, we can also analyze the patterns of gene expression to draw inferences about the underlying network. Finally, it is possible that the network architecture and parameters have been chosen to optimize the flow of information, and we see signatures of this optimization. Joint work with CG Callan, JO Dubuis, T Gregor, D Krotov, M Petkova, TR Sokolowski, G Tkacik, AM Walczak, and EF Wieschaus.

  10. Owning genetic information and gene enhancement techniques: why privacy and property rights may undermine social control of the human genome.

    PubMed

    Moore, A D

    2000-04-01

    In this article I argue that the proper subjects of intangible property claims include medical records, genetic profiles, and gene enhancement techniques. Coupled with a right to privacy these intangible property rights allow individuals a zone of control that will, in most cases, justifiably exclude governmental or societal invasions into private domains. I argue that the threshold for overriding privacy rights and intangible property rights is higher, in relation to genetic enhancement techniques and sensitive personal information, than is commonly suggested. Once the bar is raised, so-to-speak, the burden of overriding it is formidable. Thus many policy decisions that have been recently proposed or enacted--citywide audio and video surveillance, law enforcement DNA sweeps, genetic profiling, national bans on genetic testing and enhancement of humans, to name a few--will have to be backed by very strong arguments. PMID:11765764

  11. Estimates of genetic diversity in the brown cattle population of Switzerland obtained from pedigree information.

    PubMed

    Hagger, C

    2005-12-01

    The study investigates the genetic diversity present as well as its development in the Brown Cattle population of Switzerland from pedigree information. The population consisted of three subpopulations, the Braunvieh (BV), the original Braunvieh (OB) and the US-Brown Swiss (BS). The BV is a cross of OB with BS where crossing still continues. The OB is without any genetic influence of BS. The diversity measures effective population size, effective number of ancestors (explaining 99% of reference genome) and founder genome equivalents were calculated for 11 reference populations of animals born in a single year from 1992 onwards. The BS-subpopulation consisted of animals and their known ancestors which were used in the crossing scheme and was, therefore, quite small. The youngest animals were born in 2002, the oldest ones in the 1920s. Average inbreeding was by far the highest in BS, in spite of the lowest quality of pedigrees, and lowest in OB. Effective population size obtained from the difference between average inbreeding of offspring and their parents was, mostly due to the heavy use of few highly inbred BS-sires, strongly overestimated in some BV-reference populations. If this parameter was calculated from the yearly rate of inbreeding and a generation interval of 5 years, no bias was observed and ranking of populations from high to low was OB-BV-BS, i.e. equal to the other diversity parameters. The high genetic diversity found in OB was a consequence of the use of many natural service sires. Rate of decrease of effective number of ancestors was steeper in BV than OB was, however, equal for founder genome equivalents. Founder genome equivalents were more stable than effective population sizes calculated from the difference between average inbreeding of offspring and parents. The five most important ancestors contributed one-third of the 2002-reference genomes of BV and OB, in BV all were BS-sires. The relative amount of BS-genes in the BV-genome increased from

  12. The application of genetic information for regulatory standard setting under the clean air act: a decision-analytic approach.

    PubMed

    Cullen, Alison C; Corrales, Mark A; Kramer, C Bradley; Faustman, Elaine M

    2008-08-01

    In 2002, the U.S. Environmental Protection Agency (EPA) released an "Interim Policy on Genomics," stating a commitment to developing guidance on the inclusion of genetic information in regulatory decision making. This statement was followed in 2004 by a document exploring the potential implications. Genetic information can play a key role in understanding and quantifying human susceptibility, an essential step in many of the risk assessments used to shape policy. For example, the federal Clean Air Act (CAA) requires EPA to set National Ambient Air Quality Standards (NAAQS) for criteria pollutants at levels to protect even sensitive populations from adverse health effects with an adequate margin of safety. Asthmatics are generally regarded as a sensitive population, yet substantial research gaps in understanding genetic susceptibility and disease have hindered quantitative risk analysis. This case study assesses the potential role of genomic information regarding susceptible populations in the NAAQS process for fine particulate matter (PM(2.5)) under the CAA. In this initial assessment, we model the contribution of a single polymorphism to asthma risk and mortality risk; however, multiple polymorphisms and interactions (gene-gene and gene-environment) are known to play key roles in the disease process. We show that the impact of new information about susceptibility on estimates of population risk or average risk derived from large epidemiological studies depends on the circumstances. We also suggest that analysis of a single polymorphism, or other risk factor such as health status, may or may not change estimates of individual risk enough to alter a particular regulatory decision, but this depends on specific characteristics of the decision and risk information. We also show how new information about susceptibility in the context of the NAAQS for PM(2.5) could have a large impact on the estimated distribution of individual risk. This would occur if a group were

  13. Relationships between Parental Negativity and Childhood Antisocial Behavior over Time: A Bidirectional Effects Model in a Longitudinal Genetically Informative Design

    ERIC Educational Resources Information Center

    Larsson, Henrik; Viding, Essi; Rijsdijk, Fruhling V.; Plomin, Robert

    2008-01-01

    This study examined the direction and etiology underlying the relationships between parental negativity and early childhood antisocial behavior using a bidirectional effects model in a longitudinal genetically informative design. We analyzed parent reports of parental negativity and early childhood antisocial behavior in 6,230 pairs of twins at 4…

  14. Increased Reliability Of Genetic Evaluations For Dairy Cattle In The United States From Use Of Genomic Information

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Use of genomic information increased reliability of genetic evaluations compared to parent averages by 28.4% for Holsteins, 20.7% for Jerseys and 12.8% for Brown Swiss when averaged across milk, fat and protein yields and three functional traits. Correlations of genomic predictions based on evaluati...

  15. Learning Syntactic Rules and Tags with Genetic Algorithms for Information Retrieval and Filtering: An Empirical Basis for Grammatical Rules.

    ERIC Educational Resources Information Center

    Losee, Robert M.

    1996-01-01

    The grammars of natural languages may be learned by using genetic algorithm systems such as LUST (Linguistics Using Sexual Techniques) that reproduce and mutate grammatical rules and parts-of-speech tags. In document retrieval or filtering systems, applying tags to the list of terms representing a document provides additional information about…

  16. Effectiveness of the Conceptual Change Texts Accompanied by Concept Maps about Students' Understanding of the Molecules Carrying Genetical Information

    ERIC Educational Resources Information Center

    Tastan, Ibrahim; Dikmenli, Musa; Cardak, Osman

    2008-01-01

    This study aims to investigate the effects of concept maps, together with conceptual change texts, given to 11th grade students' on the subject of molecules carrying genetical information. The semistructured individual interviews were conducted with 5 upper class students to find misconceptions related to the subject. A success test was developed…

  17. How Are Genetic Conditions Diagnosed?

    MedlinePlus

    ... Consultation How are genetic conditions diagnosed? How are genetic conditions diagnosed? A doctor may suspect a diagnosis ... and advocacy resources. For more information about diagnosing genetic conditions: Genetics Home Reference provides information about genetic ...

  18. Accurate whole human genome sequencing using reversible terminator chemistry.

    PubMed

    Bentley, David R; Balasubramanian, Shankar; Swerdlow, Harold P; Smith, Geoffrey P; Milton, John; Brown, Clive G; Hall, Kevin P; Evers, Dirk J; Barnes, Colin L; Bignell, Helen R; Boutell, Jonathan M; Bryant, Jason; Carter, Richard J; Keira Cheetham, R; Cox, Anthony J; Ellis, Darren J; Flatbush, Michael R; Gormley, Niall A; Humphray, Sean J; Irving, Leslie J; Karbelashvili, Mirian S; Kirk, Scott M; Li, Heng; Liu, Xiaohai; Maisinger, Klaus S; Murray, Lisa J; Obradovic, Bojan; Ost, Tobias; Parkinson, Michael L; Pratt, Mark R; Rasolonjatovo, Isabelle M J; Reed, Mark T; Rigatti, Roberto; Rodighiero, Chiara; Ross, Mark T; Sabot, Andrea; Sankar, Subramanian V; Scally, Aylwyn; Schroth, Gary P; Smith, Mark E; Smith, Vincent P; Spiridou, Anastassia; Torrance, Peta E; Tzonev, Svilen S; Vermaas, Eric H; Walter, Klaudia; Wu, Xiaolin; Zhang, Lu; Alam, Mohammed D; Anastasi, Carole; Aniebo, Ify C; Bailey, David M D; Bancarz, Iain R; Banerjee, Saibal; Barbour, Selena G; Baybayan, Primo A; Benoit, Vincent A; Benson, Kevin F; Bevis, Claire; Black, Phillip J; Boodhun, Asha; Brennan, Joe S; Bridgham, John A; Brown, Rob C; Brown, Andrew A; Buermann, Dale H; Bundu, Abass A; Burrows, James C; Carter, Nigel P; Castillo, Nestor; Chiara E Catenazzi, Maria; Chang, Simon; Neil Cooley, R; Crake, Natasha R; Dada, Olubunmi O; Diakoumakos, Konstantinos D; Dominguez-Fernandez, Belen; Earnshaw, David J; Egbujor, Ugonna C; Elmore, David W; Etchin, Sergey S; Ewan, Mark R; Fedurco, Milan; Fraser, Louise J; Fuentes Fajardo, Karin V; Scott Furey, W; George, David; Gietzen, Kimberley J; Goddard, Colin P; Golda, George S; Granieri, Philip A; Green, David E; Gustafson, David L; Hansen, Nancy F; Harnish, Kevin; Haudenschild, Christian D; Heyer, Narinder I; Hims, Matthew M; Ho, Johnny T; Horgan, Adrian M; Hoschler, Katya; Hurwitz, Steve; Ivanov, Denis V; Johnson, Maria Q; James, Terena; Huw Jones, T A; Kang, Gyoung-Dong; Kerelska, Tzvetana H; Kersey, Alan D; Khrebtukova, Irina; Kindwall, Alex P; Kingsbury, Zoya; Kokko-Gonzales, Paula I; Kumar, Anil; Laurent, Marc A; Lawley, Cynthia T; Lee, Sarah E; Lee, Xavier; Liao, Arnold K; Loch, Jennifer A; Lok, Mitch; Luo, Shujun; Mammen, Radhika M; Martin, John W; McCauley, Patrick G; McNitt, Paul; Mehta, Parul; Moon, Keith W; Mullens, Joe W; Newington, Taksina; Ning, Zemin; Ling Ng, Bee; Novo, Sonia M; O'Neill, Michael J; Osborne, Mark A; Osnowski, Andrew; Ostadan, Omead; Paraschos, Lambros L; Pickering, Lea; Pike, Andrew C; Pike, Alger C; Chris Pinkard, D; Pliskin, Daniel P; Podhasky, Joe; Quijano, Victor J; Raczy, Come; Rae, Vicki H; Rawlings, Stephen R; Chiva Rodriguez, Ana; Roe, Phyllida M; Rogers, John; Rogert Bacigalupo, Maria C; Romanov, Nikolai; Romieu, Anthony; Roth, Rithy K; Rourke, Natalie J; Ruediger, Silke T; Rusman, Eli; Sanches-Kuiper, Raquel M; Schenker, Martin R; Seoane, Josefina M; Shaw, Richard J; Shiver, Mitch K; Short, Steven W; Sizto, Ning L; Sluis, Johannes P; Smith, Melanie A; Ernest Sohna Sohna, Jean; Spence, Eric J; Stevens, Kim; Sutton, Neil; Szajkowski, Lukasz; Tregidgo, Carolyn L; Turcatti, Gerardo; Vandevondele, Stephanie; Verhovsky, Yuli; Virk, Selene M; Wakelin, Suzanne; Walcott, Gregory C; Wang, Jingwen; Worsley, Graham J; Yan, Juying; Yau, Ling; Zuerlein, Mike; Rogers, Jane; Mullikin, James C; Hurles, Matthew E; McCooke, Nick J; West, John S; Oaks, Frank L; Lundberg, Peter L; Klenerman, David; Durbin, Richard; Smith, Anthony J

    2008-11-01

    DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.

  19. Transport and transformation of genetic information in the critical zone: The case of antibiotic resistance genes

    NASA Astrophysics Data System (ADS)

    Zhu, Y. G.

    2015-12-01

    In addition to material and energy flows, the dynamics and functions of the Earth's critical zone are intensively mediated by biological actions performed by diverse organisms. These biological actions are modulated by the expression of functional genes and their translation into enzymes that catalyze geochemical reactions, such as nutrient turnover and pollutant biodegradation. Although geobiology, as an interdisciplinary research area, is playing and vital role in linking biological and geochemical processes at different temporal and spatial scales, the distribution and transport of functional genes have rarely been investigated from the Earth's critical zone perspectives. To illustrate the framework of studies on the transport and transformation of genetic information in the critical zone, antibiotic resistance is taken as an example. Antibiotic resistance genes are considered as a group of emerging contaminants, and their emergence and spread within the critical zone on one hand are induced by anthropogenic activities, and on other hand are threatening human health worldwide. The transport and transformation of antibiotic resistance genes are controlled by both horizontal gene transfer between bacterial cells and the movement of bacteria harboring antibiotic resistance genes. In this paper, the fate and behavior of antibiotic resistance genes will be discussed in the following aspects: 1) general overview of environmental antibiotic resistance; 2) high through quantification of the resistome in various environmental media; 3) pathways of resistance gene flow within the critical zone; and 4) potential strategies in mitigating antibiotic resistance, particularly from the critical zone perspectives.

  20. Regulations Under the Americans With Disabilities Act; Genetic Information Nondiscrimination Act. Final rule.

    PubMed

    2016-05-17

    The Equal Employment Opportunity Commission (EEOC or Commission) is issuing its final rule to amend the regulations and interpretive guidance implementing Title I of the Americans with Disabilities Act (ADA) to provide guidance on the extent to which employers may use incentives to encourage employees to participate in wellness programs that ask them to respond to disability-related inquiries and/or undergo medical examinations. This rule applies to all wellness programs that include disability-related inquiries and/or medical examinations whether they are offered only to employees enrolled in an employer-sponsored group health plan, offered to all employees regardless of whether they are enrolled in such a plan, or offered as a benefit of employment by employers that do not sponsor a group health plan or group health insurance. Published elsewhere in this issue of the Federal Register, the EEOC also issued a final rule to amend the regulations implementing Title II of the Genetic Information Nondiscrimination Act (GINA) that addresses the extent to which employers may offer incentives for an employee's spouse to participate in a wellness program. PMID:27192736

  1. Molecular weight-dependent genetic information transfer with disulfide-linked polyethylenimine-based nonviral vectors.

    PubMed

    Parhiz, Hamideh; Hashemi, Maryam; Hatefi, Arash; Shier, Wayne Thomas; Farzad, Sara Amel; Ramezani, Mohammad

    2013-07-01

    One strategy for improving gene vector properties of polyethylenimine is to facilitate individual transfection mechanism steps. This study investigates (i) improving transfection efficiency by attaching peptide nuclear localization signals (nuclear localization signals: SV40 large T antigen nuclear localization signal or C-terminus of histone H1) to polyethylenimine (10 kDa) and (ii) using disulfide linkages, which are expected to be stable during polyplex formation, but cleaved inside cells giving improved gene release. Nuclear localization signal-containing polyplexes exhibited low cytotoxicity, whereas transfection efficiency with high molecular weight plasmid DNA increased up to 3.6 times that of underivatized polyethylenimine in Neuro2A cells at higher molar ratio of polyethylenimine-nitrogen to DNA-phosphate (N/P) ratios. However, with luciferase-specific low molecular weight small interfering RNA in Neuro2A/EGFPLuc cells, nuclear localization signal-containing polyplexes with disulfide linkages caused substantial cytotoxicity at N/P ratios >15 and no consistent significant reduction in luciferase expression. Possible explanations for molecular weight-dependent differences in genetic information transfer by polyplexes containing disulfide-linked nuclear localization signals are discussed.

  2. Information and redundancy: key concepts in understanding the genetic control of health and intelligence.

    PubMed

    Morris, J A

    1999-08-01

    A model is proposed in which information from the environment is analysed by complex biological decision-making systems which are highly redundant. A correct response is intelligent behaviour which preserves health; incorrect responses lead to disease. Mutations in genes which code for the redundant systems will accumulate in the genome and impair decision-making. The number of mutant genes will depend upon a balance between the new mutation rate per generation and systems of elimination based on synergistic interaction in redundant systems. This leads to a polygenic pattern of inheritance for intelligence and the common diseases. The model also gives a simple explanation for some of the hitherto puzzling aspects of work on the genetic basis of intelligence including the recorded rise in IQ this century. There is a prediction that health, intelligence and socio-economic position will be correlated generating a health differential in the social hierarchy. Furthermore, highly competitive societies will place those least able to cope in the harshest environment and this will impair health overall. The model points to a need for population monitoring of somatic mutation in order to preserve the health and intelligence of future generations.

  3. Regulations Under the Americans With Disabilities Act; Genetic Information Nondiscrimination Act. Final rule.

    PubMed

    2016-05-17

    The Equal Employment Opportunity Commission (EEOC or Commission) is issuing its final rule to amend the regulations and interpretive guidance implementing Title I of the Americans with Disabilities Act (ADA) to provide guidance on the extent to which employers may use incentives to encourage employees to participate in wellness programs that ask them to respond to disability-related inquiries and/or undergo medical examinations. This rule applies to all wellness programs that include disability-related inquiries and/or medical examinations whether they are offered only to employees enrolled in an employer-sponsored group health plan, offered to all employees regardless of whether they are enrolled in such a plan, or offered as a benefit of employment by employers that do not sponsor a group health plan or group health insurance. Published elsewhere in this issue of the Federal Register, the EEOC also issued a final rule to amend the regulations implementing Title II of the Genetic Information Nondiscrimination Act (GINA) that addresses the extent to which employers may offer incentives for an employee's spouse to participate in a wellness program.

  4. Application of automation and information systems to forensic genetic specimen processing.

    PubMed

    Leclair, Benoît; Scholl, Tom

    2005-03-01

    During the last 10 years, the introduction of PCR-based DNA typing technologies in forensic applications has been highly successful. This technology has become pervasive throughout forensic laboratories and it continues to grow in prevalence. For many criminal cases, it provides the most probative evidence. Criminal genotype data banking and victim identification initiatives that follow mass-fatality incidents have benefited the most from the introduction of automation for sample processing and data analysis. Attributes of offender specimens including large numbers, high quality and identical collection and processing are ideal for the application of laboratory automation. The magnitude of kinship analysis required by mass-fatality incidents necessitates the application of computing solutions to automate the task. More recently, the development activities of many forensic laboratories are focused on leveraging experience from these two applications to casework sample processing. The trend toward increased prevalence of forensic genetic analysis will continue to drive additional innovations in high-throughput laboratory automation and information systems.

  5. Genetic assessments and parentage analysis of captive Bolson tortoises (Gopherus flavomarginatus) inform their "rewilding" in New Mexico.

    PubMed

    Edwards, Taylor; Cox, Elizabeth Canty; Buzzard, Vanessa; Wiese, Christiane; Hillard, L Scott; Murphy, Robert W

    2014-01-01

    The Bolson tortoise (Gopherus flavomarginatus) is the first species of extirpated megafauna to be repatriated into the United States. In September 2006, 30 individuals were translocated from Arizona to New Mexico with the long-term objective of restoring wild populations via captive propagation. We evaluated mtDNA sequences and allelic diversity among 11 microsatellite loci from the captive population and archived samples collected from wild individuals in Durango, Mexico (n = 28). Both populations exhibited very low genetic diversity and the captive population captured roughly 97.5% of the total wild diversity, making it a promising founder population. Genetic screening of other captive animals (n = 26) potentially suitable for reintroduction uncovered multiple hybrid G. flavomarginatus×G. polyphemus, which were ineligible for repatriation; only three of these individuals were verified as purebred G. flavomarginatus. We used these genetic data to inform mate pairing, reduce the potential for inbreeding and to monitor the maintenance of genetic diversity in the captive population. After six years of successful propagation, we analyzed the parentage of 241 hatchlings to assess the maintenance of genetic diversity. Not all adults contributed equally to successive generations. Most yearly cohorts of hatchlings failed to capture the diversity of the parental population. However, overlapping generations of tortoises helped to alleviate genetic loss because the entire six-year cohort of hatchlings contained the allelic diversity of the parental population. Polyandry and sperm storage occurred in the captives and future management strategies must consider such events.

  6. Genetic Assessments and Parentage Analysis of Captive Bolson Tortoises (Gopherus flavomarginatus) Inform Their “Rewilding” in New Mexico

    PubMed Central

    Edwards, Taylor; Cox, Elizabeth Canty; Buzzard, Vanessa; Wiese, Christiane; Hillard, L. Scott; Murphy, Robert W.

    2014-01-01

    The Bolson tortoise (Gopherus flavomarginatus) is the first species of extirpated megafauna to be repatriated into the United States. In September 2006, 30 individuals were translocated from Arizona to New Mexico with the long-term objective of restoring wild populations via captive propagation. We evaluated mtDNA sequences and allelic diversity among 11 microsatellite loci from the captive population and archived samples collected from wild individuals in Durango, Mexico (n = 28). Both populations exhibited very low genetic diversity and the captive population captured roughly 97.5% of the total wild diversity, making it a promising founder population. Genetic screening of other captive animals (n = 26) potentially suitable for reintroduction uncovered multiple hybrid G. flavomarginatus×G. polyphemus, which were ineligible for repatriation; only three of these individuals were verified as purebred G. flavomarginatus. We used these genetic data to inform mate pairing, reduce the potential for inbreeding and to monitor the maintenance of genetic diversity in the captive population. After six years of successful propagation, we analyzed the parentage of 241 hatchlings to assess the maintenance of genetic diversity. Not all adults contributed equally to successive generations. Most yearly cohorts of hatchlings failed to capture the diversity of the parental population. However, overlapping generations of tortoises helped to alleviate genetic loss because the entire six-year cohort of hatchlings contained the allelic diversity of the parental population. Polyandry and sperm storage occurred in the captives and future management strategies must consider such events. PMID:25029369

  7. Genetic assessments and parentage analysis of captive Bolson tortoises (Gopherus flavomarginatus) inform their "rewilding" in New Mexico.

    PubMed

    Edwards, Taylor; Cox, Elizabeth Canty; Buzzard, Vanessa; Wiese, Christiane; Hillard, L Scott; Murphy, Robert W

    2014-01-01

    The Bolson tortoise (Gopherus flavomarginatus) is the first species of extirpated megafauna to be repatriated into the United States. In September 2006, 30 individuals were translocated from Arizona to New Mexico with the long-term objective of restoring wild populations via captive propagation. We evaluated mtDNA sequences and allelic diversity among 11 microsatellite loci from the captive population and archived samples collected from wild individuals in Durango, Mexico (n = 28). Both populations exhibited very low genetic diversity and the captive population captured roughly 97.5% of the total wild diversity, making it a promising founder population. Genetic screening of other captive animals (n = 26) potentially suitable for reintroduction uncovered multiple hybrid G. flavomarginatus×G. polyphemus, which were ineligible for repatriation; only three of these individuals were verified as purebred G. flavomarginatus. We used these genetic data to inform mate pairing, reduce the potential for inbreeding and to monitor the maintenance of genetic diversity in the captive population. After six years of successful propagation, we analyzed the parentage of 241 hatchlings to assess the maintenance of genetic diversity. Not all adults contributed equally to successive generations. Most yearly cohorts of hatchlings failed to capture the diversity of the parental population. However, overlapping generations of tortoises helped to alleviate genetic loss because the entire six-year cohort of hatchlings contained the allelic diversity of the parental population. Polyandry and sperm storage occurred in the captives and future management strategies must consider such events. PMID:25029369

  8. Patterns of genetic structure and evidence of gene flow among Tunisian Citrus species based on informative nSSR markers.

    PubMed

    Ben Romdhane, Meriam; Riahi, Leila; Selmi, Ayet; Zoghlami, Nejia

    2016-01-01

    This study investigates the extent of genetic diversity, phylogenetic relationships and the amount of gene flow among Tunisian Citrus species based on a set of 15 informative nuclear SSR molecular markers. Genotyping data highlighted an allelic richness among Tunisian Citrus species and has allowed the detection of 168 alleles among them 104.19 were effective. The partition of the total genetic diversity (HT=0.832) showed that the highest amount of variation within the Citrus species is HS=0.550, while the relative amount of the between-species genetic diversity GST does not exceed 0.338. This pattern of genetic structure was supported by low-to-moderate FST pairwise values and the presence of a gene flow (Nm) among the eight Citrus species. The lowest genetic differentiation was revealed between the species C. sinensis and C. insitorum (FST=0.111, Nm=1.99), while the highest genetic differentiation was recorded between the species C. aurantifolia and C. paradisi (FST=0.367, Nm=0.43). The established Neighbor Joining analysis showed that all genotypes were widely discriminated and clearly pooled according to their species of origin, with minor exceptions. PMID:27522638

  9. Considerations for Using Genetic and Epigenetic Information in Occupational Health Risk Assessment and Standard Setting

    PubMed Central

    Schulte, P. A.; Whittaker, C.; Curran, C. P.

    2015-01-01

    Risk assessment forms the basis for both occupational health decision-making and the development of occupational exposure limits (OELs). Although genetic and epigenetic data have not been widely used in risk assessment and ultimately, standard setting, it is possible to envision such uses. A growing body of literature demonstrates that genetic and epigenetic factors condition biological responses to occupational and environmental hazards or serve as targets of them. This presentation addresses the considerations for using genetic and epigenetic information in risk assessments, provides guidance on using this information within the classic risk assessment paradigm, and describes a framework to organize thinking about such uses. The framework is a 4 × 4 matrix involving the risk assessment functions (hazard identification, dose-response modeling, exposure assessment, and risk characterization) on one axis and inherited and acquired genetic and epigenetic data on the other axis. The cells in the matrix identify how genetic and epigenetic data can be used for each risk assessment function. Generally, genetic and epigenetic data might be used as endpoints in hazard identification, as indicators of exposure, as effect modifiers in exposure assessment and dose-response modeling, as descriptors of mode of action, and to characterize toxicity pathways. Vast amounts of genetic and epigenetic data may be generated by high-throughput technologies. These data can be useful for assessing variability and reducing uncertainty in extrapolations, and they may serve as the foundation upon which identification of biological perturbations would lead to a new paradigm of toxicity pathway-based risk assessments. PMID:26583908

  10. Information Technology Support for Clinical Genetic Testing within an Academic Medical Center

    PubMed Central

    Aronson, Samuel; Mahanta, Lisa; Ros, Lei Lei; Clark, Eugene; Babb, Lawrence; Oates, Michael; Rehm, Heidi; Lebo, Matthew

    2016-01-01

    Academic medical centers require many interconnected systems to fully support genetic testing processes. We provide an overview of the end-to-end support that has been established surrounding a genetic testing laboratory within our environment, including both laboratory and clinician facing infrastructure. We explain key functions that we have found useful in the supporting systems. We also consider ways that this infrastructure could be enhanced to enable deeper assessment of genetic test results in both the laboratory and clinic. PMID:26805890

  11. Specific Secondary Genetic Alterations in Mantle Cell Lymphoma Provide Prognostic Information Independent of the Gene Expression–Based Proliferation Signature

    PubMed Central

    Salaverria, Itziar; Zettl, Andreas; Beà, Sílvia; Moreno, Victor; Valls, Joan; Hartmann, Elena; Ott, German; Wright, George; Lopez-Guillermo, Armando; Chan, Wing C.; Weisenburger, Dennis D.; Gascoyne, Randy D.; Grogan, Thomas M.; Delabie, Jan; Jaffe, Elaine S.; Montserrat, Emili; Muller-Hermelink, Hans-Konrad; Staudt, Louis M.; Rosenwald, Andreas

    2008-01-01

    Purpose To compare the genetic relationship between cyclin D1–positive and cyclin D1–negative mantle cell lymphomas (MCLs) and to determine whether specific genetic alterations may add prognostic information to survival prediction based on the proliferation signature of MCLs. Patients and Methods Seventy-one cyclin D1–positive and six cyclin D1–negative MCLs previously characterized by gene expression profiling were examined by comparative genomic hybridization (CGH). Results Cyclin D1–negative MCLs were genetically characterized by gains of 3q, 8q, and 15q, and losses of 1p, 8p23-pter, 9p21-pter, 11q21–q23, and 13q that were also the most common alterations in conventional MCLs. Parallel analysis of CGH aberrations and locus-specific gene expression profiles in cyclin D1–positive patients showed that chromosomal imbalances had a substantial impact on the expression levels of the genes located in the altered regions. The analysis of prognostic factors revealed that the proliferation signature, the number of chromosomal aberrations, gains of 3q, and losses of 8p, 9p, and 9q predicted survival of MCL patients. A multivariate analysis showed that the gene expression-based proliferation signature was the strongest predictor for shorter survival. However, 3q gains and 9q losses provided prognostic information that was independent of the proliferative activity. Conclusion Cyclin D1–positive and –negative MCLs share the same secondary genetic aberrations, supporting the concept that they correspond to the same genetic entity. The integration of genetic information on chromosome 3q and 9q alterations into a proliferation signature-based model may improve the ability to predict survival in patients with MCL. PMID:17296973

  12. Soma to germline inheritance of extrachromosomal genetic information via a LINE-1 reverse transcriptase-based mechanism.

