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Sample records for accurate genetic information

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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...

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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.

  11. Bayesian statistical treatment of the fluorescence of AFLP bands leads to accurate genetic structure inference.

    PubMed

    Gaggiotti, Oscar E

    2010-11-01

    Ever since the introduction of allozymes in the 1960s, evolutionary biologists and ecologists have continued to search for more powerful molecular markers to estimate important parameters such as effective population size and migration rates and to make inferences about the demographic history of populations, the relationships between individuals and the genetic architecture of phenotypic variation (Bensch & Akesson 2005; Bonin et al. 2007). Choosing a marker requires a thorough consideration of the trade-offs associated with the different techniques and the type of data obtained from them. Some markers can be very informative but require substantial amounts of start-up time (e.g. microsatellites), while others require very little time but are much less polymorphic. Amplified fragment length polymorphism (AFLP) is a firmly established molecular marker technique that falls in this latter category. AFLPs are widely distributed throughout the genome and can be used on organisms for which there is no a priori sequence information (Meudt & Clarke 2007). These properties together with their moderate cost and short start-up time have made them the method of choice for many molecular ecology studies of wild species (Bensch & Akesson 2005). However, they have a major disadvantage, they are dominant. This represents a very important limitation because many statistical genetics methods appropriate for molecular ecology studies require the use of codominant markers. In this issue, Foll et al. (2010) present an innovative hierarchical Bayesian method that overcomes this limitation. The proposed approach represents a comprehensive statistical treatment of the fluorescence of AFLP bands and leads to accurate inferences about the genetic structure of natural populations. Besides allowing a quasi-codominant treatment of AFLPs, this new method also solves the difficult problems posed by subjectivity in the scoring of AFLP bands. PMID:20958811

  12. Fast and Accurate Construction of Ultra-Dense Consensus Genetic Maps Using Evolution Strategy Optimization

    PubMed Central

    Mester, David; Ronin, Yefim; Schnable, Patrick; Aluru, Srinivas; Korol, Abraham

    2015-01-01

    Our aim was to develop a fast and accurate algorithm for constructing consensus genetic maps for chip-based SNP genotyping data with a high proportion of shared markers between mapping populations. Chip-based genotyping of SNP markers allows producing high-density genetic maps with a relatively standardized set of marker loci for different mapping populations. The availability of a standard high-throughput mapping platform simplifies consensus analysis by ignoring unique markers at the stage of consensus mapping thereby reducing mathematical complicity of the problem and in turn analyzing bigger size mapping data using global optimization criteria instead of local ones. Our three-phase analytical scheme includes automatic selection of ~100-300 of the most informative (resolvable by recombination) markers per linkage group, building a stable skeletal marker order for each data set and its verification using jackknife re-sampling, and consensus mapping analysis based on global optimization criterion. A novel Evolution Strategy optimization algorithm with a global optimization criterion presented in this paper is able to generate high quality, ultra-dense consensus maps, with many thousands of markers per genome. This algorithm utilizes "potentially good orders" in the initial solution and in the new mutation procedures that generate trial solutions, enabling to obtain a consensus order in reasonable time. The developed algorithm, tested on a wide range of simulated data and real world data (Arabidopsis), outperformed two tested state-of-the-art algorithms by mapping accuracy and computation time. PMID:25867943

  13. 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

  14. 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

  15. 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.

  16. The Good, the Strong, and the Accurate: Preschoolers' Evaluations of Informant Attributes

    ERIC Educational Resources Information Center

    Fusaro, Maria; Corriveau, Kathleen H.; Harris, Paul L.

    2011-01-01

    Much recent evidence shows that preschoolers are sensitive to the accuracy of an informant. Faced with two informants, one of whom names familiar objects accurately and the other inaccurately, preschoolers subsequently prefer to learn the names and functions of unfamiliar objects from the more accurate informant. This study examined the inference…

  17. [Informed consent for genetic information management in Colombian law].

    PubMed

    Gómez Córdoba, Ana Isabel

    2011-01-01

    Deciphering the human genome has allowed the development of new health care ways which have been generically referred to as genomic medicine. However, this new knowledge is not devoid of risks related to the access and use of genetic information, involving not only the individual, but also the biological family, ethnic group and community to which he/she belong to. This affects both individual and collective rights, which must be protected by law. This manuscript reviews the Colombian law, specifically in terms of the access and use of genetic information for diagnostic and treatment purposes, focusing on the informed consent process. The concept of genetic information, the risks and benefits associated with genetic data management and the description and critical analysis of the present Colombian regulations were thus reviewed. As a conclusion, the juridical framework of Colombia shows deficiencies regarding the protection of both individual and collective rights linked to the access and use of genetic information. PMID:22984754

  18. Accurate Inference of Subtle Population Structure (and Other Genetic Discontinuities) Using Principal Coordinates

    PubMed Central

    Reeves, Patrick A.; Richards, Christopher M.

    2009-01-01

    Background Accurate inference of genetic discontinuities between populations is an essential component of intraspecific biodiversity and evolution studies, as well as associative genetics. The most widely-used methods to infer population structure are model-based, Bayesian MCMC procedures that minimize Hardy-Weinberg and linkage disequilibrium within subpopulations. These methods are useful, but suffer from large computational requirements and a dependence on modeling assumptions that may not be met in real data sets. Here we describe the development of a new approach, PCO-MC, which couples principal coordinate analysis to a clustering procedure for the inference of population structure from multilocus genotype data. Methodology/Principal Findings PCO-MC uses data from all principal coordinate axes simultaneously to calculate a multidimensional “density landscape”, from which the number of subpopulations, and the membership within subpopulations, is determined using a valley-seeking algorithm. Using extensive simulations, we show that this approach outperforms a Bayesian MCMC procedure when many loci (e.g. 100) are sampled, but that the Bayesian procedure is marginally superior with few loci (e.g. 10). When presented with sufficient data, PCO-MC accurately delineated subpopulations with population Fst values as low as 0.03 (G'st>0.2), whereas the limit of resolution of the Bayesian approach was Fst = 0.05 (G'st>0.35). Conclusions/Significance We draw a distinction between population structure inference for describing biodiversity as opposed to Type I error control in associative genetics. We suggest that discrete assignments, like those produced by PCO-MC, are appropriate for circumscribing units of biodiversity whereas expression of population structure as a continuous variable is more useful for case-control correction in structured association studies. PMID:19172174

  19. 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…

  20. 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

  1. 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. PMID:26956430

  2. Alignment of capillary electrophoresis-mass spectrometry datasets using accurate mass information.

    PubMed

    Nevedomskaya, Ekaterina; Derks, Rico; Deelder, André M; Mayboroda, Oleg A; Palmblad, Magnus

    2009-12-01

    Capillary electrophoresis-mass spectrometry (CE-MS) is a powerful technique for the analysis of small soluble compounds in biological fluids. A major drawback of CE is the poor migration time reproducibility, which makes it difficult to combine data from different experiments and correctly assign compounds. A number of alignment algorithms have been developed but not all of them can cope with large and irregular time shifts between CE-MS runs. Here we present a genetic algorithm designed for alignment of CE-MS data using accurate mass information. The utility of the algorithm was demonstrated on real data, and the results were compared with one of the existing packages. The new algorithm showed a significant reduction of elution time variation in the aligned datasets. The importance of mass accuracy for the performance of the algorithm was also demonstrated by comparing alignments of datasets from a standard time-of-flight (TOF) instrument with those from the new ultrahigh resolution TOF maXis (Bruker Daltonics). PMID:19826795

  3. 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. PMID:25624198

  4. 16 CFR 1101.32 - Reasonable steps to assure information is accurate.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... Reasonable Steps Commission Will Take To Assure Information It Discloses Is Accurate, and That Disclosure Is..., injuries or safety-related incidents involving such a product. Such persons would include, for example, a... set forth below are the steps the Commission will take to analyze the accuracy of information which...

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

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Reasonable Steps Commission Will Take To Assure Information It Discloses Is Accurate, and That Disclosure Is..., injuries or safety-related incidents involving such a product. Such persons would include, for example, a... set forth below are the steps the Commission will take to analyze the accuracy of information which...

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

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Reasonable Steps Commission Will Take To Assure Information It Discloses Is Accurate, and That Disclosure Is..., injuries or safety-related incidents involving such a product. Such persons would include, for example, a... set forth below are the steps the Commission will take to analyze the accuracy of information which...

  7. 16 CFR 1101.32 - Reasonable steps to assure information is accurate.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... Reasonable Steps Commission Will Take To Assure Information It Discloses Is Accurate, and That Disclosure Is..., injuries or safety-related incidents involving such a product. Such persons would include, for example, a... set forth below are the steps the Commission will take to analyze the accuracy of information which...

  8. 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 accurate. 1101.32 Section 1101.32 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY ACT REGULATIONS INFORMATION DISCLOSURE UNDER SECTION 6(b) OF THE CONSUMER PRODUCT SAFETY ACT Reasonable Steps Commission Will Take...

  9. 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.

  10. Genetic information and self-organized criticality

    NASA Astrophysics Data System (ADS)

    Wills, P. R.; Marshall, J. M.; Smith, P. J.

    2004-12-01

    The numerical fitnesses of species defined in the Bak-Sneppen model of self-organized criticality are interpreted as binary strings. This allows new species to be generated by mutation of survivors. It is shown that selection in Bak-Sneppen systems defined on both uniform and random lattices produces genotypes in conformity with the Eigen criterion for the accumulation of genetic information in macromolecular sequences.

  11. 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...

  12. Genetic information transfer promotes cooperation in bacteria.

    PubMed

    Dimitriu, Tatiana; Lotton, Chantal; Bénard-Capelle, Julien; Misevic, Dusan; Brown, Sam P; Lindner, Ariel B; Taddei, François

    2014-07-29

    Many bacterial species are social, producing costly secreted "public good" molecules that enhance the growth of neighboring cells. The genes coding for these cooperative traits are often propagated via mobile genetic elements and can be virulence factors from a biomedical perspective. Here, we present an experimental framework that links genetic information exchange and the selection of cooperative traits. Using simulations and experiments based on a synthetic bacterial system to control public good secretion and plasmid conjugation, we demonstrate that horizontal gene transfer can favor cooperation. In a well-mixed environment, horizontal transfer brings a direct infectious advantage to any gene, regardless of its cooperation properties. However, in a structured population transfer selects specifically for cooperation by increasing the assortment among cooperative alleles. Conjugation allows cooperative alleles to overcome rarity thresholds and invade bacterial populations structured purely by stochastic dilution effects. Our results provide an explanation for the prevalence of cooperative genes on mobile elements, and suggest a previously unidentified benefit of horizontal gene transfer for bacteria. PMID:25024219

  13. Genetic information transfer promotes cooperation in bacteria

    PubMed Central

    Dimitriu, Tatiana; Lotton, Chantal; Bénard-Capelle, Julien; Misevic, Dusan; Brown, Sam P.; Lindner, Ariel B.; Taddei, François

    2014-01-01

    Many bacterial species are social, producing costly secreted “public good” molecules that enhance the growth of neighboring cells. The genes coding for these cooperative traits are often propagated via mobile genetic elements and can be virulence factors from a biomedical perspective. Here, we present an experimental framework that links genetic information exchange and the selection of cooperative traits. Using simulations and experiments based on a synthetic bacterial system to control public good secretion and plasmid conjugation, we demonstrate that horizontal gene transfer can favor cooperation. In a well-mixed environment, horizontal transfer brings a direct infectious advantage to any gene, regardless of its cooperation properties. However, in a structured population transfer selects specifically for cooperation by increasing the assortment among cooperative alleles. Conjugation allows cooperative alleles to overcome rarity thresholds and invade bacterial populations structured purely by stochastic dilution effects. Our results provide an explanation for the prevalence of cooperative genes on mobile elements, and suggest a previously unidentified benefit of horizontal gene transfer for bacteria. PMID:25024219

  14. Accurate genetic diagnosis of Finnish pulmonary arterial hypertension patients using oligonucleotide-selective sequencing

    PubMed Central

    Vattulainen, Sanna; Aho, Joonas; Salmenperä, Pertteli; Bruce, Siina; Tallila, Jonna; Gentile, Massimiliano; Sankelo, Marja; Laitinen, Tarja; Koskenvuo, Juha W; Alastalo, Tero-Pekka; Myllykangas, Samuel

    2015-01-01

    The genetic basis of pulmonary arterial hypertension (PAH) among Finnish PAH patients is poorly understood. We adopted a novel-targeted next-generation sequencing (NGS) approach called Oligonucleotide-Selective Sequencing (OS-Seq) and developed a custom data analysis and interpretation pipeline to identify pathogenic base substitutions, insertions, and deletions in seven genes associated with PAH (BMPR2, BMPR1B, ACVRL1, ENG, SMAD9, CAV1, and KCNK3) from Finnish PAH patients. This study represents the first clinical study with OS-Seq technology on patients suffering from a rare genetic disorder. We analyzed DNA samples from 21 Finnish PAH patients, whose BMPR2 and ACVRL1 mutation status had been previously studied using Sanger sequencing. Our sequencing panel covered 100% of the targeted base pairs with >15× sequencing depth. Pathogenic base substitutions were identified in the BMPR2 gene in 29% of the Finnish PAH cases. Two of the pathogenic variant-positive patients had been previously tested negative using Sanger sequencing. No clinically significant variants were identified in the six other PAH genes. Our study validates the use of targeted OS-Seq for genetic diagnostics of PAH and revealed pathogenic variants that had been previously missed using Sanger sequencing. PMID:26247051

  15. 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

  16. Genetics

    MedlinePlus

    Homozygous; 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 ...

  17. 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 ...

  18. 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

  19. Cas9-chromatin binding information enables more accurate CRISPR off-target prediction

    PubMed Central

    Singh, Ritambhara; Kuscu, Cem; Quinlan, Aaron; Qi, Yanjun; Adli, Mazhar

    2015-01-01

    The CRISPR system has become a powerful biological tool with a wide range of applications. However, improving targeting specificity and accurately predicting potential off-targets remains a significant goal. Here, we introduce a web-based CRISPR/Cas9 Off-target Prediction and Identification Tool (CROP-IT) that performs improved off-target binding and cleavage site predictions. Unlike existing prediction programs that solely use DNA sequence information; CROP-IT integrates whole genome level biological information from existing Cas9 binding and cleavage data sets. Utilizing whole-genome chromatin state information from 125 human cell types further enhances its computational prediction power. Comparative analyses on experimentally validated datasets show that CROP-IT outperforms existing computational algorithms in predicting both Cas9 binding as well as cleavage sites. With a user-friendly web-interface, CROP-IT outputs scored and ranked list of potential off-targets that enables improved guide RNA design and more accurate prediction of Cas9 binding or cleavage sites. PMID:26032770

  20. Accurate protein structure modeling using sparse NMR data and homologous structure information

    PubMed Central

    Thompson, James M.; Sgourakis, Nikolaos G.; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L.; Szyperski, Thomas; Montelione, Gaetano T.; Baker, David

    2012-01-01

    While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining , 13C, and 15N backbone and 13Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2–1.9 Å relative to the conventional determined NMR ensembles and of 0.9–1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments. PMID:22665781

  1. The Basingstoke Orthopaedic Database: a high quality accurate information system for audit.

    PubMed

    Barlow, I W; Flynn, N A; Britton, J M

    1994-11-01

    The accuracy of a computerised audit system custom produced for the Orthopaedic Department has been validated by comparison with operating theatre records and patients' case notes. The study revealed only 2.5 per cent missed entries; of the recorded entries information regarding the nature of the operation was found to be 92.5 per cent complete and 98 per cent accurate. The high percentage accuracy reflects the high degree of medical input in operation of the system. The Basingstoke Orthopaedic Database is flexible, cheap and easy to maintain. Data is stored in a form that is readily applicable to standard software packages. PMID:7598401

  2. 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.

  3. Providing community-based health practitioners with timely and accurate discharge medicines information

    PubMed Central

    2012-01-01

    Background Accurate and timely medication information at the point of discharge is essential for continuity of care. There are scarce data on the clinical significance if poor quality medicines information is passed to the next episode of care. This study aimed to compare the number and clinical significance of medication errors and omission in discharge medicines information, and the timeliness of delivery of this information to community-based health practitioners, between the existing Hospital Discharge Summary (HDS) and a pharmacist prepared Medicines Information Transfer Fax (MITF). Method The study used a sample of 80 hospital patients who were at high risk of medication misadventure, and who had a MITF completed in the study period June – October 2009 at a tertiary referral hospital. The medicines information in participating patients’ MITFs was validated against their Discharge Prescriptions (DP). Medicines information in each patient’s HDS was then compared with their validated MITF. An expert clinical panel reviewed identified medication errors and omissions to determine their clinical significance. The time between patient discharge and the dispatching of the MITF and the HDS to each patient’s community-based practitioners was calculated from hospital records. Results DPs for 77 of the 80 patients were available for comparison with their MITFs. Medicines information in 71 (92%) of the MITFs matched that of the DP. Comparison of the HDS against the MITF revealed that no HDS was prepared for 16 (21%) patients. Of the remaining 61 patients; 33 (54%), had required medications omitted and 38 (62%) had medication errors in their HDS. The Clinical Panel rated the significance of errors or omissions for 70 patients (16 with no HDS prepared and 54 who’s HDS was inconsistent with the validated MITF). In 17 patients the error or omission was rated as insignificant to minor; 23 minor to moderate; 24 moderate to major and 6 major to catastrophic. 28 (35

  4. 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).

  5. 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…

  6. 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…

  7. 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 ...

  8. Genetic and Rare Diseases Information Center

    MedlinePlus

    ... GARD Information Specialists can provide you with current, reliable, and easy to understand information about rare or ... GARD provides the public with access to current, reliable, and easy-to-understand information about rare or ...

  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. PMID:25539927

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

    PubMed Central

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

    2015-01-01

    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. PMID:25539927

  11. Fostering Informed Choice: Alleviating the Trauma of Genetic Abortions.

    PubMed

    Asbury, Bret D

    2015-01-01

    Each year, thousands of pregnant women learn of fetal abnormalities through prenatal genetic analysis. This discovery--made after a woman has initially declined to exercise her right to abort an unwanted pregnancy—raises the difficult and heart-wrenching question of whether to terminate on genetic grounds. Women considering a genetic abortion rely on information and support from health care providers to assist them in making their choice. Though intended to be objective and nondirective, the support women receive frequently provides them within complete and incomprehensible information having the effect of encouraging them to abort genetically anomalous fetuses. As a result, genetic terminations--which cause severe and long-standing psychological impacts such as pathological grief, depression and post-traumatic stress—are often the result of something other than a fully informed choice.Congress and eleven states have recognized the importance of better informing choice by passing legislation aimed at providing clearer and more balanced information to expectant mothers learning of fetal genetic abnormalities. But existing legislative remedies do not adequately address this problem, and this inadequacy will become more pronounced in future years as increases in access to prenatal genetic analysis further stretch the capabilities of the available support services.This Article describes the unique characteristics of terminations for a fetal abnormality, their troubling and persistent psychological impacts,and the reasons why they will become more common in future years. It then offers proposals for how to reconfigure the prenatal genetic counseling landscape in order to reduce the incidence of genetic terminations based on incomplete or misleading information, thereby alleviating their distinct psychological costs. Its overall objective is to ensure that women learning of prenatal genetic abnormalities have access to complete and comprehensible information prior to

  12. Computer Center: BASIC String Models of Genetic Information Transfer.

    ERIC Educational Resources Information Center

    Spain, James D., Ed.

    1984-01-01

    Discusses some of the major genetic information processes which may be modeled by computer program string manipulation, focusing on replication and transcription. Also discusses instructional applications of using string models. (JN)

  13. Autopoiesis and natural drift: genetic information, reproduction, and evolution revisited.

    PubMed

    Etxeberria, Arantza

    2004-01-01

    The contribution of the theory of autopoiesis to the definition of life and biological theory affirms biological autonomy as a central notion of scientific and philosophical inquiry, and opposes other biological approaches, based on the notion of genetic information, that consider reproduction and evolution to be the central aspects of life and living phenomenology. This article reviews the autopoietic criticisms of genetic information, reproduction, and evolution in the light of a biology that can solve the problem of living organization. PMID:15245632

  14. 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

  15. Data quality control in social surveys using genetic information.

    PubMed

    Li, Yi; Guo, Guang

    2014-01-01

    This article introduces a novel way of taking advantage of genetic data in social surveys for the purposes of data quality control. Genetic information could detect and repair data issues such as missing data, reporting errors, differences in measures of the same variable, and flawed data. Using data from two surveys, the College Roommate Study (ROOM) and the National Longitudinal Study of Adolescent Health (Add Health), we show that proportion identical by descent score (a measure of genetic relationships) can identify "misreported" and unreported sibling type and detect misrepresented participants, bio-ancestry score (a measure of ancestral population memberships) can repair and recover missing race and discrepancies among different measures of self-reported race, and sex chromosomal information may help cross-check self-reported sex. This article represents an initial effort to utilize genetic data for the purposes of data quality control. As genetic data become increasingly available, researchers may explore more approaches to improving data quality. PMID:25343368

  16. 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. PMID:24354624

  17. 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

  18. 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

  19. 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…

  20. 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…

  1. 29 CFR 1635.8 - Acquisition of genetic information.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... genetic information from a social media platform which he or she was given permission to access by the... demonstrate that the accommodation would impose an undue hardship on the operation of its business.” 29 CFR 1630.2(o)(1)(iii); 29 CFR 1630.9(a). In addition, if the employer's wellness program provides...

  2. 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.…

  3. 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

  4. 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…

  5. 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…

  6. Uncertainty principle of genetic information in a living cell

    PubMed Central

    Strippoli, Pierluigi; Canaider, Silvia; Noferini, Francesco; D'Addabbo, Pietro; Vitale, Lorenza; Facchin, Federica; Lenzi, Luca; Casadei, Raffaella; Carinci, Paolo; Zannotti, Maria; Frabetti, Flavia

    2005-01-01

    Background Formal description of a cell's genetic information should provide the number of DNA molecules in that cell and their complete nucleotide sequences. We pose the formal problem: can the genome sequence forming the genotype of a given living cell be known with absolute certainty so that the cell's behaviour (phenotype) can be correlated to that genetic information? To answer this question, we propose a series of thought experiments. Results We show that the genome sequence of any actual living cell cannot physically be known with absolute certainty, independently of the method used. There is an associated uncertainty, in terms of base pairs, equal to or greater than μs (where μ is the mutation rate of the cell type and s is the cell's genome size). Conclusion This finding establishes an "uncertainty principle" in genetics for the first time, and its analogy with the Heisenberg uncertainty principle in physics is discussed. The genetic information that makes living cells work is thus better represented by a probabilistic model rather than as a completely defined object. PMID:16197549

  7. Race-specific genetic risk score is more accurate than nonrace-specific genetic risk score for predicting prostate cancer and high-grade diseases

    PubMed Central

    Na, Rong; Ye, Dingwei; Qi, Jun; Liu, Fang; Lin, Xiaoling; Helfand, Brian T; Brendler, Charles B; Conran, Carly; Gong, Jian; Wu, Yishuo; Gao, Xu; Chen, Yaqing; Zheng, S Lilly; Mo, Zengnan; Ding, Qiang; Sun, Yinghao; Xu, Jianfeng

    2016-01-01

    Genetic risk score (GRS) based on disease risk-associated single nucleotide polymorphisms (SNPs) is an informative tool that can be used to provide inherited information for specific diseases in addition to family history. However, it is still unknown whether only SNPs that are implicated in a specific racial group should be used when calculating GRSs. The objective of this study is to compare the performance of race-specific GRS and nonrace-specific GRS for predicting prostate cancer (PCa) among 1338 patients underwent prostate biopsy in Shanghai, China. A race-specific GRS was calculated with seven PCa risk-associated SNPs implicated in East Asians (GRS7), and a nonrace-specific GRS was calculated based on 76 PCa risk-associated SNPs implicated in at least one racial group (GRS76). The means of GRS7 and GRS76 were 1.19 and 1.85, respectively, in the study population. Higher GRS7 and GRS76 were independent predictors for PCa and high-grade PCa in univariate and multivariate analyses. GRS7 had a better area under the receiver-operating curve (AUC) than GRS76 for discriminating PCa (0.602 vs 0.573) and high-grade PCa (0.603 vs 0.575) but did not reach statistical significance. GRS7 had a better (up to 13% at different cutoffs) positive predictive value (PPV) than GRS76. In conclusion, a race-specific GRS is more robust and has a better performance when predicting PCa in East Asian men than a GRS calculated using SNPs that are not shown to be associated with East Asians. PMID:27140652

  8. Race-specific genetic risk score is more accurate than nonrace-specific genetic risk score for predicting prostate cancer and high-grade diseases.

    PubMed

    Na, Rong; Ye, Dingwei; Qi, Jun; Liu, Fang; Lin, Xiaoling; Helfand, Brian T; Brendler, Charles B; Conran, Carly; Gong, Jian; Wu, Yishuo; Gao, Xu; Chen, Yaqing; Zheng, S Lilly; Mo, Zengnan; Ding, Qiang; Sun, Yinghao; Xu, Jianfeng

    2016-01-01

    Genetic risk score (GRS) based on disease risk-associated single nucleotide polymorphisms (SNPs) is an informative tool that can be used to provide inherited information for specific diseases in addition to family history. However, it is still unknown whether only SNPs that are implicated in a specific racial group should be used when calculating GRSs. The objective of this study is to compare the performance of race-specific GRS and nonrace-specific GRS for predicting prostate cancer (PCa) among 1338 patients underwent prostate biopsy in Shanghai, China. A race-specific GRS was calculated with seven PCa risk-associated SNPs implicated in East Asians (GRS7), and a nonrace-specific GRS was calculated based on 76 PCa risk-associated SNPs implicated in at least one racial group (GRS76). The means of GRS7 and GRS76 were 1.19 and 1.85, respectively, in the study population. Higher GRS7 and GRS76 were independent predictors for PCa and high-grade PCa in univariate and multivariate analyses. GRS7 had a better area under the receiver-operating curve (AUC) than GRS76 for discriminating PCa (0.602 vs 0.573) and high-grade PCa (0.603 vs 0.575) but did not reach statistical significance. GRS7 had a better (up to 13% at different cutoffs) positive predictive value (PPV) than GRS76. In conclusion, a race-specific GRS is more robust and has a better performance when predicting PCa in East Asian men than a GRS calculated using SNPs that are not shown to be associated with East Asians. PMID:27140652

  9. 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

  10. Dinucleotide repeat loci contribute highly informative genetic markers to the human chromosome 2 linkage map

    SciTech Connect

    Todd, S. ); Sherman, S.L. ); Naylor, S.L. )

    1993-06-01

    Microsatellite repeat loci can provide informative markers for genetic linkage. Currently, the human chromosome 2 genetic linkage map has very few highly polymorphic markers. Being such a large chromosome, it will require a large number of informative markers for the dense coverage desired to allow disease genes to be mapped quickly and accurately. Dinucleotide repeat loci from two anonymous chromosome 2 genomic DNA clones were sequenced so that oligonucleotide primers could be designed for amplifying each locus using the polymerase chain reaction (PCR). Five sets of PCR primers were also generated from nucleotide sequences in the GenBank Database of chromosome 2 genes containing dinucleotide repeats. In addition, one PCR primer pair was made that amplifies a restriction fragment length polymorphism on the TNP1 gene. These markers were placed on the CEPH genetic linkage map by screening the CEPH reference DNA panel with each primer set, combining these data with those of other markers previously placed on the map, and analyzing the combined data set using CRI-MAP and LINKAGE. The microsatellite loci are highly informative markers and the TNP1 locus, as expected, is only moderately informative. A map was constructed with 38 ordered loci (odds [ge] 1000:1) spanning 296 cM (male) and 476 cM (female) of chromosome 2 compared with 306 cM (male) and 529 cM (female) for a previous map of 20 markers. 32 refs., 2 figs., 3 tabs.

  11. The benefits of using genetic information to design prevention trials.

    PubMed

    Hu, Youna; Li, Li; Ehm, Margaret G; Bing, Nan; Song, Kijoung; Nelson, Matthew R; Talmud, Philippa J; Hingorani, Aroon D; Kumari, Meena; Kivimäki, Mika; Xu, Chun-Fang; Waterworth, Dawn M; Whittaker, John C; Abecasis, Gonçalo R; Spino, Cathie; Kang, Hyun Min

    2013-04-01

    Clinical trials for preventative therapies are complex and costly endeavors focused on individuals likely to develop disease in a short time frame, randomizing them to treatment groups, and following them over time. In such trials, statistical power is governed by the rate of disease events in each group and cost is determined by randomization, treatment, and follow-up. Strategies that increase the rate of disease events by enrolling individuals with high risk of disease can significantly reduce study size, duration, and cost. Comprehensive study of common, complex diseases has resulted in a growing list of robustly associated genetic markers. Here, we evaluate the utility--in terms of trial size, duration, and cost--of enriching prevention trial samples by combining clinical information with genetic risk scores to identify individuals at greater risk of disease. We also describe a framework for utilizing genetic risk scores in these trials and evaluating the associated cost and time savings. With type 1 diabetes (T1D), type 2 diabetes (T2D), myocardial infarction (MI), and advanced age-related macular degeneration (AMD) as examples, we illustrate the potential and limitations of using genetic data for prevention trial design. We illustrate settings where incorporating genetic information could reduce trial cost or duration considerably, as well as settings where potential savings are negligible. Results are strongly dependent on the genetic architecture of the disease, but we also show that these benefits should increase as the list of robustly associated markers for each disease grows and as large samples of genotyped individuals become available. PMID:23541341

  12. 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

  13. 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…

  14. QuShape: Rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis

    PubMed Central

    Karabiber, Fethullah; McGinnis, Jennifer L.; Favorov, Oleg V.; Weeks, Kevin M.

    2013-01-01

    Chemical probing of RNA and DNA structure is a widely used and highly informative approach for examining nucleic acid structure and for evaluating interactions with protein and small-molecule ligands. Use of capillary electrophoresis to analyze chemical probing experiments yields hundreds of nucleotides of information per experiment and can be performed on automated instruments. Extraction of the information from capillary electrophoresis electropherograms is a computationally intensive multistep analytical process, and no current software provides rapid, automated, and accurate data analysis. To overcome this bottleneck, we developed a platform-independent, user-friendly software package, QuShape, that yields quantitatively accurate nucleotide reactivity information with minimal user supervision. QuShape incorporates newly developed algorithms for signal decay correction, alignment of time-varying signals within and across capillaries and relative to the RNA nucleotide sequence, and signal scaling across channels or experiments. An analysis-by-reference option enables multiple, related experiments to be fully analyzed in minutes. We illustrate the usefulness and robustness of QuShape by analysis of RNA SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) experiments. PMID:23188808

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

    PubMed Central

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

    2015-01-01

    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. PMID:26713437

  16. 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

  17. 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. PMID:24375512

  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. A generalized information function applied to the genetic code.

    PubMed

    Alvager, T; Graham, G; Hilleke, R; Hutchison, D; Westgard, J

    1990-01-01

    The problem of the partitioning of the degeneracy of the codons in the genetic code is considered in the framework of a generalized information function IG = c sigma kpk(ln pk + G(Ek] where k represents the number of codons in a specific degeneracy class and G(Ek) is an arbitrary real valued function. For G(Ek) = 0 the Shannon information function is recovered. For a particular choice of G(Ek) that takes the dominance of even degeneracies into account, it is found by direct numerical calculations that the correct degeneracy partitioning appears as optimal values of the Ig function. This results is also supported by optimization calculations in which the generalized information function is regarded as a continuous function in the degeneracy variables. PMID:2073543

  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. PMID:19438445

  1. 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.

  2. 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

  3. 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

  4. 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

  5. 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

  6. Individual olfactory perception reveals meaningful nonolfactory genetic information

    PubMed Central

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

    2015-01-01

    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. PMID:26100865

  7. The Double Helix: Applying an Ethic of Care to the Duty to Warn Genetic Relatives of Genetic Information.

    PubMed

    Weaver, Meaghann

    2016-03-01

    Genetic testing reveals information about a patient's health status and predictions about the patient's future wellness, while also potentially disclosing health information relevant to other family members. With the increasing availability and affordability of genetic testing and the integration of genetics into mainstream medicine, the importance of clarifying the scope of confidentiality and the rules regarding disclosure of genetic findings to genetic relatives is prime. The United Nations International Declaration on Human Genetic Data urges an appreciation for principles of equality, justice, solidarity and responsibility in the context of genetic testing, including a commitment to honoring the privacy and security of the person tested. Considering this global mandate and recent professional statements in the context of a legal amendment to patient privacy policies in Australia, a fresh scrutiny of the legal history of a physician's duty to warn is warranted. This article inquiries whether there may be anything ethically or socially amiss with a potential future recommendation for health professionals or patients to universally disclose particular cancer predisposition genetic diagnosis to genetic family members. While much of the discussion remains applicable to all genetic diagnosis, the article focuses on the practice of disclosure within the context of BRCA1/2 diagnosis. An 'ethic of care' interpretation of legal tradition and current practice will serve to reconcile law and medical policy on the issue of physician disclosure of genetic results to family members without patient consent. PMID:26194147

  8. 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

  9. 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 ...