    PubMed

    Spadafora, Corrado

    2016-08-01

    Mature spermatozoa are permeable to foreign DNA and RNA molecules. Here I propose a model, whereby extrachromosomal genetic information, mostly encoded in the form of RNA in somatic cells, can cross the Weismann barrier and reach epididymal spermatozoa. LINE-1 retrotransposon-derived reverse transcriptase (RT) can play key roles in the process by expanding the RNA-encoded information. Retrotransposon-encoded RT is stored in mature gametes, is highly expressed in early embryos and undifferentiated cells, and becomes downregulated in differentiated cells. In turn, RT plays a role in developmental control, as its inhibition arrests developmental progression of early embryos with globally altered transcriptomic profiles. Thus, sperm cells act as recipients, and transgenerational vectors of somatically derived genetic information which they pass to the next generation with the potential to modify the fate of the developing embryos. PMID:27315018

  13. Relative contributions of neutral and non-neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes

    PubMed Central

    Matala, Andrew P; Ackerman, Michael W; Campbell, Matthew R; Narum, Shawn R

    2014-01-01

    Mounting evidence of climatic effects on riverine environments and adaptive responses of fishes have elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non-neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the Columbia River Basin, which supports diverse populations distributed among dynamic landscapes. We categorized 188 SNP loci as either putatively neutral or candidates for divergent selection (non-neutral) using a multitest association approach. Neutral variation distinguished lineages and defined broad-scale population structure consistent with previous studies, but fine-scale resolution was also detected at levels not previously observed. Within distinct coastal and inland lineages, we identified nine and 22 candidate loci commonly associated with precipitation or temperature variables and putatively under divergent selection. Observed patterns of non-neutral variation suggest overall climate is likely to shape local adaptation (e.g., potential rapid evolution) of steelhead trout in the Columbia River region. Broad geographic patterns of neutral and non-neutral variation demonstrated here can be used to accommodate priorities for regional management and inform long-term conservation of this species. PMID:25067950

  14. Profitable capitation requires accurate costing.

    PubMed

    West, D A; Hicks, L L; Balas, E A; West, T D

    1996-01-01

    In the name of costing accuracy, nurses are asked to track inventory use on per treatment basis when more significant costs, such as general overhead and nursing salaries, are usually allocated to patients or treatments on an average cost basis. Accurate treatment costing and financial viability require analysis of all resources actually consumed in treatment delivery, including nursing services and inventory. More precise costing information enables more profitable decisions as is demonstrated by comparing the ratio-of-cost-to-treatment method (aggregate costing) with alternative activity-based costing methods (ABC). Nurses must participate in this costing process to assure that capitation bids are based upon accurate costs rather than simple averages. PMID:8788799

  15. A rigorous approach to facilitate and guarantee the correctness of the genetic testing management in human genome information systems

    PubMed Central

    2011-01-01

    Background Recent medical and biological technology advances have stimulated the development of new testing systems that have been providing huge, varied amounts of molecular and clinical data. Growing data volumes pose significant challenges for information processing systems in research centers. Additionally, the routines of genomics laboratory are typically characterized by high parallelism in testing and constant procedure changes. Results This paper describes a formal approach to address this challenge through the implementation of a genetic testing management system applied to human genome laboratory. We introduced the Human Genome Research Center Information System (CEGH) in Brazil, a system that is able to support constant changes in human genome testing and can provide patients updated results based on the most recent and validated genetic knowledge. Our approach uses a common repository for process planning to ensure reusability, specification, instantiation, monitoring, and execution of processes, which are defined using a relational database and rigorous control flow specifications based on process algebra (ACP). The main difference between our approach and related works is that we were able to join two important aspects: 1) process scalability achieved through relational database implementation, and 2) correctness of processes using process algebra. Furthermore, the software allows end users to define genetic testing without requiring any knowledge about business process notation or process algebra. Conclusions This paper presents the CEGH information system that is a Laboratory Information Management System (LIMS) based on a formal framework to support genetic testing management for Mendelian disorder studies. We have proved the feasibility and showed usability benefits of a rigorous approach that is able to specify, validate, and perform genetic testing using easy end user interfaces. PMID:22369688

  16. [Genetics and genetic counseling].

    PubMed

    Izzi, Claudia; Liut, Francesca; Dallera, Nadia; Mazza, Cinzia; Magistroni, Riccardo; Savoldi, Gianfranco; Scolari, Francesco

    2016-01-01

    Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most frequent genetic disease, characterized by progressive development of bilateral renal cysts. Two causative genes have been identified: PKD1 and PKD2. ADPKD phenotype is highly variable. Typically, ADPKD is an adult onset disease. However, occasionally, ADPKD manifests as very early onset disease. The phenotypic variability of ADPKD can be explained at three genetic levels: genic, allelic and gene modifier effects. Recent advances in molecular screening for PKD gene mutations and the introduction of the new next generation sequencing (NGS)- based genotyping approach have generated considerable improvement regarding the knowledge of genetic basis of ADPKD. The purpose of this article is to provide a comprehensive review of the genetics of ADPKD, focusing on new insights in genotype-phenotype correlation and exploring novel clinical approach to genetic testing. Evaluation of these new genetic information requires a multidisciplinary approach involving a nephrologist and a clinical geneticist. PMID:27067213

  17. Information Seeking and Intentions to Have Genetic Testing for Hereditary Cancers in Rural and Appalachian Kentuckians

    ERIC Educational Resources Information Center

    Kelly, Kimberly M.; Andrews, James E; Case, Donald O.; Allard, Suzanne L.; Johnson, J. David

    2007-01-01

    Context: Research is limited regarding the potential of genetic testing for cancer risk in rural Appalachia. Purpose: This study examined perceptions of genetic testing in a population sample of Kentuckians, with a focus on Appalachian and rural differences. The goals were to examine cultural and psychosocial factors that may predict intentions to…

  18. Using genetically informed, randomized prevention trials to test etiological hypotheses about child and adolescent drug use and psychopathology.

    PubMed

    Brody, Gene H; Beach, Steven R H; Hill, Karl G; Howe, George W; Prado, Guillermo; Fullerton, Stephanie M

    2013-10-01

    In this essay, we describe a new era of public health research in which prevention science principles are combined with genomic science to produce gene × intervention (G × I) research. We note the roles of behavioral and molecular genetics in risk and protective mechanisms for drug use and psychopathology among children and adolescents, and the results of first-generation genetically informed prevention trials are reviewed. We also consider the need for second-generation research that focuses on G × I effects on mediators or intermediate processes. This research can be used to further understanding of etiological processes, to identify individual differences in children's and adolescents' responses to risk, and to increase the precision of prevention programs. We note the caveats about using genetic data to select intervention participants.

  19. Accurate monotone cubic interpolation

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1991-01-01

    Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.

  20. Accurate Finite Difference Algorithms

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  1. 'I don't see any point in telling them': attitudes to sharing genetic information in the family and carrier testing of relatives among British Pakistani adults referred to a genetics clinic.

    PubMed

    Shaw, Alison; Hurst, Jane A

    2009-04-01

    The sharing of genetic information following the diagnosis of a genetic condition can be important for managing familial risks for genetic conditions. This paper explores factors that impede or facilitate the sharing of genetic information within a sample of British Pakistani families. It draws from research investigating understandings of genetics and inheritance, attitudes to prenatal diagnosis and risk communication in the family that used methods of participant observation and interview with adults from 66 families of Pakistani origin referred to a genetics clinic in southern England. We found a lack of English often restricted one partner's access to genetic information and partners fluent in English sometimes withheld information to protect a partner (usually the wife) from blame, stigma or feelings of marital insecurity. Many couples felt genetic information was private to them as a couple and were unwilling to share it with the wider family, commenting on its potentially stigmatizing and emotionally and socially disruptive effects on themselves, their child and their marriage, as well as on the marriage prospects of other family members. Those who sought carrier testing because of a family history did so when considering their own marriage or parenting, sometimes on the insistence of an affected relative, but did not readily discuss carrier testing with other relatives. Despite the complex consanguinity in some families, a family-based approach to risk management is not necessarily any easier among British Pakistanis than other ethnic groups. PMID:19052940

  2. Mathematical modeling of erythrocyte chimerism informs genetic intervention strategies for sickle cell disease.

    PubMed

    Altrock, Philipp M; Brendel, Christian; Renella, Raffaele; Orkin, Stuart H; Williams, David A; Michor, Franziska

    2016-09-01

    Recent advances in gene therapy and genome-engineering technologies offer the opportunity to correct sickle cell disease (SCD), a heritable disorder caused by a point mutation in the β-globin gene. The developmental switch from fetal γ-globin to adult β-globin is governed in part by the transcription factor (TF) BCL11A. This TF has been proposed as a therapeutic target for reactivation of γ-globin and concomitant reduction of β-sickle globin. In this and other approaches, genetic alteration of a portion of the hematopoietic stem cell (HSC) compartment leads to a mixture of sickling and corrected red blood cells (RBCs) in periphery. To reverse the sickling phenotype, a certain proportion of corrected RBCs is necessary; the degree of HSC alteration required to achieve a desired fraction of corrected RBCs remains unknown. To address this issue, we developed a mathematical model describing aging and survival of sickle-susceptible and normal RBCs; the former can have a selective survival advantage leading to their overrepresentation. We identified the level of bone marrow chimerism required for successful stem cell-based gene therapies in SCD. Our findings were further informed using an experimental mouse model, where we transplanted mixtures of Berkeley SCD and normal murine bone marrow cells to establish chimeric grafts in murine hosts. Our integrative theoretical and experimental approach identifies the target frequency of HSC alterations required for effective treatment of sickling syndromes in humans. Our work replaces episodic observations of such target frequencies with a mathematical modeling framework that covers a large and continuous spectrum of chimerism conditions. Am. J. Hematol. 91:931-937, 2016. © 2016 Wiley Periodicals, Inc.

  3. Endogenous bioelectrical networks store non-genetic patterning information during development and regeneration.

    PubMed

    Levin, Michael

    2014-06-01

    Pattern formation, as occurs during embryogenesis or regeneration, is the crucial link between genotype and the functions upon which selection operates. Even cancer and aging can be seen as challenges to the continuous physiological processes that orchestrate individual cell activities toward the anatomical needs of an organism. Thus, the origin and maintenance of complex biological shape is a fundamental question for cell, developmental, and evolutionary biology, as well as for biomedicine. It has long been recognized that slow bioelectrical gradients can control cell behaviors and morphogenesis. Here, I review recent molecular data that implicate endogenous spatio-temporal patterns of resting potentials among non-excitable cells as instructive cues in embryogenesis, regeneration, and cancer. Functional data have implicated gradients of resting potential in processes such as limb regeneration, eye induction, craniofacial patterning, and head-tail polarity, as well as in metastatic transformation and tumorigenesis. The genome is tightly linked to bioelectric signaling, via ion channel proteins that shape the gradients, downstream genes whose transcription is regulated by voltage, and transduction machinery that converts changes in bioelectric state to second-messenger cascades. However, the data clearly indicate that bioelectric signaling is an autonomous layer of control not reducible to a biochemical or genetic account of cell state. The real-time dynamics of bioelectric communication among cells are not fully captured by transcriptomic or proteomic analyses, and the necessary-and-sufficient triggers for specific changes in growth and form can be physiological states, while the underlying gene loci are free to diverge. The next steps in this exciting new field include the development of novel conceptual tools for understanding the anatomical semantics encoded in non-neural bioelectrical networks, and of improved biophysical tools for reading and writing

  4. Age-specific Parkinson disease risk in GBA mutation carriers: information for genetic counseling

    PubMed Central

    Rana, Huma Q.; Balwani, Manisha; Bier, Louise; Alcalay, Roy N.

    2012-01-01

    Purpose We sought to estimate age-specific risk of Parkinson disease in relatives of patients with Gaucher disease, who are obligate carriers of GBA mutations and who were not ascertained by family history of Parkinson disease. Methods A validated family history of Parkinson disease questionnaire was administered to 119 patients with Gaucher disease who were evaluated at the Mount Sinai School of Medicine from 2009 to 2012; the ages of their parents, siblings, and children, history of Parkinson disease, age at onset of Parkinson disease, and ethnic background were obtained. Kaplan–Meier survival curves were used to estimate age-specific Parkinson disease penetrance among parents of patients with Gaucher disease, who are obligatory GBA mutation carriers. Results Two participants with Gaucher disease were affected by Parkinson disease (5.4% of those who were 60 years or older). Of the 224 informative parents of patients with Gaucher disease, 11 had Parkinson disease (4.9%). Among the parents (obligatory carriers), cumulative risk of Parkinson disease by ages 65 and 85 was estimated to be 2.2% ±2.1% and 10.9% ±7.2%, respectively. Conclusion We provide useful age-specific estimates of Parkinson disease penetrance in patients with Gaucher disease and GBA heterozygous carriers for genetic counseling. Although GBA mutations may increase the risk for PD, the vast majority of patients with Gaucher disease and heterozygotes may not develop the disease. Further studies are needed to identify what modifies the risk of Parkinson disease in GBA mutation carriers. PMID:22935721

  5. Endogenous bioelectrical networks store non-genetic patterning information during development and regeneration

    PubMed Central

    Levin, Michael

    2014-01-01

    Pattern formation, as occurs during embryogenesis or regeneration, is the crucial link between genotype and the functions upon which selection operates. Even cancer and aging can be seen as challenges to the continuous physiological processes that orchestrate individual cell activities toward the anatomical needs of an organism. Thus, the origin and maintenance of complex biological shape is a fundamental question for cell, developmental, and evolutionary biology, as well as for biomedicine. It has long been recognized that slow bioelectrical gradients can control cell behaviors and morphogenesis. Here, I review recent molecular data that implicate endogenous spatio-temporal patterns of resting potentials among non-excitable cells as instructive cues in embryogenesis, regeneration, and cancer. Functional data have implicated gradients of resting potential in processes such as limb regeneration, eye induction, craniofacial patterning, and head-tail polarity, as well as in metastatic transformation and tumorigenesis. The genome is tightly linked to bioelectric signaling, via ion channel proteins that shape the gradients, downstream genes whose transcription is regulated by voltage, and transduction machinery that converts changes in bioelectric state to second-messenger cascades. However, the data clearly indicate that bioelectric signaling is an autonomous layer of control not reducible to a biochemical or genetic account of cell state. The real-time dynamics of bioelectric communication among cells are not fully captured by transcriptomic or proteomic analyses, and the necessary-and-sufficient triggers for specific changes in growth and form can be physiological states, while the underlying gene loci are free to diverge. The next steps in this exciting new field include the development of novel conceptual tools for understanding the anatomical semantics encoded in non-neural bioelectrical networks, and of improved biophysical tools for reading and writing

  6. The genetic variance for multiple linked quantitative trait loci conditional on marker information in a crossed population.

    PubMed

    Matsuda, H; Iwaisaki, H

    2002-01-01

    In the prediction of genetic values and quantitative trait loci (QTLs) mapping via the mixed model method incorporating marker information in animal populations, it is important to model the genetic variance for individuals with an arbitrary pedigree structure. In this study, for a crossed population originated from different genetic groups such as breeds or outbred strains, the variance of additive genetic values for multiple linked QTLs that are contained in a chromosome segment, especially the segregation variance, is investigated assuming the use of marker data. The variance for a finite number of QTLs in one chromosomal segment is first examined for the crossed population with the general pedigree. Then, applying the concept of the expectation of identity-by-descent proportion, an approximation to the mean of the conditional probabilities for the linked QTLs over all loci is obtained, and using it an expression for the variance in the case of an infinite number of linked QTLs marked by flanking markers is derived. It appears that the approach presented can be useful in the segment mapping using, and in the genetic evaluation of, crosses with general pedigrees in the population of concern. The calculation of the segregation variance through the current approach is illustrated numerically, using a small data-set.

  7. Development of a tiered and binned genetic counseling model for informed consent in the era of multiplex testing for cancer susceptibility

    PubMed Central

    Bradbury, Angela R.; Patrick-Miller, Linda; Long, Jessica; Powers, Jacquelyn; Stopfer, Jill; Forman, Andrea; Rybak, Christina; Mattie, Kristin; Brandt, Amanda; Chambers, Rachelle; Chung, Wendy K.; Churpek, Jane; Daly, Mary B.; Digiovanni, Laura; Farengo-Clark, Dana; Fetzer, Dominique; Ganschow, Pamela; Grana, Generosa; Gulden, Cassandra; Hall, Michael; Kohler, Lynne; Maxwell, Kara; Merrill, Shana; Montgomery, Susan; Mueller, Rebecca; Nielsen, Sarah; Olopade, Olufunmilayo; Rainey, Kimberly; Seelaus, Christina; Nathanson, Katherine L.; Domchek, Susan M.

    2016-01-01

    Purpose Multiplex genetic testing, including both moderate- and high-penetrance genes for cancer susceptibility, is associated with greater uncertainty than traditional testing, presenting challenges to informed consent and genetic counseling. We sought to develop a new model for informed consent and genetic counseling for four ongoing studies. Methods Drawing from professional guidelines, literature, conceptual frameworks, and clinical experience, a multidisciplinary group developed a tiered-binned genetic counseling approach proposed to facilitate informed consent and improve outcomes of cancer susceptibility multiplex testing. Results In this model, tier 1 “indispensable” information is presented to all patients. More specific tier 2 information is provided to support variable informational needs among diverse patient populations. Clinically relevant information is “binned” into groups to minimize information overload, support informed decision making, and facilitate adaptive responses to testing. Seven essential elements of informed consent are provided to address the unique limitations, risks, and uncertainties of multiplex testing. Conclusion A tiered-binned model for informed consent and genetic counseling has the potential to address the challenges of multiplex testing for cancer susceptibility and to support informed decision making and adaptive responses to testing. Future prospective studies including patient-reported outcomes are needed to inform how to best incorporate multiplex testing for cancer susceptibility into clinical practice. PMID:25297947

  8. Professional opportunities and responsibilities in the provision of genetic information to children relinquished for adoption.

    PubMed

    Venne, Vickie L; Botkin, Jeffrey R; Buys, Saundra S

    2003-05-15

    We report a case involving the disclosure of BRCA1 mutation results to a woman who had placed a child for adoption 30 years prior to learning her mutation status. The disclosure of the mother's genetic test result to the son resulted in unexpected subsequent communications. This article briefly describes the experience and discusses the unique issues that arise in counseling a parent who has relinquished a child who is subsequently at risk to inherit a mutation for an adult onset genetic condition.

  9. Closing the gap: inverting the genetics curriculum to ensure an informed public.

    PubMed

    Dougherty, Michael J

    2009-07-01

    Over the past 20 years, the focus of national efforts to improve K-12 science education has ranged from curriculum and professional development of teachers to the adoption of science standards and high-stakes testing. In spite of this work, students in the United States continue to lag behind their peers in other countries. This underperformance is true for genetics, as well as for science and math in general, and is particularly worrisome given the accelerating need for scientists and engineers in our increasingly technology-driven economy. A scientifically literate public is essential if citizens are to engage effectively with policymakers on issues of scientific importance. Perhaps nowhere is this conjunction more personally meaningful than in human genetics and medicine. Rapid changes in our field have the potential to revolutionize healthcare, but the public is ill prepared to participate in this transformation. One potential solution is to modernize the genetics curriculum so that it matches the science of the 21(st) century. This paper highlights changes in human genetics that support a curricular reorganization, outlines the problems with current genetics instruction, and proposes a new genetics curriculum. PMID:19559400

  10. Closing the Gap: Inverting the Genetics Curriculum to Ensure an Informed Public

    PubMed Central

    Dougherty, Michael J.

    2009-01-01

    Over the past 20 years, the focus of national efforts to improve K-12 science education has ranged from curriculum and professional development of teachers to the adoption of science standards and high-stakes testing. In spite of this work, students in the United States continue to lag behind their peers in other countries. This underperformance is true for genetics, as well as for science and math in general, and is particularly worrisome given the accelerating need for scientists and engineers in our increasingly technology-driven economy. A scientifically literate public is essential if citizens are to engage effectively with policymakers on issues of scientific importance. Perhaps nowhere is this conjunction more personally meaningful than in human genetics and medicine. Rapid changes in our field have the potential to revolutionize healthcare, but the public is ill prepared to participate in this transformation. One potential solution is to modernize the genetics curriculum so that it matches the science of the 21st century. This paper highlights changes in human genetics that support a curricular reorganization, outlines the problems with current genetics instruction, and proposes a new genetics curriculum. PMID:19559400

  11. Can sexual selection theory inform genetic management of captive populations? A review

    PubMed Central

    Chargé, Rémi; Teplitsky, Céline; Sorci, Gabriele; Low, Matthew

    2014-01-01

    Captive breeding for conservation purposes presents a serious practical challenge because several conflicting genetic processes (i.e., inbreeding depression, random genetic drift and genetic adaptation to captivity) need to be managed in concert to maximize captive population persistence and reintroduction success probability. Because current genetic management is often only partly successful in achieving these goals, it has been suggested that management insights may be found in sexual selection theory (in particular, female mate choice). We review the theoretical and empirical literature and consider how female mate choice might influence captive breeding in the context of current genetic guidelines for different sexual selection theories (i.e., direct benefits, good genes, compatible genes, sexy sons). We show that while mate choice shows promise as a tool in captive breeding under certain conditions, for most species, there is currently too little theoretical and empirical evidence to provide any clear guidelines that would guarantee positive fitness outcomes and avoid conflicts with other genetic goals. The application of female mate choice to captive breeding is in its infancy and requires a goal-oriented framework based on the needs of captive species management, so researchers can make honest assessments of the costs and benefits of such an approach, using simulations, model species and captive animal data. PMID:25553072

  12. Can sexual selection theory inform genetic management of captive populations? A review.

    PubMed

    Chargé, Rémi; Teplitsky, Céline; Sorci, Gabriele; Low, Matthew

    2014-11-01

    Captive breeding for conservation purposes presents a serious practical challenge because several conflicting genetic processes (i.e., inbreeding depression, random genetic drift and genetic adaptation to captivity) need to be managed in concert to maximize captive population persistence and reintroduction success probability. Because current genetic management is often only partly successful in achieving these goals, it has been suggested that management insights may be found in sexual selection theory (in particular, female mate choice). We review the theoretical and empirical literature and consider how female mate choice might influence captive breeding in the context of current genetic guidelines for different sexual selection theories (i.e., direct benefits, good genes, compatible genes, sexy sons). We show that while mate choice shows promise as a tool in captive breeding under certain conditions, for most species, there is currently too little theoretical and empirical evidence to provide any clear guidelines that would guarantee positive fitness outcomes and avoid conflicts with other genetic goals. The application of female mate choice to captive breeding is in its infancy and requires a goal-oriented framework based on the needs of captive species management, so researchers can make honest assessments of the costs and benefits of such an approach, using simulations, model species and captive animal data. PMID:25553072

  13. Founded: Genetic Reconstruction of Lineage Diversity and Kinship Informs Ex situ Conservation of Cuban Amazon Parrots (Amazona leucocephala).

    PubMed

    Milián-García, Yoamel; Jensen, Evelyn L; Madsen, Jeanette; Álvarez Alonso, Suleiky; Serrano Rodríguez, Aryamne; Espinosa López, Georgina; Russello, Michael A

    2015-01-01

    Captive breeding is a widespread conservation strategy, yet such programs rarely include empirical genetic data for assessing management assumptions and meeting conservation goals. Cuban Amazon parrots (Amazona leucocephala) are considered vulnerable, and multiple on-island captive populations have been established from wild-caught and confiscated individuals of unknown ancestry. Here, we used mitochondrial haplotypic and nuclear genotypic data at 9 microsatellite loci to quantify the extent and distribution of genetic variation within and among captive populations in Zapata Swamp and Managua, Cuba, and to estimate kinship among breeders (n = 88). Using Bayesian clustering analysis, we detected 2 distinct clusters within the Zapata population, one of which was shared with Managua. Individuals from the cluster unique to Zapata possessed mitochondrial haplotypes with affinities to Cuban subspecies (A. l. leucocephala, A. l. palmarum); the shared cluster was similar, but also included haplotypes closely related to the subspecies restricted to Cayman Brac (A. l. hesterna). Overall mean kinship was low within each captive population (-0.026 to -0.012), with 19 and 11 recommended breeding pairs in Zapata and Managua, respectively, ranked according to mean kinship and informed by molecular sexing. Our results highlight the importance of understanding population history within ex situ management programs, while providing genetic information to directly inform Cuban parrot conservation.

  14. [The public perception of information about the potential risks of genetically modified crops in the food chain].

    PubMed

    Furnival, Ariadne Chloë; Pinheiro, Sônia Maria

    2008-01-01

    At a time when genetically modified (GM) crops are entering the Brazilian food chain, we present the findings of a study that makes use of a qualitative technique involving focal groups to look into the public's interpretation of the information available about this biotechnological innovation. This methodology produced results that revealed the interconnections drawn by the research subjects between this form of biotechnology, changes to the environment, and food production in general. The mistrust expressed about GM crops was particularly attributed by the participants to the non-availability of comprehensible information in the mass media or on product labels.

  15. Disclosure of genetic information to at-risk relatives: recent amendments to the Privacy Act 1988 (Cwlth).

    PubMed

    Otlowski, Margaret F A

    2007-10-01

    The federal Privacy Act 1988 (Cwlth) has recently been amended to permit the disclosure of genetic information to an at-risk relative when there is a serious (although not necessarily imminent) threat to that person's life, health, or safety. This represents a significant exception to the statutory obligations to maintain the privacy of a patient's health information. However, its scope of operation is limited in that it applies only to doctors and other health professionals working in the private sector, and does not cover those working in State public hospitals or for Commonwealth Government agencies. PMID:17908004

  16. Reactions to genetically modified food crops and how perception of risks and benefits influences consumers' information gathering.

    PubMed

    Wilson, Carlene; Evans, Greg; Leppard, Phil; Syrette, Julie

    2004-10-01

    Previous research has reported strong consumer perception that genetically modified (GM) food crops may lead to adverse outcomes in a number of different areas. This is despite the widespread promulgation of the potential benefits and opportunities ascribed to the same technology by many scientists and other experts. A computer-based information gathering and evaluation task was completed by 198 adults to assess the extent to which their initial focus on the dangers or opportunities of genetic modification, or both, could be ascribed to the manner in which they gathered information on the topic (heuristically vs. systematically). Results did not confirm the hypothesis that initial focus (risks, benefits, or both) predicted ongoing information gathering and evaluation behavior. Moreover, also contrary to prediction, most participants primarily used systematic strategies when deriving their initial position, regardless of that opinion. Participants found it difficult to achieve a balanced perspective on GM food crop, even though balanced argument, as measured by order of story selection and time spent reading, was preferred as the source of information. Perceived importance is probably the most influential variable determining information gathering about issues or events to which a level of risk is attached.