  10. Learning the Structure of High-Dimensional Manifolds with Self-Organizing Maps for Accurate Information Extraction

    NASA Astrophysics Data System (ADS)

    Zhang, Lili

    This work aims to improve the capability of accurate information extraction from high-dimensional data, with a specific neural learning paradigm, the Self-Organizing Map (SOM). The SOM is an unsupervised learning algorithm that can faithfully sense the manifold structure and support supervised learning of relevant information from the data. Yet open problems regarding SOM learning exist. We focus on the following two issues. (1) Evaluation of topology preservation. Topology preservation is essential for SOMs in faithful representation of manifold structure. However, in reality, topology violations are not unusual, especially when the data have complicated structure. Measures capable of accurately quantifying and informatively expressing topology violations are lacking. One contribution of this work is a new measure, the Weighted Differential Topographic Function (WDTF), which differentiates an existing measure, the Topographic Function (TF), and incorporates detailed data distribution as an importance weighting of violations to distinguish severe violations from insignificant ones. Another contribution is an interactive visual tool, TopoView, which facilitates the visual inspection of violations on the SOM lattice. We show the effectiveness of the combined use of the WDTF and TopoView through a simple two-dimensional data set and two hyperspectral images. (2) Learning multiple latent variables from high-dimensional data. We use an existing two-layer SOM-hybrid supervised architecture, which captures the manifold structure in its SOM hidden layer, and then, uses its output layer to perform the supervised learning of latent variables. In the customary way, the output layer only uses the strongest output of the SOM neurons. This severely limits the learning capability. We allow multiple, k, strongest responses of the SOM neurons for the supervised learning. Moreover, the fact that different latent variables can be best learned with different values of k motivates a

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

    PubMed Central

    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. PMID:15746980

  12. Preferences for Genetic and Behavioral Health Information: The Impact of Risk Factors and Disease Attributions

    PubMed Central

    O'Neill, Suzanne C.; McBride, Colleen M.; Alford, Sharon Hensley; Kaphingst, Kimberly A.

    2012-01-01

    Background Increased availability of genetic risk information may lead the public to give precedence to genetic causation over behavioral/environmental factors, decreasing behavior change motivation. Few population-based data inform these concerns. Purpose We assess the association of family history, behavioral risks, and causal attributions for diseases and the perceived value of pursuing information emphasizing health habits or genes. Method 1959 healthy adults completed a survey that assessed behavioral risk factors, family history, causal attributions of eight diseases, and health information preferences. Results Participants’ causal beliefs favored health behaviors over genetics. Interest in behavioral information was higher than in genetic information. As behavioral risk factors increased, inclination toward genetic explanations increased; interest in how health habits affect disease risk decreased. Conclusions Those at greatest need for behavior change may hold attributions that diminish interest in behavior change information. Enhancing understanding of gene-environment influences could be explored to increase engagement with health information. PMID:20532842

  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. PMID:26567205

  14. 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

  15. 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

  16. What Are Pregnant Women’s Information Needs and Information Seeking Behaviors Prior to Their Prenatal Genetic Counseling?

    PubMed Central

    Hsieh, Yichuan; Brennan, Patricia Flatley

    2005-01-01

    As a result of the Human Genome Project, more genetic diagnostic tests have become available to the public and genetic-related information has also grown exponentially. Pregnant women are now routinely offered tests for chromosomal disorders and screenings for genetic conditions that are relevant to their situations. In order to facilitate the information system (IS) development to support their informed decision-making, it is imperative for the IS designer to recognize their unique information needs and patterns of information seeking behavior (ISB) first. This paper presents results of a pilot study that examined pregnant women’s information needs, ISBs, and information resources used prior to their prenatal genetic counseling. Findings suggest three distinctive areas, content, format, and timing, for IS design considerations. PMID:16779061

  17. Finding Markers That Make a Difference: DNA Pooling and SNP-Arrays Identify Population Informative Markers for Genetic Stock Identification

    PubMed Central

    Ozerov, Mikhail; Vasemägi, Anti; Wennevik, Vidar; Diaz-Fernandez, Rogelio; Kent, Matthew; Gilbey, John; Prusov, Sergey; Niemelä, Eero; Vähä, Juha-Pekka

    2013-01-01

    Genetic stock identification (GSI) using molecular markers is an important tool for management of migratory species. Here, we tested a cost-effective alternative to individual genotyping, known as allelotyping, for identification of highly informative SNPs for accurate genetic stock identification. We estimated allele frequencies of 2880 SNPs from DNA pools of 23 Atlantic salmon populations using Illumina SNP-chip. We evaluated the performance of four common strategies (global FST, pairwise FST, Delta and outlier approach) for selection of the most informative set of SNPs and tested their effectiveness for GSI compared to random sets of SNP and microsatellite markers. For the majority of cases, SNPs selected using the outlier approach performed best followed by pairwise FST and Delta methods. Overall, the selection procedure reduced the number of SNPs required for accurate GSI by up to 53% compared with randomly chosen SNPs. However, GSI accuracy was more affected by populations in the ascertainment group rather than the ranking method itself. We demonstrated for the first time the compatibility of different large-scale SNP datasets by compiling the largest population genetic dataset for Atlantic salmon to date. Finally, we showed an excellent performance of our top SNPs on an independent set of populations covering the main European distribution range of Atlantic salmon. Taken together, we demonstrate how combination of DNA pooling and SNP arrays can be applied for conservation and management of salmonids as well as other species. PMID:24358184

  18. Finding markers that make a difference: DNA pooling and SNP-arrays identify population informative markers for genetic stock identification.

    PubMed

    Ozerov, Mikhail; Vasemägi, Anti; Wennevik, Vidar; Diaz-Fernandez, Rogelio; Kent, Matthew; Gilbey, John; Prusov, Sergey; Niemelä, Eero; Vähä, Juha-Pekka

    2013-01-01

    Genetic stock identification (GSI) using molecular markers is an important tool for management of migratory species. Here, we tested a cost-effective alternative to individual genotyping, known as allelotyping, for identification of highly informative SNPs for accurate genetic stock identification. We estimated allele frequencies of 2880 SNPs from DNA pools of 23 Atlantic salmon populations using Illumina SNP-chip. We evaluated the performance of four common strategies (global F ST, pairwise F ST, Delta and outlier approach) for selection of the most informative set of SNPs and tested their effectiveness for GSI compared to random sets of SNP and microsatellite markers. For the majority of cases, SNPs selected using the outlier approach performed best followed by pairwise F ST and Delta methods. Overall, the selection procedure reduced the number of SNPs required for accurate GSI by up to 53% compared with randomly chosen SNPs. However, GSI accuracy was more affected by populations in the ascertainment group rather than the ranking method itself. We demonstrated for the first time the compatibility of different large-scale SNP datasets by compiling the largest population genetic dataset for Atlantic salmon to date. Finally, we showed an excellent performance of our top SNPs on an independent set of populations covering the main European distribution range of Atlantic salmon. Taken together, we demonstrate how combination of DNA pooling and SNP arrays can be applied for conservation and management of salmonids as well as other species. PMID:24358184

  19. Parents’ experiences of receiving their child’s genetic diagnosis: A qualitative study to inform clinical genetics practice

    PubMed Central

    Ashtiani, Setareh; Makela, Nancy; Carrion, Prescilla; Austin, Jehannine

    2014-01-01

    Purpose Little is currently known about how parents experience the medical genetics appointment at which their child receives a genetic diagnosis. Methods We conducted semi-structured in-person interviews with 13 parents of 10 index children to explore their experience in the medical genetics appointment in which they received their child’s genetic diagnosis. Guided by grounded theory, we used a constant comparative approach to data analysis, and the transcribed interviews were coded and sorted, and thematic categories identified. Results 61.5% of parents experienced the diagnosis session as negative, 23% felt the experience was positive, and 15.5% were ambivalent. Receiving emotional support, an outline of the follow-up plans, and messages of hope and perspective during the session seemed to positively influence parents’ experience, while feeling that their role was as a passive receiver of information and using difficult medical terminology negatively influenced parents’ overall experience. Parental preparedness for the information, and the parents’ emotional reaction to the diagnosis were also factors that influenced the parental experience. Few participants understood the role of the genetic counselor. Conclusion Our results provide in-depth insight into the parental experience of the pediatric medical genetics diagnosis session. We propose a mechanism through which parental experience shapes their perception of the medical genetics session. PMID:24706543

  20. 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

  1. 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

    ... information collection was previously published in the Federal Register on July 27, 2011, (76 FR 44937) and... information about genetic tests. The overarching goal of the GTR is to advance the public health and research... tests; and (3) facilitating genetic and genomic data-sharing for research and new scientific...

  2. Development of a Novel Reference Plasmid for Accurate Quantification of Genetically Modified Kefeng6 Rice DNA in Food and Feed Samples

    PubMed Central

    Zhang, Xiujie; Wan, Yusong

    2013-01-01

    Reference plasmids are an essential tool for the quantification of genetically modified (GM) events. Quantitative real-time PCR (qPCR) is the most commonly used method to characterize and quantify reference plasmids. However, the precision of this method is often limited by calibration curves, and qPCR data can be affected by matrix differences between the standards and samples. Here, we describe a digital PCR (dPCR) approach that can be used to accurately measure the novel reference plasmid pKefeng6 and quantify the unauthorized variety of GM rice Kefeng6, eliminating the issues associated with matrix effects in calibration curves. The pKefeng6 plasmid was used as a calibrant for the quantification of Kefeng6 rice by determining the copy numbers of event- (77 bp) and taxon-specific (68 bp) fragments, their ratios, and their concentrations. The plasmid was diluted to five different concentrations. The third sample (S3) was optimized for the quantification range of dPCR according to previous reports. The ratio between the two fragments was 1.005, which closely approximated the value certified by sequencing, and the concentration was found to be 792 copies/μL. This method was precise, with an RSD of ~3%. These findings demonstrate the advantages of using the dPCR method to characterize reference materials. PMID:24324952

  3. 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.)…

  4. 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.

  5. 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

  6. The commercialization of human genetic information and related circumstances within Turkish law.

    PubMed

    Memiş, Tekin

    2011-01-01

    Today, human genetic information is used for commercial purposes as well. This means, based on the case, the direct or indirect commercialization of genetic information. In this study, this specific issue is analyzed in light of the new legal regulations as to the subject in the Turkish Law. Specifically, this study focuses on the issue of whether the commercialization of genetic information is allowed under the Turkish Law. This study also attempts to clarify the issue of whether there is any limitations for the commercialization of genetic information in the Turkish Law provided that the commercialization of genetic information is permitted. Prior to this legal analysis, the problems of the legal ownership for genetic information and of whether genetic information should be considered as an organ of human body is discussed. Accordingly, relevant Turkish laws and regulations are individually analyzed within this context. In the mean time legal regulations of some countries in this respect are taken into account with a comparative approach. In the end a general evaluation and suggestions are provided to the reader. PMID:22984751

  7. 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

  8. 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…

  9. Therapeutic Targets of Triglyceride Metabolism as Informed by Human Genetics.

    PubMed

    Bauer, Robert C; Khetarpal, Sumeet A; Hand, Nicholas J; Rader, Daniel J

    2016-04-01

    Human genetics has contributed to the development of multiple drugs to treat hyperlipidemia and coronary artery disease (CAD), most recently including antibodies targeting PCSK9 to reduce LDL cholesterol. Despite these successes, a large burden of CAD remains. Genetic and epidemiological studies have suggested that circulating triglyceride (TG)-rich lipoproteins (TRLs) are a causal risk factor for CAD, presenting an opportunity for novel therapeutic strategies. We discuss recent unbiased human genetics testing, including genome-wide association studies (GWAS) and whole-genome or -exome sequencing, that have identified the lipoprotein lipase (LPL) and hepatic lipogenesis pathways as important mechanisms in the regulation of circulating TRLs. Further strengthening the causal relationship between TRLs and CAD, findings such as these may provide novel targets for much-needed potential therapeutic interventions. PMID:26988439

  10. Food labels, genetic information, and the right not to know.

    PubMed

    Loi, Michele

    2014-12-01

    Many people believe that individuals have a right not to know their genetic disease risk. Here it is argued that, if this is correct, individuals also have a right not to know their diet-related disease risk. Reasons to remain ignorant are analogous in the case of risk related to diet and genetic susceptibilities. It follows that any policy to promote healthy diets (e.g. through "judgmental" food labels, such as traffic light labels, or, hypothetically, scary pictures similar to those found in cigarette packets) ought to protect the individual right not to know. PMID:25638946

  11. Biomedical text summarization to support genetic database curation: using Semantic MEDLINE to create a secondary database of genetic information

    PubMed Central

    Fiszman, Marcelo; Hurdle, John F; Rindflesch, Thomas C

    2010-01-01

    Objective: This paper examines the development and evaluation of an automatic summarization system in the domain of molecular genetics. The system is a potential component of an advanced biomedical information management application called Semantic MEDLINE and could assist librarians in developing secondary databases of genetic information extracted from the primary literature. Methods: An existing summarization system was modified for identifying biomedical text relevant to the genetic etiology of disease. The summarization system was evaluated on the task of identifying data describing genes associated with bladder cancer in MEDLINE citations. A gold standard was produced using records from Genetics Home Reference and Online Mendelian Inheritance in Man. Genes in text found by the system were compared to the gold standard. Recall, precision, and F-measure were calculated. Results: The system achieved recall of 46%, and precision of 88% (F-measure = 0.61) by taking Gene References into Function (GeneRIFs) into account. Conclusion: The new summarization schema for genetic etiology has potential as a component in Semantic MEDLINE to support the work of data curators. PMID:20936065

  12. 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)

  13. A survey of medical directors of life insurance companies concerning use of genetic information.

    PubMed Central

    McEwen, J E; McCarty, K; Reilly, P R

    1993-01-01

    Rapid advances in our ability to test persons presymptomatically for genetic diseases have generated increasing concern that genetic information will be abused by insurance companies. Reasoning that the insurance companies may have the strongest interest in using genetic data and that the medical directors of those companies with responsibility for rating applicants would be a good source of information on the use of such data, we conducted a large survey of medical directors of North American life insurance companies. We received responses from 27 medical directors. Our results suggest that (1) few insurers perform genetic tests on applicants, but most are interested in accessing genetic test information about applicants that already exists; (2) the degree of insurers' interest in using genetic test results may depend on the face amount of the policy applied for and on the specificity and sensitivity of the test; (3) many companies employ underwriting guidelines with respect to certain genetic conditions but may not always have specific actuarial data in house to support their rating decisions; (4) a considerable degree of subjectivity is involved in most insurers' rating decisions; and (5) some of the medical directors who responded to our survey are not fully informed about certain basic principles of medical genetics. PMID:8317496

  14. 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)

  15. A Genetically Informed Study of Associations between Family Functioning and Child Psychosocial Adjustment

    ERIC Educational Resources Information Center

    Schermerhorn, Alice C.; D'Onofrio, Brian M.; Turkheimer, Eric; Ganiban, Jody M.; Spotts, Erica L.; Lichtenstein, Paul; Reiss, David; Neiderhiser, Jenae M.

    2011-01-01

    Research has documented associations between family functioning and offspring psychosocial adjustment, but questions remain regarding whether these associations are partly due to confounding genetic factors and other environmental factors. The current study used a genetically informed approach, the Children of Twins design, to explore the…

  16. 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.…

  17. 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…

  18. 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…

  19. 78 FR 13286 - Sharing Certain Business Information Regarding the Introduction of Genetically Engineered...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-27

    ... produced through genetic engineering that are plant pests or that there is reason to believe are plant pests under 7 CFR part 340, ``Introduction of Organisms and Products Altered or Produced Through Genetic... officials. The APHIS FOIA Office oversees any information release requested under FOIA. \\1\\ See 50 FR...

  20. 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

  1. 78 FR 70617 - Open Government: Use of Genetic Information in Documenting and Evaluating Disability

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-26

    ... From the Federal Register Online via the Government Publishing Office SOCIAL SECURITY ADMINISTRATION Open Government: Use of Genetic Information in Documenting and Evaluating Disability AGENCY: Social Security Administration. ACTION: Notice of open government forum. SUMMARY: We will host an...

  2. Different concepts and models of information for family-relevant genetic findings: comparison and ethical analysis.

    PubMed

    Lenk, Christian; Frommeld, Debora

    2015-08-01

    Genetic predispositions often concern not only individual persons, but also other family members. Advances in the development of genetic tests lead to a growing number of genetic diagnoses in medical practice and to an increasing importance of genetic counseling. In the present article, a number of ethical foundations and preconditions for this issue are discussed. Four different models for the handling of genetic information are presented and analyzed including a discussion of practical implications. The different models' ranges of content reach from a strictly autonomous position over self-governed arrangements in the practice of genetic counseling up to the involvement of official bodies and committees. The different models show a number of elements which seem to be very useful for the handling of genetic data in families from an ethical perspective. In contrast, the limitations of the standard medical attempt regarding confidentiality and personal autonomy in the context of genetic information in the family are described. Finally, recommendations for further ethical research and the development of genetic counseling in families are given. PMID:25894235

  3. 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

  4. Integrating genetic and genomic information into effective cancer care in diverse populations

    PubMed Central

    Fashoyin-Aje, L.; Sanghavi, K.; Bjornard, K.; Bodurtha, J.