  17. Confidentiality versus duty to inform--an empirical study on attitudes towards the handling of genetic information.

    PubMed

    Wolff, Katharina; Brun, Wibecke; Kvale, Gerd; Nordin, Karin

    2007-01-15

    We set out to investigate whether potential relatives want to be informed about the existence of hereditary conditions within their family and under which conditions they want healthcare providers to breach confidentiality to inform them. We hypothesized that the willingness to be informed about a hereditary condition in the family would be influenced by characteristics of the disease and by individual characteristics. Surveys were administered to a Norwegian random sample (N = 2,400) to a Swedish random sample (N = 1,200), and to a Norwegian student sample (n = 607). Eight different disease scenarios were constructed, systematically varying three disease characteristics: fatality, penetrance, and availability of treatment. Results show that a majority of participants wished to be informed about the existence of a hereditary disease within their family. The desire to be informed and the acceptability of breaches of confidentiality were predicted by the treatability of the disease, uncertainty avoidance, and age, but not by self-efficacy or worry.

  18. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  19. Misusing informed consent: a critique of limitations on research subjects' access to genetic research results.

    PubMed

    Banks, T M

    2000-01-01

    Express denials of access to genetic research results are being drafted into consent instruments. Some commentators suggest that the principle of beneficence can justify such a denial of access. This paper provides an ethical and legal critique of the use of consent instruments to disclaim responsibility for on-going disclosure by genetic researchers. Currently, the law of torts provides only weak protection for on-going disclosure for research subjects. The most substantive rights are to be found in the law of fiduciary obligations. The author concludes that, notwithstanding arguments to the contrary, there should be a presumption of disclosure in genetic research, unless the research subject elects otherwise. The author outlines one possible exception to this general presumption.

  20. Genetics and cardiovascular disease: the impact of molecular diagnosis.

    PubMed

    Vengoechea, Jaime; McKelvey, Kent D

    2013-04-01

    Information technology is exponentially reducing the cost of genetic testing while multiple clinical applications emerge. Genetic diagnosis increasingly impacts prevention, diagnosis and treatment of disease. In cardiovascular medicine, the establishment of a specific genetic diagnosis may affect management of cardiomyopathy, arrhythmia, connective tissue and metabolic disease. Econometric studies have determined that genetic testing is cost-effective in hypertrophic cardiomyopathy and disease-specific interventions are now available for specific conditions. Identification of a specific genetic disorder now allows for more precise medicine in the affected individual and more accurate preventive care for asymptomatic family members.

  1. Informed Choice in Direct-to-Consumer Genetic Testing for Alzheimer and Other Diseases: Lessons from Two Cases

    PubMed Central

    Messner, Donna A.

    2011-01-01

    Health-related direct-to-consumer (DTC) genetic testing has been a controversial practice. Especially problematic is predictive testing for Alzheimer disease (AD), since the disease is incurable, prevention is inconclusive, and testing does not definitively predict an individual’s future disease status. In this paper, I examine two contrasting cases of subjects who learn through genetic testing that they have an elevated risk of developing AD later in life. In these cases, the subject’s emotional response to the result is related to how well prepared she was for the real-life personal implications of possible test results. Analysis leads to the conclusion that when groups of health-related genetic tests are offered as packages by DTC companies, informed consumer choice is rendered impossible. Moreover, I argue, this marketing approach contravenes U.S. Federal Trade Commission policies for non-deceptive commercial communications. I conclude by suggesting ways to improve the prospects for informed consumer choice in DTC testing. PMID:21603253

  2. Preimplantation Genetic Diagnosis (PGD) on In-Vitro Fertilization (IVF) Websites: Presentations of Risks, Benefits and Other Information

    PubMed Central

    Klitzman, Robert; Zolovska, Beata; Folberth, William; Sauer, Mark V.; Chung, Wendy; Appelbaum, Paul

    2010-01-01

    Objective To examine information on Preimplantation Genetic Diagnosis (PGD) presented on In-Vitro Fertilization (IVF) clinic websites. Design We systematically sampled every third IVF clinic on the 2004 CDC provider list. Setting The Internet. Patients None. Interventions None. Main Outcome Measures Benefits, risks and other types of information mentioned regarding PGD. Results Of 135 sites examined, 88.1% had websites, and 70% mentioned PGD, of which 27% were university/hospital-based and 63% were private clinics. Sites mentioning PGD listed uses/benefits of PGD far more than the risks involved. Of these sites, 76% described testing for single gene diseases, but fewer mentioned risks of missing target diagnoses (35%), or risks for loss of embryo (18%); and 14% described PGD as new or controversial. Private clinics were more likely than other programs to: be on either the East or West Coasts; list certain PGD risks (e.g., diagnostic error); note that PGD was new or controversial; reference source of PGD information; provide accuracy rates of genetic testing of embryos; and offer gender selection for social reasons. Conclusions Most IVF clinics advertise PGD on-line, but the scope and quality of information about it varies widely, emphasizing benefits while minimizing risks. Clinics and patients may benefit from more thorough and consistent presentation of PGD, drawing on available evidence to best provide a realistic portrayal of PGD. PMID:18829009

  3. How Is Genetic Testing Done?

    MedlinePlus

    ... Testing How is genetic testing done? How is genetic testing done? Once a person decides to proceed ... is called informed consent . For more information about genetic testing procedures: The Genetic Science Learning Center at ...

  4. Accurate and Accidental Empathy.

    ERIC Educational Resources Information Center

    Chandler, Michael

    The author offers two controversial criticisms of what are rapidly becoming standard assessment procedures for the measurement of empathic skill. First, he asserts that assessment procedures which attend exclusively to the accuracy with which subjects are able to characterize other people's feelings provide little or no useful information about…

  5. Testing the limits of the 'joint account' model of genetic information: a legal thought experiment.

    PubMed

    Foster, Charles; Herring, Jonathan; Boyd, Magnus

    2015-05-01

    We examine the likely reception in the courtroom of the 'joint account' model of genetic confidentiality. We conclude that the model, as modified by Gilbar and others, is workable and reflects, better than more conventional legal approaches, both the biological and psychological realities and the obligations owed under Articles 8 and 10 of the European Convention on Human Rights (ECHR).

  6. The Genetic and Environmental Contributions to Oppositional Defiant Behavior: A Multi-informant Twin Study

    ERIC Educational Resources Information Center

    Hudziak, James J.; Derks, Eske M.; Althoff, Robert R.; Copeland, William; Boomsma, Dorret I.

    2005-01-01

    Objective: To estimate the genetic and environmental contributions to oppositional defiant behavior (ODB) from mother, father, and teacher report using the Conners Revised Short Forms in a large twin sample. Method: ODB data were collected from 1,595 mothers, 1,114 fathers, and 793 teachers of 7-year-old twin pairs from the Netherlands Twin…

  7. Network‐Informed Gene Ranking Tackles Genetic Heterogeneity in Exome‐Sequencing Studies of Monogenic Disease

    PubMed Central

    Schulz, Reiner; Weale, Michael E.; Southgate, Laura; Oakey, Rebecca J.; Simpson, Michael A.; Schlitt, Thomas

    2015-01-01

    ABSTRACT Genetic heterogeneity presents a significant challenge for the identification of monogenic disease genes. Whole‐exome sequencing generates a large number of candidate disease‐causing variants and typical analyses rely on deleterious variants being observed in the same gene across several unrelated affected individuals. This is less likely to occur for genetically heterogeneous diseases, making more advanced analysis methods necessary. To address this need, we present HetRank, a flexible gene‐ranking method that incorporates interaction network data. We first show that different genes underlying the same monogenic disease are frequently connected in protein interaction networks. This motivates the central premise of HetRank: those genes carrying potentially pathogenic variants and whose network neighbors do so in other affected individuals are strong candidates for follow‐up study. By simulating 1,000 exome sequencing studies (20,000 exomes in total), we model varying degrees of genetic heterogeneity and show that HetRank consistently prioritizes more disease‐causing genes than existing analysis methods. We also demonstrate a proof‐of‐principle application of the method to prioritize genes causing Adams‐Oliver syndrome, a genetically heterogeneous rare disease. An implementation of HetRank in R is available via the Website http://sourceforge.net/p/hetrank/. PMID:26394720

  8. 29 CFR 2590.702-1 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40, or at age 30 for those with increased risk for breast cancer, including individuals with BRCA1 or... evidence of increased risk of breast cancer, such as the results of a genetic test or a family history of breast cancer, before the claim for the mammogram is paid. This policy is applied uniformly to...

  9. 26 CFR 54.9802-3T - Additional requirements prohibiting discrimination based on genetic information (temporary).

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... increased risk for breast cancer, including individuals with BRCA1 or BRCA2 gene mutations. B is 33 years... reimbursement. Following an established policy, the plan asks B for evidence of increased risk of breast cancer, such as the results of a genetic test or a family history of breast cancer, before the claim for...

  10. 29 CFR 2590.702-1 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40, or at age 30 for those with increased risk for breast cancer, including individuals with BRCA1 or... evidence of increased risk of breast cancer, such as the results of a genetic test or a family history of breast cancer, before the claim for the mammogram is paid. This policy is applied uniformly to...

  11. 45 CFR 148.180 - Prohibition of discrimination based on genetic information.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... participants starting at age 40, or at age 30 for those with increased risk for breast cancer, including... breast cancer, such as the results of a genetic test, before the claim for the mammogram is paid. (ii...). Example 3. (i) Facts. Individual K was previously diagnosed with and treated for breast cancer, which...

  12. 29 CFR 2590.702-1 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40, or at age 30 for those with increased risk for breast cancer, including individuals with BRCA1 or... evidence of increased risk of breast cancer, such as the results of a genetic test or a family history of breast cancer, before the claim for the mammogram is paid. This policy is applied uniformly to...

  13. 45 CFR 146.122 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 40, or at age 30 for those with increased risk for breast cancer, including individuals with BRCA1 or... evidence of increased risk of breast cancer, such as the results of a genetic test or a family history of breast cancer, before the claim for the mammogram is paid. This policy is applied uniformly to...

  14. 26 CFR 54.9802-3T - Additional requirements prohibiting discrimination based on genetic information (temporary).

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... increased risk for breast cancer, including individuals with BRCA1 or BRCA2 gene mutations. B is 33 years... reimbursement. Following an established policy, the plan asks B for evidence of increased risk of breast cancer, such as the results of a genetic test or a family history of breast cancer, before the claim for...

  15. 45 CFR 146.122 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 40, or at age 30 for those with increased risk for breast cancer, including individuals with BRCA1 or... evidence of increased risk of breast cancer, such as the results of a genetic test or a family history of breast cancer, before the claim for the mammogram is paid. This policy is applied uniformly to...

  16. 26 CFR 54.9802-3T - Additional requirements prohibiting discrimination based on genetic information (temporary).

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... increased risk for breast cancer, including individuals with BRCA1 or BRCA2 gene mutations. B is 33 years... reimbursement. Following an established policy, the plan asks B for evidence of increased risk of breast cancer, such as the results of a genetic test or a family history of breast cancer, before the claim for...

  17. 45 CFR 148.180 - Prohibition of discrimination based on genetic information.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... participants starting at age 40, or at age 30 for those with increased risk for breast cancer, including... breast cancer, such as the results of a genetic test, before the claim for the mammogram is paid. (ii...). Example 3. (i) Facts. Individual K was previously diagnosed with and treated for breast cancer, which...

  18. 45 CFR 148.180 - Prohibition of discrimination based on genetic information.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... participants starting at age 40, or at age 30 for those with increased risk for breast cancer, including... breast cancer, such as the results of a genetic test, before the claim for the mammogram is paid. (ii...). Example 3. (i) Facts. Individual K was previously diagnosed with and treated for breast cancer, which...

  19. 45 CFR 148.180 - Prohibition of discrimination based on genetic information.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... participants starting at age 40, or at age 30 for those with increased risk for breast cancer, including... breast cancer, such as the results of a genetic test, before the claim for the mammogram is paid. (ii...). Example 3. (i) Facts. Individual K was previously diagnosed with and treated for breast cancer, which...

  20. 29 CFR 2590.702-1 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40, or at age 30 for those with increased risk for breast cancer, including individuals with BRCA1 or... evidence of increased risk of breast cancer, such as the results of a genetic test or a family history of breast cancer, before the claim for the mammogram is paid. This policy is applied uniformly to...

  1. 29 CFR 2590.702-1 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40, or at age 30 for those with increased risk for breast cancer, including individuals with BRCA1 or... evidence of increased risk of breast cancer, such as the results of a genetic test or a family history of breast cancer, before the claim for the mammogram is paid. This policy is applied uniformly to...

  2. 45 CFR 148.180 - Prohibition of discrimination based on genetic information.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... participants starting at age 40, or at age 30 for those with increased risk for breast cancer, including... breast cancer, such as the results of a genetic test, before the claim for the mammogram is paid. (ii...). Example 3. (i) Facts. Individual K was previously diagnosed with and treated for breast cancer, which...

  3. 26 CFR 54.9802-3T - Additional requirements prohibiting discrimination based on genetic information (temporary).

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... increased risk for breast cancer, including individuals with BRCA1 or BRCA2 gene mutations. B is 33 years... reimbursement. Following an established policy, the plan asks B for evidence of increased risk of breast cancer, such as the results of a genetic test or a family history of breast cancer, before the claim for...

  4. 26 CFR 54.9802-3T - Additional requirements prohibiting discrimination based on genetic information (temporary).

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... increased risk for breast cancer, including individuals with BRCA1 or BRCA2 gene mutations. B is 33 years... reimbursement. Following an established policy, the plan asks B for evidence of increased risk of breast cancer, such as the results of a genetic test or a family history of breast cancer, before the claim for...

  5. 45 CFR 146.122 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 40, or at age 30 for those with increased risk for breast cancer, including individuals with BRCA1 or... evidence of increased risk of breast cancer, such as the results of a genetic test or a family history of breast cancer, before the claim for the mammogram is paid. This policy is applied uniformly to...

  6. 45 CFR 146.122 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 40, or at age 30 for those with increased risk for breast cancer, including individuals with BRCA1 or... evidence of increased risk of breast cancer, such as the results of a genetic test or a family history of breast cancer, before the claim for the mammogram is paid. This policy is applied uniformly to...

  7. 45 CFR 146.122 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 40, or at age 30 for those with increased risk for breast cancer, including individuals with BRCA1 or... evidence of increased risk of breast cancer, such as the results of a genetic test or a family history of breast cancer, before the claim for the mammogram is paid. This policy is applied uniformly to...

  8. The genetics of dilated cardiomyopathy

    PubMed Central

    Dellefave, Lisa; McNally, Elizabeth M.

    2010-01-01

    Purpose of review More than forty different individual genes have been implicated in the inheritance of dilated cardiomyopathy. For a subset of these genes, mutations can lead to a spectrum of cardiomyopathy that extends to hypertrophic cardiomyopathy and left ventricular noncompaction. In nearly all cases, there is an increased risk of arrhythmias. With some genetic mutations, extracardiac manifestations are likely to be present. The precise genetic etiology can usually not be discerned from the cardiac and/or extracardiac manifestations and requires molecular genetic diagnosis for prognostic determination and cardiac care. Recent findings Newer technologies are influencing genetic testing, especially cardiomyopathy genetic testing, where an increased number of genes are now routinely being tested simultaneously. While this approach to testing multiple genes is increasing the diagnostic yield, the analysis of multiple genes in one test is also resulting in a large amount of genetic information of unclear significance. Summary Genetic testing is highly useful in the care of patients and families, since it guides diagnosis, influences care and aids in prognosis. However, the large amount of benign human genetic variation may complicate genetic results, and often requires a skilled team to accurately interpret the findings. PMID:20186049

  9. Do Other People's Plights Matter? A Genetically Informed Twin Study of the Role of Social Context in the Link between Peer Victimization and Children's Aggression and Depression Symptoms

    ERIC Educational Resources Information Center

    Brendgen, Mara; Vitaro, Frank; Barker, Edward D.; Girard, Alain; Dionne, Ginette; Tremblay, Richard E.; Boivin, Michel

    2013-01-01

    Using a genetically informed design, this study examined the additive and interactive effects of genetic risk, personal peer victimization experiences, and peer victimization experienced by others on children's aggression and depression symptoms. Of major interest was whether these effects varied depending on whether or not the victimized others…

  10. Genetically determined ancestry is more informative than self-reported race in HIV-infected and -exposed children.

    PubMed

    Spector, Stephen A; Brummel, Sean S; Nievergelt, Caroline M; Maihofer, Adam X; Singh, Kumud K; Purswani, Murli U; Williams, Paige L; Hazra, Rohan; Van Dyke, Russell; Seage, George R

    2016-09-01

    The Pediatric HIV/AIDS Cohort Study (PHACS), the largest ongoing longitudinal study of perinatal HIV-infected (PHIV) and HIV-exposed, uninfected (PHEU) children in the United States, comprises the Surveillance Monitoring of Antiretroviral Therapy [ART] Toxicities (SMARTT) Study in PHEU children and the Adolescent Master Protocol (AMP) that includes PHIV and PHEU children ≥7 years. Although race/ethnicity is often used to assess health outcomes, this approach remains controversial and may fail to accurately reflect the backgrounds of ancestry-diverse populations as represented in the PHACS participants.In this study, we compared genetically determined ancestry (GDA) and self-reported race/ethnicity (SRR) in the PHACS cohort. GDA was estimated using a highly discriminative panel of 41 single nucleotide polymorphisms and compared to SRR. Because SRR was similar between the PHIV and PHEU, and between the AMP and SMARTT cohorts, data for all unique 1958 participants were combined.According to SRR, 63% of study participants identified as Black/African-American, 27% White, and 34% Hispanic. Using the highest percentage of ancestry/ethnicity to identify GDA, 9.5% of subjects were placed in the incorrect superpopulation based on SRR. When ≥50% or ≥75% GDA of a given superpopulation was required, 12% and 25%, respectively, of subjects were placed in the incorrect superpopulation based on SRR, and the percent of subjects classified as multiracial increased. Of 126 participants with unidentified SRR, 71% were genetically identified as Eurasian.GDA provides a more robust assessment of race/ethnicity when compared to self-report, and study participants with unidentified SRR could be assigned GDA using genetic markers. In addition, identification of continental ancestry removes the taxonomic identification of race as a variable when identifying risk for clinical outcomes. PMID:27603370

  11. Genetically determined ancestry is more informative than self-reported race in HIV-infected and -exposed children

    PubMed Central

    Spector, Stephen A.; Brummel, Sean S.; Nievergelt, Caroline M.; Maihofer, Adam X.; Singh, Kumud K.; Purswani, Murli U.; Williams, Paige L.; Hazra, Rohan; Van Dyke, Russell; Seage, George R.

    2016-01-01

    Abstract The Pediatric HIV/AIDS Cohort Study (PHACS), the largest ongoing longitudinal study of perinatal HIV-infected (PHIV) and HIV-exposed, uninfected (PHEU) children in the United States, comprises the Surveillance Monitoring of Antiretroviral Therapy [ART] Toxicities (SMARTT) Study in PHEU children and the Adolescent Master Protocol (AMP) that includes PHIV and PHEU children ≥7 years. Although race/ethnicity is often used to assess health outcomes, this approach remains controversial and may fail to accurately reflect the backgrounds of ancestry-diverse populations as represented in the PHACS participants. In this study, we compared genetically determined ancestry (GDA) and self-reported race/ethnicity (SRR) in the PHACS cohort. GDA was estimated using a highly discriminative panel of 41 single nucleotide polymorphisms and compared to SRR. Because SRR was similar between the PHIV and PHEU, and between the AMP and SMARTT cohorts, data for all unique 1958 participants were combined. According to SRR, 63% of study participants identified as Black/African-American, 27% White, and 34% Hispanic. Using the highest percentage of ancestry/ethnicity to identify GDA, 9.5% of subjects were placed in the incorrect superpopulation based on SRR. When ≥50% or ≥75% GDA of a given superpopulation was required, 12% and 25%, respectively, of subjects were placed in the incorrect superpopulation based on SRR, and the percent of subjects classified as multiracial increased. Of 126 participants with unidentified SRR, 71% were genetically identified as Eurasian. GDA provides a more robust assessment of race/ethnicity when compared to self-report, and study participants with unidentified SRR could be assigned GDA using genetic markers. In addition, identification of continental ancestry removes the taxonomic identification of race as a variable when identifying risk for clinical outcomes. PMID:27603370

  12. 'Is this knowledge mine and nobody else's? I don't feel that.' Patient views about consent, confidentiality and information-sharing in genetic medicine.

    PubMed

    Dheensa, Sandi; Fenwick, Angela; Lucassen, Anneke

    2016-03-01

    In genetic medicine, a patient's diagnosis can mean their family members are also at risk, raising a question about how consent and confidentiality should function in clinical genetics. This question is particularly pressing when it is unclear whether a patient has shared information. Conventionally, healthcare professionals view confidentiality at an individual level and 'disclosure without consent' as the exception, not the rule. The relational joint account model, by contrast, conceptualises genetic information as confidential at the familial level and encourages professionals to take disclosure as the default position. In this study, we interviewed 33 patients about consent and confidentiality and analysed data thematically. Our first theme showed that although participants thought of certain aspects of genetic conditions--for example, the way they affect day-to-day health--as somewhat personal, they perceived genetic information--for example, the mutation in isolation--as familial. Most thought these elements were separable and thought family members had a right to know the latter, identifying a broad range of harms that would justify disclosure. Our second theme illustrated that participants nonetheless had some concerns about what, if any, implications there would be of professionals treating such information as familial and they emphasised the importance of being informed about the way their information would be shared. Based on these results, we recommend that professionals take disclosure as the default position, but make clear that they will treat genetic information as familial during initial consultations and address any concerns therein.

  13. Design and implementation of a library-based information service in molecular biology and genetics at the University of Pittsburgh

    PubMed Central

    Chattopadhyay, Ansuman; Tannery, Nancy Hrinya; Silverman, Deborah A. L.; Bergen, Phillip; Epstein, Barbara A.

    2006-01-01

    Setting: In summer 2002, the Health Sciences Library System (HSLS) at the University of Pittsburgh initiated an information service in molecular biology and genetics to assist researchers with identifying and utilizing bioinformatics tools. Program Components: This novel information service comprises hands-on training workshops and consultation on the use of bioinformatics tools. The HSLS also provides an electronic portal and networked access to public and commercial molecular biology databases and software packages. Evaluation Mechanisms: Researcher feedback gathered during the first three years of workshops and individual consultation indicate that the information service is meeting user needs. Next Steps/Future Directions: The service's workshop offerings will expand to include emerging bioinformatics topics. A frequently asked questions database is also being developed to reuse advice on complex bioinformatics questions. PMID:16888665

  14. Informational content, literacy demands, and usability of websites offering health-related genetic tests directly to consumers

    PubMed Central

    Lachance, Christina R.; Erby, Lori A. H.; Ford, Beth M.; Allen, Vincent C.; Kaphingst, Kimberly A.

    2010-01-01

    Purpose As direct to consumer (DTC) genetic testing becomes more available, a diverse group of consumers, including those with limited health literacy, may consider testing. In light of concerns raised about DTC genetic testing, this study sought to critically examine whether the informational content, literacy demands, and usability of health-related DTC websites met existing recommendations. Methods A content analysis was performed on 29 health-related DTC websites. Two coders independently evaluated each website for informational content (e.g., benefits, limitations), literacy demands (e.g., reading level), and usability (e.g., ease of navigation). Results Most sites presented health conditions and some markers for which they tested, benefits of testing, a description of the testing process, and their privacy policy. Fewer cited scientific literature, explained test limitations or provided an opportunity to consult a health professional. Key informational content was difficult to locate on most sites. Few sites gave sample disease risk estimates, or used common language and explained technical terms consistently. Average reading level was grade 15. Conclusion The quality of informational content, literacy demands, and usability across health-related DTC websites varied widely. Many users would struggle to find and understand the important information. In order for consumers to better understand the content on these sites and evaluate the meaning of the tests for their health, sites should lower the demands placed on users by distilling and prioritizing the key informational content while simultaneously attending to the reading level and usability elements. In the absence of regulation compelling such changes, government agencies or professional organizations may need to increase consumer and provider awareness of these issues. PMID:20386454

  15. Accurate Optical Reference Catalogs

    NASA Astrophysics Data System (ADS)

    Zacharias, N.

    2006-08-01

    Current and near future all-sky astrometric catalogs on the ICRF are reviewed with the emphasis on reference star data at optical wavelengths for user applications. The standard error of a Hipparcos Catalogue star position is now about 15 mas per coordinate. For the Tycho-2 data it is typically 20 to 100 mas, depending on magnitude. The USNO CCD Astrograph Catalog (UCAC) observing program was completed in 2004 and reductions toward the final UCAC3 release are in progress. This all-sky reference catalogue will have positional errors of 15 to 70 mas for stars in the 10 to 16 mag range, with a high degree of completeness. Proper motions for the about 60 million UCAC stars will be derived by combining UCAC astrometry with available early epoch data, including yet unpublished scans of the complete set of AGK2, Hamburg Zone astrograph and USNO Black Birch programs. Accurate positional and proper motion data are combined in the Naval Observatory Merged Astrometric Dataset (NOMAD) which includes Hipparcos, Tycho-2, UCAC2, USNO-B1, NPM+SPM plate scan data for astrometry, and is supplemented by multi-band optical photometry as well as 2MASS near infrared photometry. The Milli-Arcsecond Pathfinder Survey (MAPS) mission is currently being planned at USNO. This is a micro-satellite to obtain 1 mas positions, parallaxes, and 1 mas/yr proper motions for all bright stars down to about 15th magnitude. This program will be supplemented by a ground-based program to reach 18th magnitude on the 5 mas level.

  16. A colorful origin for the genetic code: information theory, statistical mechanics and the emergence of molecular codes.

    PubMed

    Tlusty, Tsvi

    2010-09-01

    The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. While the biochemical details of this code were unraveled long ago, its origin is still obscure. We review information-theoretic approaches to the problem of the code's origin and discuss the results of a recent work that treats the code in terms of an evolving, error-prone information channel. Our model - which utilizes the rate-distortion theory of noisy communication channels - suggests that the genetic code originated as a result of the interplay of the three conflicting evolutionary forces: the needs for diverse amino-acids, for error-tolerance and for minimal cost of resources. The description of the code as an information channel allows us to mathematically identify the fitness of the code and locate its emergence at a second-order phase transition when the mapping of codons to amino-acids becomes nonrandom. The noise in the channel brings about an error-graph, in which edges connect codons that are likely to be confused. The emergence of the code is governed by the topology of the error-graph, which determines the lowest modes of the graph-Laplacian and is related to the map coloring problem. PMID:20558115

  17. A colorful origin for the genetic code: Information theory, statistical mechanics and the emergence of molecular codes

    NASA Astrophysics Data System (ADS)

    Tlusty, Tsvi

    2010-09-01

    The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. While the biochemical details of this code were unraveled long ago, its origin is still obscure. We review information-theoretic approaches to the problem of the code's origin and discuss the results of a recent work that treats the code in terms of an evolving, error-prone information channel. Our model - which utilizes the rate-distortion theory of noisy communication channels - suggests that the genetic code originated as a result of the interplay of the three conflicting evolutionary forces: the needs for diverse amino-acids, for error-tolerance and for minimal cost of resources. The description of the code as an information channel allows us to mathematically identify the fitness of the code and locate its emergence at a second-order phase transition when the mapping of codons to amino-acids becomes nonrandom. The noise in the channel brings about an error-graph, in which edges connect codons that are likely to be confused. The emergence of the code is governed by the topology of the error-graph, which determines the lowest modes of the graph-Laplacian and is related to the map coloring problem.

  18. Using genetic diversity information to establish core collections of Stylosanthes capitata and Stylosanthes macrocephala

    PubMed Central

    Santos-Garcia, Melissa Oliveira; de Toledo-Silva, Guilherme; Sassaki, Rodrigo Possidonio; Ferreira, Thais Helena; Resende, Rosângela Maria Simeão; Chiari, Lucimara; Karia, Cláudio Takao; Carvalho, Marcelo Ayres; Faleiro, Fábio Gelape; Zucchi, Maria Imaculada; de Souza, Anete Pereira

    2012-01-01

    Stylosanthes species are important forage legumes in tropical and subtropical areas. S. macrocephala and S. capitata germplasm collections that consist of 134 and 192 accessions, respectively, are maintained at the Brazilian Agricultural Research Corporation Cerrados (Embrapa-Cerrados). Polymorphic microsatellite markers were used to assess genetic diversity and population structure with the aim to assemble a core collection. The mean values of HO and HE for S. macrocephala were 0.08 and 0.36, respectively, whereas the means for S. capitata were 0.48 and 0.50, respectively. Roger’s genetic distance varied from 0 to 0.83 for S. macrocephala and from 0 to 0.85 for S. capitata. Analysis with STRUCTURE software distinguished five groups among the S. macrocephala accessions and four groups among those of S. capitata. Nei’s genetic diversity was 27% in S. macrocephala and 11% in S. capitata. Core collections were assembled for both species. For S. macrocephala, all of the allelic diversity was represented by 23 accessions, whereas only 13 accessions were necessary to represent all allelic diversity for S. capitata. The data presented herein evidence the population structure present in the Embrapa-Cerrados germplasm collections of S. macrocephala and S. capitata, which may be useful for breeding programs and germplasm conservation. PMID:23271947

  19. Vehicles, Replicators, and Intercellular Movement of Genetic Information: Evolutionary Dissection of a Bacterial Cell

    PubMed Central

    Jalasvuori, Matti

    2012-01-01

    Prokaryotic biosphere is vastly diverse in many respects. Any given bacterial cell may harbor in different combinations viruses, plasmids, transposons, and other genetic elements along with their chromosome(s). These agents interact in complex environments in various ways causing multitude of phenotypic effects on their hosting cells. In this discussion I perform a dissection for a bacterial cell in order to simplify the diversity into components that may help approach the ocean of details in evolving microbial worlds. The cell itself is separated from all the genetic replicators that use the cell vehicle for preservation and propagation. I introduce a classification that groups different replicators according to their horizontal movement potential between cells and according to their effects on the fitness of their present host cells. The classification is used to discuss and improve the means by which we approach general evolutionary tendencies in microbial communities. Moreover, the classification is utilized as a tool to help formulating evolutionary hypotheses and to discuss emerging bacterial pathogens as well as to promote understanding on the average phenotypes of different replicators in general. It is also discussed that any given biosphere comprising prokaryotic cell vehicles and genetic replicators may naturally evolve to have horizontally moving replicators of various types. PMID:22567533

  20. Reproductive decisions after fetal genetic counselling.

    PubMed

    Pergament, Eugene; Pergament, Deborah

    2012-10-01

    A broad range of testing modalities for fetal genetic disease has been established. These include carrier screening for single-gene mutations, first-trimester and second-trimester screening for chromosome abnormalities and open neural-tube defects, prenatal diagnosis by means of chorionic villus sampling and amniocentesis, and preimplantation genetic diagnosis. Reproductive decisions before and after fetal genetic counselling represent the culmination of a dynamic interaction between prospective parents, obstetrician and genetic counsellor. The decision to undergo genetic testing before and after genetic counselling is influenced by a host of interrelated factors, including patient-partner and family relationships, patient-physician communication, societal mores, religious beliefs, and the media. Because of the complexity of personal and societal factors involved, it is not surprising that genetic counselling concerning reproductive decision-making must be individualised. A limited number of principles, guidelines and standards apply when counselling about testing for fetal genetic disease. These principles are that genetic counselling should be non-directive and unbiased and that parental decisions should be supported regardless of the reproductive choice. A critical responsibility of the obstetrician and genetic counsellor is to provide accurate and objective information about the implications, advantages, disadvantages and consequences of any genetic testing applied to prospective parents and their fetuses. These principles and responsibilities will be tested as newer technologies, such as array comparative genome hybridisation, non-invasive prenatal diagnosis and sequencing of the entire genome are introduced into the field of reproductive genetics and become routine practice.

  1. Blood and Intestine eQTLs from an Anti-TNF-Resistant Crohn's Disease Cohort Inform IBD Genetic Association Loci

    PubMed Central

    Di Narzo, Antonio F; Peters, Lauren A; Argmann, Carmen; Stojmirovic, Aleksandar; Perrigoue, Jacqueline; Li, Katherine; Telesco, Shannon; Kidd, Brian; Walker, Jennifer; Dudley, Joel; Cho, Judy; Schadt, Eric E; Kasarskis, Andrew; Curran, Mark; Dobrin, Radu; Hao, Ke

    2016-01-01

    OBJECTIVES: Genome-wide association studies (GWAS) have identified loci reproducibly associated with inflammatory bowel disease (IBD) and other immune-mediated diseases; however, the molecular mechanisms underlying most of genetic susceptibility remain undefined. Expressional quantitative trait loci (eQTL) of disease-relevant tissue can be employed in order to elucidate the genes and pathways affected by disease-specific genetic variance. METHODS: In this study, we derived eQTLs for human whole blood and intestine tissues of anti-tumor necrosis factor-resistant Crohn's disease (CD) patients. We interpreted these eQTLs in the context of published IBD GWAS hits to inform on the disease process. RESULTS: At 10% false discovery rate, we discovered that 5,174 genes in blood and 2,063 genes in the intestine were controlled by a nearby single-nucleotide polymorphism (SNP) (i.e., cis-eQTL), among which 1,360 were shared between the two tissues. A large fraction of the identified eQTLs were supported by the regulomeDB database, showing that the eQTLs reside in regulatory elements (odds ratio; OR=3.44 and 3.24 for blood and intestine eQTLs, respectively) as opposed to protein-coding regions. Published IBD GWAS hits as a whole were enriched for blood and intestine eQTLs (OR=2.88 and 2.05; and P value=2.51E-9 and 0.013, respectively), thereby linking genetic susceptibility to control of gene expression in these tissues. Through a systematic search, we used eQTL data to inform 109 out of 372 IBD GWAS SNPs documented in National Human Genome Research Institute catalog, and we categorized the genes influenced by eQTLs according to their functions. Many of these genes have experimentally validated roles in specific cell types contributing to intestinal inflammation. CONCLUSIONS: The blood and intestine eQTLs described in this study represent a powerful tool to link GWAS loci to a regulatory function and thus elucidate the mechanisms underlying the genetic loci associated with IBD

  2. Behavior genetics of personality disorders: informing classification and conceptualization in DSM-5.

    PubMed

    South, Susan C; DeYoung, Nathaniel J

    2013-07-01

    Personality pathology is currently captured in the Diagnostic and Statistical Manual through 10 categorical personality disorder (PD) diagnoses grouped into three descriptive clusters. This classification system has been criticized by many for using discrete categories and arbitrary thresholds when making clinical decisions. To address these critiques, the DSM-5 Personality and Personality Disorders Work Group has put forth a proposal that significantly alters the structure and content of the DSM-IV PD section. If this DSM-5 Work Group has conducted its own systematic review of the empirical literature, this review has not been released or made widely available. As such, it is up to the psychology community at large to determine how well the suggested changes align with findings from extant PD research. The current article joins this effort by addressing the contribution of behavior genetic findings to the revision process for classification of PDs in DSM-5. First, we provide a brief review of the history of PD classification in the DSM. Next, we present an overview and rationale for each of the five major suggested changes to PD diagnoses. For each suggested change, we outline the available evidence from behavior genetics and interpretations of these findings. Finally, we offer a summary of considerations for PD classification as the DSM-5 moves forward. Review of the behavior genetics literature suggests that several features of the DSM-5 proposal, including the elimination of 4 PDs, merging clinical disorders and PDs on a single axis, and the implementation of a trait rating system, require significantly greater explication before a product is finalized.

  3. Genetic information and ecosystem health: arguments for the application of chaos theory to identify boundary conditions for ecosystem management.

    PubMed Central

    Stomp, A M

    1994-01-01

    To meet the demands for goods and services of an exponentially growing human population, global ecosystems will come under increasing human management. The hallmark of successful ecosystem management will be long-term ecosystem stability. Ecosystems and the genetic information and processes which underlie interactions of organisms with the environment in populations and communities exhibit behaviors which have nonlinear characteristics. Nonlinear mathematical formulations describing deterministic chaos have been used successfully to model such systems in physics, chemistry, economics, physiology, and epidemiology. This approach can be extended to ecotoxicology and can be used to investigate how changes in genetic information determine the behavior of populations and communities. This article seeks to provide the arguments for such an approach and to give initial direction to the search for the boundary conditions within which lies ecosystem stability. The identification of a theoretical framework for ecotoxicology and the parameters which drive the underlying model is a critical component in the formulation of a prioritized research agenda and appropriate ecosystem management policy and regulation. PMID:7713038

  4. The impact of sleep duration on adolescent development: a genetically informed analysis of identical twin pairs.

    PubMed

    Barnes, J C; Meldrum, Ryan C

    2015-02-01

    Recent work provides evidence that reduced sleep duration has detrimental effects on a range of developmentally related outcomes during adolescence. Yet, the potential confounding influence of genetic and shared environmental effects has not been sufficiently addressed. This study addresses this issue by analyzing cross-sectional data from the twin sub-sample of the first wave of the National Longitudinal Study of Adolescent Health [N ≈ 287 MZ (monozygotic) twin pairs; 50% male; 22% Black; mean age = 15.75]. Associations between sleep duration (measured through two different strategies, one tapping number of hours slept at night and the other measuring weeknight bedtimes) and seven outcomes (self-control, depressive symptoms, suicidal ideation, body mass index, violent delinquency, non-violent delinquency, and drug use) were estimated. Consistent with prior research, associations between sleep duration and several outcomes were statistically significant when using standard social science analytic methods. Yet, when employing a methodology that accounts for genetic and shared environmental influences, some of these associations were reduced to non-significance. Still, two consistent associations remained in that participants who reported sleeping fewer hours at night (or who reported later bedtimes) exhibited lower levels of self-control and more depressive symptoms. Implications of the findings and directions for future research are discussed.

  5. Golden rice: scientific, regulatory and public information processes of a genetically modified organism.

    PubMed

    Moghissi, A Alan; Pei, Shiqian; Liu, Yinzuo

    2016-01-01

    Historically, agricultural development evolved in three phases. During the first phase the plants were selected on the basis of the availability of a plant with desirable properties at a specific location. The second phase provided the agricultural community with crossbreeding plants to achieve improvement in agricultural production. The evolution of biological knowledge has provided the ability to genetically engineer (GE) crops, one of the key processes within genetically modified organisms (GMO). This article uses golden rice, a species of transgenic Asian rice which contains a precursor of vitamin A in the edible part of the plant as an example of GE/GMO emphasizing Chinese experience in agricultural evolution. It includes a brief review of agricultural evolution to be followed by a description of golden rice development. Golden rice was created as a humanitarian project and has received positive comments by the scientific community and negative voices from certain environmental groups. In this article, we use the Best Available Science (BAS) Concept and Metrics for Evaluation of Scientific Claims (MESC) derived from it to evaluate claims and counter claims on scientific aspects of golden rice. This article concludes that opposition to golden rice is based on belief rather than any of its scientifically derived nutritional, safety or environmental properties.

  6. Phylogeographic Triangulation: Using Predator-Prey-Parasite Interactions to Infer Population History from Partial Genetic Information

    PubMed Central

    Barbosa, A. Márcia; Thode, Guillermo; Real, Raimundo; Feliu, Carlos; Vargas, J. Mario

    2012-01-01

    Phylogeographic studies, which infer population history and dispersal movements from intra-specific spatial genetic variation, require expensive and time-consuming analyses that are not always feasible, especially in the case of rare or endangered species. On the other hand, comparative phylogeography of species involved in close biotic interactions may show congruent patterns depending on the specificity of the relationship. Consequently, the phylogeography of a parasite that needs two hosts to complete its life cycle should reflect population history traits of both hosts. Population movements evidenced by the parasite’s phylogeography that are not reflected in the phylogeography of one of these hosts may thus be attributed to the other host. Using the wild rabbit (Oryctolagus cuniculus) and a parasitic tapeworm (Taenia pisiformis) as an example, we propose comparing the phylogeography of easily available organisms such as game species and their specific heteroxenous parasites to infer population movements of definitive host/predator species, independently of performing genetic analyses on the latter. This may be an interesting approach for indirectly studying the history of species whose phylogeography is difficult to analyse directly. PMID:23209834

  7. The impact of sleep duration on adolescent development: a genetically informed analysis of identical twin pairs.

    PubMed

    Barnes, J C; Meldrum, Ryan C

    2015-02-01

    Recent work provides evidence that reduced sleep duration has detrimental effects on a range of developmentally related outcomes during adolescence. Yet, the potential confounding influence of genetic and shared environmental effects has not been sufficiently addressed. This study addresses this issue by analyzing cross-sectional data from the twin sub-sample of the first wave of the National Longitudinal Study of Adolescent Health [N ≈ 287 MZ (monozygotic) twin pairs; 50% male; 22% Black; mean age = 15.75]. Associations between sleep duration (measured through two different strategies, one tapping number of hours slept at night and the other measuring weeknight bedtimes) and seven outcomes (self-control, depressive symptoms, suicidal ideation, body mass index, violent delinquency, non-violent delinquency, and drug use) were estimated. Consistent with prior research, associations between sleep duration and several outcomes were statistically significant when using standard social science analytic methods. Yet, when employing a methodology that accounts for genetic and shared environmental influences, some of these associations were reduced to non-significance. Still, two consistent associations remained in that participants who reported sleeping fewer hours at night (or who reported later bedtimes) exhibited lower levels of self-control and more depressive symptoms. Implications of the findings and directions for future research are discussed. PMID:24915970

  8. Estimating Information Processing in a Memory System: The Utility of Meta-analytic Methods for Genetics

    PubMed Central

    Yildizoglu, Tugce; Weislogel, Jan-Marek; Mohammad, Farhan; Chan, Edwin S.-Y.; Assam, Pryseley N.; Claridge-Chang, Adam

    2015-01-01

    Genetic studies in Drosophila reveal that olfactory memory relies on a brain structure called the mushroom body. The mainstream view is that each of the three lobes of the mushroom body play specialized roles in short-term aversive olfactory memory, but a number of studies have made divergent conclusions based on their varying experimental findings. Like many fields, neurogenetics uses null hypothesis significance testing for data analysis. Critics of significance testing claim that this method promotes discrepancies by using arbitrary thresholds (α) to apply reject/accept dichotomies to continuous data, which is not reflective of the biological reality of quantitative phenotypes. We explored using estimation statistics, an alternative data analysis framework, to examine published fly short-term memory data. Systematic review was used to identify behavioral experiments examining the physiological basis of olfactory memory and meta-analytic approaches were applied to assess the role of lobular specialization. Multivariate meta-regression models revealed that short-term memory lobular specialization is not supported by the data; it identified the cellular extent of a transgenic driver as the major predictor of its effect on short-term memory. These findings demonstrate that effect sizes, meta-analysis, meta-regression, hierarchical models and estimation methods in general can be successfully harnessed to identify knowledge gaps, synthesize divergent results, accommodate heterogeneous experimental design and quantify genetic mechanisms. PMID:26647168

  9. Estimating Information Processing in a Memory System: The Utility of Meta-analytic Methods for Genetics.

    PubMed

    Yildizoglu, Tugce; Weislogel, Jan-Marek; Mohammad, Farhan; Chan, Edwin S-Y; Assam, Pryseley N; Claridge-Chang, Adam

    2015-12-01

    Genetic studies in Drosophila reveal that olfactory memory relies on a brain structure called the mushroom body. The mainstream view is that each of the three lobes of the mushroom body play specialized roles in short-term aversive olfactory memory, but a number of studies have made divergent conclusions based on their varying experimental findings. Like many fields, neurogenetics uses null hypothesis significance testing for data analysis. Critics of significance testing claim that this method promotes discrepancies by using arbitrary thresholds (α) to apply reject/accept dichotomies to continuous data, which is not reflective of the biological reality of quantitative phenotypes. We explored using estimation statistics, an alternative data analysis framework, to examine published fly short-term memory data. Systematic review was used to identify behavioral experiments examining the physiological basis of olfactory memory and meta-analytic approaches were applied to assess the role of lobular specialization. Multivariate meta-regression models revealed that short-term memory lobular specialization is not supported by the data; it identified the cellular extent of a transgenic driver as the major predictor of its effect on short-term memory. These findings demonstrate that effect sizes, meta-analysis, meta-regression, hierarchical models and estimation methods in general can be successfully harnessed to identify knowledge gaps, synthesize divergent results, accommodate heterogeneous experimental design and quantify genetic mechanisms. PMID:26647168

  10. Inconsistencies in pedigree symbols in human genetics publications: A need for standardization

    SciTech Connect

    Steinhaus, K.A.; Bennett, R.L.; Resta, R.G.

    1995-04-10

    To determine consistency in usage of pedigree symbols by genetics professionals, we reviewed pedigrees printed in 10 human genetic and medical journals and 24 medical genetics textbooks. We found no consistent symbolization for common situations such as pregnancy, spontaneous abortion, death, or test results. Inconsistency in pedigree design can create difficulties in the interpretation of family studies and detract from the pedigree`s basic strength of simple and accurate communication of medical information. We recommend the development of standard pedigree symbols, and their incorporation into genetic publications, professional genetics training programs, pedigree software programs, and genetic board examinations. 5 refs., 11 figs., 2 tabs.

  11. Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information

    PubMed Central

    2012-01-01

    Background Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton. Results In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium. Conclusion This study will serve as a valuable genomic resource

  12. Genetics Home Reference: Turner syndrome

    MedlinePlus

    ... pregnancies that do not survive to term (miscarriages and stillbirths). Related Information What information about a genetic condition can statistics provide? Why are some genetic conditions more common ...

  13. NO RELATIONSHIP BETWEEN INTELLIGENCE AND FACIAL ATTRACTIVENESS IN A LARGE, GENETICALLY INFORMATIVE SAMPLE

    PubMed Central

    Mitchem, Dorian G.; Zietsch, Brendan P.; Wright, Margaret J.; Martin, Nicholas G.; Hewitt, John K.; Keller, Matthew C.

    2015-01-01

    Theories in both evolutionary and social psychology suggest that a positive correlation should exist between facial attractiveness and general intelligence, and several empirical observations appear to corroborate this expectation. Using highly reliable measures of facial attractiveness and IQ in a large sample of identical and fraternal twins and their siblings, we found no evidence for a phenotypic correlation between these traits. Likewise, neither the genetic nor the environmental latent factor correlations were statistically significant. We supplemented our analyses of new data with a simple meta-analysis that found evidence of publication bias among past studies of the relationship between facial attractiveness and intelligence. In view of these results, we suggest that previously published reports may have overestimated the strength of the relationship and that the theoretical bases for the predicted attractiveness-intelligence correlation may need to be reconsidered. PMID:25937789

  14. Jurisprudence and genetics.

    PubMed

    Kaveny, M C

    1999-03-01

    This section of the Notes in Moral Theology attempts to grapple with the proper relation of law and morality in three emerging issues connected with genetics: cloning, discrimination on the basis of genetic information, and patenting of genetic material.

  15. Information theoretical methods to deconvolute genetic regulatory networks applied to thyroid neoplasms

    NASA Astrophysics Data System (ADS)

    Hernández-Lemus, Enrique; Velázquez-Fernández, David; Estrada-Gil, Jesús K.; Silva-Zolezzi, Irma; Herrera-Hernández, Miguel F.; Jiménez-Sánchez, Gerardo

    2009-12-01

    Most common pathologies in humans are not caused by the mutation of a single gene, rather they are complex diseases that arise due to the dynamic interaction of many genes and environmental factors. This plethora of interacting genes generates a complexity landscape that masks the real effects associated with the disease. To construct dynamic maps of gene interactions (also called genetic regulatory networks) we need to understand the interplay between thousands of genes. Several issues arise in the analysis of experimental data related to gene function: on the one hand, the nature of measurement processes generates highly noisy signals; on the other hand, there are far more variables involved (number of genes and interactions among them) than experimental samples. Another source of complexity is the highly nonlinear character of the underlying biochemical dynamics. To overcome some of these limitations, we generated an optimized method based on the implementation of a Maximum Entropy Formalism (MaxEnt) to deconvolute a genetic regulatory network based on the most probable meta-distribution of gene-gene interactions. We tested the methodology using experimental data for Papillary Thyroid Cancer (PTC) and Thyroid Goiter tissue samples. The optimal MaxEnt regulatory network was obtained from a pool of 25,593,993 different probability distributions. The group of observed interactions was validated by several (mostly in silico) means and sources. For the associated Papillary Thyroid Cancer Gene Regulatory Network (PTC-GRN) the majority of the nodes (genes) have very few links (interactions) whereas a small number of nodes are highly connected. PTC-GRN is also characterized by high clustering coefficients and network heterogeneity. These properties have been recognized as characteristic of topological robustness, and they have been largely described in relation to biological networks. A number of biological validity outcomes are discussed with regard to both the

  16. Direct-to-consumer genetic testing: perceptions, problems, and policy responses.

    PubMed

    Caulfield, Timothy; McGuire, Amy L

    2012-01-01

    Direct-to-consumer (DTC) genetic testing has attracted a great amount of attention from policy makers, the scientific community, professional groups, and the media. Although it is unclear what the public demand is for these services, there does appear to be public interest in personal genetic risk information. As a result, many commentators have raised a variety of social, ethical, and regulatory issues associated with this emerging industry, including privacy issues, ensuring that DTC companies provide accurate information about the risks and limitations of their services, the possible adverse impact of DTC genetic testing on healthcare systems, and concern about how individuals may interpret and react to genetic risk information.

  17. Genetic barcodes

    DOEpatents

    Weier, Heinz -Ulrich G

    2015-08-04

    Herein are described multicolor FISH probe sets termed "genetic barcodes" targeting several cancer or disease-related loci to assess gene rearrangements and copy number changes in tumor cells. Two, three or more different fluorophores are used to detect the genetic barcode sections thus permitting unique labeling and multilocus analysis in individual cell nuclei. Gene specific barcodes can be generated and combined to provide both numerical and structural genetic information for these and other pertinent disease associated genes.

  18. Hot topic: a unified approach to utilize phenotypic, full pedigree, and genomic information for genetic evaluation of Holstein final score.

    PubMed

    Aguilar, I; Misztal, I; Johnson, D L; Legarra, A; Tsuruta, S; Lawlor, T J

    2010-02-01

    The first national single-step, full-information (phenotype, pedigree, and marker genotype) genetic evaluation was developed for final score of US Holsteins. Data included final scores recorded from 1955 to 2009 for 6,232,548 Holsteins cows. BovineSNP50 (Illumina, San Diego, CA) genotypes from the Cooperative Dairy DNA Repository (Beltsville, MD) were available for 6,508 bulls. Three analyses used a repeatability animal model as currently used for the national US evaluation. The first 2 analyses used final scores recorded up to 2004. The first analysis used only a pedigree-based relationship matrix. The second analysis used a relationship matrix based on both pedigree and genomic information (single-step approach). The third analysis used the complete data set and only the pedigree-based relationship matrix. The fourth analysis used predictions from the first analysis (final scores up to 2004 and only a pedigree-based relationship matrix) and prediction using a genomic based matrix to obtain genetic evaluation (multiple-step approach). Different allele frequencies were tested in construction of the genomic relationship matrix. Coefficients of determination between predictions of young bulls from parent average, single-step, and multiple-step approaches and their 2009 daughter deviations were 0.24, 0.37 to 0.41, and 0.40, respectively. The highest coefficient of determination for a single-step approach was observed when using a genomic relationship matrix with assumed allele frequencies of 0.5. Coefficients for regression of 2009 daughter deviations on parent-average, single-step, and multiple-step predictions were 0.76, 0.68 to 0.79, and 0.86, respectively, which indicated some inflation of predictions. The single-step regression coefficient could be increased up to 0.92 by scaling differences between the genomic and pedigree-based relationship matrices with little loss in accuracy of prediction. One complete evaluation took about 2h of computing time and 2

  19. University Students' Knowledge Structures and Informal Reasoning on the Use of Genetically Modified Foods: Multidimensional Analyses

    NASA Astrophysics Data System (ADS)

    Wu, Ying-Tien

    2012-12-01

    This study aims to provide insights into the role of learners' knowledge structures about a socio-scientific issue (SSI) in their informal reasoning on the issue. A total of 42 non-science major university students' knowledge structures and informal reasoning were assessed with multidimensional analyses. With both qualitative and quantitative analyses, this study revealed that those students with more extended and better-organized knowledge structures, as well as those who more frequently used higher-order information processing modes, were more oriented towards achieving a higher-level informal reasoning quality. The regression analyses further showed that the "richness" of the students' knowledge structures explained 25 % of the variation in their rebuttal construction, an important indicator of reasoning quality, indicating the significance of the role of students' sophisticated knowledge structure in SSI reasoning. Besides, this study also provides some initial evidence for the significant role of the "core" concept within one's knowledge structure in one's SSI reasoning. The findings in this study suggest that, in SSI-based instruction, science instructors should try to identify students' core concepts within their prior knowledge regarding the SSI, and then they should try to guide students to construct and structure relevant concepts or ideas regarding the SSI based on their core concepts. Thus, students could obtain extended and well-organized knowledge structures, which would then help them achieve better learning transfer in dealing with SSIs.

  20. Information Entropy Analysis of the H1N1 Genetic Code

    NASA Astrophysics Data System (ADS)

    Martwick, Andy

    2010-03-01

    During the current H1N1 pandemic, viral samples are being obtained from large numbers of infected people world-wide and are being sequenced on the NCBI Influenza Virus Resource Database. The information entropy of the sequences was computed from the probability of occurrence of each nucleotide base at every position of each set of sequences using Shannon's definition of information entropy, [ H=∑bpb,2( 1pb ) ] where H is the observed information entropy at each nucleotide position and pb is the probability of the base pair of the nucleotides A, C, G, U. Information entropy of the current H1N1 pandemic is compared to reference human and swine H1N1 entropy. As expected, the current H1N1 entropy is in a low entropy state and has a very large mutation potential. Using the entropy method in mature genes we can identify low entropy regions of nucleotides that generally correlate to critical protein function.