    2013-01-01

    This paper provides an overview of issues in the integration of genetic (related to hereditary DNA) and genomic (related to genes and their functions) information in cancer care for individuals and families who are part of health care systems worldwide, from low to high resourced. National and regional cancer plans have the potential to integrate genetic and genomic information with a goal of identifying and helping individuals and families with and at risk of cancer. Healthcare professionals and the public have the opportunity to increase their genetic literacy and communication about cancer family history to enhance cancer control, prevention, and tailored therapies. PMID:24001763

  5. 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

  6. Communal discourse as a supplement to informed consent for genetic research.

    PubMed

    Foster, M W; Eisenbraun, A J; Carter, T H

    1997-11-01

    Genetic technologies present unique problems for the practice of informed consent. They provide information that may affect a study participant's family or kindred, which may be identifiable as an ethnic or locally isolated population. That information may be used to construct adverse perceptions of such identifiable populations, including non-participants who may not have been informed of or consented to the analyses. To address collective implications of genetic research, we describe a process that can supplement individual consent. Our approach engages pre-existing social units in discourses about proposed research. Communal discourses can influence individuals' decisions to participate in research studies. PMID:9354789

  7. 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

  8. [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

  9. The adequacy of informed consent forms in genetic research in Oman: a pilot study.

    PubMed

    Al-Riyami, Asya; Jaju, Deepali; Jaju, Sanjay; Silverman, Henry J

    2011-08-01

    Genetic research presents ethical challenges to the achievement of valid informed consent, especially in developing countries with areas of low literacy. During the last several years, a number of genetic research proposals involving Omani nationals were submitted to the Department of Research and Studies, Ministry of Health, Oman. The objective of this paper is to report on the results of an internal quality assurance initiative to determine the extent of the information being provided in genetic research informed consent forms. In order to achieve this, we developed checklists to assess the inclusion of basic elements of informed consent as well as elements related to the collection and future storage of biological samples. Three of the authors independently evaluated and reached consensus on seven informed consent forms that were available for review. Of the seven consent forms, four had less than half of the basic elements of informed consent. None contained any information regarding whether genetic information relevant to health would be disclosed, whether participants may share in commercial products, the extent of confidentiality protections, and the inclusion of additional consent forms for future storage and use of tissue samples. Information regarding genetic risks and withdrawal of samples were rarely mentioned (1/7), whereas limits on future use of samples were mentioned in 3 of 7 consent forms. Ultimately, consent forms are not likely to address key issues regarding genetic research that have been recommended by research ethics guidelines. We recommend enhanced educational efforts to increase awareness, on the part of researchers, of information that should be included in consent forms. PMID:21266001

  10. 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

  11. Accurate 3D rigid-body target motion and structure estimation by using GMTI/HRR with template information

    NASA Astrophysics Data System (ADS)

    Wu, Shunguang; Hong, Lang

    2008-04-01

    A framework of simultaneously estimating the motion and structure parameters of a 3D object by using high range resolution (HRR) and ground moving target indicator (GMTI) measurements with template information is given. By decoupling the motion and structure information and employing rigid-body constraints, we have developed the kinematic and measurement equations of the problem. Since the kinematic system is unobservable by using only one scan HRR and GMTI measurements, we designed an architecture to run the motion and structure filters in parallel by using multi-scan measurements. Moreover, to improve the estimation accuracy in large noise and/or false alarm environments, an interacting multi-template joint tracking (IMTJT) algorithm is proposed. Simulation results have shown that the averaged root mean square errors for both motion and structure state vectors have been significantly reduced by using the template information.

  12. 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

  13. Valuations of Genetic Test Information for Treatable Conditions: The Case of Colorectal Cancer Screening

    PubMed Central

    Kilambi, Vikram; Johnson, F. Reed; González, Juan Marcos; Mohamed, Ateesha F.

    2014-01-01

    Background The value of the information that genetic testing services provide can be questioned for insurance-based health systems. The results of genetic tests oftentimes may not lead to well-defined clinical interventions; however, Lynch syndrome, a genetic mutation for which carriers are at an increased risk for colorectal cancer, can be identified through genetic testing, and meaningful health interventions are available via increased colonoscopic surveillance. Valuations of test information for such conditions ought to account for the full impact of interventions and contingent outcomes. Objectives To conduct a discrete-choice experiment to elicit individuals’ preferences for genetic test information. Methods A Web-enabled discrete-choice experiment survey was administered to a representative sample of US residents aged 50 years and older. In addition to specifying expenditures on colonoscopies, respondents were asked to make a series of nine selections between two hypothetical genetic tests or a no-test option under the premise that a relative had Lynch syndrome. The hypothetical genetic tests were defined by the probability of developing colorectal cancer, the probability of a false-negative test result, privacy of the result, and out-of-pocket cost. A model specification identifying necessary interactions was derived from assumptions of risk behavior and the decision context and was estimated using random-parameters logit. Results A total of 650 respondents were contacted, and 385 completed the survey. The monetary equivalent of test information was approximately $1800. Expenditures on colonoscopies to reduce mortality risks affected valuations. Respondents with lower income or who reported being employed significantly valued genetic tests more. Conclusion Genetic testing may confer benefits through the impact of subsequent interventions on private individuals. PMID:25498779

  14. 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.

  15. Applying Multivariate Discrete Distributions to Genetically Informative Count Data.

    PubMed

    Kirkpatrick, Robert M; Neale, Michael C

    2016-03-01

    We present a novel method of conducting biometric analysis of twin data when the phenotypes are integer-valued counts, which often show an L-shaped distribution. Monte Carlo simulation is used to compare five likelihood-based approaches to modeling: our multivariate discrete method, when its distributional assumptions are correct, when they are incorrect, and three other methods in common use. With data simulated from a skewed discrete distribution, recovery of twin correlations and proportions of additive genetic and common environment variance was generally poor for the Normal, Lognormal and Ordinal models, but good for the two discrete models. Sex-separate applications to substance-use data from twins in the Minnesota Twin Family Study showed superior performance of two discrete models. The new methods are implemented using R and OpenMx and are freely available. PMID:26497008

  16. Doctor's expertise and managing discrepant information from other sources in genetic counseling: a conversation analytic perspective.

    PubMed

    Lehtinen, Esa; Kääriäinen, Helena

    2005-12-01

    The study examines a recurrent interactional pattern in genetic counseling. It describes clinical geneticists' responses in situations in which clients have presented information from other sources that is potentially discrepant with information given by the doctor. The data consists of 12 video-recorded sessions of genetic counseling in Finland, and the method is conversation analysis. There are two primary ways the doctors respond: either they accept the client's information as such, but show that it is not discrepant with the doctor's information, or they reject the client's information. In the latter case they mitigate the 'wrongness' of the client's information. The clinical geneticists seem to be working with a dilemma: they need to find a balance between ensuring correct understanding of the information and showing respect for the expertise of others. A particularly complex case is also analyzed and reflected on. PMID:16388324

  17. 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. PMID:18312122

  18. 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…

  19. 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…

  20. Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information

    PubMed Central

    Pollastri, Gianluca; Martin, Alberto JM; Mooney, Catherine; Vullo, Alessandro

    2007-01-01

    Background Structural properties of proteins such as secondary structure and solvent accessibility contribute to three-dimensional structure prediction, not only in the ab initio case but also when homology information to known structures is available. Structural properties are also routinely used in protein analysis even when homology is available, largely because homology modelling is lower throughput than, say, secondary structure prediction. Nonetheless, predictors of secondary structure and solvent accessibility are virtually always ab initio. Results Here we develop high-throughput machine learning systems for the prediction of protein secondary structure and solvent accessibility that exploit homology to proteins of known structure, where available, in the form of simple structural frequency profiles extracted from sets of PDB templates. We compare these systems to their state-of-the-art ab initio counterparts, and with a number of baselines in which secondary structures and solvent accessibilities are extracted directly from the templates. We show that structural information from templates greatly improves secondary structure and solvent accessibility prediction quality, and that, on average, the systems significantly enrich the information contained in the templates. For sequence similarity exceeding 30%, secondary structure prediction quality is approximately 90%, close to its theoretical maximum, and 2-class solvent accessibility roughly 85%. Gains are robust with respect to template selection noise, and significant for marginal sequence similarity and for short alignments, supporting the claim that these improved predictions may prove beneficial beyond the case in which clear homology is available. Conclusion The predictive system are publicly available at the address . PMID:17570843

  1. 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.

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

    PubMed

    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. PMID:26172739

  3. 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.

  4. 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

  5. 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

  6. The Complex Trial Protocol (CTP): a new, countermeasure-resistant, accurate, P300-based method for detection of concealed information.

    PubMed

    Rosenfeld, J Peter; Labkovsky, Elena; Winograd, Michael; Lui, Ming A; Vandenboom, Catherine; Chedid, Erica

    2008-11-01

    A new P300-based concealed information test is described. A rare probe or frequent irrelevant stimulus appears in the same trial in which a target or nontarget later appears. One response follows the first stimulus and uses the same button press regardless of stimulus type. A later second stimulus then appears: target or nontarget. The subject presses one button for a target, another for a nontarget. A P300 to the first stimulus indicates probe recognition. One group was tested in 3 weeks for denied recognition of familiar information. Weeks 1 and 3 were guilty conditions; Week 2 was a countermeasure (CM) condition. The probe-irrelevant differences were significant in all weeks, and percent hits were >90%. Attempted CM use was detectable via elevated reaction time to the first stimulus. In a replication, results were similar. False positive rates for both studies varied from 0 to .08, yielding J. B. Grier (1971) A' values from .9 to 1.0. PMID:18823418

  7. 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. PMID:9807244

  8. 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.

  9. 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

  10. 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

  11. American Academy of Orthopaedic Surgeons Disclosure Policy Fails to Accurately Inform Its Members of Potential Conflicts of Interest.

    PubMed

    Tanzer, Dylan; Smith, Karen; Tanzer, Michael

    2015-07-01

    The American Academy of Orthopaedic Surgeons (AAOS) disclosure policy is designed to ensure that members involved in education or policy development remain free of outside influence. Although mandatory for these members, it is voluntary for the rest of the AAOS membership. To determine surgeon compliance with disclosure policy, we conducted a study in which we compared surgeon-consultants' disclosures as posted on 6 major orthopedic companies' websites in 2011 with those surgeons' disclosures as listed in AAOS disclosure program records. We found that 549 AAOS members were identified by at least 1 company as having received consulting payments. Overall, 44% of AAOS members did not comply with disclosure policy, or their information was not available on the AAOS website (range, 37%-61%). This study demonstrated that AAOS's policy of mandatory disclosure for select members and voluntary disclosure for all other members is ineffective. The AAOS disclosure program and the potential consequences of noncompliance need to be reevaluated by the organization if it wants its program to succeed. PMID:26161764

  12. 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

  13. 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. PMID:25998783

  14. Etiology and measurement of relational aggression: A multi-informant behavior genetic investigation.

    PubMed

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

    2009-11-01

    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 1,981 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 the maternal report (66%) than it did in the youth report (9%). In addition, informant-specific additive genetic and shared environmental influences were found only for the youth report, with all remaining variance in the 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

  15. 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

  16. Genetic evaluation by best linear unbiased prediction using marker and trait information in a multibreed population.

    PubMed Central

    Wang, T; Fernando, R L; Grossman, M

    1998-01-01

    Genetic evaluation by best linear unbiased prediction (BLUP) requires modeling genetic means, variances, and covariances. This paper presents theory to model means, variances, and covariances in a multibreed population, given marker and breed information, in the presence of gametic disequilibrium between the marker locus (ML) and linked quantitative trait locus (MQTL). Theory and algorithms are presented to construct the matrix of conditional covariances between relatives (Gv) for the MQTL effects in a multibreed population and to obtain the inverse of Gv efficiently. Theory presented here accounts for heterogeneity of variances among pure breeds and for segregation variances between pure breeds. A numerical example was used to illustrate how the theory and algorithms can be used for genetic evaluation by BLUP using marker and trait information in a multibreed population. PMID:9475759

  17. 45 CFR 146.122 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 1 2011-10-01 2011-10-01 false Additional requirements prohibiting discrimination based on genetic information. 146.122 Section 146.122 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES REQUIREMENTS RELATING TO HEALTH CARE ACCESS REQUIREMENTS FOR THE GROUP HEALTH INSURANCE MARKET Requirements Relating to Access...

  18. 26 CFR 54.9802-3T - Additional requirements prohibiting discrimination based on genetic information (temporary).

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 26 Internal Revenue 17 2014-04-01 2014-04-01 false Additional requirements prohibiting discrimination based on genetic information (temporary). 54.9802-3T Section 54.9802-3T Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) MISCELLANEOUS EXCISE TAXES (CONTINUED) PENSION EXCISE TAXES § 54.9802-3T...

  19. 29 CFR 2590.702-1 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 29 Labor 9 2014-07-01 2014-07-01 false Additional requirements prohibiting discrimination based on genetic information. 2590.702-1 Section 2590.702-1 Labor Regulations Relating to Labor (Continued) EMPLOYEE BENEFITS SECURITY ADMINISTRATION, DEPARTMENT OF LABOR GROUP HEALTH PLANS RULES AND REGULATIONS FOR GROUP HEALTH PLANS Health...

  20. 26 CFR 54.9802-3T - Additional requirements prohibiting discrimination based on genetic information (temporary).

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 26 Internal Revenue 17 2012-04-01 2012-04-01 false Additional requirements prohibiting discrimination based on genetic information (temporary). 54.9802-3T Section 54.9802-3T Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) MISCELLANEOUS EXCISE TAXES (CONTINUED) PENSION EXCISE TAXES § 54.9802-3T...

  1. 26 CFR 54.9802-3T - Additional requirements prohibiting discrimination based on genetic information (temporary).

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 26 Internal Revenue 17 2013-04-01 2013-04-01 false Additional requirements prohibiting discrimination based on genetic information (temporary). 54.9802-3T Section 54.9802-3T Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) MISCELLANEOUS EXCISE TAXES (CONTINUED) PENSION EXCISE TAXES § 54.9802-3T...

  2. 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...

  3. 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

  4. 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…

  5. Mutual information image registration based on improved bee evolutionary genetic algorithm

    NASA Astrophysics Data System (ADS)

    Xu, Gang; Tu, Jingzhi

    2009-07-01

    In recent years, the mutual information is regarded as a more efficient similarity metrics in the image registration. According to the features of mutual information image registration, the Bee Evolution Genetic Algorithm (BEGA) is chosen for optimizing parameters, which imitates swarm mating. Besides, we try our best adaptively set the initial parameters to improve the BEGA. The programming result shows the wonderful precision of the algorithm.

  6. Infant development in family context: call for a genetically informed approach

    PubMed Central

    Parade, Stephanie H.; McGeary, John; Seifer, Ronald; Knopik, Valerie

    2012-01-01

    We call for a genetically informed approach in the examination of infant social and emotional development in family context. We recommend that scholars conceptualize family functioning as occurring on three unique levels: the parent-child dyad, the inter-parental dyad, and whole family functioning. Although advances in the area of understanding genetic variation in infants as a potential moderator of the influence of parent-child dyadic functioning have been made over the past decade, it is time to widen this inquiry to consider genetic variation in infants as a potential moderator of the influence of inter-parental dyadic and whole family functioning as well. A critical review of the literature also calls for additional examination of genetic variation in infants as a moderator of positive contextual influences, the integration of unique temperament variables with studies of infant genotype, consideration of the role of the gene-environment correlation, and epigenetic effects. Furthermore, we call for the application of genetically-informed research methods to these questions. Expanding knowledge in this area has the potential to refine treatment and prevention efforts aimed at promoting infant social and emotional development. PMID:22969793

  7. A preliminary investigation of genetic counselors’ information needs when receiving a variant of uncertain significance result: a mixed methods study

    PubMed Central

    Scherr, Courtney L.; Lindor, Noralane M.; Malo, Teri L.; Couch, Fergus J.; Vadaparampil, Susan T.

    2015-01-01

    Purpose To explore genetic counselors’ information preferences on reports of variant of uncertain significance (VUS) results from cancer genetic testing. Methods This mixed methods report (quantitative and qualitative approaches) utilized a survey of genetic counselors containing closed- and open-ended questions to explore genetic counselors’ information needs and perceptions of the industry’s current information sharing practices. Descriptive statistics were calculated for responses to the closed-ended questions and thematic analysis guided the interpretation of the open-ended questions. Results Of the 267 participants (28.6% response rate), the majority indicated a perceived lack of information on VUS laboratory reports, were concerned about the perceived practice of withholding information, and stated the information they wanted to see. Although most did not indicate how additional information would be used, some reported they would provide information directly to patients, and others reported the information would be used to contextualize the VUS result when counseling patients. Conclusion This analysis identified information genetic counselors believe is needed on VUS reports indicating what they believe are best practices in lieu of guidelines for laboratories currently providing genetic testing services, and implies needed guidelines for reporting VUS. Future studies should explore how genetic counselors use additional information contained on VUS reports. PMID:25569439

  8. 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 ...

  9. Neural network and genetic algorithm technology in data mining of manufacturing quality information

    NASA Astrophysics Data System (ADS)

    Song, Limei; Qu, Xing-Hua; Ye, Shenghua

    2002-03-01

    Data Mining of Manufacturing Quality Information (MQI) is the key technology in Quality Lead Control. Of all the data mining methods, Neural Network and Genetic Algorithm is widely used for their strong advantages, such as non-linear, collateral, veracity etc. But if you singly use them, there will be some limitations preventing your research, such as convergence slowly, searching blindness etc. This paper combines their merits and use Genetic BP Algorithm in Data Mining of MQI. It has been successfully used in the key project of Natural Science Foundation of China (NSFC) - Quality Control and Zero-defect Engineering (Project No. 59735120).