  1. Using genetic information from candidate gene and genome-wide association studies in risk prediction for alcohol dependence

    PubMed Central

    Yan, Jia; Aliev, Fazil; Webb, Bradley T; Kendler, Kenneth S; Williamson, Vernell S; Edenberg, Howard J; Agrawal, Arpana; Kos, Mark Z; Almasy, Laura; Nurnberger, John I; Schuckit, Marc A; Kramer, John R; Rice, John P; Kuperman, Samuel; Goate, Alison M; Tischfield, Jay A; Porjesz, Bernice; Dick, Danielle M

    2013-01-01

    Family-based and genome-wide association studies (GWAS) of alcohol dependence (AD) have reported numerous associated variants. The clinical validity of these variants for predicting AD compared to family history information has not been reported. Using the Collaborative Study on the Genetics of Alcoholism (COGA) and the Study of Addiction: Genes and Environment (SAGE) GWAS samples, we examined the aggregate impact of multiple single nucleotide polymorphisms (SNPs) on risk prediction. We created genetic sum scores by adding risk alleles associated in discovery samples, and then tested the scores for their ability to discriminate between cases and controls in validation samples. Genetic sum scores were assessed separately for SNPs associated with AD in candidate gene studies and SNPs from GWAS analyses that met varying p-value thresholds. Candidate gene sum scores did not exhibit significant predictive accuracy. Family history was a better classifier of case-control status, with a significant area under the receiver operating characteristic curve (AUC) of 0.686 in COGA and 0.614 in SAGE. SNPs that met less stringent p-value thresholds of 0.01 to 0.50 in GWAS analyses yielded significant AUC estimates, ranging from mean estimates of 0.549 for SNPs with p < 0.01 to 0.565 for SNPs with p < 0.50. This study suggests that SNPs currently have limited clinical utility, but there is potential for enhanced predictive ability with better understanding of the large number of variants that might contribute to risk. PMID:23362995

  2. Perspectives for the use of structural information and chemical genetics to develop inhibitors of Janus kinases

    PubMed Central

    Haan, Claude; Behrmann, Iris; Haan, Serge

    2010-01-01

    Abstract Gain-of-function mutations in the genes encoding Janus kinases have been discovered in various haematologic diseases. Jaks are composed of a FERM domain, an SH2 domain, a pseudokinase domain and a kinase domain, and a complex interplay of the Jak domains is involved in regulation of catalytic activity and association to cytokine receptors. Most activating mutations are found in the pseudokinase domain. Here we present recently discovered mutations in the context of our structural models of the respective domains. We describe two structural hotspots in the pseudokinase domain of Jak2 that seem to be associated either to myeloproliferation or to lymphoblastic leukaemia, pointing at the involvement of distinct signalling complexes in these disease settings. The different domains of Jaks are discussed as potential drug targets. We present currently available inhibitors targeting Jaks and indicate structural differences in the kinase domains of the different Jaks that may be exploited in the development of specific inhibitors. Moreover, we discuss recent chemical genetic approaches which can be applied to Jaks to better understand the role of these kinases in their biological settings and as drug targets. PMID:20132407

  3. How the neurocircuitry and genetics of fear inhibition may inform our understanding of PTSD.

    PubMed

    Jovanovic, Tanja; Ressler, Kerry J

    2010-06-01

    Exposure to traumatic events that produce extreme fear and horror is all too common in both military and civilian populations, but not all individuals develop posttraumatic stress disorder (PTSD) as a result of the exposure. What mediates risk and resilience in the development of PTSD and other stress-related psychopathology is of paramount importance to our further understanding of trauma-related psychopathology as well as the development of new treatment approaches. Biological factors, such as genotype and neurobiology, interact with environmental factors, such as childhood background and trauma load, to affect vulnerability and resilience in the aftermath of trauma exposure. One of the core symptoms of PTSD is the inability to control fear, which has led some investigators and clinicians to conceptualize PTSD as a disorder of fear or, more importantly, its inhibition. This review focuses on translational methods that have been used to examine fear conditioning and inhibition of fear in PTSD and summarizes genetic and neurobiological factors related to fear inhibition. The authors also discuss different pharmacological approaches that enhance fear inhibition and may improve treatment outcomes for patients with PTSD. PMID:20231322

  4. European population genetic substructure: further definition of ancestry informative markers for distinguishing among diverse European ethnic groups.

    PubMed

    Tian, Chao; Kosoy, Roman; Nassir, Rami; Lee, Annette; Villoslada, Pablo; Klareskog, Lars; Hammarström, Lennart; Garchon, Henri-Jean; Pulver, Ann E; Ransom, Michael; Gregersen, Peter K; Seldin, Michael F

    2009-01-01

    The definition of European population genetic substructure and its application to understanding complex phenotypes is becoming increasingly important. In the current study using over 4,000 subjects genotyped for 300,000 single-nucleotide polymorphisms (SNPs), we provide further insight into relationships among European population groups and identify sets of SNP ancestry informative markers (AIMs) for application in genetic studies. In general, the graphical description of these principal components analyses (PCA) of diverse European subjects showed a strong correspondence to the geographical relationships of specific countries or regions of origin. Clearer separation of different ethnic and regional populations was observed when northern and southern European groups were considered separately and the PCA results were influenced by the inclusion or exclusion of different self-identified population groups including Ashkenazi Jewish, Sardinian, and Orcadian ethnic groups. SNP AIM sets were identified that could distinguish the regional and ethnic population groups. Moreover, the studies demonstrated that most allele frequency differences between different European groups could be controlled effectively in analyses using these AIM sets. The European substructure AIMs should be widely applicable to ongoing studies to confirm and delineate specific disease susceptibility candidate regions without the necessity of performing additional genome-wide SNP studies in additional subject sets.

  5. The effect of genetic test-based risk information on behavioral outcomes: A critical examination of failed trials and a call to action.

    PubMed

    Austin, Jehannine

    2015-12-01

    Encouraging individuals at risk for common complex disease like heart disease, cancer, and diabetes to adopt lifestyle changes (e.g., smoking cessation, exercise, proper nutrition, increased screening) could be powerful public health tools to decrease the enormous personal and economic burden of these conditions. Theoretically, genetic risk information appears to be a compelling tool that could be used to provoke at-risk individuals to adopt these lifestyle changes. Unfortunately, however, numerous studies now have shown that providing individuals with genetic test-based risk information has little to no impact on their behavior. In this article (a commentary not a systematic review), the failed trials in which genetic information has been used as a tool to induce behavior change will be critically examined in order to identify new and potentially more effective ways forward.

  6. Genetic variation and population structure in a threatened species, the Utah prairie dog Cynomys parvidens: the use of genetic data to inform conservation actions.

    PubMed

    Brown, Nathanael L; Peacock, Mary M; Ritchie, Mark E

    2016-01-01

    The Utah prairie dog (Cynomys parvidens), listed as threatened under the United States Endangered Species Act, was the subject of an extensive eradication program throughout its range during the 20th century. Eradication campaigns, habitat destruction/fragmentation/conversion, and epizootic outbreaks (e.g., sylvatic plague) have reduced prairie dog numbers from an estimated 95,000 individuals in the 1920s to approximately 14,000 (estimated adult spring count) today. As a result of these anthropogenic actions, the species is now found in small isolated sets of subpopulations. We characterized the levels of genetic diversity and population genetic structure using 10 neutral nuclear microsatellite loci for twelve populations (native and transplanted) representative of the three management designated "recovery units," found in three distinct biogeographic regions, sampled across the species' range. The results indicate (1) low levels of genetic diversity within colonies (H e = 0.109-0.357; H o = 0.106- 0.313), (2) high levels of genetic differentiation among colonies (global F ST = 0.296), (3) very small genetic effective population sizes, and (4) evidence of genetic bottlenecks. The genetic data reveal additional subdivision such that colonies within recovery units do not form single genotype clusters consistent with recovery unit boundaries. Genotype cluster membership support historical gene flow among colonies in the easternmost West Desert Recovery Unit with the westernmost Pausaugunt colonies and among the eastern Pausaugunt colonies and the Awapa Recovery unit to the north. In order to maintain the long-term viability of the species, there needs to be an increased focus on maintaining suitable habitat between groups of existing populations that can act as connective corridors. The location of future translocation sites should be located in areas that will maximize connectivity, leading to maintenance of genetic variation and evolutionary potential. PMID

  7. Public Awareness of Direct-to-Consumer Genetic Tests: Findings from the 2013 U.S. Health Information National Trends Survey.

    PubMed

    Agurs-Collins, Tanya; Ferrer, Rebecca; Ottenbacher, Allison; Waters, Erika A; O'Connell, Mary E; Hamilton, Jada G

    2015-12-01

    Although the availability of direct-to-consumer (DTC) genetic testing has increased in recent years, the general public's awareness of this testing is not well understood. This study examined levels of public awareness of DTC genetic testing, sources of information about testing, and psychosocial factors associated with awareness of testing in the USA. Data were obtained from the nationally representative 2013 U.S. Health Information National Trends Survey. Guided by a social-cognitive conceptual framework, univariable and multivariable logistic regressions were conducted to identify factors associated with awareness of DTC genetic tests. Of 3185 participants, 35.6% were aware of DTC genetic tests, with the majority learning about these tests through radio, television, and the Internet. In the final adjusted model, participants with annual incomes of $99,999 or less had lower odds of being aware of DTC genetic testing (ORs ranging from 0.46-0.61) than did those participants with incomes of $100,000 or more. The odds of awareness of DTC genetic tests were significantly higher for those who actively seek cancer information (OR=1.91, 95% CI=1.36-2.69), use the Internet (OR=1.81, 95% CI=1.05-3.13), and have high numeracy skills (OR=1.67, 95% CI=1.17-2.38). It will be critical for healthcare researchers and practitioners to understand predictors and consequences of the public's awareness of DTC genetic tests, as well as how such awareness may translate into DTC genetic testing uptake, health behavior change, and ultimately disease prevention. PMID:25600375

  8. Public Awareness of Direct-to-Consumer Genetic Tests: Findings from the 2013 U.S. Health Information National Trends Survey

    PubMed Central

    Agurs-Collins, Tanya; Ferrer, Rebecca; Ottenbacher, Allison; Waters, Erika A.; O’Connell, Mary E.; Hamilton, Jada G.

    2015-01-01

    Although the availability of direct-to-consumer (DTC) genetic testing has increased in recent years, the general public’s awareness of this testing is not well understood. This study examined levels of public awareness of DTC genetic testing, sources of information about testing, and psychosocial factors associated with awareness of testing in the U.S. Data were obtained from the nationally representative 2013 U.S. Health Information National Trends Survey. Guided by a social-cognitive conceptual framework, univariable and multivariable logistic regressions were conducted to identify factors associated with awareness of DTC genetic tests. Of 3,185 participants, 35.6% were aware of DTC genetic tests, with the majority learning about these tests through radio, television, and the Internet. In the final adjusted model, participants with annual incomes of $99,999 or less had lower odds of being aware of DTC genetic testing (ORs ranging from 0.46–0.61) than did those participants with incomes of $100,000 or more. The odds of awareness of DTC genetic tests were significantly higher for those who actively seek cancer information (OR = 1.91, 95% CI = 1.36–2.69), use the Internet (OR = 1.81, 95% CI = 1.05–3.13) and have high numeracy skills (OR = 1.67, 95% CI = 1.17–2.38). It will be critical for healthcare researchers and practitioners to understand predictors and consequences of the public’s awareness of DTC genetic tests, as well as how such awareness may translate into DTC genetic testing uptake, health behavior change, and ultimately disease prevention. PMID:25600375

  9. Public Awareness of Direct-to-Consumer Genetic Tests: Findings from the 2013 U.S. Health Information National Trends Survey.

    PubMed

    Agurs-Collins, Tanya; Ferrer, Rebecca; Ottenbacher, Allison; Waters, Erika A; O'Connell, Mary E; Hamilton, Jada G

    2015-12-01

    Although the availability of direct-to-consumer (DTC) genetic testing has increased in recent years, the general public's awareness of this testing is not well understood. This study examined levels of public awareness of DTC genetic testing, sources of information about testing, and psychosocial factors associated with awareness of testing in the USA. Data were obtained from the nationally representative 2013 U.S. Health Information National Trends Survey. Guided by a social-cognitive conceptual framework, univariable and multivariable logistic regressions were conducted to identify factors associated with awareness of DTC genetic tests. Of 3185 participants, 35.6% were aware of DTC genetic tests, with the majority learning about these tests through radio, television, and the Internet. In the final adjusted model, participants with annual incomes of $99,999 or less had lower odds of being aware of DTC genetic testing (ORs ranging from 0.46-0.61) than did those participants with incomes of $100,000 or more. The odds of awareness of DTC genetic tests were significantly higher for those who actively seek cancer information (OR=1.91, 95% CI=1.36-2.69), use the Internet (OR=1.81, 95% CI=1.05-3.13), and have high numeracy skills (OR=1.67, 95% CI=1.17-2.38). It will be critical for healthcare researchers and practitioners to understand predictors and consequences of the public's awareness of DTC genetic tests, as well as how such awareness may translate into DTC genetic testing uptake, health behavior change, and ultimately disease prevention.

  10. DTC genetic testing: pendulum swings and policy paradoxes.

    PubMed

    Caulfield, T

    2012-01-01

    After decades of optimistic portrayals, there has been a shift in the way that the popular press represents genomic research. A skeptical view has become more common. The central reason for this pendulum swing away from popular support is the harsh truth that most genetic risk information just isn't that predictive. This reality has created a fascinating policy paradox. If, as many in the scientific community are now saying, genetic information is not the oracle of our future health as we were once led to believe, and if access does not, for most, cause harm, why regulate the area? Why worry about shoddy direct-to-consumer (DTC) genetic testing companies? One primary justification, and one endorsed by the recent Canadian College of Medical Geneticists (CCMG) Policy Statement on DTC Genetics Testing, is that information that is conveyed to the public about genetics via marketing and to those who access DTC tests should, at a minimum, be accurate.

  11. Experiences with community engagement and informed consent in a genetic cohort study of severe childhood diseases in Kenya

    PubMed Central

    2010-01-01

    Background The potential contribution of community engagement to addressing ethical challenges for international biomedical research is well described, but there is relatively little documented experience of community engagement to inform its development in practice. This paper draws on experiences around community engagement and informed consent during a genetic cohort study in Kenya to contribute to understanding the strengths and challenges of community engagement in supporting ethical research practice, focusing on issues of communication, the role of field workers in 'doing ethics' on the ground and the challenges of community consultation. Methods The findings are based on action research methods, including analysis of community engagement documentation and the observations of the authors closely involved in their development and implementation. Qualitative and quantitative content analysis has been used for documentation of staff meetings and trainings, a meeting with 24 community leaders, and 40 large public and 70 small community group meetings. Meeting minutes from a purposive sample of six community representative groups have been analysed using a thematic framework approach. Results Field workers described challenges around misunderstandings about research, perceived pressure for recruitment and challenges in explaining the study. During consultation, leaders expressed support for the study and screening for sickle cell disease. In community meetings, there was a common interpretation of research as medical care. Concerns centred on unfamiliar procedures. After explanations of study procedures to leaders and community members, few questions were asked about export of samples or the archiving of samples for future research. Conclusions Community engagement enabled researchers to take account of staff and community opinions and issues during the study and adapt messages and methods to address emerging ethical challenges. Field workers conducting informed

  12. Attitudes of physicians and patients towards disclosure of genetic information to spouse and first-degree relatives: a case study from Turkey

    PubMed Central

    2014-01-01

    Background When considering the principle of medical confidentiality, disclosure of genetic information constitutes a special case because of the impact that this information can have on the health and the lives of relatives. The aim of this study is to explore the attitudes of Turkish physicians and patients about sharing information obtained from genetic tests. Methods The study was carried out in Kocaeli, Turkey. Participants were either paediatricians and gynaecologists registered in Kocaeli, or patients coming to the genetic diagnosis centre for karyotype analysis in 2008. A self-administered paper questionnaire was given to the physicians, and face-to-face structured interviews were conducted with patients. We used a case study involving a man who was found to be a balanced chromosome carrier as a result of a test conducted after his first baby was born with Down's syndrome. However, he refused to share this information with his wife or his siblings. Percentages of characteristics and preferences of the participants were calculated, and the results were analysed using Kruskal-Wallis test. Results A total of 155 physicians (68% response rate) and 104 patients (46% response rate) were participated in the study. Twenty-six percent of physicians and 49% of patients believed that genetic information belongs to the whole family. When participants were asked with whom genetic information should be shared for the case study, most of the physicians and patients thought the physician should inform the spouse (79%, 85%, respectively). They were less likely to support a physician informing a sibling (41%, 53%, respectively); whereas, many thought the testee has an obligation to inform siblings (70%, 94%, respectively). Conclusions Although Turkey’s national regulations certainly protect the right of privacy of the testee, the participants in our study appear to believe that informing the spouse, who is not personally at risk of serious damage, is the physician

  13. NNLOPS accurate associated HW production

    NASA Astrophysics Data System (ADS)

    Astill, William; Bizon, Wojciech; Re, Emanuele; Zanderighi, Giulia

    2016-06-01

    We present a next-to-next-to-leading order accurate description of associated HW production consistently matched to a parton shower. The method is based on reweighting events obtained with the HW plus one jet NLO accurate calculation implemented in POWHEG, extended with the MiNLO procedure, to reproduce NNLO accurate Born distributions. Since the Born kinematics is more complex than the cases treated before, we use a parametrization of the Collins-Soper angles to reduce the number of variables required for the reweighting. We present phenomenological results at 13 TeV, with cuts suggested by the Higgs Cross section Working Group.

  14. A highly accurate heuristic algorithm for the haplotype assembly problem

    PubMed Central

    2013-01-01

    Background Single nucleotide polymorphisms (SNPs) are the most common form of genetic variation in human DNA. The sequence of SNPs in each of the two copies of a given chromosome in a diploid organism is referred to as a haplotype. Haplotype information has many applications such as gene disease diagnoses, drug design, etc. The haplotype assembly problem is defined as follows: Given a set of fragments sequenced from the two copies of a chromosome of a single individual, and their locations in the chromosome, which can be pre-determined by aligning the fragments to a reference DNA sequence, the goal here is to reconstruct two haplotypes (h1, h2) from the input fragments. Existing algorithms do not work well when the error rate of fragments is high. Here we design an algorithm that can give accurate solutions, even if the error rate of fragments is high. Results We first give a dynamic programming algorithm that can give exact solutions to the haplotype assembly problem. The time complexity of the algorithm is O(n × 2t × t), where n is the number of SNPs, and t is the maximum coverage of a SNP site. The algorithm is slow when t is large. To solve the problem when t is large, we further propose a heuristic algorithm on the basis of the dynamic programming algorithm. Experiments show that our heuristic algorithm can give very accurate solutions. Conclusions We have tested our algorithm on a set of benchmark datasets. Experiments show that our algorithm can give very accurate solutions. It outperforms most of the existing programs when the error rate of the input fragments is high. PMID:23445458

  15. 75 FR 33317 - Request for Information (RFI) on the National Institutes of Health Plan To Develop the Genetic...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-11

    ... Health Plan To Develop the Genetic Testing Registry ACTION: Notice. SUMMARY: The National Institutes of... on its plan to develop the Genetic Testing Registry (GTR); a centralized public resource that will..., (3) health care providers, (4) clinical laboratory professionals, (5) payers, (6) genetic...

  16. Impact on maternal parenting stress of receipt of genetic information regarding risk of diabetes in newborn infants.

    PubMed

    Yu, M S; Norris, J M; Mitchell, C M; Butler-Simon, N; Groshek, M; Follansbee, D; Erlich, H; Rewers, M; Klingensmith, G J

    1999-09-17

    Our objective was to investigate whether notification of high-risk status for type 1 diabetes in newborn infants results in an increased maternal-parenting stress level when compared with notification of low-risk status for type 1 diabetes. Maternal parenting stress level was assessed at 5-7 weeks postpartum (baseline) and was reassessed 4-5 months after parents were informed of their newborn infants' genetic screening results (follow-up). Parenting stress level was measured using the total stress score (TSS) of the Parenting Stress Index/Short Form. The outcome variable, change in TSS, was calculated by subtracting the baseline TSS from the follow-up TSS. Demographic variables such as maternal race, maternal age, maternal education level, maternal marital status, child's birth order, and total family income were assessed through a structured phone interview at the time of baseline assessment. The risk factor of interest was the child's human leukocyte antigen (HLA) status for type 1 diabetes, i.e., whether child was at a high or moderate (combined into "high") genetic risk or at a low genetic risk for type 1 diabetes. A sample of 88 mothers (23 with a high-risk child and 65 with a low-risk child) was evaluated. Baseline median TSSs were 65 and 74 for mothers of low-risk infants and mothers of high-risk infants, respectively. Both groups' median TSS decreased between baseline and follow-up. No significant differences were found between change in TSS and maternal age, race, education level, marital status, total family income, or child's birth order. Although the median decrease in TSS was smaller in mothers with a high-risk child when compared with mothers of a low-risk child, this difference was not statistically significant. We did not find an association between newborn's HLA status and change in maternal TSS. The results of this study suggest that notification of high-risk status for type 1 diabetes in newborn infants may not result in an increased level of

  17. Frequently Asked Questions about Genetic Testing

    MedlinePlus

    ... sobre las pruebas genéticas Frequently Asked Questions About Genetic Testing What is genetic testing? What can I ... find more information about genetic testing? What is genetic testing? Genetic testing uses laboratory methods to look ...

  18. Accurate mask model for advanced nodes

    NASA Astrophysics Data System (ADS)

    Zine El Abidine, Nacer; Sundermann, Frank; Yesilada, Emek; Ndiaye, El Hadji Omar; Mishra, Kushlendra; Paninjath, Sankaranarayanan; Bork, Ingo; Buck, Peter; Toublan, Olivier; Schanen, Isabelle

    2014-07-01

    Standard OPC models consist of a physical optical model and an empirical resist model. The resist model compensates the optical model imprecision on top of modeling resist development. The optical model imprecision may result from mask topography effects and real mask information including mask ebeam writing and mask process contributions. For advanced technology nodes, significant progress has been made to model mask topography to improve optical model accuracy. However, mask information is difficult to decorrelate from standard OPC model. Our goal is to establish an accurate mask model through a dedicated calibration exercise. In this paper, we present a flow to calibrate an accurate mask enabling its implementation. The study covers the different effects that should be embedded in the mask model as well as the experiment required to model them.

  19. 78 FR 40541 - GDT Tek, Inc., Gemini Explorations, Inc., Genetic Vectors, Inc., and Global Gate Property Corp...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-05

    ... From the Federal Register Online via the Government Publishing Office SECURITIES AND EXCHANGE COMMISSION GDT Tek, Inc., Gemini Explorations, Inc., Genetic Vectors, Inc., and Global Gate Property Corp... accurate information concerning the securities of Genetic Vectors, Inc. because it has not filed...

  20. Modifications to the HIPAA Privacy, Security, Enforcement, and Breach Notification rules under the Health Information Technology for Economic and Clinical Health Act and the Genetic Information Nondiscrimination Act; other modifications to the HIPAA rules.

    PubMed

    2013-01-25

    The Department of Health and Human Services (HHS or ``the Department'') is issuing this final rule to: Modify the Health Insurance Portability and Accountability Act (HIPAA) Privacy, Security, and Enforcement Rules to implement statutory amendments under the Health Information Technology for Economic and Clinical Health Act (``the HITECH Act'' or ``the Act'') to strengthen the privacy and security protection for individuals' health information; modify the rule for Breach Notification for Unsecured Protected Health Information (Breach Notification Rule) under the HITECH Act to address public comment received on the interim final rule; modify the HIPAA Privacy Rule to strengthen the privacy protections for genetic information by implementing section 105 of Title I of the Genetic Information Nondiscrimination Act of 2008 (GINA); and make certain other modifications to the HIPAA Privacy, Security, Breach Notification, and Enforcement Rules (the HIPAA Rules) to improve their workability and effectiveness and to increase flexibility for and decrease burden on the regulated entities.

  1. Practical implications for genetic modeling in the genomics era

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic models convert data into estimated breeding values and other information useful to breeders. The goal is to provide accurate and timely predictions of the future performance for each animal (or embryo). Modeling involves defining traits, editing raw data, removing environmental effects, incl...

  2. Investigation of the Ethical Concepts that Inform the Laws Limiting Genetic Screening in Employment Decisions: Privacy, Human Dignity, Equality, Autonomy, Efficiency

    SciTech Connect

    Pasquerella, Lynn; Rothstein, Lawrence E.

    2003-01-16

    The broad question addressed in our research is : What is the influence of ethical concepts on legislative outcomes? The research focuses on the important ethical concerns that surround the use of genetic information in employment matters and in American state legislatures. By analyzing the contents of hearings, interviews and advocacy documents involved in the legislative process, the research seeks to answer the question: How might the dominance of a particular ethical concept informing the discussion of a bill influence the legislative outcome?

  3. The high cost of accurate knowledge.

    PubMed

    Sutcliffe, Kathleen M; Weber, Klaus

    2003-05-01

    Many business thinkers believe it's the role of senior managers to scan the external environment to monitor contingencies and constraints, and to use that precise knowledge to modify the company's strategy and design. As these thinkers see it, managers need accurate and abundant information to carry out that role. According to that logic, it makes sense to invest heavily in systems for collecting and organizing competitive information. Another school of pundits contends that, since today's complex information often isn't precise anyway, it's not worth going overboard with such investments. In other words, it's not the accuracy and abundance of information that should matter most to top executives--rather, it's how that information is interpreted. After all, the role of senior managers isn't just to make decisions; it's to set direction and motivate others in the face of ambiguities and conflicting demands. Top executives must interpret information and communicate those interpretations--they must manage meaning more than they must manage information. So which of these competing views is the right one? Research conducted by academics Sutcliffe and Weber found that how accurate senior executives are about their competitive environments is indeed less important for strategy and corresponding organizational changes than the way in which they interpret information about their environments. Investments in shaping those interpretations, therefore, may create a more durable competitive advantage than investments in obtaining and organizing more information. And what kinds of interpretations are most closely linked with high performance? Their research suggests that high performers respond positively to opportunities, yet they aren't overconfident in their abilities to take advantage of those opportunities.

  4. Variance Decomposition of MRI-Based Covariance Maps Using Genetically-Informative Samples and Structural Equation Modeling

    PubMed Central

    Schmitt, J. Eric; Lenroot, Rhoshel; Ordaz, Sarah E.; Wallace, Gregory L.; Lerch, Jason P.; Evans, Alan C.; Prom, Elizabeth C.; Kendler, Kenneth S.; Neale, Michael C.; Giedd, Jay N.

    2010-01-01

    The role of genetics in driving intracortical relationships is an important question that has rarely been studied in humans. In particular, there are no extant high-resolution imaging studies on genetic covariance. In this article, we describe a novel method that combines classical quantitative genetic methodologies for variance decomposition with recently-developed semi-multivariate algorithms for high-resolution measurement of phenotypic covariance. Using these tools, we produced correlational maps of genetic and environmental (i.e. nongenetic) relationships between several regions of interest and the cortical surface in a large pediatric sample of 600 twins, siblings, and singletons. These analyses demonstrated high, fairly uniform, statistically significant genetic correlations between the entire cortex and global mean cortical thickness. In agreement with prior reports on phenotypic covariance using similar methods, we found mean cortical thickness was most strongly correlated with association cortices. However, the present study suggests that genetics plays a large role in global brain patterning of cortical thickness in this manner. Further, using specific gyri with known high heritabilities as seed regions, we found a consistent pattern of high bilateral genetic correlations between structural homologues, with environmental correlations more restricted to the same hemisphere as the seed region, suggesting that interhemispheric covariance is largely genetically mediated. These findings are consistent with the limited existing knowledge on the genetics of cortical variability as well as our prior multivariate studies on cortical gyri. PMID:18672072

  5. Genetic test reporting enhances understanding of risk information and acceptance of prevention recommendations compared to family history-based counseling alone

    PubMed Central

    Taber, Jennifer M.; Aspinwall, Lisa G.; Stump, Tammy K.; Kohlmann, Wendy; Champine, Marjan; Leachman, Sancy A.

    2015-01-01

    It is unknown whether or why genetic test reporting confers benefits in the understanding and management of cancer risk beyond what patients learn from counseling based on family history. A prospective nonexperimental control group study compared participants from melanoma-prone families who underwent CDKN2A/p16 (p16) genetic testing (27 carriers, 38 noncarriers) to participants from equivalently melanoma-prone families known not to carry a deleterious p16 mutation (31 no-test controls). All participants received equivalent counseling concerning elevated lifetime melanoma risk and corresponding recommendations for prevention and screening. Both immediately and one month after counseling, participants receiving a genetic test result reported greater understanding of their risk, decreased derogation of the risk information, and greater personal applicability of prevention recommendations than no-test controls. Decreased derogation of risk information after test reporting predicted further increases in understanding of melanoma risk and applicability of prevention recommendations one month later. Results suggest unique benefits of genetic test reporting in promoting understanding and acceptance of information about hereditary cancer risk and its management. PMID:26178773

  6. Genetic Interaction Scoring Procedure for Bacterial Species.

    PubMed

    Wagih, Omar; Parts, Leopold

    2015-01-01

    A genetic interaction occurs when the phenotype of an organism carrying two mutant genes differs from what should have been observed given their independent influence. Such unexpected outcome indicates a mechanistic connection between the perturbed genes, providing a key source of functional information about the cell. Large-scale screening for genetic interactions involves measuring phenotypes of single and double mutants, which for microorganisms is usually done by automated analysis of images of ordered colonies. Obtaining accurate colony sizes, and using them to identify genetic interactions from such screens remains a challenging and time-consuming task. Here, we outline steps to compute genetic interaction scores in E. coli by measuring colony sizes from plate images, performing normalisation, and quantifying the strength of the effect. PMID:26621468

  7. Accurate phase-shift velocimetry in rock.

    PubMed

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R; Holmes, William M

    2016-06-01

    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models. PMID:27111139

  8. Accurate phase-shift velocimetry in rock

    NASA Astrophysics Data System (ADS)

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R.; Holmes, William M.