  10. Genetically informative designs in the study of resilience in developmental psychopathology.

    PubMed

    Bartels, Meike; Hudziak, James J

    2007-04-01

    The study of resilience, defined here as the ability to recover from a prior illness or the capacity to remain well in the face of extraordinary genetic or environmental risk factors, is the focus of this article. We believe that to study resilience in the domain of developmental psychopathology it is necessary to use genetically informative strategies. Extending this argument to the study of resilience (eg, why some kids recover) is the focus of last part this article and our research strategies in the next decade. PMID:17349511

  11. Information entropy as a measure of genetic diversity and evolvability in colonization.

    PubMed

    Day, Troy

    2015-05-01

    In recent years, several studies have examined the relationship between genetic diversity and establishment success in colonizing species. Many of these studies have shown that genetic diversity enhances establishment success. There are several hypotheses that might explain this pattern, and here I focus on the possibility that greater genetic diversity results in greater evolvability during colonization. Evaluating the importance of this mechanism first requires that we quantify evolvability. Currently, most measures of evolvability have been developed for quantitative traits whereas many studies of colonization success deal with discrete molecular markers or phenotypes. The purpose of this study is to derive a suitable measure of evolvability for such discrete data. I show that under certain assumptions, Shannon's information entropy of the allelic distribution provides a natural measure of evolvability. This helps to alleviate previous concerns about the interpretation of information entropy for genetic data. I also suggest that information entropy provides a natural generalization to previous measures of evolvability for quantitative traits when the trait distributions are not necessarily multivariate normal. PMID:25604806

  12. 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

  13. 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...

  14. 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. PMID:25953490

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

    NASA Astrophysics Data System (ADS)

    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.

  16. 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

  17. 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

  18. SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models

    PubMed Central

    2014-01-01

    Background Locating the protein-coding genes in novel genomes is essential to understanding and exploiting the genomic information but it is still difficult to accurately predict all the genes. The recent availability of detailed information about transcript structure from high-throughput sequencing of messenger RNA (RNA-Seq) delineates many expressed genes and promises increased accuracy in gene prediction. Computational gene predictors have been intensively developed for and tested in well-studied animal genomes. Hundreds of fungal genomes are now or will soon be sequenced. The differences of fungal genomes from animal genomes and the phylogenetic sparsity of well-studied fungi call for gene-prediction tools tailored to them. Results SnowyOwl is a new gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions and to evaluate the resulting models. The pipeline has been developed and streamlined by comparing its predictions to manually curated gene models in three fungal genomes and validated against the high-quality gene annotation of Neurospora crassa; SnowyOwl predicted N. crassa genes with 83% sensitivity and 65% specificity. SnowyOwl gains sensitivity by repeatedly running the HMM gene predictor Augustus with varied input parameters and selectivity by choosing the models with best homology to known proteins and best agreement with the RNA-Seq data. Conclusions SnowyOwl efficiently uses RNA-Seq data to produce accurate gene models in both well-studied and novel fungal genomes. The source code for the SnowyOwl pipeline (in Python) and a web interface (in PHP) is freely available from http://sourceforge.net/projects/snowyowl/. PMID:24980894

  19. Genetic and environmental bases of childhood antisocial behavior: a multi-informant twin study.

    PubMed

    Baker, Laura A; Jacobson, Kristen C; Raine, Adrian; Lozano, Dora Isabel; Bezdjian, Serena

    2007-05-01

    Genetic and environmental influences on childhood antisocial and aggressive behavior (ASB) during childhood were examined in 9- to 10-year-old twins, using a multi-informant approach. The sample (605 families of twins or triplets) was socioeconomically and ethnically diverse, representative of the culturally diverse urban population in Southern California. Measures of ASB included symptom counts for conduct disorder, ratings of aggression, delinquency, and psychopathic traits obtained through child self-reports, teacher, and caregiver ratings. Multivariate analysis revealed a common ASB factor across informants that was strongly heritable (heritability was .96), highlighting the importance of a broad, general measure obtained from multiple sources as a plausible construct for future investigations of specific genetic mechanisms in ASB. The best fitting multivariate model required informant-specific genetic, environmental, and rater effects for variation in observed ASB measures. The results suggest that parents, children, and teachers have only a partly "shared view" and that the additional factors that influence the "rater-specific" view of the child's antisocial behavior vary for different informants. This is the first study to demonstrate strong heritable effects on ASB in ethnically and economically diverse samples. PMID:17516756

  20. Genetic and Environmental Bases of Childhood Antisocial Behavior: A Multi-Informant Twin Study

    PubMed Central

    Baker, Laura A.; Jacobson, Kristen C.; Raine, Adrian; Lozano, Dora Isabel; Bezdjian, Serena

    2007-01-01

    Genetic and environmental influences on childhood antisocial and aggressive behavior (ASB) during childhood were examined in 9- to 10-year-old twins, using a multi-informant approach. The sample (605 families of twins or triplets) was socioeconomically and ethnically diverse, representative of the culturally diverse urban population in Southern California. Measures of ASB included symptom counts for conduct disorder, ratings of aggression, delinquency, and psychopathic traits obtained through child self-reports, teacher, and caregiver ratings. Multivariate analysis revealed a common ASB factor across informants that was strongly heritable (heritability was .96), highlighting the importance of a broad, general measure obtained from multiple sources as a plausible construct for future investigations of specific genetic mechanisms in ASB. The best fitting multivariate model required informant-specific genetic, environmental, and rater effects for variation in observed ASB measures. The results suggest that parent, children, and teachers have only a partly “shared view” and that the additional factors that influence the “rater-specific” view of the child's antisocial behavior vary for different informants. This is the first study to demonstrate strong heritable effects on ASB in ethnically and economically diverse samples. PMID:17516756

  1. 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. PMID:24617293

  2. Nurse capacity, fertility, and litter size in crossbred sows and genetic correlation to purebred sow information.

    PubMed

    Nielsen, B; Christensen, O F; Velander, I

    2016-05-01

    In pigs litter size has increased during the last decades and number of weaned piglets is an important issue. The aim of this study was to develop a new trait of nurse capacity (NC) of crossbred sows viewed as crossbred performances in the two purebred parent lines, and estimate the genetic correlation to fertility and litter size five days after birth. An experiment recording phenotypes of crossbred sows was conducted in three large production herds with 11,247 first litter Danish Landrace x Yorkshire sows. All terminal sires used were Duroc AI boars. The experiment was running from 2010 to 2013. At farrowing, the total number born (TNB) was recorded. Five days after farrowing the litter size of the biological mother (LS5) was recorded. During the first three days after farrowing the number of piglets at each nurse sow was equalized to 14 piglets and after three weeks the NC was recorded and defined as the number of piglets nursed. Additional records on TNB and LS5 from related sows in nucleus and multiplier herds were added to obtain a data set with both purebred and crossbred information. A reduced animal model including both purebred and crossbred records was used and parameters were estimated. The results show that NC recorded on crossbred first litter sows had heritabilities of 0.05 and 0.07 for crossbred performance in the purebred populations of Landrace and Yorkshire, respectively. Estimated genetic correlations between TNB in purebreds and crossbreds show that nearly 50% of genetic gain in the purebred populations was transferred to crossbreds. Unfavorable genetic correlations between TNB in purebreds and NC in crossbreds were observed. For LS5 the genetic (co)variances show that 61% of the genetic gain in the two purebred lines was transferred to the commercial pig production of crossbred first litter sows, but no statistically significant genetic correlation to NC was obtained. PMID:27285680

  3. 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. PMID:25540896

  4. 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

  5. A Genetically Informed Study of Associations between Family Functioning and Child Psychosocial Adjustment

    PubMed Central

    Schermerhorn, Alice C.; D’Onofrio, Brian M.; Turkheimer, Eric; Ganiban, Jody M.; Spotts, Erica L.; Lichtenstein, Paul; Reiss, David; Neiderhiser, Jenae M.

    2010-01-01

    Research has documented associations between family functioning and offspring psychosocial adjustment, but questions remain regarding whether these associations are partly due to confounding genetic factors and other environmental factors. The current study used a genetically informed approach, the Children of Twins design, to explore the associations between family functioning (family conflict, marital quality, and agreement about parenting) and offspring psychopathology. Participants were 867 twin pairs (388 MZ; 479 DZ) from the Twin and Offspring Study in Sweden (TOSS), their spouses, and children (51.7% female; M = 15.75 years). The results suggested associations between exposure to family conflict (assessed by the mother, father, and child) and child adjustment were independent of genetic factors and other environmental factors. However, when family conflict was assessed using only children’s reports, the results indicated that genetic factors also influenced these associations. In addition, the analyses indicated that exposure to low marital quality and agreement about parenting was associated with children’s internalizing and externalizing problems, and that genetic factors also contributed to the associations of marital quality and agreement about parenting with offspring externalizing problems. PMID:21142367

  6. 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...

  7. 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

  8. 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

  9. 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

    2016-01-01

    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. PMID:26866982

  10. Large-Scale Phenotyping of an Accurate Genetic Mouse Model of JNCL Identifies Novel Early Pathology Outside the Central Nervous System

    PubMed Central

    Staropoli, John F.; Haliw, Larissa; Biswas, Sunita; Garrett, Lillian; Hölter, Sabine M.; Becker, Lore; Skosyrski, Sergej; Da Silva-Buttkus, Patricia; Calzada-Wack, Julia; Neff, Frauke; Rathkolb, Birgit; Rozman, Jan; Schrewe, Anja; Adler, Thure; Puk, Oliver; Sun, Minxuan; Favor, Jack; Racz, Ildikó; Bekeredjian, Raffi; Busch, Dirk H.; Graw, Jochen; Klingenspor, Martin; Klopstock, Thomas; Wolf, Eckhard; Wurst, Wolfgang; Zimmer, Andreas; Lopez, Edith; Harati, Hayat; Hill, Eric; Krause, Daniela S.; Guide, Jolene; Dragileva, Ella; Gale, Evan; Wheeler, Vanessa C.; Boustany, Rose-Mary; Brown, Diane E.; Breton, Sylvie; Ruether, Klaus; Gailus-Durner, Valérie; Fuchs, Helmut; de Angelis, Martin Hrabě; Cotman, Susan L.

    2012-01-01

    Cln3Δex7/8 mice harbor the most common genetic defect causing juvenile neuronal ceroid lipofuscinosis (JNCL), an autosomal recessive disease involving seizures, visual, motor and cognitive decline, and premature death. Here, to more thoroughly investigate the manifestations of the common JNCL mutation, we performed a broad phenotyping study of Cln3Δex7/8 mice. Homozygous Cln3Δex7/8 mice, congenic on a C57BL/6N background, displayed subtle deficits in sensory and motor tasks at 10–14 weeks of age. Homozygous Cln3Δex7/8 mice also displayed electroretinographic changes reflecting cone function deficits past 5 months of age and a progressive decline of retinal post-receptoral function. Metabolic analysis revealed increases in rectal body temperature and minimum oxygen consumption in 12–13 week old homozygous Cln3Δex7/8mice, which were also seen to a lesser extent in heterozygous Cln3Δex7/8 mice. Heart weight was slightly increased at 20 weeks of age, but no significant differences were observed in cardiac function in young adults. In a comprehensive blood analysis at 15–16 weeks of age, serum ferritin concentrations, mean corpuscular volume of red blood cells (MCV), and reticulocyte counts were reproducibly increased in homozygous Cln3Δex7/8 mice, and male homozygotes had a relative T-cell deficiency, suggesting alterations in hematopoiesis. Finally, consistent with findings in JNCL patients, vacuolated peripheral blood lymphocytes were observed in homozygous Cln3Δex7/8 neonates, and to a greater extent in older animals. Early onset, severe vacuolation in clear cells of the epididymis of male homozygous Cln3Δex7/8 mice was also observed. These data highlight additional organ systems in which to study CLN3 function, and early phenotypes have been established in homozygous Cln3Δex7/8 mice that merit further study for JNCL biomarker development. PMID:22701626

  11. 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

  12. The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency

    PubMed Central

    Rubinstein, Wendy S.; Maglott, Donna R.; Lee, Jennifer M.; Kattman, Brandi L.; Malheiro, Adriana J.; Ovetsky, Michael; Hem, Vichet; Gorelenkov, Viatcheslav; Song, Guangfeng; Wallin, Craig; Husain, Nora; Chitipiralla, Shanmuga; Katz, Kenneth S.; Hoffman, Douglas; Jang, Wonhee; Johnson, Mark; Karmanov, Fedor; Ukrainchik, Alexander; Denisenko, Mikhail; Fomous, Cathy; Hudson, Kathy; Ostell, James M.

    2013-01-01

    The National Institutes of Health Genetic Testing Registry (GTR; available online at http://www.ncbi.nlm.nih.gov/gtr/) maintains comprehensive information about testing offered worldwide for disorders with a genetic basis. Information is voluntarily submitted by test providers. The database provides details of each test (e.g. its purpose, target populations, methods, what it measures, analytical validity, clinical validity, clinical utility, ordering information) and laboratory (e.g. location, contact information, certifications and licenses). Each test is assigned a stable identifier of the format GTR000000000, which is versioned when the submitter updates information. Data submitted by test providers are integrated with basic information maintained in National Center for Biotechnology Information’s databases and presented on the web and through FTP (ftp.ncbi.nih.gov/pub/GTR/_README.html). PMID:23193275

  13. 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

  14. A genetically informative developmental study of the relationship between conduct disorder and peer deviance in males

    PubMed Central

    Kendler, K. S.; Jacobson, K.; Myers, J. M.; Eaves, L. J.

    2014-01-01

    Background Conduct disorder (CD) and peer deviance (PD) both powerfully predict future externalizing behaviors. Although levels of CD and PD are strongly correlated, the causal relationship between them has remained controversial and has not been examined by a genetically informative study. Method Levels of CD and PD were assessed in 746 adult male–male twin pairs at personal interview for ages 8–11, 12–14 and 15–17 years using a life history calendar. Model fitting was performed using the Mx program. Results The best-fit model indicated an active developmental relationship between CD and PD including forward transmission of both traits over time and strong causal relationships between CD and PD within time periods. The best-fit model indicated that the causal relationship for genetic risk factors was from CD to PD and was constant over time. For common environmental factors, the causal pathways ran from PD to CD and were stronger in earlier than later age periods. Conclusions A genetically informative model revealed causal pathways difficult to elucidate by other methods. Genes influence risk for CD, which, through social selection, impacts on the deviance of peers. Shared environment, through family and community processes, encourages or discourages adolescent deviant behavior, which, via social influence, alters risk for CD. Social influence is more important than social selection in childhood, but by late adolescence social selection becomes predominant. These findings have implications for prevention efforts for CD and associated externalizing disorders. PMID:17935643

  15. 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

  16. 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

  17. 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. PMID:26280323

  18. 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

  19. 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

  20. 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

  1. Brain eQTL Mapping Informs Genetic Studies of Psychiatric Diseases

    PubMed Central

    Liu, Chunyu

    2011-01-01

    Genome-wide association studies (GWASs) have been used to identify genes that increase risk of psychiatric diseases. However, much of the variation in disease risk is still unexplained, suggesting that there are genes still to be discovered. Functional annotation of genetic variants may increase the power of GWASs to identify disease genes by providing prior information that can be used in Bayesian analysis or in reducing the number of tests. Genetic mapping of expression quantitative trait loci (eQTLs) is helping us to reveal novel functional effects of thousands of single nucleotide polymorphisms (SNPs). The published brain eQTL studies are reviewed here, and major methodological issues and their possible solutions are discussed. We emphasize the frequently-ignored problems of batch effects, covariates, and multiple testing, all of which can lead to false positives and false negatives. The future application of eQTL data to the GWAS analysis is also discussed. PMID:21441974

  2. Parent Involvement, Sibling Companionship, and Adolescent Substance Use: A Longitudinal, Genetically-Informed Design

    PubMed Central

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

    2015-01-01

    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 two 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

  3. 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

  4. Motivating donors to genetic research? Anthropological reasons to rethink the role of informed consent.

    PubMed

    Hoeyer, Klaus; Lynöe, Niels

    2006-01-01

    In this article we explore the contribution from social anthropology to the medical ethical debates about the use of informed consent in research, based on blood samples and other forms of tissue. The article springs from a project exploring donors' motivation for providing blood and healthcare data for genetic research to be executed by a Swedish start-up genomics company. This article is not confined to empirical findings, however, as we suggest that anthropology provides reason to reassess the theoretical understanding of autonomy as generally defined by Beauchamp and Childress. Careful consideration of the trust expressed by donors through the act of donation, furthermore, suggests that there is reason to redirect the ethical scrutiny from informed consent to issues concerning institutional arrangements and social responsibility. In particular, we suggest that an anthropological approach could facilitate a reconsideration of the political implications of using informed consent as a regulatory practice in tissue-based research. PMID:16645794

  5. 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

  6. Interplay between heritability, genetic correlation and economic weighting in a selection index with and without genomic information.