    2016-06-01

    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models.

  9. Accurate phase-shift velocimetry in rock.

    PubMed

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R; Holmes, William M

    2016-06-01

    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models.

  10. No Additional Prognostic Value of Genetic Information in the Prediction of Vascular Events after Cerebral Ischemia of Arterial Origin: The PROMISe Study

    PubMed Central

    Achterberg, Sefanja; Kappelle, L. Jaap; de Bakker, Paul I. W.; Traylor, Matthew; Algra, Ale

    2015-01-01

    Background Patients who have suffered from cerebral ischemia have a high risk of recurrent vascular events. Predictive models based on classical risk factors typically have limited prognostic value. Given that cerebral ischemia has a heritable component, genetic information might improve performance of these risk models. Our aim was to develop and compare two models: one containing traditional vascular risk factors, the other also including genetic information. Methods and Results We studied 1020 patients with cerebral ischemia and genotyped them with the Illumina Immunochip. Median follow-up time was 6.5 years; the annual incidence of new ischemic events (primary outcome, n=198) was 3.0%. The prognostic model based on classical vascular risk factors had an area under the receiver operating characteristics curve (AUC-ROC) of 0.65 (95% confidence interval 0.61-0.69). When we added a genetic risk score based on prioritized SNPs from a genome-wide association study of ischemic stroke (using summary statistics from the METASTROKE study which included 12389 cases and 62004 controls), the AUC-ROC remained the same. Similar results were found for the secondary outcome ischemic stroke. Conclusions We found no additional value of genetic information in a prognostic model for the risk of ischemic events in patients with cerebral ischemia of arterial origin. This is consistent with a complex, polygenic architecture, where many genes of weak effect likely act in concert to influence the heritable risk of an individual to develop (recurrent) vascular events. At present, genetic information cannot help clinicians to distinguish patients at high risk for recurrent vascular events. PMID:25906364

  11. Strong genetic admixture in the Altai at the Middle Bronze Age revealed by uniparental and ancestry informative markers.

    PubMed

    Hollard, Clémence; Keyser, Christine; Giscard, Pierre-Henri; Tsagaan, Turbat; Bayarkhuu, Noost; Bemmann, Jan; Crubézy, Eric; Ludes, Bertrand

    2014-09-01

    The Altai Mountains have been a long-term boundary zone between the Eurasian Steppe populations and South and East Asian populations. To disentangle some of the historical population movements in this area, 14 ancient human specimens excavated in the westernmost part of the Mongolian Altai were studied. Thirteen of them were dated from the Middle to the End of the Bronze Age and one of them to the Eneolithic period. The environmental conditions encountered in this region led to the good preservation of DNA in the human remains. Therefore, a multi-markers approach was adopted for the genetic analysis of identity, ancestry and phenotype markers. Mitochondrial DNA analyses revealed that the ancient Altaians studied carried both Western (H, U, T) and Eastern (A, C, D) Eurasian lineages. In the same way, the patrilineal gene pool revealed the presence of different haplogroups (Q1a2a1-L54, R1a1a1b2-Z93 and C), probably marking different origins for the male paternal lineages. To go further in the search of the origin of these ancient specimens, phenotypical characters (i.e. hair and eye color) were determined. For this purpose, we adapted the HIrisPlex assay recently described to MALDI-TOF mass spectrometry. In addition, some ancestry informative markers were analyzed with this assay. The results revealed mixed phenotypes among this group confirming the probable admixed ancestry of the studied Altaian population at the Middle Bronze Age. The good results obtained from ancient DNA samples suggest that this approach might be relevant for forensic casework too. PMID:25016250

  12. FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads

    PubMed Central

    Zhang, Gong; Fedyunin, Ivan; Kirchner, Sebastian; Xiao, Chuanle; Valleriani, Angelo; Ignatova, Zoya

    2012-01-01

    The most crucial step in data processing from high-throughput sequencing applications is the accurate and sensitive alignment of the sequencing reads to reference genomes or transcriptomes. The accurate detection of insertions and deletions (indels) and errors introduced by the sequencing platform or by misreading of modified nucleotides is essential for the quantitative processing of the RNA-based sequencing (RNA-Seq) datasets and for the identification of genetic variations and modification patterns. We developed a new, fast and accurate algorithm for nucleic acid sequence analysis, FANSe, with adjustable mismatch allowance settings and ability to handle indels to accurately and quantitatively map millions of reads to small or large reference genomes. It is a seed-based algorithm which uses the whole read information for mapping and high sensitivity and low ambiguity are achieved by using short and non-overlapping reads. Furthermore, FANSe uses hotspot score to prioritize the processing of highly possible matches and implements modified Smith–Watermann refinement with reduced scoring matrix to accelerate the calculation without compromising its sensitivity. The FANSe algorithm stably processes datasets from various sequencing platforms, masked or unmasked and small or large genomes. It shows a remarkable coverage of low-abundance mRNAs which is important for quantitative processing of RNA-Seq datasets. PMID:22379138

  13. Genetics Home Reference: porphyria

    MedlinePlus

    ... of iron in the liver, alcohol consumption, smoking, hepatitis C or HIV infection, or certain hormones. Mutations in ... Diagnostic Tests Drug Therapy Surgery and Rehabilitation Genetic Counseling Palliative Care Related Information How are genetic conditions ...

  14. Genetics of Hearing Loss

    MedlinePlus

    ... in Latin America Information For... Media Policy Makers Genetics of Hearing Loss Language: English Español (Spanish) Recommend ... of hearing loss in babies is due to genetic causes. There are also a number of things ...

  15. New law requires 'medically accurate' lesson plans.

    PubMed

    1999-09-17

    The California Legislature has passed a bill requiring all textbooks and materials used to teach about AIDS be medically accurate and objective. Statements made within the curriculum must be supported by research conducted in compliance with scientific methods, and published in peer-reviewed journals. Some of the current lesson plans were found to contain scientifically unsupported and biased information. In addition, the bill requires material to be "free of racial, ethnic, or gender biases." The legislation is supported by a wide range of interests, but opposed by the California Right to Life Education Fund, because they believe it discredits abstinence-only material.

  16. New law requires 'medically accurate' lesson plans.

    PubMed

    1999-09-17

    The California Legislature has passed a bill requiring all textbooks and materials used to teach about AIDS be medically accurate and objective. Statements made within the curriculum must be supported by research conducted in compliance with scientific methods, and published in peer-reviewed journals. Some of the current lesson plans were found to contain scientifically unsupported and biased information. In addition, the bill requires material to be "free of racial, ethnic, or gender biases." The legislation is supported by a wide range of interests, but opposed by the California Right to Life Education Fund, because they believe it discredits abstinence-only material. PMID:11366835

  17. Horizontal integration of OMIM across the medical school preclinical curriculum for early reinforcement of clinical genetics principles

    PubMed Central

    Diehl, Adam C.; Reader, Lauren; Hamosh, Ada; Bodurtha, Joann N.

    2016-01-01

    Purpose With the relentless expansion of genetics into every field of medicine, stronger preclinical and clinical medical student education in genetics is needed. The explosion of genetic information cannot be addressed by simply adding content hours. We proposed that students be provided a tool to access accurate clinical information on genetic conditions and, through this tool, build life-long learning habits to carry them through their medical careers. Methods Surveys conducted at the Johns Hopkins University School of Medicine revealed that medical students in all years lacked confidence when approaching genetic conditions and lacked a reliable resource for accurate genetic information. In response, the school created a horizontal thread that stretches across the first-year curriculum and is devoted to teaching students how to use Online Mendelian Inheritance in Man (OMIM) (http://omim.org) and the databases to which it links as a starting point for approaching genetic conditions. Results The thread improved the first-year students’ confidence in clinical genetics concepts and encouraged use of OMIM as a primary source for genetic information. Most students showed confidence in OMIM as a learning tool and wanted to see the thread repeated in subsequent years. Conclusion Incorporating OMIM into the preclinical curriculum improved students’ confidence in clinical genetics concepts. PMID:25032988

  18. Risk Information Exposure and Direct to Consumer Genetic Testing for BRCA Mutations among Women with a Personal or Family History of Breast or Ovarian Cancer

    PubMed Central

    Gray, Stacy W.; O’Grady, Cristin; Karp, Lauren; Smith, Daniel; Schwartz, J. Sanford; Hornik, Robert C.; Armstrong, Katrina

    2009-01-01

    Background Direct to consumer (DTC) BRCA testing may expand access to genetic testing and enhance cancer prevention efforts. However, it is not know if current DTC websites provide adequate risk information for informed medical decision-making. Methods 284 women with a personal or family history of breast/ovarian cancer were randomly assigned to view a “mock” DTC commercial website (control condition: CC, n=93) or the same “mock” website that included information on the potential risks of obtaining genetic testing online. Risk information was framed two ways: risk information attributed to expert sources (ES, n=98) and unattributed risk information (URI, n=93). Participants completed an online survey. Endpoints were intentions to get BRCA testing, testing site preference and beliefs about DTC BRCA testing. Results Sample characteristics: mean age 39 (range 18–70), 82% white, mean education 3 yrs. college. Women exposed to risk information had lower intentions to get BRCA testing than women in the CC (adjusted odds ratio (OR) 0.48; 95% confidence interval (CI) 0.26–0.87, p=0.016), less positive beliefs about online BRCA testing (adjusted OR 0.48; 95% 0.27–0.86, p=0.014). Women in the ES condition were more likely to prefer clinic based testing than women in the CC (adjusted OR 2.05; 95% CI 1.07–3.90, p=0.030). Conclusion Exposing women to information on the potential risks of online BRCA testing altered their intentions, beliefs and preferences for BRCA testing. Policy makers may want to consider content and framing of risk information on DTC websites as they formulate regulation for this rapidly growing industry. PMID:19318436

  19. Accurate documentation and wound measurement.

    PubMed

    Hampton, Sylvie

    This article, part 4 in a series on wound management, addresses the sometimes routine yet crucial task of documentation. Clear and accurate records of a wound enable its progress to be determined so the appropriate treatment can be applied. Thorough records mean any practitioner picking up a patient's notes will know when the wound was last checked, how it looked and what dressing and/or treatment was applied, ensuring continuity of care. Documenting every assessment also has legal implications, demonstrating due consideration and care of the patient and the rationale for any treatment carried out. Part 5 in the series discusses wound dressing characteristics and selection.

  20. Accurate calculation of the absolute free energy of binding for drug molecules† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c5sc02678d Click here for additional data file.

    PubMed Central

    Aldeghi, Matteo; Heifetz, Alexander; Bodkin, Michael J.; Knapp, Stefan

    2016-01-01

    Accurate prediction of binding affinities has been a central goal of computational chemistry for decades, yet remains elusive. Despite good progress, the required accuracy for use in a drug-discovery context has not been consistently achieved for drug-like molecules. Here, we perform absolute free energy calculations based on a thermodynamic cycle for a set of diverse inhibitors binding to bromodomain-containing protein 4 (BRD4) and demonstrate that a mean absolute error of 0.6 kcal mol–1 can be achieved. We also show a similar level of accuracy (1.0 kcal mol–1) can be achieved in pseudo prospective approach. Bromodomains are epigenetic mark readers that recognize acetylation motifs and regulate gene transcription, and are currently being investigated as therapeutic targets for cancer and inflammation. The unprecedented accuracy offers the exciting prospect that the binding free energy of drug-like compounds can be predicted for pharmacologically relevant targets. PMID:26798447

  1. Advances in Genetic Testing for Hereditary Cancer Syndromes.

    PubMed

    Thomas, Ellen; Mohammed, Shehla

    2016-01-01

    The ability to identify genetic mutations causing an increased risk of cancer represents the first widespread example of personalised medicine, in which genetic information is used to inform patients of their cancer risks and direct an appropriate strategy to minimise those risks. Increasingly, an understanding of the genetic basis of many cancers also facilitates selection of the most effective therapeutic options. The technology underlying genetic testing has been revolutionised in the years since the completion of the Human Genome Project in 2001. This has advanced knowledge of the genetic factors underlying familial cancer risk, and has also improved genetic testing capacity allowing a larger number of patients to be tested for a constitutional cancer predisposition. To use these tests safely and effectively, they must be assessed for their ability to provide accurate and useful results, and be requested and interpreted by health professionals with an understanding of their strengths and limitations. Genetic testing is increasing in its scope and ambition with each year that passes, requiring a greater proportion of the healthcare workforce to acquire a working knowledge of genetics and genetic testing to manage their patients safely and sensitively. PMID:27075345

  2. Genetic Structure and Demographic History Should Inform Conservation: Chinese Cobras Currently Treated as Homogenous Show Population Divergence

    PubMed Central

    Lin, Long-Hui; Qu, Yan-Fu; Li, Hong; Zhou, Kai-Ya; Ji, Xiang

    2012-01-01

    An understanding of population structure and genetic diversity is crucial for wildlife conservation and for determining the integrity of wildlife populations. The vulnerable Chinese cobra (Naja atra) has a distribution from the mouth of the Yangtze River down to northern Vietnam and Laos, within which several large mountain ranges and water bodies may influence population structure. We combined 12 microsatellite loci and 1117 bp of the mitochondrial cytochrome b gene to explore genetic structure and demographic history in this species, using 269 individuals from various localities in Mainland China and Vietnam. High levels of genetic variation were identified for both mtDNA and microsatellites. mtDNA data revealed two main (Vietnam + southern China + southwestern China; eastern + southeastern China) and one minor (comprising only two individuals from the westernmost site) clades. Microsatellite data divided the eastern + southeastern China clade further into two genetic clusters, which include individuals from the eastern and southeastern regions, respectively. The Luoxiao and Nanling Mountains may be important barriers affecting the diversification of lineages. In the haplotype network of cytchrome b, many haplotypes were represented within a “star” cluster and this and other tests suggest recent expansion. However, microsatellite analyses did not yield strong evidence for a recent bottleneck for any population or genetic cluster. The three main clusters identified here should be considered as independent management units for conservation purposes. The release of Chinese cobras into the wild should cease unless their origin can be determined, and this will avoid problems arising from unnatural homogenization. PMID:22558439

  3. How Are Genetic Conditions Treated or Managed?

    MedlinePlus

    ... are genetic conditions treated or managed? How are genetic conditions treated or managed? Many genetic disorders result ... out more about the treatment and management of genetic conditions: Links to information about the treatment of ...

  4. SPLASH: Accurate OH maser positions

    NASA Astrophysics Data System (ADS)

    Walsh, Andrew; Gomez, Jose F.; Jones, Paul; Cunningham, Maria; Green, James; Dawson, Joanne; Ellingsen, Simon; Breen, Shari; Imai, Hiroshi; Lowe, Vicki; Jones, Courtney

    2013-10-01

    The hydroxyl (OH) 18 cm lines are powerful and versatile probes of diffuse molecular gas, that may trace a largely unstudied component of the Galactic ISM. SPLASH (the Southern Parkes Large Area Survey in Hydroxyl) is a large, unbiased and fully-sampled survey of OH emission, absorption and masers in the Galactic Plane that will achieve sensitivities an order of magnitude better than previous work. In this proposal, we request ATCA time to follow up OH maser candidates. This will give us accurate (~10") positions of the masers, which can be compared to other maser positions from HOPS, MMB and MALT-45 and will provide full polarisation measurements towards a sample of OH masers that have not been observed in MAGMO.

  5. Accurate thickness measurement of graphene

    NASA Astrophysics Data System (ADS)

    Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.

    2016-03-01

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  6. Accurate thickness measurement of graphene.

    PubMed

    Shearer, Cameron J; Slattery, Ashley D; Stapleton, Andrew J; Shapter, Joseph G; Gibson, Christopher T

    2016-03-29

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  7. Beyond the Genetic Diagnosis: Providing Parents What They Want to Know.

    PubMed

    Saul, Robert A; Meredith, Stephanie Hall

    2016-07-01

    Clinicians need to provide accurate, up-to-date, and balanced information to parents following a prenatal or postnatal diagnosis of Down syndrome and other genetic conditions. Families want information about the genomic outcomes and medical issues, but they also want information about life outcomes and social supports. Because the anticipated outcomes of a condition can change significantly based on available social support, health care, and services, it is important for clinicians to stay up-to-date about new developments and credible, medically reviewed information about Down syndrome and other genetic conditions to access resources for clinical care. PMID:27368358

  8. The NLSY Kinship Links: Using the NLSY79 and NLSY-Children Data to Conduct Genetically-Informed and Family-Oriented Research.

    PubMed

    Rodgers, Joseph Lee; Beasley, William H; Bard, David E; Meredith, Kelly M; D Hunter, Michael; Johnson, Amber B; Buster, Maury; Li, Chengchang; May, Kim O; Mason Garrison, S; Miller, Warren B; van den Oord, Edwin; Rowe, David C

    2016-07-01

    The National Longitudinal Survey of Youth datasets (NLSY79; NLSY-Children/Young Adults; NLSY97) have extensive family pedigree information contained within them. These data sources are based on probability sampling, a longitudinal design, and a cross-generational and within-family data structure, with hundreds of phenotypes relevant to behavior genetic (BG) researchers, as well as to other developmental and family researchers. These datasets provide a unique and powerful source of information for BG researchers. But much of the information required for biometrical modeling has been hidden, and has required substantial programming effort to uncover-until recently. Our research team has spent over 20 years developing kinship links to genetically inform biometrical modeling. In the most recent release of kinship links from two of the NLSY datasets, the direct kinship indicators included in the 2006 surveys allowed successful and unambiguous linking of over 94 % of the potential pairs. In this paper, we provide details for research teams interested in using the NLSY data portfolio to conduct BG (and other family-oriented) research.

  9. Genetics Home Reference: diastrophic dysplasia

    MedlinePlus

    ... my area? Other Names for This Condition Diastrophic dwarfism DTD Related Information How are genetic conditions and ... 2 links) Health Topic: Bone Diseases Health Topic: Dwarfism Genetic and Rare Diseases Information Center (1 link) ...

  10. A Genetically Informed Study of the Processes Underlying the Association between Parental Marital Instability and Offspring Adjustment

    ERIC Educational Resources Information Center

    D'Onofrio, Brian M.; Turkheimer, Eric; Emery, Robert E.; Slutske, Wendy S.; Heath, Andrew C.; Madden, Pamela A.; Martin, Nicholas G.

    2006-01-01

    Parental divorce is associated with problematic offspring adjustment, but the relation may be due to shared genetic or environmental factors. One way to test for these confounds is to study offspring of twins discordant for divorce. The current analyses used this design to separate the mechanisms responsible for the association between parental…

  11. Project 6: Cumulative Risk Assessment Methods and Applications: Task 6.3. Applying Genetic and Epigenetic Data to Inform Susceptibility

    EPA Science Inventory

    Susceptibility is defined by the NRC (2009) as the capacity to be affected. A person can be at greater or less risk relative to population median risk because of susceptibility factors such as life stage, sex, genetics, socioeconomic status, prior exposure to chemicals, and non-c...

  12. Informing a Learning Progression in Genetics: Which Should Be Taught First, Mendelian Inheritance or the Central Dogma of Molecular Biology?

    ERIC Educational Resources Information Center

    Duncan, Ravit Golan; Castro-Faix, Moraima; Choi, Jinnie

    2016-01-01

    The Framework for Science Education and the Next Generation Science Standards in the USA emphasize learning progressions (LPs) that support conceptual coherence and the gradual building of knowledge over time. In the domain of genetics there are two independently developed alternative LPs. In essence, the difference between the two progressions…

  13. Current status of genetics and genomics of reared penaeid shrimp: information relevant to access and benefit sharing.

    PubMed

    Andriantahina, Farafidy; Liu, Xiaolin; Feng, Tingting; Xiang, Jianhai

    2013-08-01

    At present, research and progress in shrimp genomics and genetics show significant developments. Shrimp genetics and genomics also show immense potential for an increased production in a way that meets shrimp culture progress goals for the third millennium. This review article aims to provide an overview of its current status and future direction, discusses questions that need focused research to address them, and summarizes areas where genetics and genomics knowledge can make a positive difference to shrimp culture sustainability. Sustainable progress of penaeid shrimps will depend upon feasible solutions for environmental, research, economic, consumer problems, proper development, and planning policy enforcement. It is recommended that increased funding for biotechnology research and progress be directed to expand worldwide commercial shrimp culture and address environmental and public health issues. For any researcher or shrimp company member who has attempted to or whom would like to thoroughly search the literature to gain a complete understanding of the current state of shrimp genetics and genomics, this publication will be an invaluable source of reference materials, some of which is reported here for the first time.

  14. Elephant behaviour and conservation: social relationships, the effects of poaching, and genetic tools for management.

    PubMed

    Archie, Elizabeth A; Chiyo, Patrick I

    2012-02-01

    Genetic tools are increasingly valuable for understanding the behaviour, evolution, and conservation of social species. In African elephants, for instance, genetic data provide basic information on the population genetic causes and consequences of social behaviour, and how human activities alter elephants' social and genetic structures. As such, African elephants provide a useful case study to understand the relationships between social behaviour and population genetic structure in a conservation framework. Here, we review three areas where genetic methods have made important contributions to elephant behavioural ecology and conservation: (1) understanding kin-based relationships in females and the effects of poaching on the adaptive value of elephant relationships, (2) understanding patterns of paternity in elephants and how poaching can alter these patterns, and (3) conservation genetic tools to census elusive populations, track ivory, and understand the behavioural ecology of crop-raiding. By comparing studies from populations that have experienced a range of poaching intensities, we find that human activities have a large effect on elephant behaviour and genetic structure. Poaching disrupts kin-based association patterns, decreases the quality of elephant social relationships, and increases male reproductive skew, with important consequences for population health and the maintenance of genetic diversity. In addition, we find that genetic tools to census populations or gather forensic information are almost always more accurate than non-genetic alternatives. These results contribute to a growing understanding of poaching on animal behaviour, and how genetic tools can be used to understand and conserve social species.

  15. Elephant behaviour and conservation: social relationships, the effects of poaching, and genetic tools for management.

    PubMed

    Archie, Elizabeth A; Chiyo, Patrick I

    2012-02-01

    Genetic tools are increasingly valuable for understanding the behaviour, evolution, and conservation of social species. In African elephants, for instance, genetic data provide basic information on the population genetic causes and consequences of social behaviour, and how human activities alter elephants' social and genetic structures. As such, African elephants provide a useful case study to understand the relationships between social behaviour and population genetic structure in a conservation framework. Here, we review three areas where genetic methods have made important contributions to elephant behavioural ecology and conservation: (1) understanding kin-based relationships in females and the effects of poaching on the adaptive value of elephant relationships, (2) understanding patterns of paternity in elephants and how poaching can alter these patterns, and (3) conservation genetic tools to census elusive populations, track ivory, and understand the behavioural ecology of crop-raiding. By comparing studies from populations that have experienced a range of poaching intensities, we find that human activities have a large effect on elephant behaviour and genetic structure. Poaching disrupts kin-based association patterns, decreases the quality of elephant social relationships, and increases male reproductive skew, with important consequences for population health and the maintenance of genetic diversity. In addition, we find that genetic tools to census populations or gather forensic information are almost always more accurate than non-genetic alternatives. These results contribute to a growing understanding of poaching on animal behaviour, and how genetic tools can be used to understand and conserve social species. PMID:21880086

  16. Genetics Home Reference: short QT syndrome

    MedlinePlus

    ... Information What information about a genetic condition can statistics provide? Why are some genetic conditions more common in particular ethnic groups? Genetic Changes Mutations in the KCNH2 , KCNJ2 , and KCNQ1 genes can cause short QT syndrome . These ...

  17. Qualitative analysis of mouse specific-locus mutations: information on genetic organization, gene expression, and the chromosomal nature of induced lesions

    SciTech Connect

    Russell, L.B.

    1982-01-01

    Analysis of mouse specific-locus (SL) mutations at three loci has identified over 33 distinct complementation groups - most of which are probably overlapping deficiencies - and 13 to 14 new functional units. The complementation maps that have been generated for the d-se and c regions include numerous vital functions; however, some of the genes in these regions are non-vital. At such loci, hypomorphic mutants must represent intragenic alterations, and some viable nulls could conceivably be intragenic lesions also. Analysis of SL mutations has provided information on genetic expression. Homozygous deficiencies can be completely viable or can kill at any one of a range of developmental stages. Heterozygonus deficiencies of up to 6 cM or more in genetic length have been recovered and propagated. The time of death of homozygous and the degree of inviability of heterozygous deficiencies are related more to specific content of the missing segment than to its length. Combinations of deficiencies with x-autosome translocations that inactivate the homologous region in a mosaic fashion have shown that organismic lethals are not necessarily cell lethal. The spectrum of mutations induced depends on the nature of the mutagen and the type of germ cell exposed. Radiation of spermatogonia produces intragenic as well as null mutations. Spontaneous mutations have an admixture of types not present in populations of mutations induced in germ cells, and this raises doubts concerning the accuracy of doubling-dose calculations in genetic risk estimation. The analysis of SL mutations has yielded genetic tools for the construction of detailed gene-dosage series, cis-trans comparisons, the mapping of known genes and identification of new genes, genetic rescue of various types, and the identification and isolation of DNA sequences. (ERB)

  18. Advances in the Understanding of the Genetic Causes of Hearing Loss in Children Inform a Rational Approach to Evaluation.

    PubMed

    Carey, John C; Palumbos, Janice C

    2016-10-01

    Hearing loss represents the most common sensory disability of children. Remarkable advances in the identification of genes underlying nonsyndromic and syndromic hearing loss in just the last 2 decades have led to the ability to determine the specific genetic cause of hearing loss in many children. Surprisingly one gene, GJB2, encoding the protein connexin-26, accounts for about 20 % of sensorineural hearing loss (including in India) and is considered the first tier test in evaluating an infant with unexplained congenital hearing loss. Using the knowledge of the etiology of hearing loss, the authors propose a diagnostic reasoning process for the assessment of a child in the pediatric setting. Second tier testing consists of the multiple gene panels using whole exome sequencing strategies, and is becoming available in some regions of the world including the US. Referral to medical genetics is always a consideration in a child with no explanation for the hearing loss and in families with questions about recurrence risk.

  19. Information content in genome-wide scans: concordance between patterns of genetic differentiation and linkage mapping associations

    PubMed Central

    2011-01-01

    Background Scanning the genome with high density SNP markers has become a standard approach for identifying regions of the genome showing substantial between-population genetic differentiation, and thus evidence of diversifying selection. Such regions may contain genes of large phenotypic effect. However, few studies have attempted to address the power or efficacy of such an approach. Results In this study, the patterns of allele frequency differences between two cattle breeds based on the Bovine HapMap study were compared with statistical evidence for QTL based on a linkage mapping study of an experimental population formed by a cross between the same breeds. Concordance between the two datasets was seen for chromosomes carrying QTL with strong statistical support, such as BTA5 and BTA18, which carry genes associated with coat color. For these chromosomes, there was a correspondence between the strength of the QTL signal along the chromosome and the degree of genetic differentiation between breeds. However, such an association was not seen in a broader comparison that also included chromosomes carrying QTL with lower significance levels. In addition, other chromosomal regions with substantial QTL effects did not include markers showing extreme between-breed genetic differentiation. Furthermore, the overall consistency between the two studies was weak, with low genome-wide correlation between the statistical values obtained in the linkage mapping study and between-breed genetic differentiation from the HapMap study. Conclusions These results suggest that genomic diversity scans are capable of detecting regions associated with qualitative traits but may be limited in their power to detect regions associated with quantitative phenotypic differences between populations, which may depend on the marker resolution of the study and the level of LD in the populations under investigation. PMID:21269469

  20. Genetic testing of children for familial cancers: a comparative legal perspective on consent, communication of information and confidentiality.