    PubMed

    Haberland, A M; Pimentel, E C G; Ytournel, F; Erbe, M; Simianer, H

    2013-12-01

    The availability of genomic information demands proper evaluation on how the kind (phenotypic versus genomic) and the amount of information influences the interplay of heritability (h(2)), genetic correlation (r(GiGj)) and economic weighting of traits with regard to the standard deviation of the index (σI). As σI is directly proportional to response to selection, it was the chosen parameter for comparing the indices. Three selection indices incorporating conventional and genomic information for a two trait (i and j) breeding goal were compared. Information sources were chosen corresponding to pig breeding applications. Index I incorporating an own performance in trait j served as reference scenario. In index II, additional information in both traits was contributed by a varying number of full-sibs (2, 7, 50). In index III, the conventional own performance in trait j was combined with genomic information for both traits. The number of animals in the reference population (NP = 1000, 5000, 10,000) and thus the accuracy of GBVs were varied. With more information included in the index, σI became more independent of r(GiGj), h(j)(2) and relative economic weighting. This applied for index II (more full-sibs) and for index III (more accurate GBVs). Standard deviations of index II with seven full-sibs and index III with NP = 1000 were similar when both traits had the same heritability. If the heritability of trait j was reduced (h(j)(2) = 0.1), σI of index III with NP = 1000 was clearly higher than for index II with seven full-sibs. When enhancing the relative economic weight of trait j, the decrease in σI of the conventional full-sib index was much stronger than for index III. Our results imply that NP = 1000 can be considered a minimum size for a reference population in pig breeding. These conclusions also hold for comparing the accuracies of the indices. PMID:24236608

  7. 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…

  8. 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

  9. An Approach to Extract Informative Rules for Web Page Recommendation by Genetic Programming

    NASA Astrophysics Data System (ADS)

    Kim, Jaekwang; Yoon, Kwangho; Lee, Jee-Hyong

    Clickstreams in users' navigation logs have various data which are related to users' web surfing. Those are visit counts, stay times, product types, etc. When we observe these data, we can divide clickstreams into sub-clickstreams so that the pages in a sub-clickstream share more contexts with each other than with the pages in other sub-clickstreams. In this paper, we propose a method which extracts more informative rules from clickstreams for web page recommendation based on genetic programming and association rules. First, we split clickstreams into sub-clickstreams by contexts for generating more informative rules. In order to split clickstreams in consideration of context, we extract six features from users' navigation logs. A set of split rules is generated by combining those features through genetic programming, and then informative rules for recommendation are extracted with the association rule mining algorithm. Through experiments, we verify that the proposed method is more effective than the other methods in various conditions.

  10. 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

  11. 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.

  12. 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.

  13. 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. PMID:26494459

  14. 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

  15. 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

  16. 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. PMID:23088795

  17. Mining the Unknown: A Systems Approach to Metabolite Identification Combining Genetic and Metabolic Information

    PubMed Central

    Krumsiek, Jan; Suhre, Karsten; Evans, Anne M.; Mitchell, Matthew W.; Mohney, Robert P.; Milburn, Michael V.; Wägele, Brigitte; Römisch-Margl, Werner; Illig, Thomas; Adamski, Jerzy; Gieger, Christian; Theis, Fabian J.; Kastenmüller, Gabi

    2012-01-01

    Recent genome-wide association studies (GWAS) with metabolomics data linked genetic variation in the human genome to differences in individual metabolite levels. A strong relevance of this metabolic individuality for biomedical and pharmaceutical research has been reported. However, a considerable amount of the molecules currently quantified by modern metabolomics techniques are chemically unidentified. The identification of these “unknown metabolites” is still a demanding and intricate task, limiting their usability as functional markers of metabolic processes. As a consequence, previous GWAS largely ignored unknown metabolites as metabolic traits for the analysis. Here we present a systems-level approach that combines genome-wide association analysis and Gaussian graphical modeling with metabolomics to predict the identity of the unknown metabolites. We apply our method to original data of 517 metabolic traits, of which 225 are unknowns, and genotyping information on 655,658 genetic variants, measured in 1,768 human blood samples. We report previously undescribed genotype–metabotype associations for six distinct gene loci (SLC22A2, COMT, CYP3A5, CYP2C18, GBA3, UGT3A1) and one locus not related to any known gene (rs12413935). Overlaying the inferred genetic associations, metabolic networks, and knowledge-based pathway information, we derive testable hypotheses on the biochemical identities of 106 unknown metabolites. As a proof of principle, we experimentally confirm nine concrete predictions. We demonstrate the benefit of our method for the functional interpretation of previous metabolomics biomarker studies on liver detoxification, hypertension, and insulin resistance. Our approach is generic in nature and can be directly transferred to metabolomics data from different experimental platforms. PMID:23093944

  18. 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

  19. 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.

  20. 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

  1. 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

  2. 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.)…

  3. MolabIS - An integrated information system for storing and managing molecular genetics data

    PubMed Central

    2011-01-01

    Background Long-term sample storage, tracing of data flow and data export for subsequent analyses are of great importance in genetics studies. Therefore, molecular labs do need a proper information system to handle an increasing amount of data from different projects. Results We have developed a molecular labs information management system (MolabIS). It was implemented as a web-based system allowing the users to capture original data at each step of their workflow. MolabIS provides essential functionality for managing information on individuals, tracking samples and storage locations, capturing raw files, importing final data from external files, searching results, accessing and modifying data. Further important features are options to generate ready-to-print reports and convert sequence and microsatellite data into various data formats, which can be used as input files in subsequent analyses. Moreover, MolabIS also provides a tool for data migration. Conclusions MolabIS is designed for small-to-medium sized labs conducting Sanger sequencing and microsatellite genotyping to store and efficiently handle a relative large amount of data. MolabIS not only helps to avoid time consuming tasks but also ensures the availability of data for further analyses. The software is packaged as a virtual appliance which can run on different platforms (e.g. Linux, Windows). MolabIS can be distributed to a wide range of molecular genetics labs since it was developed according to a general data model. Released under GPL, MolabIS is freely available at http://www.molabis.org. PMID:22040322

  4. Nonparametric Methods for Incorporating Genomic Information Into Genetic Evaluations: An Application to Mortality in Broilers

    PubMed Central

    González-Recio, Oscar; Gianola, Daniel; Long, Nanye; Weigel, Kent A.; Rosa, Guilherme J. M.; Avendaño, Santiago

    2008-01-01

    Four approaches using single-nucleotide polymorphism (SNP) information (F∞-metric model, kernel regression, reproducing kernel Hilbert spaces (RKHS) regression, and a Bayesian regression) were compared with a standard procedure of genetic evaluation (E-BLUP) of sires using mortality rates in broilers as a response variable, working in a Bayesian framework. Late mortality (14–42 days of age) records on 12,167 progeny of 200 sires were precorrected for fixed and random (nongenetic) effects used in the model for genetic evaluation and for the mate effect. The average of the corrected records was computed for each sire. Twenty-four SNPs seemingly associated with late mortality were included in three methods used for genomic assisted evaluations. One thousand SNPs were included in the Bayesian regression, to account for markers along the whole genome. The posterior mean of heritability of mortality was 0.02 in the E-BLUP approach, suggesting that genetic evaluation could be improved if suitable molecular markers were available. Estimates of posterior means and standard deviations of the residual variance were 24.38 (3.88), 29.97 (3.22), 17.07 (3.02), and 20.74 (2.87) for E-BLUP, the linear model on SNPs, RKHS regression, and the Bayesian regression, respectively, suggesting that RKHS accounted for more variance in the data. The two nonparametric methods (kernel and RKHS regression) fitted the data better, having a lower residual sum of squares. Predictive ability, assessed by cross-validation, indicated advantages of the RKHS approach, where accuracy was increased from 25 to 150%, relative to other methods. PMID:18430951

  5. 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

  6. "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

  7. 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

  8. 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. PMID:26833494

  9. 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.

  10. 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

  11. Using the Internet to Seek Information About Genetic and Rare Diseases: A Case Study Comparing Data From 2006 and 2011

    PubMed Central

    Schmidt, Johanna; Haakonsen, Christy; Lewis, Janine; Della Rocca, Maria; Morrison, Stephanie; Biesecker, Barbara; Kaphingst, Kimberly A

    2014-01-01

    Background The Genetic and Rare Disease Information Center (GARD) is a major provider of Web-based information on genetic and rare diseases. Little is known about the type of Web-based information individuals seek about genetic and rare diseases or their reasons for seeking. Objective The objective of this paper is to describe the types of Web-based information sought about genetic and rare diseases and the reasons for seeking it from GARD by examining inquiries from 2006 and 2011. Methods There were 278 English-language email and Web-based inquiries posed to GARD by lay individuals (ie, patients, parents, and relatives), which were randomly selected from inquiries in 2006 (n=68) and 2011 (n=210) and examined using content analysis. Results Most often in both years, individuals sought basic disease information (51/68, 75.0% and 132/210, 62.8%; P=.067) and information about treatment (17/51, 33.3% and 62/132, 47.0%; P=.095). Specifically, inquirers requested information about their disease prognosis (6/51, 11.8% and 23/132, 17.4%; P=.347) and made requests for specialists (8/68, 11.8% and 31/210, 14.8%; P=.536). In both 2006 and 2011, a substantial subset of inquirers requested information related to undiagnosed symptoms, representing 16.2% (11/68) and 11.9% (25/210; P=.362) of inquiries, respectively. Inquirers were significantly more likely to have seen a health care provider before contacting GARD (99/210, 47.1% vs 20/68, 29.4%; P=.010) and to ask about clinical research studies in 2011 than in 2006 (24/210, 11.4% vs 2/68, 2.9%; P=.037). In the 2011 data set, the majority of the inquirers were women (201/210, 95.7%). In our 2006 sample, men were the majority source of inquiries (54/68, 79.4%). Conclusions Findings from this study indicate that lay people contacting a genetic and rare disease information center most often seek information about disease prognosis, finding a specialist, and obtaining a diagnosis for symptoms. Unique characteristics of individuals

  12. 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.

  13. 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

  14. 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 ...

  15. 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

  16. 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

  17. Mouse models of human AML accurately predict chemotherapy response.

    PubMed

    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

    2009-04-01

    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

  18. 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

  19. 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...

  20. 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…

  1. 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…

  2. [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

  3. A Genetically Informed Cross-Lagged Analysis of Autistic-Like Traits and Affective Problems in Early Childhood.

    PubMed

    Micalizzi, Lauren; Ronald, Angelica; Saudino, Kimberly J

    2016-07-01

    A genetically informed cross-lagged model was applied to twin data to explore etiological links between autistic-like traits and affective problems in early childhood. The sample comprised 310 same-sex twin pairs (143 monozygotic and 167 dizygotic; 53 % male). Autistic-like traits and affective problems were assessed at ages 2 and 3 using parent ratings. Both constructs were related within and across age (r = 0.30-0.53) and showed moderate stability (r = 0.45-0.54). Autistic-like traits and affective problems showed genetic and environmental influences at both ages. Whereas at age 2, the covariance between autistic-like traits and affective problems was entirely due to environmental influences (shared and nonshared), at age 3, genetic factors also contributed to the covariance between constructs. The stability paths, but not the cross-lagged paths, were significant, indicating that there is stability in both autistic-like traits and affective problems but they do not mutually influence each other across age. Stability effects were due to genetic, shared, and nonshared environmental influences. Substantial novel genetic and nonshared environmental influences emerge at age 3 and suggest change in the etiology of these constructs over time. During early childhood, autistic-like traits tend to occur alongside affective problems and partly overlapping genetic and environmental influences explain this association. PMID:26456961

  4. 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

  5. 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

  6. 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.

  7. 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

  8. Whole genome association scan for genetic polymorphisms influencing information processing speed

    PubMed Central

    Luciano, Michelle; Hansell, Narelle K.; Lahti, Jari; Davies, Gail; Medland, Sarah E.; Räikkönen, Katri; Tenesa, Albert; Widen, Elisabeth; McGhee, Kevin A.; Palotie, Aarno; Liewald, David; Porteous, David J.; Starr, John M.; Montgomery, Grant W.; Martin, Nicholas G.; Eriksson, Johan G.; Wright, Margaret J.; Deary, Ian J.

    2012-01-01

    Processing speed is an important cognitive function that is compromised in psychiatric illness (e.g., schizophrenia, depression) and old age; it shares genetic background with complex cognition (e.g., working memory, reasoning). To find genes influencing speed we performed a genome-wide association scan in up to three cohorts: Brisbane (mean age 16 years; N = 1659); LBC1936 (mean age 70 years, N = 992); LBC1921 (mean age 82 years, N = 307), and; HBCS (mean age 64 years, N = 1080). Meta-analysis of the common measures highlighted various suggestively significant (p < 1.21 × 10−5) SNPs and plausible candidate genes (e.g., TRIB3). A biological pathways analysis of the speed factor identified two common pathways from the KEGG database (cell junction, focal adhesion) in two cohorts, while a pathway analysis linked to the GO database revealed common pathways across pairs of speed measures (e.g., receptor binding, cellular metabolic process). These highlighted genes and pathways will be able to inform future research, including results for psychiatric disease. PMID:21130836

  9. 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

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

    PubMed

    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. An Online Resource of Digital Stories About Cancer Genetics: Qualitative Study of Patient Preferences and Information Needs

    PubMed Central

    Mundy, Lisa; Hilgart, Jennifer

    2011-01-01

    Background The Cancer Genetics Service for Wales (CGSW) was established in 1998 as an all-Wales service for individuals with concerns about their family history of cancer. CGSW offers a range of services such as risk assessment, genetic counseling, and genetic testing. Individuals referred to cancer genetics services often have unmet information and support needs, and they value access to practical and experiential information from other patients and health professionals. As a result of the lifelong nature of genetic conditions, a fundamental challenge is to meet the ongoing needs of these patients by providing easily accessible and reliable information. Objectives Our aims were to explore how the long-term information and support needs of CGSW patients could be met and to assess whether an online bank of digital stories about cancer genetics would be acceptable to patients. Methods In 2009, CGSW organized patient panels across Wales. During these events, 169 patients were asked for their feedback about a potential online resource of digital stories from CGSW patients and staff. A total of 75 patients registered to take part in the project and 23 people from across Wales agreed to share their story. All participants took part in a follow-up interview. Results Patient preferences for an online collection of cancer genetics stories were collected at the patient panels. Key topics to be covered by the stories were identified, and this feedback informed the development of the website to ensure that patients’ needs would be met. The 23 patient storytellers were aged between 28 and 75 years, and 19 were female. The digital stories reflect patients’ experiences within CGSW and the implications of living with or at risk of cancer. Follow-up interviews with patient storytellers showed that they shared their experiences as a means of helping other patients and to increase understanding of the cancer genetics service. Digital stories were also collected from 12 members of

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

    PubMed

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

    2014-06-01

    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

  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. Pharmacogenomic Testing for Neuropsychiatric Drugs: Current Status of Drug Labeling, Guidelines for Using Genetic Information, and Test Options

    PubMed Central

    Drozda, Katarzyna; Müller, Daniel J.; Bishop, Jeffrey R.

    2014-01-01

    Advancements in pharmacogenomics have introduced an increasing number of opportunities to bring personalized medicine into clinical practice. Understanding how and when to use this technology to help guide pharmacotherapy used to treat neuropsychiatric conditions remains a challenge for many clinicians. Currently, guidelines exist to assist clinicians in the use of genetic information for drug selection and/or dosing for the tricyclic antidepressants, carbamazepine, and phenytoin. Additional language in the product labeling suggests that genetic information may also be useful for assessing the starting and target doses, as well as drug interaction potential, for a number of other medications used to treat psychiatric and neurological conditions. In this review, we outline the current status of pharmacogenomic testing for neuropsychiatric drugs as it pertains to information contained in drug labeling, consensus guidelines, and test panels, as well as considerations related to obtaining tests for patients. PMID:24523097

  15. 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

  16. Lost in translation: preclinical studies on 3,4-methylenedioxymethamphetamine provide information on mechanisms of action, but do not allow accurate prediction of adverse events in humans

    PubMed Central

    Green, AR; King, MV; Shortall, SE; Fone, KCF

    2012-01-01

    3,4-Methylenedioxymethamphetamine (MDMA) induces both acute adverse effects and long-term neurotoxic loss of brain 5-HT neurones in laboratory animals. However, when choosing doses, most preclinical studies have paid little attention to the pharmacokinetics of the drug in humans or animals. The recreational use of MDMA and current clinical investigations of the drug for therapeutic purposes demand better translational pharmacology to allow accurate risk assessment of its ability to induce adverse events. Recent pharmacokinetic studies on MDMA in animals and humans are reviewed and indicate that the risks following MDMA ingestion should be re-evaluated. Acute behavioural and body temperature changes result from rapid MDMA-induced monoamine release, whereas long-term neurotoxicity is primarily caused by metabolites of the drug. Therefore acute physiological changes in humans are fairly accurately mimicked in animals by appropriate dosing, although allometric dosing calculations have little value. Long-term changes require MDMA to be metabolized in a similar manner in experimental animals and humans. However, the rate of metabolism of MDMA and its major metabolites is slower in humans than rats or monkeys, potentially allowing endogenous neuroprotective mechanisms to function in a species specific manner. Furthermore acute hyperthermia in humans probably limits the chance of recreational users ingesting sufficient MDMA to produce neurotoxicity, unlike in the rat. MDMA also inhibits the major enzyme responsible for its metabolism in humans thereby also assisting in preventing neurotoxicity. These observations question whether MDMA alone produces long-term 5-HT neurotoxicity in human brain, although when taken in combination with other recreational drugs it may induce neurotoxicity. LINKED ARTICLES This article is commented on by Parrott, pp. 1518–1520 of this issue. To view this commentary visit http://dx.doi.org/10.1111/j.1476-5381.2012.01941.x and to view the the

  17. 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…

  18. Genetic parameters for growth and faecal worm egg count following Haemonchus contortus experimental infestations using pedigree and molecular information

    PubMed Central

    2014-01-01

    Background Haemonchosis is a parasitic disease that causes severe economic losses in sheep industry. In recent years, the increasing resistance of the parasite to anthelmintics has raised the need for alternative control strategies. Genetic selection is a promising alternative but its efficacy depends on the availability of genetic variation and on the occurrence of favourable genetic correlations between the traits included in the breeding goal. The objective of this study was twofold. First, to estimate both the heritability of and the genetic correlations between growth traits and parasite resistance traits, using bivariate linear mixed animal models, from the phenotypes and genotypes of 1004 backcross lambs (considered as a single population), which underwent two subsequent experimental infestations protocols with Haemonchus contortus. Second, to compare the precision of the estimates when using two different relationship matrices: including pedigree information only or including also SNP (single nucleotide polymorphism) information. Results Heritabilities were low for average daily gain before infestation (0.10 to 0.15) and average daily gain during the first infestation (0.11 to 0.16), moderate for faecal egg counts during the first infestation (0.21 to 0.38) and faecal egg counts during the second infestation (0.48 to 0.55). Genetic correlations between both growth traits and faecal egg count during the naïve infestation were equal to zero but the genetic correlation between faecal egg count during the second infestation and growth was positive in a Haemonchus contortus free environment and negative in a contaminated environment. The standard errors of the estimates obtained by including SNP information were smaller than those obtained by including pedigree information only. Conclusions The genetic parameters estimates suggest that growth performance can be selected for independently of selection on resistance to naïve infestation. Selection for increased

  19. 45 CFR 146.122 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... individual has a genetic variant associated with hereditary nonpolyposis colorectal cancer is a genetic test... manifested with respect to A. Example 2. (i) Facts. Individual B has several family members with colon cancer... hereditary nonpolyposis colorectal cancer (HNPCC). B's physician, a health care professional with...

  20. 45 CFR 146.122 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... individual has a genetic variant associated with hereditary nonpolyposis colorectal cancer is a genetic test... manifested with respect to A. Example 2. (i) Facts. Individual B has several family members with colon cancer... hereditary nonpolyposis colorectal cancer (HNPCC). B's physician, a health care professional with...

  1. 45 CFR 146.122 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... individual has a genetic variant associated with hereditary nonpolyposis colorectal cancer is a genetic test... manifested with respect to A. Example 2. (i) Facts. Individual B has several family members with colon cancer... hereditary nonpolyposis colorectal cancer (HNPCC). B's physician, a health care professional with...

  2. 45 CFR 146.122 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... individual has a genetic variant associated with hereditary nonpolyposis colorectal cancer is a genetic test... manifested with respect to A. Example 2. (i) Facts. Individual B has several family members with colon cancer... hereditary nonpolyposis colorectal cancer (HNPCC). B's physician, a health care professional with...

  3. Molecular genetic variation in cultivated peanut cultivars and breeding lines revealed by highly informative SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Groundnut or peanut (Arachis hypogaea L.) is an economically important crop worldwide as a source of protein and cooking oil, particularly in developing countries. Because of its narrow genetic background and shortage of polymorphic genetic markers, molecular characterization of cultivated peanuts e...

  4. Robust and Highly Informative Microsatellite-Based Genetic Identity Kit for Potato

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The fingerprinting of 742 potato landraces with 51 simple sequence repeat (SSR, microsatellite) markers resulted in improving a previously constructed potato genetic identity (PGI) kit. In addition, we mapped 27 new SSR markers on at least one of three potato genetic linkage maps. All SSR marker loc...

  5. 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…

  6. Gene by Social-Context Interactions for Number of Sexual Partners Among White Male Youths: Genetics-informed Sociology

    PubMed Central

    Guo, Guang; Tong, Yuying; Cai, Tianji

    2010-01-01

    In this study, we set out to investigate whether introducing molecular genetic measures into an analysis of sexual partner variety will yield novel sociological insights. The data source is the white male DNA sample in the National Longitudinal Study of Adolescent Health. Our empirical analysis has produced a robust protective effect of the 9R/9R genotype relative to the Any10R genotype in the dopamine transporter gene (DAT1). The gene-environment interaction analysis demonstrates that the protective effect of 9R/9R tends to be lost in schools in which higher proportions of students start having sex early or among those with relatively low levels of cognitive ability. Our genetics-informed sociological analysis suggests that the “one size” of a single social theory may not fit all. Explaining a human trait or behavior may require a theory that accommodates the complex interplay between social contextual and individual influences and genetic predispositions. PMID:19569400

  7. Using Genetically Informed, Randomized Prevention Trials to Test Etiological Hypotheses About Child and Adolescent Drug Use and Psychopathology

    PubMed Central

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

    2013-01-01

    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. PMID:23927515

  8. Relationships between parental negativity and childhood antisocial behavior over time: a bidirectional effects model in a longitudinal genetically informative design.

    PubMed

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

    2008-07-01

    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 and 7 years of age. Results from a cross-lagged twin model contribute to the understanding of the mechanisms underlying the bidirectional processes involved in parental negativity and childhood antisocial behavior. Specifically, the findings of this study suggest that the association between parenting and child antisocial behavior is best explained by both parent-driven and child-driven effects. We found support for the notion that parent's negative feelings towards their children environmentally mediate the risk for child antisocial behavior. We also found evidence of genetically mediated child effects; in which genetically influenced antisocial behavior evoke parental negativity towards the child. PMID:17602294

  9. 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. PMID:23927515

  10. Improved weight management using genetic information to personalize a calorie controlled diet

    PubMed Central

    Arkadianos, Ioannis; Valdes, Ana M; Marinos, Efstathios; Florou, Anna; Gill, Rosalynn D; Grimaldi, Keith A

    2007-01-01

    Background Gene-environment studies demonstrate variability in nutrient requirements depending upon individual variations in genes affecting nutrient metabolism and transport. This study investigated whether the inclusion of genetic information to personalize a patient's diet (nutrigenetics) could improve long term weight management. Methods Patients with a history of failures at weight loss were offered a nutrigenetic test screening 24 variants in 19 genes involved in metabolism. 50 patients were in the nutrigenetic group and 43 patients attending the same clinic were selected for comparison using algorithms to match the characteristics: age, sex, frequency of clinical visits and BMI at initial clinic visit. The second group of 43 patients did not receive a nutrigenetic test. BMI reduction at 100 and > 300 days and blood fasting glucose were measured. Results After 300 days of follow-up individuals in the nutrigenetic group were more likely to have maintained some weight loss (73%) than those in the comparison group (32%), resulting in an age and gender adjusted OR of 5.74 (95% CI 1.74–22.52). Average BMI reduction in the nutrigenetic group was 1.93 kg/m2(5.6% loss) vs. an average BMI gain of 0.51 kg/m2(2.2% gain) (p < 0.023). Among patients with a starting blood fasting glucose of > 100 mg/dL, 57% (17/30) of the nutrigenetic group but only 25% (4/16) of the non-tested group had levels reduced to < 100 mg/dL after > 90 days of weight management therapy (OR for lowering glucose to < 100 mg/dL due to diet = 1.98 95%CI 1.01, 3.87, p < 0.046). Conclusion Addition of nutrigenetically tailored diets resulted in better compliance, longer-term BMI reduction and improvements in blood glucose levels. PMID:17945020

  11. 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. PMID:27299299

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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. PMID:26245792

  19. Accurate prediction of protein structural classes by incorporating predicted secondary structure information into the general form of Chou's pseudo amino acid composition.

    PubMed

    Kong, Liang; Zhang, Lichao; Lv, Jinfeng

    2014-03-01

    Extracting good representation from protein sequence is fundamental for protein structural classes prediction tasks. In this paper, we propose a novel and powerful method to predict protein structural classes based on the predicted secondary structure information. At the feature extraction stage, a 13-dimensional feature vector is extracted to characterize general contents and spatial arrangements of the secondary structural elements of a given protein sequence. Specially, four segment-level features are designed to elevate discriminative ability for proteins from the α/β and α+β classes. After the features are extracted, a multi-class non-linear support vector machine classifier is used to implement protein structural classes prediction. We report extensive experiments comparing the proposed method to the state-of-the-art in protein structural classes prediction on three widely used low-similarity benchmark datasets: FC699, 1189 and 640. Our method achieves competitive performance on prediction accuracies, especially for the overall prediction accuracies which have exceeded the best reported results on all of the three datasets. PMID:24316044

  20. Grading More Accurately

    ERIC Educational Resources Information Center

    Rom, Mark Carl

    2011-01-01

    Grades matter. College grading systems, however, are often ad hoc and prone to mistakes. This essay focuses on one factor that contributes to high-quality grading systems: grading accuracy (or "efficiency"). I proceed in several steps. First, I discuss the elements of "efficient" (i.e., accurate) grading. Next, I present analytical results…

  1. 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

  2. The intersection of relational autonomy and narrative ethics for the patient unwilling to disclose genetic diagnosis information.

    PubMed

    Gallagher, Michael

    2014-12-01

    The rare case of the patient unwilling to disclose genetic data to his or her family provides an opportunity to expand the atomistic conception of the autonomous individual in medical decision-making. Medical practitioners naturally avoid violating patient autonomy and privacy. However, unwilling disclosure can damage the health of people other than the patient. In this situation, professionals must weigh the principle of autonomy against the nature of relationships, duties, and confidentialities between patient, professional, and family. The paradigm case studied is that of a patient with a potentially dangerous heart condition, Long QT Syndrome 3. Patients with Long QT 3 are at high risk for dying of ventricular tachycardia during rest, especially from ages 40-60. Once familial genetic testing was completed, the proband's mother, who was positive for the mutation, chose not to inform her estranged sister of the diagnosis.This paper examines the ethical duties of the physician to inform a patient's extended family of a serious genetic diagnosis, with a focus on the emotional and psychological effects of genetic testing. The need to adapt the process of violating confidentiality around considerations for the patient's emotional state and narrative will be addressed. This approach considers the patient's narrative, standpoint, and relationships as a way to develop a support plan and will present a guideline for cases where the probability of significant harm to others supersedes the patient's preference of non-disclosure as well as the physician's respect of confidentiality. The paper seeks to expand the conversation on genetic testing and autonomy beyond principles by considering all parties involved and emphasizes the use of the varied resources available to medical practitioners, especially to provide the best help possible without overburdening physicians with duties. PMID:26085443

  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 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.

  5. 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.

  6. 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

  7. 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

  8. The Locus Lookup Tool at MaizeGDB: Identification of Genomic Regions in Maize by Integrating Sequence Information with Physical and Genetic Maps

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Methods to automatically integrate sequence information with physical and genetic maps are scarce. The Locus Lookup Tool enables researchers to define windows of genomic sequence likely to contain loci of interest where only genetic or physical mapping associations are reported. Using the Locus Look...

  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. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. THE SOYBEAN BREEDER'S TOOLBOX: A NEW RESOURCE FOR SOYBEAN GENETIC AND GENOMIC INFORMATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In order to make soybean genetic data more accessible and retrievable, data contained in the current SoyBase AceDB database was converted to a relational database schema. This data is now available through an internet interface titled “The Soybean Breeder’s Toolbox”. The interface was designed to ...

  16. 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). PMID:24965717

  17. 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

  18. Genetic differentiation of chinese indigenous meat goats ascertained using microsatellite information.

    PubMed

    Ling, Y H; Zhang, X D; Yao, N; Ding, J P; Chen, H Q; Zhang, Z J; Zhang, Y H; Ren, C H; Ma, Y H; Zhang, X R

    2012-02-01

    To investigate the genetic diversity of seven Chinese indigenous meat goat breeds (Tibet goat, Guizhou white goat, Shannan white goat, Yichang white goat, Matou goat, Changjiangsanjiaozhou white goat and Anhui white goat), explain their genetic relationship and assess their integrity and degree of admixture, 302 individuals from these breeds and 42 Boer goats introduced from Africa as reference samples were genotyped for 11 microsatellite markers. Results indicated that the genetic diversity of Chinese indigenous meat goats was rich. The mean heterozygosity and the mean allelic richness (AR) for the 8 goat breeds varied from 0.697 to 0.738 and 6.21 to 7.35, respectively. Structure analysis showed that Tibet goat breed was genetically distinct and was the first to separate and the other Chinese goats were then divided into two sub-clusters: Shannan white goat and Yichang white goat in one cluster; and Guizhou white goat, Matou goat, Changjiangsanjiaozhou white goat and Anhui white goat in the other cluster. This grouping pattern was further supported by clustering analysis and Principal component analysis. These results may provide a scientific basis for the characteristization, conservation and utilization of Chinese meat goats. PMID:25049548

  19. 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

  20. '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. PMID:26744307

  1. Risk estimation and value-of-information analysis for three proposed genetic screening programs for chronic beryllium disease prevention

    SciTech Connect

    Bartell, S.M.; Ponce, R.A.; Takaro, T.K.; Zerbe, R.O.; Omenn, G.S.; Faustman, E.M.

    2000-02-01

    Genetic differences (polymorphisms) among members of a population are thought to influence susceptibility to various environmental exposures. In practice, however, this information is rarely incorporated into quantitative risk assessment and risk management. The authors describe an analytic framework for predicting the risk reduction and value-of-information (VOI) resulting from specific risk management applications of genetic biomarkers, and they apply the framework to the example of occupational chronic beryllium disease (CBD), an immune-mediated pulmonary granulomatous disease. One described Human Leukocyte Antigen gene variant, HLA-DP{beta}1*0201, contains a substitution of glutamate for lysine at position 69 that appears to have high sensitivity ({approximately}94%) but low specificity ({approximately}70%) with respect to CBD among individuals occupationally exposed to respirable beryllium. The expected postintervention CBD prevalence rates for using the genetic variant (1) as a required job placement screen, (2) as a medical screen for semiannual in place of annual lymphocyte proliferation testing, or (3) as a voluntary job placement screen are 0.08%, 0.8%, and 0.6%, respectively, in a hypothetical cohort with 1% baseline CBD prevalence. VOI analysis is used to examine the reduction in total social cost, calculated as the net value of disease reduction and financial expenditures, expected for proposed CBD intervention programs based on the genetic susceptibility test. For the example cohort the expected net VOI per beryllium worker for genetically based testing and intervention is $13,000, $1,800, and $5,100, respectively, based on a health valuation of $1.45 million per CBD case avoided. VOI results for alternative CBD valuations are also presented. Despite large parameter uncertainty, probabilistic analysis predicts generally positive utility for each of the three evaluated programs when avoidance of a CBD case is valued at $1 million or higher. Although

  2. 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

  3. 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

  4. Using a genetically informative design to examine the relationship between breastfeeding and childhood conduct problems.

    PubMed

    Shelton, Katherine H; Collishaw, Stephan; Rice, Frances J; Harold, Gordon T; Thapar, Anita

    2011-12-01

    A number of public health interventions aimed at increasing the uptake of breastfeeding are in place in the United States and other Western countries. While the physical health and nutritional benefits of breastfeeding for the mother and child are relatively well established, the evidence for psychological effects is less clear. This study aimed to examine whether there is an association between breastfeeding and later conduct problems in children. It also considered the extent to which any relationship is attributable to maternally-provided inherited characteristics that influence both likelihood of breastfeeding and child conduct problems. A prenatal cross-fostering design with a sample of 870 families with a child aged 4-11 years was used. Mothers were genetically related or unrelated to their child as a result of assisted reproductive technologies. The relationship between breastfeeding and conduct problems was assessed while controlling for theorised measured confounders by multivariate regression (e.g. maternal smoking, education, and antisocial behaviour), and for unmeasured inherited factors by testing associations separately for related and unrelated mother-child pairs. Breastfeeding was associated with lower levels of conduct disorder symptoms in offspring in middle childhood. Breastfeeding was associated with lower levels of conduct problems even after controlling for observed confounders in the genetically related group, but not in the genetically unrelated group. In contrast, maternal antisocial behaviour showed robust associations with child conduct problems after controlling for measured and inherited confounders. These findings highlight the importance of using genetically sensitive designs in order to test causal environmental influences. PMID:22028070

  5. 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

  6. 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

  7. A model for the emergence of the genetic code as a transition in a noisy information channel.

    PubMed

    Tlusty, Tsvi

    2007-11-21

    The genetic code maps the 64 nucleotide triplets (codons) to 20 amino acids. Some argue that the specific form of the code with its 20 amino acids might be a 'frozen accident' because of the overwhelming effects of any further change. Others see it as a consequence of primordial biochemical pathways and their evolution. Here we examine a scenario in which evolution drives the emergence of a genetic code by selecting for an amino acid map that minimizes the impact of errors. We treat the stochastic mapping of codons to amino acids as a noisy information channel with a natural fitness measure. Organisms compete by the fitness of their codes and, as a result, a genetic code emerges at a supercritical transition in the noisy channel, when the mapping of codons to amino acids becomes non-random. At the phase transition, a small expansion is valid and the emergent code is governed by smooth modes of the Laplacian of errors. These modes are in turn governed by the topology of the error-graph, in which codons are connected if they are likely to be confused. This topology sets an upper bound-which is related to the classical map-coloring problem-on the number of possible amino acids. The suggested scenario is generic and may describe a mechanism for the formation of other error-prone biological codes, such as the recognition of DNA sites by proteins in the transcription regulatory network. PMID:17826800

  8. 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

  9. Accurate measurement of time

    NASA Astrophysics Data System (ADS)

    Itano, Wayne M.; Ramsey, Norman F.