    PubMed

    Gilbar, Roy

    2010-03-01

    Genetic testing of children is the subject of ethical and legal debate. On the one hand, the literature emphasises the personal interests and rights of the individual child. On the other, the interests of the parents and the family as a whole are discussed. English law relies by and large on a patient-centred approach where the child has some say about his/her medical care. The view reflected in Anglo-American guidelines, more specifically, is that testing is potentially harmful and may compromise the child's autonomy and confidentiality. This explains the reluctance to submit children to predictive genetic testing. An analysis of Israeli law, however, reflects a different approach, where the benefit to the child is defined more widely. This accords with the general communitarian position adopted by Israeli law, a legal position that reflects the duality of Israeli society in simultaneously promoting both fundamental human rights and family ethics. In practice, however, there may be little difference, as children in both jurisdictions have access to similar genetic services.

  1. Makeup of the genetic correlation between milk production traits using genome-wide single nucleotide polymorphism information.

    PubMed

    van Binsbergen, R; Veerkamp, R F; Calus, M P L

    2012-04-01

    The correlated responses between traits may differ depending on the makeup of genetic covariances, and may differ from the predictions of polygenic covariances. Therefore, the objective of the present study was to investigate the makeup of the genetic covariances between the well-studied traits: milk yield, fat yield, protein yield, and their percentages in more detail. Phenotypic records of 1,737 heifers of research farms in 4 different countries were used after homogenizing and adjusting for management effects. All cows had a genotype for 37,590 single nucleotide polymorphisms (SNP). A bayesian stochastic search variable selection model was used to estimate the SNP effects for each trait. About 0.5 to 1.0% of the SNP had a significant effect on 1 or more traits; however, the SNP without a significant effect explained most of the genetic variances and covariances of the traits. Single nucleotide polymorphism correlations differed from the polygenic correlations, but only 10 regions were found with an effect on multiple traits; in 1 of these regions the DGAT1 gene was previously reported with an effect on multiple traits. This region explained up to 41% of the variances of 4 traits and explained a major part of the correlation between fat yield and fat percentage and contributes to asymmetry in correlated response between fat yield and fat percentage. Overall, for the traits in this study, the infinitesimal model is expected to be sufficient for the estimation of the variances and covariances.

  2. What Is Direct-to-Consumer Genetic Testing?

    MedlinePlus

    ... consumer genetic testing? What is direct-to-consumer genetic testing? Traditionally, genetic tests have been available only ... testing. For more information about direct-to-consumer genetic testing: The American College of Medical Genetics, which ...

  3. ‘Is this knowledge mine and nobody else's? I don't feel that.’ Patient views about consent, confidentiality and information-sharing in genetic medicine

    PubMed Central

    Dheensa, Sandi; Fenwick, Angela; Lucassen, Anneke

    2016-01-01

    In genetic medicine, a patient's diagnosis can mean their family members are also at risk, raising a question about how consent and confidentiality should function in clinical genetics. This question is particularly pressing when it is unclear whether a patient has shared information. Conventionally, healthcare professionals view confidentiality at an individual level and ‘disclosure without consent’ as the exception, not the rule. The relational joint account model, by contrast, conceptualises genetic information as confidential at the familial level and encourages professionals to take disclosure as the default position. In this study, we interviewed 33 patients about consent and confidentiality and analysed data thematically. Our first theme showed that although participants thought of certain aspects of genetic conditions—for example, the way they affect day-to-day health—as somewhat personal, they perceived genetic information—for example, the mutation in isolation—as familial. Most thought these elements were separable and thought family members had a right to know the latter, identifying a broad range of harms that would justify disclosure. Our second theme illustrated that participants nonetheless had some concerns about what, if any, implications there would be of professionals treating such information as familial and they emphasised the importance of being informed about the way their information would be shared. Based on these results, we recommend that professionals take disclosure as the default position, but make clear that they will treat genetic information as familial during initial consultations and address any concerns therein. PMID:26744307

  4. Processing of data discrepancies for U.S. dairy cattle and effect on genetic evaluations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic evaluations depend on accurate data in three ways: 1) the accuracy of the recorded trait (e.g. milk weight), 2) information on how much influence it should receive and how it should be adjusted (e.g. milking frequency, number of milkings weighed) and 3) which other animals it should influen...

  5. Practical implications for genetic modeling in the genomics era for the dairy industry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic models convert data into estimated breeding values and other information useful to breeders. The goal is to provide accurate and timely predictions of the future performance for each animal (or embryo). Modeling involves defining traits, editing raw data, removing environmental effects, incl...

  6. Genetics Home Reference: hypochondrogenesis

    MedlinePlus

    ... and Rare Diseases Information Center Frequency Hypochondrogenesis and achondrogenesis , type 2 (a similar skeletal disorder) together affect ... of hypochondrogenesis: Genetic Testing Registry: ... Achondrogenesis These resources from MedlinePlus offer information about the ...

  7. Non-targeted analysis of electronics waste by comprehensive two-dimensional gas chromatography combined with high-resolution mass spectrometry: Using accurate mass information and mass defect analysis to explore the data.

    PubMed

    Ubukata, Masaaki; Jobst, Karl J; Reiner, Eric J; Reichenbach, Stephen E; Tao, Qingping; Hang, Jiliang; Wu, Zhanpin; Dane, A John; Cody, Robert B

    2015-05-22

    Comprehensive two-dimensional gas chromatography (GC×GC) and high-resolution mass spectrometry (HRMS) offer the best possible separation of their respective techniques. Recent commercialization of combined GC×GC-HRMS systems offers new possibilities for the analysis of complex mixtures. However, such experiments yield enormous data sets that require new informatics tools to facilitate the interpretation of the rich information content. This study reports on the analysis of dust obtained from an electronics recycling facility by using GC×GC in combination with a new high-resolution time-of-flight (TOF) mass spectrometer. New software tools for (non-traditional) Kendrick mass defect analysis were developed in this research and greatly aided in the identification of compounds containing chlorine and bromine, elements that feature in most persistent organic pollutants (POPs). In essence, the mass defect plot serves as a visual aid from which halogenated compounds are recognizable on the basis of their mass defect and isotope patterns. Mass chromatograms were generated based on specific ions identified in the plots as well as region of the plot predominantly occupied by halogenated contaminants. Tentative identification was aided by database searches, complementary electron-capture negative ionization experiments and elemental composition determinations from the exact mass data. These included known and emerging flame retardants, such as polybrominated diphenyl ethers (PBDEs), hexabromobenzene, tetrabromo bisphenol A and tris (1-chloro-2-propyl) phosphate (TCPP), as well as other legacy contaminants such as polychlorinated biphenyls (PCBs) and polychlorinated terphenyls (PCTs).

  8. University Students' Knowledge Structures and Informal Reasoning on the Use of Genetically Modified Foods: Multidimensional Analyses

    ERIC Educational Resources Information Center

    Wu, Ying-Tien

    2013-01-01

    This study aims to provide insights into the role of learners' knowledge structures about a socio-scientific issue (SSI) in their informal reasoning on the issue. A total of 42 non-science major university students' knowledge structures and informal reasoning were assessed with multidimensional analyses. With both qualitative and…

  9. Human genetics

    SciTech Connect

    Carlson, E.A.

    1984-01-01

    This text provides full and balanced coverage of the concepts requisite for a thorough understanding of human genetics. Applications to both the individual and society are integrated throughout the lively and personal narrative, and the essential principles of heredity are clearly presented to prepare students for informed participation in public controversies. High-interest, controversial topics, including recombinant DNA technology, oncogenes, embryo transfer, environmental mutagens and carcinogens, IQ testing, and eugenics encourage understanding of important social issues.

  10. The Impact of Risk Information Exposure on Women’s Beliefs about Direct-to-Consumer Genetic Testing for BRCA Mutations

    PubMed Central

    Gray, Stacy W.; Hornik, Robert C.; Schwartz, J. Sanford; Armstrong, Katrina

    2011-01-01

    Despite an increase in direct-to-consumer (DTC) genetic testing, little is known about how variations in website content might alter consumer behavior. We evaluated the impact of risk information provision on women’s attitudes about DTC BRCA testing. We conducted a randomized experiment; women viewed a “mock” BRCA testing website without (control group: CG) or with information on the potential risks of DTC testing (RG; framed two ways: unattributed information [UR] and information presented by experts [ER]). 767 women participated; mean age was 37 years, mean education was 15 years, and 79% of subjects were white. Women in the RG had less positive beliefs about DTC testing (mean RG=23.8, CG=25.2; p=0.001), lower intentions to get tested (RG= 2.8, CG= 3.1; p=0.03), were more likely to prefer clinic-based testing (RG=5.1, CG=4.8; p=0.03) and to report that they had seen enough risk information (RG=5.3, CG= 4.7; p<0.001). UR and ER exposure produced similar effects. Effects did not differ for women with or without a personal/family history of breast/ovarian cancer. Exposing women to the potential risks of DTC BRCA testing altered their beliefs, preferences, and intentions. Risk messages appear to be salient to women irrespective of their chance of having a BRCA mutation. PMID:21992449

  11. Genetic testing in hyperlipidemia.

    PubMed

    Bilen, Ozlem; Pokharel, Yashashwi; Ballantyne, Christie M

    2015-05-01

    Hereditary dyslipidemias are often underdiagnosed and undertreated, yet with significant health implications, most importantly causing preventable premature cardiovascular diseases. The commonly used clinical criteria to diagnose hereditary lipid disorders are specific but are not very sensitive. Genetic testing may be of value in making accurate diagnosis and improving cascade screening of family members, and potentially, in risk assessment and choice of therapy. This review focuses on using genetic testing in the clinical setting for lipid disorders, particularly familial hypercholesterolemia.

  12. Genetic Testing in Hyperlipidemia.

    PubMed

    Bilen, Ozlem; Pokharel, Yashashwi; Ballantyne, Christie M

    2016-03-01

    Hereditary dyslipidemias are often underdiagnosed and undertreated, yet with significant health implications, most importantly causing preventable premature cardiovascular diseases. The commonly used clinical criteria to diagnose hereditary lipid disorders are specific but are not very sensitive. Genetic testing may be of value in making accurate diagnosis and improving cascade screening of family members, and potentially, in risk assessment and choice of therapy. This review focuses on using genetic testing in the clinical setting for lipid disorders, particularly familial hypercholesterolemia.

  13. A DArT marker genetic map of perennial ryegrass (Lolium perenne L.) integrated with detailed comparative mapping information; comparison with existing DArT marker genetic maps of Lolium perenne, L. multiflorum and Festuca pratensis

    PubMed Central

    2013-01-01

    Background Ryegrasses and fescues (genera, Lolium and Festuca) are species of forage and turf grasses which are used widely in agricultural and amenity situations. They are classified within the sub-family Pooideae and so are closely related to Brachypodium distachyon, wheat, barley, rye and oats. Recently, a DArT array has been developed which can be used in generating marker and mapping information for ryegrasses and fescues. This represents a potential common marker set for ryegrass and fescue researchers which can be linked through to comparative genomic information for the grasses. Results A F2 perennial ryegrass genetic map was developed consisting of 7 linkage groups defined by 1316 markers and deriving a total map length of 683 cM. The marker set included 866 DArT and 315 gene sequence-based markers. Comparison with previous DArT mapping studies in perennial and Italian ryegrass (L. multiflorum) identified 87 and 105 DArT markers in common, respectively, of which 94% and 87% mapped to homoeologous linkage groups. A similar comparison with meadow fescue (F. pratensis) identified only 28 DArT markers in common, of which c. 50% mapped to non-homoelogous linkage groups. In L. perenne, the genetic distance spanned by the DArT markers encompassed the majority of the regions that could be described in terms of comparative genomic relationships with rice, Brachypodium distachyon, and Sorghum bicolor. Conclusions DArT markers are likely to be a useful common marker resource for ryegrasses and fescues, though the success in aligning different populations through the mapping of common markers will be influenced by degrees of population interrelatedness. The detailed mapping of DArT and gene-based markers in this study potentially allows comparative relationships to be derived in future mapping populations characterised using solely DArT markers. PMID:23819624

  14. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  15. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2013-07-01 2013-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  16. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2011-07-01 2011-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  17. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2014-07-01 2014-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  18. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2012-07-01 2012-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  19. Pathways to support genetically modified (GM) foods in South Korea: Deliberate reasoning, information shortcuts, and the role of formal education.

    PubMed

    Kim, Sei-Hill; Kim, Jeong-Nam; Besley, John C

    2013-02-01

    Analyzing survey data on the issue of GM foods in South Korea, this study examines two competing routes - deliberate reasoning versus information shortcuts - to forming opinions on controversial science. Findings indicated that both deliberate reasoning and information shortcuts were in play; but the process was moderated by a person's education level. The well educated were more likely than the less educated to engage in deliberate reasoning when shaping their support for GM foods. Implications of the findings are discussed in detail.

  20. Accurate On-Line Intervention Practices for Efficient Improvement of Reading Skills in Africa

    ERIC Educational Resources Information Center

    Marshall, Minda B.

    2016-01-01

    Lifelong learning is the only way to sustain proficient learning in a rapidly changing world. Knowledge and information are exploding across the globe. We need accurate ways to facilitate the process of drawing external factual information into an internal perceptive advantage from which to interpret and argue new information. Accurate and…

  1. The importance of accurate atmospheric modeling

    NASA Astrophysics Data System (ADS)

    Payne, Dylan; Schroeder, John; Liang, Pang

    2014-11-01

    This paper will focus on the effect of atmospheric conditions on EO sensor performance using computer models. We have shown the importance of accurately modeling atmospheric effects for predicting the performance of an EO sensor. A simple example will demonstrated how real conditions for several sites in China will significantly impact on image correction, hyperspectral imaging, and remote sensing. The current state-of-the-art model for computing atmospheric transmission and radiance is, MODTRAN® 5, developed by the US Air Force Research Laboratory and Spectral Science, Inc. Research by the US Air Force, Navy and Army resulted in the public release of LOWTRAN 2 in the early 1970's. Subsequent releases of LOWTRAN and MODTRAN® have continued until the present. Please verify that (1) all pages are present, (2) all figures are correct, (3) all fonts and special characters are correct, and (4) all text and figures fit within the red margin lines shown on this review document. Complete formatting information is available at http://SPIE.org/manuscripts Return to the Manage Active Submissions page at http://spie.org/submissions/tasks.aspx and approve or disapprove this submission. Your manuscript will not be published without this approval. Please contact author_help@spie.org with any questions or concerns. The paper will demonstrate the importance of using validated models and local measured meteorological, atmospheric and aerosol conditions to accurately simulate the atmospheric transmission and radiance. Frequently default conditions are used which can produce errors of as much as 75% in these values. This can have significant impact on remote sensing applications.

  2. Accurate Mass Measurements in Proteomics

    SciTech Connect

    Liu, Tao; Belov, Mikhail E.; Jaitly, Navdeep; Qian, Weijun; Smith, Richard D.

    2007-08-01

    To understand different aspects of life at the molecular level, one would think that ideally all components of specific processes should be individually isolated and studied in details. Reductionist approaches, i.e., studying one biological event at a one-gene or one-protein-at-a-time basis, indeed have made significant contributions to our understanding of many basic facts of biology. However, these individual “building blocks” can not be visualized as a comprehensive “model” of the life of cells, tissues, and organisms, without using more integrative approaches.1,2 For example, the emerging field of “systems biology” aims to quantify all of the components of a biological system to assess their interactions and to integrate diverse types of information obtainable from this system into models that could explain and predict behaviors.3-6 Recent breakthroughs in genomics, proteomics, and bioinformatics are making this daunting task a reality.7-14 Proteomics, the systematic study of the entire complement of proteins expressed by an organism, tissue, or cell under a specific set of conditions at a specific time (i.e., the proteome), has become an essential enabling component of systems biology. While the genome of an organism may be considered static over short timescales, the expression of that genome as the actual gene products (i.e., mRNAs and proteins) is a dynamic event that is constantly changing due to the influence of environmental and physiological conditions. Exclusive monitoring of the transcriptomes can be carried out using high-throughput cDNA microarray analysis,15-17 however the measured mRNA levels do not necessarily correlate strongly with the corresponding abundances of proteins,18-20 The actual amount of functional proteins can be altered significantly and become independent of mRNA levels as a result of post-translational modifications (PTMs),21 alternative splicing,22,23 and protein turnover.24,25 Moreover, the functions of expressed

  3. Wavelets meet genetic imaging

    NASA Astrophysics Data System (ADS)

    Wang, Yu-Ping

    2005-08-01

    Genetic image analysis is an interdisciplinary area, which combines microscope image processing techniques with the use of biochemical probes for the detection of genetic aberrations responsible for cancers and genetic diseases. Recent years have witnessed parallel and significant progress in both image processing and genetics. On one hand, revolutionary multiscale wavelet techniques have been developed in signal processing and applied mathematics in the last decade, providing sophisticated tools for genetic image analysis. On the other hand, reaping the fruit of genome sequencing, high resolution genetic probes have been developed to facilitate accurate detection of subtle and cryptic genetic aberrations. In the meantime, however, they bring about computational challenges for image analysis. In this paper, we review the fruitful interaction between wavelets and genetic imaging. We show how wavelets offer a perfect tool to address a variety of chromosome image analysis problems. In fact, the same word "subband" has been used in the nomenclature of cytogenetics to describe the multiresolution banding structure of the chromosome, even before its appearance in the wavelet literature. The application of wavelets to chromosome analysis holds great promise in addressing several computational challenges in genetics. A variety of real world examples such as the chromosome image enhancement, compression, registration and classification will be demonstrated. These examples are drawn from fluorescence in situ hybridization (FISH) and microarray (gene chip) imaging experiments, which indicate the impact of wavelets on the diagnosis, treatments and prognosis of cancers and genetic diseases.

  4. Patient expectations and attitudes towards specialist genetic eye services.

    PubMed

    Clarke, E; Combs, R; Black, G; Hall, G

    2015-04-01

    Little research has explored the views of patients referred to specialist genetic eye clinics. Future service development must be informed by the perspectives of patients to ensure services are accessible and meet their needs. Semi-structured telephone interviews were undertaken with patients referred to the Genetic Eye Clinic in Manchester, UK. Participants were interviewed before their first appointment. The interview transcripts were analysed using Interpretative Phenomenological Analysis (IPA). Nine interviews took place. Five participants were adults with sight loss and 4 were the parent/carer of a child patient. The major themes identified were: expectations of a medical-genetic focus to the clinic, psychological adjustment to the diagnosis of an eye condition impacting on counselling and support needs, lack of preparation and restricted expectations due to unfamiliarity with the service and positive attitudes towards genetic research and testing. Key motivating factors for patients attending specialist ophthalmic genetic services are medical-genetic orientated, including accurate diagnostic and prognostic information, participation in research and clarification of recurrence risks. Some barriers to patients accessing and fully engaging with services were identified. There is a need to raise awareness of the specialist service amongst the public, patient organisations and professionals. Facilitating patient preparation for clinic could improve patient outcomes, and the need for integrated services is reinforced. The results feed into the development of a best practice model for the delivery of specialist ophthalmic genetic services.

  5. Consulting communities on feedback of genetic findings in international health research: sharing sickle cell disease and carrier information in coastal Kenya

    PubMed Central

    2013-01-01

    Background International health research in malaria-endemic settings may include screening for sickle cell disease, given the relationship between this important genetic condition and resistance to malaria, generating questions about whether and how findings should be disclosed. The literature on disclosing genetic findings in the context of research highlights the role of community consultation in understanding and balancing ethically important issues from participants’ perspectives, including social forms of benefit and harm, and the influence of access to care. To inform research practice locally, and contribute to policy more widely, this study aimed to explore the views of local residents in Kilifi County in coastal Kenya on how researchers should manage study-generated information on sickle cell disease and carrier status. Methods Between June 2010 and July 2011, we consulted 62 purposively selected Kilifi residents on how researchers should manage study-generated sickle cell disease findings. Methods drew on a series of deliberative informed small group discussions. Data were analysed thematically, using charts, to describe participants’ perceptions of the importance of disclosing findings, including reasoning, difference and underlying values. Themes were derived from the underlying research questions and from issues emerging from discussions. Data interpretation drew on relevant areas of social science and bioethics literature. Results Perceived health and social benefits generated strong support for disclosing findings on sickle cell disease, but the balance of social benefits and harms was less clear for sickle cell trait. Many forms of health and social benefits and harms of information-sharing were identified, with important underlying values related to family interests and the importance of openness. The influence of micro and macro level contextual features and prioritization of values led to marked diversity of opinion. Conclusions The approach

  6. The changing landscape of genetic testing and its impact on clinical and laboratory services and research in Europe

    PubMed Central

    Hastings, Ros; de Wert, Guido; Fowler, Brian; Krawczak, Michael; Vermeulen, Eric; Bakker, Egbert; Borry, Pascal; Dondorp, Wybo; Nijsingh, Niels; Barton, David; Schmidtke, Jörg; van El, Carla G; Vermeesch, Joris; Stol, Yrrah; Carmen Howard, Heidi; Cornel, Martina C

    2012-01-01

    The arrival of new genetic technologies that allow efficient examination of the whole human genome (microarray, next-generation sequencing) will impact upon both laboratories (cytogenetic and molecular genetics in the first instance) and clinical/medical genetic services. The interpretation of analytical results in terms of their clinical relevance and the predicted health status poses a challenge to both laboratory and clinical geneticists, due to the wealth and complexity of the information obtained. There is a need to discuss how to best restructure the genetic services logistically and to determine the clinical utility of genetic testing so that patients can receive appropriate advice and genetic testing. To weigh up the questions and challenges of the new genetic technologies, the European Society of Human Genetics (ESHG) held a series of workshops on 10 June 2010 in Gothenburg. This was part of an ESHG satellite symposium on the ‘Changing landscape of genetic testing', co-organized by the ESHG Genetic Services Quality and Public and Professional Policy Committees. The audience consisted of a mix of geneticists, ethicists, social scientists and lawyers. In this paper, we summarize the discussions during the workshops and present some of the identified ways forward to improve and adapt the genetic services so that patients receive accurate and relevant information. This paper covers ethics, clinical utility, primary care, genetic services and the blurring boundaries between healthcare and research. PMID:22453292

  7. Genetic Stroke Syndromes

    PubMed Central

    Barrett, Kevin M.; Meschia, James F.

    2014-01-01

    Purpose of Review: This review describes the clinical and radiographic features, genetic determinants, and treatment options for the most well-characterized monogenic disorders associated with stroke. Recent Findings: Stroke is a phenotype of many clinically important inherited disorders. Recognition of the clinical manifestations of genetic disorders associated with stroke is important for accurate diagnosis and prognosis. Genetic studies have led to the discovery of specific mutations associated with the clinical phenotypes of many inherited stroke syndromes. Summary: Several inherited causes of stroke have established and effective therapies, further underscoring the importance of timely diagnosis. PMID:24699489

  8. Measuring Fisher information accurately in correlated neural populations.

    PubMed

    Kanitscheider, Ingmar; Coen-Cagli, Ruben; Kohn, Adam; Pouget, Alexandre

    2015-06-01

    Neural responses are known to be variable. In order to understand how this neural variability constrains behavioral performance, we need to be able to measure the reliability with which a sensory stimulus is encoded in a given population. However, such measures are challenging for two reasons: First, they must take into account noise correlations which can have a large influence on reliability. Second, they need to be as efficient as possible, since the number of trials available in a set of neural recording is usually limited by experimental constraints. Traditionally, cross-validated decoding has been used as a reliability measure, but it only provides a lower bound on reliability and underestimates reliability substantially in small datasets. We show that, if the number of trials per condition is larger than the number of neurons, there is an alternative, direct estimate of reliability which consistently leads to smaller errors and is much faster to compute. The superior performance of the direct estimator is evident both for simulated data and for neuronal population recordings from macaque primary visual cortex. Furthermore we propose generalizations of the direct estimator which measure changes in stimulus encoding across conditions and the impact of correlations on encoding and decoding, typically denoted by Ishuffle and Idiag respectively.

  9. Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis

    PubMed Central

    Caminsky, Natasha; Mucaki, Eliseos J.; Rogan, Peter K.

    2014-01-01

    The interpretation of genomic variants has become one of the paramount challenges in the post-genome sequencing era. In this review we summarize nearly 20 years of research on the applications of information theory (IT) to interpret coding and non-coding mutations that alter mRNA splicing in rare and common diseases. We compile and summarize the spectrum of published variants analyzed by IT, to provide a broad perspective of the distribution of deleterious natural and cryptic splice site variants detected, as well as those affecting splicing regulatory sequences. Results for natural splice site mutations can be interrogated dynamically with Splicing Mutation Calculator, a companion software program that computes changes in information content for any splice site substitution, linked to corresponding publications containing these mutations. The accuracy of IT-based analysis was assessed in the context of experimentally validated mutations. Because splice site information quantifies binding affinity, IT-based analyses can discern the differences between variants that account for the observed reduced (leaky) versus abolished mRNA splicing. We extend this principle by comparing predicted mutations in natural, cryptic, and regulatory splice sites with observed deleterious phenotypic and benign effects. Our analysis of 1727 variants revealed a number of general principles useful for ensuring portability of these analyses and accurate input and interpretation of mutations. We offer guidelines for optimal use of IT software for interpretation of mRNA splicing mutations. PMID:25717368

  10. Medical genetics

    SciTech Connect

    Nora, J.J.; Fraser, F.C.

    1989-01-01

    This book presents a discussion of medical genetics for the practitioner treating or counseling patients with genetic disease. It includes a discussion of the relationship of heredity and diseases, the chromosomal basis for heredity, gene frequencies, and genetics of development and maldevelopment. The authors also focus on teratology, somatic cell genetics, genetics and cancer, genetics of behavior.

  11. Parent, sibling and peer influences on smoking initiation, regular smoking and nicotine dependence. Results from a genetically informative design.

    PubMed

    Scherrer, Jeffrey F; Xian, Hong; Pan, Hui; Pergadia, Michele L; Madden, Pamela A F; Grant, Julia D; Sartor, Carolyn E; Haber, Jon Randolph; Jacob, Theodore; Bucholz, Kathleen K

    2012-03-01

    We sought to determine whether parenting, sibling and peer influences are associated with offspring ever smoking, regular smoking and nicotine dependence (ND) after controlling for familial factors. We used a twin-family design and data from structured diagnostic surveys of 1919 biological offspring (ages 12-32 years), 1107 twin fathers, and 1023 mothers. Offspring were classified into one of four familial risk groups based on twin fathers' and their co-twins' history of DSM-III-R nicotine dependence. Multivariate multinomial logistic regression was used to model familial risk, paternal and maternal parenting behavior and substance use, sibling substance use, and friend and school peer smoking, alcohol and drug use. Ever smoking was associated with increasing offspring age, white race, high maternal pressure to succeed in school, sibling drug use, and friend smoking, alcohol and drug use. Offspring regular smoking was associated with these same factors with additional contribution from maternal ND. Offspring ND was associated with increasing offspring age, male gender, biological parents divorce, high genetic risk from father and mother ND, maternal problem drinking, maternal rule inconsistency and sibling drug use, and friend smoking, alcohol and drug use. Friend smoking had the largest magnitude of association with offspring smoking. This effect remains after accounting for familial liability and numerous parent and sibling level effects. Smoking interventions may have greatest impact by targeting smoking prevention among peer groups in adolescent and young adult populations. PMID:22094168

  12. Accurate lineshape spectroscopy and the Boltzmann constant

    PubMed Central

    Truong, G.-W.; Anstie, J. D.; May, E. F.; Stace, T. M.; Luiten, A. N.

    2015-01-01

    Spectroscopy has an illustrious history delivering serendipitous discoveries and providing a stringent testbed for new physical predictions, including applications from trace materials detection, to understanding the atmospheres of stars and planets, and even constraining cosmological models. Reaching fundamental-noise limits permits optimal extraction of spectroscopic information from an absorption measurement. Here, we demonstrate a quantum-limited spectrometer that delivers high-precision measurements of the absorption lineshape. These measurements yield a very accurate measurement of the excited-state (6P1/2) hyperfine splitting in Cs, and reveals a breakdown in the well-known Voigt spectral profile. We develop a theoretical model that accounts for this breakdown, explaining the observations to within the shot-noise limit. Our model enables us to infer the thermal velocity dispersion of the Cs vapour with an uncertainty of 35 p.p.m. within an hour. This allows us to determine a value for Boltzmann's constant with a precision of 6 p.p.m., and an uncertainty of 71 p.p.m. PMID:26465085

  13. Accurate SHAPE-directed RNA structure determination

    PubMed Central

    Deigan, Katherine E.; Li, Tian W.; Mathews, David H.; Weeks, Kevin M.

    2009-01-01

    Almost all RNAs can fold to form extensive base-paired secondary structures. Many of these structures then modulate numerous fundamental elements of gene expression. Deducing these structure–function relationships requires that it be possible to predict RNA secondary structures accurately. However, RNA secondary structure prediction for large RNAs, such that a single predicted structure for a single sequence reliably represents the correct structure, has remained an unsolved problem. Here, we demonstrate that quantitative, nucleotide-resolution information from a SHAPE experiment can be interpreted as a pseudo-free energy change term and used to determine RNA secondary structure with high accuracy. Free energy minimization, by using SHAPE pseudo-free energies, in conjunction with nearest neighbor parameters, predicts the secondary structure of deproteinized Escherichia coli 16S rRNA (>1,300 nt) and a set of smaller RNAs (75–155 nt) with accuracies of up to 96–100%, which are comparable to the best accuracies achievable by comparative sequence analysis. PMID:19109441

  14. Individual genetic and genomic research results and the tradition of informed consent: exploring U.S. review board guidance

    PubMed Central

    Simon, Christian M.; Shinkunas, Laura; Brandt, Debra; Williams, Janet K.

    2015-01-01

    Background Genomic research is challenging the tradition of informed consent. Genomic researchers in the United States, Canada, and parts of Europe are encouraged to use informed consent to address the prospect of disclosing individual research results (IRRs) to study participants. In the U.S., no national policy exists to direct this use of informed consent, and it is unclear how local Institutional Review Boards (IRBs) may want researchers to respond. Objective and Methods To explore publicly accessible IRB websites for guidance in this area, using summative content analysis. Findings Three types of research results were addressed in 45 informed consent templates and instructions from 20 IRBs based at centers conducting genomic research: 1) IRRs in general 2) incidental findings (IFs), and 3) a broad and unspecified category of, “significant new findings” (SNFs). IRRs were more frequently referenced than IFs or SNFs. Most documents stated that access to IRRs would not be an option for research participants. These nondisclosure statements were found to coexist in some documents with statements that SNFs would be disclosed to participants if related to their willingness to participate in research. The median readability of template language on IRRs, IFs, and SNFs was greater than a 9th grade level. Conclusion IRB guidance may downplay the possibility of IFs, and contain conflicting messages on IRR nondisclosure and SNF disclosure. IRBs may need to clarify why separate IRR and SNF language should appear in the same consent document. The extent of these issues, nationally and internationally, needs to be determined. PMID:22361295

  15. NCI Dictionary of Genetics Terms

    Cancer.gov

    A dictionary of more than 150 genetics-related terms written for healthcare professionals, developed to support the comprehensive, evidence-based, peer-reviewed PDQ cancer genetics information summaries.

  16. Genetics Home Reference: Blau syndrome

    MedlinePlus

    ... inherited version of the disorder called early-onset sarcoidosis. Related Information What does it mean if a ... Genetic Testing Registry: Blau syndrome Genetic Testing Registry: Sarcoidosis, early-onset Merck Manual Consumer Version: Overview of ...

  17. Your Genes, Your Choices: Exploring the Issues Raised by Genetic Research

    SciTech Connect

    Baker, C.

    1999-05-31

    Your Genes, Your Choices provides accurate information about the ethical, legal, and social implications of the Human Genome Project and genetic research in an easy-to-read style and format. Each chapter in the book begins with a brief vignette, which introduces an issue within a human story, and raises a question for the reader to think about as the basic science and information are presented in the rest of the chapter.

  18. Accurate Inference of Local Phased Ancestry of Modern Admixed Populations

    PubMed Central

    Ma, Yamin; Zhao, Jian; Wong, Jian-Syuan; Ma, Li; Li, Wenzhi; Fu, Guoxing; Xu, Wei; Zhang, Kui; Kittles, Rick A.; Li, Yun; Song, Qing

    2014-01-01

    Population stratification is a growing concern in genetic-association studies. Averaged ancestry at the genome level (global ancestry) is insufficient for detecting the population substructures and correcting population stratifications in association studies. Local and phase stratification are needed for human genetic studies, but current technologies cannot be applied on the entire genome data due to various technical caveats. Here we developed a novel approach (aMAP, ancestry of Modern Admixed Populations) for inferring local phased ancestry. It took about 3 seconds on a desktop computer to finish a local ancestry analysis for each human genome with 1.4-million SNPs. This method also exhibits the scalability to larger datasets with respect to the number of SNPs, the number of samples, and the size of reference panels. It can detect the lack of the proxy of reference panels. The accuracy was 99.4%. The aMAP software has a capacity for analyzing 6-way admixed individuals. As the biomedical community continues to expand its efforts to increase the representation of diverse populations, and as the number of large whole-genome sequence datasets continues to grow rapidly, there is an increasing demand on rapid and accurate local ancestry analysis in genetics, pharmacogenomics, population genetics, and clinical diagnosis. PMID:25052506

  19. Accurate inference of local phased ancestry of modern admixed populations.

    PubMed

    Ma, Yamin; Zhao, Jian; Wong, Jian-Syuan; Ma, Li; Li, Wenzhi; Fu, Guoxing; Xu, Wei; Zhang, Kui; Kittles, Rick A; Li, Yun; Song, Qing

    2014-01-01

    Population stratification is a growing concern in genetic-association studies. Averaged ancestry at the genome level (global ancestry) is insufficient for detecting the population substructures and correcting population stratifications in association studies. Local and phase stratification are needed for human genetic studies, but current technologies cannot be applied on the entire genome data due to various technical caveats. Here we developed a novel approach (aMAP, ancestry of Modern Admixed Populations) for inferring local phased ancestry. It took about 3 seconds on a desktop computer to finish a local ancestry analysis for each human genome with 1.4-million SNPs. This method also exhibits the scalability to larger datasets with respect to the number of SNPs, the number of samples, and the size of reference panels. It can detect the lack of the proxy of reference panels. The accuracy was 99.4%. The aMAP software has a capacity for analyzing 6-way admixed individuals. As the biomedical community continues to expand its efforts to increase the representation of diverse populations, and as the number of large whole-genome sequence datasets continues to grow rapidly, there is an increasing demand on rapid and accurate local ancestry analysis in genetics, pharmacogenomics, population genetics, and clinical diagnosis. PMID:25052506

  20. Ethics and genetic testing.

    PubMed

    Grady, C

    1999-01-01

    The tremendous growth in knowledge about genes and genetic technologies will eventually enable us to know individual genotypes and susceptibilities to disease, perhaps even before birth. Each new genetic test developed raises serious issues for individuals and society on the circumstances under which genetic information should be sought and the uses that should be made of such information. Ethical reflection and analysis will help us to prepare for the responsible use of information about genotypes so that individuals, both now and in the future, are benefited and not harmed, so that justice is served, and so that confidentiality and privacy, and respect for the autonomy, dignity, and differences of each individual, are preserved.

  1. Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches

    PubMed Central

    Bérénos, Camillo; Ellis, Philip A; Pilkington, Jill G; Pemberton, Josephine M

    2014-01-01

    The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genomewide markers can potentially remove this limitation and lead to less biased and more precise estimates. We estimated heritability, maternal genetic effects and genetic correlations for body size traits in an unmanaged long-term study population of Soay sheep on St Kilda using three increasingly complete and accurate estimates of relatedness: (i) Pedigree 1, using observation-derived maternal links and microsatellite-derived paternal links; (ii) Pedigree 2, using SNP-derived assignment of both maternity and paternity; and (iii) whole-genome relatedness at 37 037 autosomal SNPs. In initial analyses, heritability estimates were strikingly similar for all three methods, while standard errors were systematically lower in analyses based on Pedigree 2 and genomic relatedness. Genetic correlations were generally strong, differed little between the three estimates of relatedness and the standard errors declined only very slightly with improved relatedness information. When partitioning maternal effects into separate genetic and environmental components, maternal genetic effects found in juvenile traits increased substantially across the three relatedness estimates. Heritability declined compared to parallel models where only a maternal environment effect was fitted, suggesting that maternal genetic effects are confounded with direct genetic effects and that more accurate estimates of relatedness were better able to separate maternal genetic effects from direct genetic effects. We found that the heritability captured by SNP markers asymptoted at about half the SNPs available, suggesting that denser marker panels are not necessarily required for precise and unbiased heritability estimates. Finally, we present guidelines for the use of genomic relatedness in future quantitative genetics

  2. Information-theoretic indices and an approximate significance test for testing the molecular clock hypothesis with genetic distances.

    PubMed

    Xia, Xuhua

    2009-09-01

    Distance-based phylogenetic methods are widely used in biomedical research. However, distance-based dating of speciation events and the test of the molecular clock hypothesis are relatively underdeveloped. Here I develop an approximate test of the molecular clock hypothesis for distance-based trees, as well as information-theoretic indices that have been used frequently in model selection, for use with distance matrices. The results are in good agreement with the conventional sequence-based likelihood ratio test. Among the information-theoretic indices, AICu is the most consistent with the sequence-based likelihood ratio test. The confidence in model selection by the indices can be evaluated by bootstrapping. I illustrate the usage of the indices and the approximate significance test with both empirical and simulated sequences. The tests show that distance matrices from protein gel electrophoresis and from genome rearrangement events do not violate the molecular clock hypothesis, and that the evolution of the third codon position conforms to the molecular clock hypothesis better than the second codon position in vertebrate mitochondrial genes. I outlined evolutionary distances that are appropriate for phylogenetic reconstruction and dating.

  3. Genetic toxicology: web resources.

    PubMed

    Young, Robert R

    2002-04-25

    Genetic toxicology is the scientific discipline dealing with the effects of chemical, physical and biological agents on the heredity of living organisms. The Internet offers a wide range of online digital resources for the field of Genetic Toxicology. The history of genetic toxicology and electronic data collections are reviewed. Web-based resources at US National Library of Medicine (NLM), including MEDLINE, PUBMED, Gateway, Entrez, and TOXNET, are discussed. Search strategies and Medical Subject Headings (MeSH) are reviewed in the context of genetic toxicology. The TOXNET group of databases are discussed with emphasis on those databases with genetic toxicology content including GENE-TOX, TOXLINE, Hazardous Substances Data Bank, Integrated Risk Information System, and Chemical Carcinogenesis Research Information System. Location of chemical information including chemical structure and linkage to health and regulatory information using CHEMIDPLUS at NLM and other databases is reviewed. Various government agencies have active genetic toxicology research programs or use genetic toxicology data to assist fulfilling the agency's mission. Online resources at the US Food and Drug Administration (FDA), the US Environmental Protection Agency (EPA), the National Institutes of Environmental Health Sciences, and the National Toxicology Program (NTP) are outlined. Much of the genetic toxicology for pharmaceuticals, industrial chemicals and pesticides that is performed in the world is regulatory-driven. Regulatory web resources are presented for the laws mandating testing, guidelines on study design, Good Laboratory Practice (GLP) regulations, and requirements for electronic data collection and reporting. The Internet provides a range of other supporting resources to the field of genetic toxicology. The web links for key professional societies and journals in genetic toxicology are listed. Distance education, educational media resources, and job placement services are also

  4. The synthesis paradigm in genetics.

    PubMed

    Rice, William R

    2014-02-01

    Experimental genetics with model organisms and mathematically explicit genetic theory are generally considered to be the major paradigms by which progress in genetics is achieved. Here I argue that this view is incomplete and that pivotal advances in genetics--and other fields of biology--are also made by synthesizing disparate threads of extant information rather than generating new information from experiments or formal theory. Because of the explosive expansion of information in numerous "-omics" data banks, and the fragmentation of genetics into numerous subdisciplines, the importance of the synthesis paradigm will likely expand with time.

  5. Medical genetics

    SciTech Connect

    Jorde, L.B.; Carey, J.C.; White, R.L.

    1995-10-01

    This book on the subject of medical genetics is a textbook aimed at a very broad audience: principally, medical students, nursing students, graduate, and undergraduate students. The book is actually a primer of general genetics as applied to humans and provides a well-balanced introduction to the scientific and clinical basis of human genetics. The twelve chapters include: Introduction, Basic Cell Biology, Genetic Variation, Autosomal Dominant and Recessive Inheritance, Sex-linked and Mitochondrial Inheritance, Clinical Cytogenetics, Gene Mapping, Immunogenetics, Cancer Genetics, Multifactorial Inheritance and Common Disease, Genetic Screening, Genetic Diagnosis and Gene Therapy, and Clinical Genetics and Genetic Counseling.

  6. Development of a database system and image viewer to assist in the correlation of histopathologic features and digital image analysis with clinical and molecular genetic information.

    PubMed

    Yagi, Yukako; Riedlinger, Gregory; Xu, Xun; Nakamura, Akira; Levy, Bruce; Iafrate, A John; Mino-Kenudson, Mari; Klepeis, Veronica E

    2016-02-01

    Pathologists are required to integrate data from multiple sources when making a diagnosis. Furthermore, whole slide imaging (WSI) and next generation sequencing will escalate data size and complexity. Development of well-designed databases that can allow efficient navigation between multiple data types is necessary for both clinical and research purposes. We developed and evaluated an interactive, web-based database that integrates clinical, histologic, immunohistochemical and genetic information to aid in pathologic diagnosis and interpretation with nine lung adenocarcinoma cases. To minimize sectioning artifacts, representative blocks were serially sectioned using automated tissue sectioning (Kurabo Industries, Osaka Japan) and selected slides were stained by multiple techniques, (hematoxylin and eosin [H&E], immunohistochemistry [IHC] or fluorescence in situ hybridization [FISH]). Slides were digitized by WSI scanners. An interactive relational database was designed based on a list of proposed fields covering a variety of clinical, pathologic and molecular parameters. By focusing on the three main tasks of 1.) efficient management of textual information, 2.) effective viewing of all varieties of stained whole slide images (WSI), and 3.) assistance in evaluating WSI with computer-aided diagnosis, this database prototype shows great promise for multi-modality research and diagnosis. PMID:26778830

  7. Population genetic dynamics of an invasion reconstructed from the sediment egg bank.

    PubMed

    Möst, Markus; Oexle, Sarah; Marková, Silvia; Aidukaite, Dalia; Baumgartner, Livia; Stich, Hans-Bernd; Wessels, Martin; Martin-Creuzburg, Dominik; Spaak, Piet

    2015-08-01

    Biological invasions are a global issue with far-reaching consequences for single species, communities and whole ecosystems. Our understanding of modes and mechanisms of biological invasions requires knowledge of the genetic processes associated with successful invasions. In many instances, this information is particularly difficult to obtain as the initial phases of the invasion process often pass unnoticed and we rely on inferences from contemporary population genetic data. Here, we combined historic information with the genetic analysis of resting eggs to reconstruct the invasion of Daphnia pulicaria into Lower Lake Constance (LLC) in the 1970s from the resting egg bank in the sediments. We identified the invader as 'European D. pulicaria' originating from meso- and eutrophic lowland lakes and ponds in Central Europe. The founding population was characterized by extremely low genetic variation in the resting egg bank that increased considerably over time. Furthermore, strong evidence for selfing and/or biparental inbreeding was found during the initial phase of the invasion, followed by a drop of selfing rate to low levels in subsequent decades. Moreover, the increase in genetic variation was most pronounced during early stages of the invasion, suggesting additional introductions during this period. Our study highlights that genetic data covering the entire invasion process from its beginning can be crucial to accurately reconstruct the invasion history of a species. We show that propagule banks can preserve such information enabling the study of population genetic dynamics and sources of genetic variation in successful invasive populations. PMID:26122166

  8. Population genetic dynamics of an invasion reconstructed from the sediment egg bank.

    PubMed

    Möst, Markus; Oexle, Sarah; Marková, Silvia; Aidukaite, Dalia; Baumgartner, Livia; Stich, Hans-Bernd; Wessels, Martin; Martin-Creuzburg, Dominik; Spaak, Piet

    2015-08-01

    Biological invasions are a global issue with far-reaching consequences for single species, communities and whole ecosystems. Our understanding of modes and mechanisms of biological invasions requires knowledge of the genetic processes associated with successful invasions. In many instances, this information is particularly difficult to obtain as the initial phases of the invasion process often pass unnoticed and we rely on inferences from contemporary population genetic data. Here, we combined historic information with the genetic analysis of resting eggs to reconstruct the invasion of Daphnia pulicaria into Lower Lake Constance (LLC) in the 1970s from the resting egg bank in the sediments. We identified the invader as 'European D. pulicaria' originating from meso- and eutrophic lowland lakes and ponds in Central Europe. The founding population was characterized by extremely low genetic variation in the resting egg bank that increased considerably over time. Furthermore, strong evidence for selfing and/or biparental inbreeding was found during the initial phase of the invasion, followed by a drop of selfing rate to low levels in subsequent decades. Moreover, the increase in genetic variation was most pronounced during early stages of the invasion, suggesting additional introductions during this period. Our study highlights that genetic data covering the entire invasion process from its beginning can be crucial to accurately reconstruct the invasion history of a species. We show that propagule banks can preserve such information enabling the study of population genetic dynamics and sources of genetic variation in successful invasive populations.

  9. Genetic algorithms

    NASA Technical Reports Server (NTRS)

    Wang, Lui; Bayer, Steven E.

    1991-01-01

    Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

  10. Genetic secrets: Protecting privacy and confidentiality in the genetic era

    SciTech Connect

    Rothstein, M.A.

    1998-07-01

    Few developments are likely to affect human beings more profoundly in the long run than the discoveries resulting from advances in modern genetics. Although the developments in genetic technology promise to provide many additional benefits, their application to genetic screening poses ethical, social, and legal questions, many of which are rooted in issues of privacy and confidentiality. The ethical, practical, and legal ramifications of these and related questions are explored in depth. The broad range of topics includes: the privacy and confidentiality of genetic information; the challenges to privacy and confidentiality that may be projected to result from the emerging genetic technologies; the role of informed consent in protecting the confidentiality of genetic information in the clinical setting; the potential uses of genetic information by third parties; the implications of changes in the health care delivery system for privacy and confidentiality; relevant national and international developments in public policies, professional standards, and laws; recommendations; and the identification of research needs.

  11. What Are the Risks and Limitations of Genetic Testing?

    MedlinePlus

    ... testing? What are the risks and limitations of genetic testing? The physical risks associated with most genetic ... more information about the risks and limitations of genetic testing: The American College of Medical Genetics and ...

  12. What Do the Results of Genetic Tests Mean?

    MedlinePlus

    ... genetic tests mean? What do the results of genetic tests mean? The results of genetic tests are ... type of result. For more information about interpreting genetic test results: The National Cancer Institute fact sheet ...

  13. Molecular genetics to inform spatial management in benthic invertebrate fisheries: a case study using the Australian greenlip abalone.

    PubMed

    Miller, K J; Mundy, C N; Mayfield, S

    2014-10-01

    Hierarchical sampling and subsequent microsatellite genotyping of >2300 Haliotis laevigata (greenlip abalone) from 19 locations distributed across five biogeographic regions have substantially advanced our knowledge of population structure and connectivity in this commercially important species. The study has found key differences in stock structure of H. laevigata compared with the sympatric and congeneric Haliotis rubra (blacklip abalone) and yielded valuable insights into the management of fisheries targeting species characterized by spatial structure at small scales (i.e. S-fisheries). As with H. rubra, H. laevigata comprise a series of metapopulations with strong self-recruitment. However, the spatial extent of H. laevigata metapopulations (reefal areas around 30 km(2) ; distances of up to 135 km are effective barriers to larval dispersal) was substantially greater than that identified for H. rubra (Miller et al. 2009). Differences in the dynamics and scale of population processes, even between congeneric haliotids as made evident in this study, imply that for S-fisheries, it is difficult to generalize about the potential consequences of life history commonalities. Consequently, species-specific management reflective of the population structure of the target species remains particularly important. This will likely require integration of information about stock structure and connectivity with data on life history and population dynamics to determine the necessary input (e.g. number of fishers, fishing effort) and output (e.g. minimum legal size, total allowable catch) controls to underpin their sustainable management.

  14. Molecular genetics to inform spatial management in benthic invertebrate fisheries: a case study using the Australian greenlip abalone.

    PubMed

    Miller, K J; Mundy, C N; Mayfield, S

    2014-10-01

    Hierarchical sampling and subsequent microsatellite genotyping of >2300 Haliotis laevigata (greenlip abalone) from 19 locations distributed across five biogeographic regions have substantially advanced our knowledge of population structure and connectivity in this commercially important species. The study has found key differences in stock structure of H. laevigata compared with the sympatric and congeneric Haliotis rubra (blacklip abalone) and yielded valuable insights into the management of fisheries targeting species characterized by spatial structure at small scales (i.e. S-fisheries). As with H. rubra, H. laevigata comprise a series of metapopulations with strong self-recruitment. However, the spatial extent of H. laevigata metapopulations (reefal areas around 30 km(2) ; distances of up to 135 km are effective barriers to larval dispersal) was substantially greater than that identified for H. rubra (Miller et al. 2009). Differences in the dynamics and scale of population processes, even between congeneric haliotids as made evident in this study, imply that for S-fisheries, it is difficult to generalize about the potential consequences of life history commonalities. Consequently, species-specific management reflective of the population structure of the target species remains particularly important. This will likely require integration of information about stock structure and connectivity with data on life history and population dynamics to determine the necessary input (e.g. number of fishers, fishing effort) and output (e.g. minimum legal size, total allowable catch) controls to underpin their sustainable management. PMID:25211183

  15. Problems and Their Solutions in Genetic Counseling Education in Japan

    PubMed Central

    Kohzaki, Hidetsugu

    2014-01-01

    With the expansion of novel chromosome testing, a career as a certified genetic counselor has been gathering a lot of attention. However, few people certified as a genetic counselor after completing postgraduate courses are able to find employment as a genetic counselor, and their salaries are quite low. It is also questionable whether or not such newly graduated genetic counselors, who have limited life experience and knowledge, can fully understand family issues and properly perform counseling sessions. To address these issues, a wide range of education and training may be necessary. In this study, we examined current problems in genetic counseling education in Japan, and proposed effective measures to address these problems. Toward creating a new society, we are currently establishing a national qualification system and cultivating qualified professionals capable of providing patients with accurate information on chromosome and genetic testing. In addition, these professionals could encourage younger generations to have an interest in genetic counseling. I also hope that these professionals will work not only in Japan but all over the world. PMID:25121085

  16. Rapid optimization of blast wave mitigation strategies using Quiet Direct Simulation and Genetic Algorithm

    NASA Astrophysics Data System (ADS)

    Smith, Matthew R.; Kuo, Fang-An; Hsieh, Chih-Wei; Yu, Jen-Perng; Wu, Jong-Shinn; Ferguson, Alex

    2010-06-01

    Presented is a rapid calculation tool for the optimization of blast wave related mitigation strategies. The motion of gas resulting from a blast wave (specified by the user) is solved by the Quiet Direct Simulation (QDS) method - a rapid kinetic theory-based finite volume method. The optimization routine employed is a newly developed Genetic Algorithm (GA) which is demonstrated to be similar to a Differential Evolution (DE) scheme with several modifications. In any Genetic Algorithm, individuals contain genetic information which is passed on to newly created individuals in successive generations. The results from unsteady QDS simulations are used to determine the individual's "genetic fitness" which is employed by the proposed Genetic Algorithm during the reproduction process. The combined QDS/GA algorithm is applied to various test cases and finally the optimization of a non-trivial blast wave mitigation strategy. Both QDS and the proposed GA are demonstrated to perform with minimal computational expense while accurately solving the optimization problems presented.

  17. Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice

    PubMed Central

    Badoni, Saurabh; Das, Sweta; Sayal, Yogesh K.; Gopalakrishnan, S.; Singh, Ashok K.; Rao, Atmakuri R.; Agarwal, Pinky; Parida, Swarup K.; Tyagi, Akhilesh K.

    2016-01-01

    We developed genome-wide 84634 ISM (intron-spanning marker) and 16510 InDel-fragment length polymorphism-based ILP (intron-length polymorphism) markers from genes physically mapped on 12 rice chromosomes. These genic markers revealed much higher amplification-efficiency (80%) and polymorphic-potential (66%) among rice accessions even by a cost-effective agarose gel-based assay. A wider level of functional molecular diversity (17–79%) and well-defined precise admixed genetic structure was assayed by 3052 genome-wide markers in a structured population of indica, japonica, aromatic and wild rice. Six major grain weight QTLs (11.9–21.6% phenotypic variation explained) were mapped on five rice chromosomes of a high-density (inter-marker distance: 0.98 cM) genetic linkage map (IR 64 x Sonasal) anchored with 2785 known/candidate gene-derived ISM and ILP markers. The designing of multiple ISM and ILP markers (2 to 4 markers/gene) in an individual gene will broaden the user-preference to select suitable primer combination for efficient assaying of functional allelic variation/diversity and realistic estimation of differential gene expression profiles among rice accessions. The genomic information generated in our study is made publicly accessible through a user-friendly web-resource, “Oryza ISM-ILP marker” database. The known/candidate gene-derived ISM and ILP markers can be enormously deployed to identify functionally relevant trait-associated molecular tags by optimal-resource expenses, leading towards genomics-assisted crop improvement in rice. PMID:27032371

  18. Genetic Analysis in Maize Foundation Parents with Mapping Population and Testcross Population: Ye478 Carried More Favorable Alleles and Using QTL Information Could Improve Foundation Parents

    PubMed Central

    Liu, Yinghong; Hou, Xianbin; Xiao, Qianlin; Yi, Qiang; Bian, Shaowei; Hu, Yufeng; Liu, Hanmei; Zhang, Junjie; Hao, Xiaoqin; Cheng, Weidong; Li, Yu; Huang, Yubi

    2016-01-01

    The development of maize foundation parents is an important part of genetics and breeding research, and applying new genetic information to produce foundation parents has been challenging. In this study, we focused on quantitative trait loci (QTLs) and general combining ability (GCA) of Ye478, a widely used foundation parent in China. We developed three sets of populations for QTL mapping and to analyze the GCA for some agronomic traits. The assessment of 15 traits resulted in the detection of 251 QTLs in six tested environments, with 119 QTLs identified through a joint analysis across all environments. Further, analyses revealed that most favorable alleles for plant type-related traits were from Ye478, and more than half of the favorable alleles for yield-related traits were from R08, another foundation parent used in southwestern China, suggesting that different types of foundation parents carried different favorable alleles. We observed that the GCA for most traits (e.g., plant height and 100-kernel weight) was maintained in the inbred lines descended from the foundation parents. Additionally, the continuous improvement in the GCA of the descendants of the foundation parents was consistent with the main trend in maize breeding programs. We identified three significant genomic regions that were highly conserved in three Ye478 descendants, including the stable QTL for plant height. The GCA for the traits in the F7 generation revealed that the QTLs for the given traits per se were affected by additive effects in the same way in different populations. PMID:27721817

  19. Genetics Home Reference: osteopetrosis

    MedlinePlus

    ... Open All Close All Description Osteopetrosis is a bone disease that makes bones abnormally dense and prone to ... Other Names for This Condition congenital osteopetrosis marble bone disease osteopetroses Related Information How are genetic conditions and ...

  20. Genetics Home Reference: alkaptonuria

    MedlinePlus

    ... homogentisate oxidase. This enzyme helps break down the amino acids phenylalanine and tyrosine, which are important building blocks ... Resources MedlinePlus (2 links) Encyclopedia: Alkaptonuria Health Topic: Amino Acid Metabolism Disorders Genetic and Rare Diseases Information Center ( ...