    1993-07-01

    The paper discusses current methods for accurate measurements of time by conventional atomic clocks, with particular attention given to the principles of operation of atomic-beam frequency standards, atomic hydrogen masers, and atomic fountain and to the potential use of strings of trapped mercury ions as a time device more stable than conventional atomic clocks. The areas of application of the ultraprecise and ultrastable time-measuring devices that tax the capacity of modern atomic clocks include radio astronomy and tests of relativity. The paper also discusses practical applications of ultraprecise clocks, such as navigation of space vehicles and pinpointing the exact position of ships and other objects on earth using the GPS.

  10. 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.

  11. 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.

  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. Donor-conceived individuals and access to information about their genetic origins: the relevance and role of rights.

    PubMed

    Tobin, John

    2012-06-01

    The discourse of rights has increasingly been used to frame debates about access to information for donor-conceived individuals. This article seeks to clarify the moral and legal basis upon which human rights are relevant to this issue. It outlines the elements of a substantive rights-based approach which is then used to resolve the competing rights of a donor and a donor-conceived individual. Three arguments are offered. First, donor anonymity must be prohibited prospectively and donor-conceived individuals must be entitled to information about their genetic parents. Secondly, a context-sensitive application of a human rights-based approach allows retrospective access to non-identifying information but precludes retrospective access to identifying information where a donor wishes to remain anonymous in circumstances where anonymity was guaranteed at the time of donation. Finally, despite this finding, a rights-based approach requires states to actively encourage such donors to consent to the release of identifying information and to take reasonable steps to support donor-conceived individuals in circumstances where donors refuse to provide their consent. PMID:22908617

  14. Genetic information and ecosystem health: arguments for the application of chaos theory to identify boundary conditions for ecosystem management.

    PubMed

    Stomp, A M

    1994-12-01

    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

  15. 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

  16. A functional–structural model of rice linking quantitative genetic information with morphological development and physiological processes

    PubMed Central

    Xu, Lifeng; Henke, Michael; Zhu, Jun; Kurth, Winfried; Buck-Sorlin, Gerhard

    2011-01-01

    Background and Aims Although quantitative trait loci (QTL) analysis of yield-related traits for rice has developed rapidly, crop models using genotype information have been proposed only relatively recently. As a first step towards a generic genotype–phenotype model, we present here a three-dimensional functional–structural plant model (FSPM) of rice, in which some model parameters are controlled by functions describing the effect of main-effect and epistatic QTLs. Methods The model simulates the growth and development of rice based on selected ecophysiological processes, such as photosynthesis (source process) and organ formation, growth and extension (sink processes). It was devised using GroIMP, an interactive modelling platform based on the Relational Growth Grammar formalism (RGG). RGG rules describe the course of organ initiation and extension resulting in final morphology. The link between the phenotype (as represented by the simulated rice plant) and the QTL genotype was implemented via a data interface between the rice FSPM and the QTLNetwork software, which computes predictions of QTLs from map data and measured trait data. Key Results Using plant height and grain yield, it is shown how QTL information for a given trait can be used in an FSPM, computing and visualizing the phenotypes of different lines of a mapping population. Furthermore, we demonstrate how modification of a particular trait feeds back on the entire plant phenotype via the physiological processes considered. Conclusions We linked a rice FSPM to a quantitative genetic model, thereby employing QTL information to refine model parameters and visualizing the dynamics of development of the entire phenotype as a result of ecophysiological processes, including the trait(s) for which genetic information is available. Possibilities for further extension of the model, for example for the purposes of ideotype breeding, are discussed. PMID:21247905

  17. 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

  18. 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

  19. 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

  20. 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. PMID:25603722

  1. 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.

  2. 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…

  3. 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

  4. A genetically informed study of the association between harsh punishment and offspring behavioral problems.

    PubMed

    Lynch, Stacy K; Turkheimer, Eric; D'Onofrio, Brian M; Mendle, Jane; Emery, Robert E; Slutske, Wendy S; Martin, Nicholas G

    2006-06-01

    Conclusions about the effects of harsh parenting on children have been limited by research designs that cannot control for genetic or shared environmental confounds. The present study used a sample of children of twins and a hierarchical linear modeling statistical approach to analyze the consequences of varying levels of punishment while controlling for many confounding influences. The sample of 887 twin pairs and 2,554 children came from the Australian Twin Registry. Although corporal punishment per se did not have significant associations with negative childhood outcomes, harsher forms of physical punishment did appear to have specific and significant effects. The observed association between harsh physical punishment and negative outcomes in children survived a relatively rigorous test of its causal status, thereby increasing the authors' conviction that harsh physical punishment is a serious risk factor for children. PMID:16756394

  5. 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

  6. Interpreting genetic risks.

    PubMed

    Pearn, J

    2016-01-01

    Prof. Peter Beighton has given a professional lifetime to helping patients and their families who have been afflicted by inherited disease. His clinical skills have brought certainty, confidence and support to those confronted with some of the most difficult decisions in life's progress. Prof. Beighton's research has led to the discovery of new syndromes and the elucidation of accurate genetic risks in many diseases. This in turn has empowered patients and their families to make informed decisions and has provided doctors with the scientific knowledge to help patients. On the occasion of this festschrift, I join with so many members of Peter's international professional family to pay tribute to his leadership and service - not only in medical genetics - but also in the broadest domains of healthcare. PMID:27245536

  7. 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

  8. 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. PMID:21888511

  9. Attitudes towards the sharing of genetic information with at-risk relatives: results of a quantitative survey.

    PubMed

    Heaton, Timothy J; Chico, Victoria

    2016-01-01

    To investigate public attitudes towards receiving genetic information arising from a test on a relative, 955 University of Sheffield students and staff were surveyed using disease vignettes. Strength of attitude was measured on whether, in the event of relevant information being discovered, they, as an at-risk relative, would want to be informed, whether the at-risk relative's interest should override proband confidentiality, and, if they had been the proband, willingness to give up confidentiality to inform such relatives. Results indicated considerably more complexity to the decision-making than simple statistical risk. Desire for information only slightly increased with risk of disease manifestation [log odds 0.05 (0.04, 0.06) per percentage point increase in manifestation risk]. Condition preventability was the primary factor increasing desire [modifiable baseline, non-preventable log odds -1.74 (-2.04, -1.44); preventable 0.64 (0.34, 0.95)]. Disease seriousness also increased desire [serious baseline, non-serious log odds -0.89 (-1.19, -0.59); fatal 0.55 (0.25, 0.86)]. Individuals with lower education levels exhibited much greater desire to be informed [GCSE log odds 1.67 (0.64, 2.66)]. Age did not affect desire. Our findings suggest that attitudes were influenced more by disease characteristics than statistical risk. Respondents generally expressed strong attitudes demonstrating that this was not an issue which people felt ambivalent about. We provide estimates of the British population in favour/against disclosure for various disease scenarios. PMID:26612611

  10. 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

  11. Incorporating information about pre-implantation genetic diagnosis into discussions about testing and risk-management for BRCA1/2 mutations: A qualitative study of patient preferences

    PubMed Central

    Hurley, Karen; Rubin, Lisa; Werner-Lin, Allison; Sagi, Michal; Kemel, Yelena; Stern, Rikki; Phillips, Aliza; Cholst, Ina; Kauff, Noah; Offit, Kenneth

    2016-01-01

    Background Studies show that BRCA1/2 mutation carriers are interested in learning about reproductive options such as pre-implantation genetic diagnosis (PGD) to prevent passing their risk onto their children. However, attitudes vary widely, and the procedure raises complex ethical and psychosocial issues. This complexity, plus the highly technical nature of PGD, makes it difficult to integrate PGD information into genetic counseling sessions that already cover probabilistic, emotionally-charged risk information. Method Thirty-three reproductive age BRCA1/2 mutation carriers who had previously undergone genetic counseling viewed a tutorial about PGD and were interviewed about attitudes towards PGD, and preferences about how to include PGD information in genetic counseling. Results Most participants preferred to be briefly informed of availability of PGD information, and to receive written materials about PGD, but with the option of deferring detailed discussion if they already feel overloaded or perceive that PGD is not immediately relevant to their risk management and/or childbearing plans. For some, the stress of testing temporarily interfered with information processing, producing states of cognitive avoidance (“in a fog,” “tuning out”). Some preferred to discuss PGD with a physician with whom they had an ongoing relationship (e.g., OB/GYN, primary care provider, oncologist). Conclusions Providers offering cancer genetic testing can consider indicating availability of PGD information, while attending to patients’ level of interest and ability to absorb information. Research is needed to link patient responses to information overload to psychosocial outcomes (e.g., distress, decision quality). Continuing medical education is needed to support providers in facilitating informed decisions about PGD. PMID:22736296

  12. Quantifying Phenotypic Plasticity Using Genetic Information for Simulating Plant Height in Winter Wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A challenge for crop simulation modeling is to incorporate existing and rapidly emerging genomic information into models to develop new and improved algorithms. The objective of this effort was to simulate plant height in winter wheat (Triticum aestivum L.) across a range of environments in Nebraska...

  13. 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.

  14. 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.

  15. 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

  16. How the Neurocircuitry and Genetics of Fear Inhibition May Inform Our Understanding of PTSD

    PubMed Central

    Jovanovic, Tanja; Ressler, Kerry J.

    2013-01-01

    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

  17. Genetic identification of horse mackerel and related species in seafood products by means of forensically informative nucleotide sequencing methodology.

    PubMed

    Lago, Fátima C; Herrero, Beatriz; Vieites, Juan M; Espiñeira, Montserrat

    2011-03-23

    In the present study, a methodology based on the amplification of a fragment of mitochondrial cytochrome b and subsequent phylogenetic analysis (FINS: forensically informative nucleotide sequencing) to genetically identify horse mackerels have been developed. This methodology makes possible the identification of more than 20 species belonging to the families Carangidae, Mullidae, and Scombridae. The main novelty of this work lies in the longest number of different horse mackerel species included and in the applicability of the developed methods to all kinds of processed products that can be found by consumers in markets around the world, including those that have undergone intensive processes of transformation, as for instance canned foods. Finally, the methods were applied to 15 commercial samples, all of them canned products. Therefore, these methods are useful for checking the fulfillment of labeling regulations for horse mackerels and horse mackerel products, verifying the correct traceability in commercial trade, and fisheries control. PMID:21332203

  18. 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. PMID:26284465

  19. 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

  20. Effect of Enhanced Information, Values Clarification, and Removal of Financial Barriers on Use of Prenatal Genetic Testing

    PubMed Central

    Kuppermann, Miriam; Pena, Sherri; Bishop, Judith T.; Nakagawa, Sanae; Gregorich, Steven E.; Sit, Anita; Vargas, Juan; Caughey, Aaron B.; Sykes, Susan; Pierce, Lasha; Norton, Mary E.

    2015-01-01

    Importance Prenatal genetic testing guidelines recommend providing patients with detailed information to allow informed, preference-based screening and diagnostic testing decisions. The effect of implementing these guidelines is not well understood. Objective Toanalyze the effect of a decision support guide and elimination of financial barriers to testing on use of prenatal genetic testing and decision-making among women of varying literacy and numeracy levels. Design Randomized trial conducted from 2010-2013. Setting Prenatal clinics at three county hospitals, a community clinic, an academic center, and three medical centers of an integrated health care delivery system in the San Francisco Bay area. Participants English- or Spanish-speaking women who had not yet undergone screening and/or diagnostic testing and remained pregnant at 11 weeks gestation (n=710). Interventions A computerized, interactive decision support guide and access to prenatal testing with no out-of-pocket expense (n=357) or usual care as per current guidelines (n=353). Main Outcome Measures The primary outcome was invasive diagnostic test use, obtained via medical record review. Secondary outcomes included testing strategy undergone, and knowledge, risk comprehension, decisional conflict and decision regret at 24-36 weeks' gestation. Results Women randomized to the intervention group, compared to those randomized to the control group, were less likely to have invasive testing [5.9% vs. 12.3%, odds ratio (OR) 0.45, 95% CI 0.25-0.80] and more likely to forego testing altogether [25.6% vs. 20.4%, OR 3.30 (reference group screening followed by invasive testing), CI 1.43-7.64]. They also had higher knowledge scores (9.4 vs. 8.6 on a 15-point scale, mean group difference 0.82, CI 0.34-1.31), and were more likely to correctly estimate the amniocentesis-related miscarriage risk (73.8% vs. 59.0%, OR 1.95, CI 1.39-2.75) and their age-adjusted chance of carrying a fetus with trisomy 21 (58.7% vs. 46

  1. 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

  2. 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

  3. 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 ...

  4. Expression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic Variation

    PubMed Central

    Raj, Towfique; McGeachie, Michael J.; Qiu, Weiliang; Ziniti, John P.; Stubbs, Benjamin J.; Liang, Liming; Martinez, Fernando D.; Strunk, Robert C.; Lemanske, Robert F.; Liu, Andrew H.; Stranger, Barbara E.; Carey, Vincent J.; Raby, Benjamin A.

    2015-01-01

    Disease-associated loci identified through genome-wide association studies (GWAS) frequently localize to non-coding sequence. We and others have demonstrated strong enrichment of such single nucleotide polymorphisms (SNPs) for expression quantitative trait loci (eQTLs), supporting an important role for regulatory genetic variation in complex disease pathogenesis. Herein we describe our initial efforts to develop a predictive model of disease-associated variants leveraging eQTL information. We first catalogued cis-acting eQTLs (SNPs within 100kb of target gene transcripts) by meta-analyzing four studies of three blood-derived tissues (n = 586). At a false discovery rate < 5%, we mapped eQTLs for 6,535 genes; these were enriched for disease-associated genes (P < 10−04), particularly those related to immune diseases and metabolic traits. Based on eQTL information and other variant annotations (distance from target gene transcript, minor allele frequency, and chromatin state), we created multivariate logistic regression models to predict SNP membership in reported GWAS. The complete model revealed independent contributions of specific annotations as strong predictors, including evidence for an eQTL (odds ratio (OR) = 1.2–2.0, P < 10−11) and the chromatin states of active promoters, different classes of strong or weak enhancers, or transcriptionally active regions (OR = 1.5–2.3, P < 10−11). This complete prediction model including eQTL association information ultimately allowed for better discrimination of SNPs with higher probabilities of GWAS membership (6.3–10.0%, compared to 3.5% for a random SNP) than the other two models excluding eQTL information. This eQTL-based prediction model of disease relevance can help systematically prioritize non-coding GWAS SNPs for further functional characterization. PMID:26474488

  5. 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

  6. Prevalence and correlates of receiving and sharing high-penetrance cancer genetic test results: Findings from the Health Information National Trends Survey

    PubMed Central

    Taber, Jennifer M.; Chang, Christine Q.; Lam, Tram Kim; Gillanders, Elizabeth M.; Hamilton, Jada G.; Schully, Sheri D.

    2015-01-01

    Background/Aims The aim of this study was to explore the prevalence and correlates of receiving and sharing high-penetrance cancer genetic test results. Methods Participants completed the population-based, cross-sectional 2013 Health Information National Trends Survey. We examined sociodemographic characteristics of participants reporting having had BRCA1/2 or Lynch syndrome genetic testing, and sociodemographic and psychosocial correlates of sharing test results with health professionals and family members. Results Participants who underwent BRCA1/2 or Lynch syndrome genetic testing (n=77; 2.42% of respondents) were more likely to be female and to have a family or personal cancer history than those not undergoing testing. Approximately three-quarters of participants shared results with health professionals and three-quarters with their family; only 4% did not share results with anyone. Participants who shared results with health professionals reported greater optimism, self-efficacy for health management, and trust in information from their doctors. Participants who shared results with family were more likely to be female and to have a personal cancer history, and had greater self-efficacy for health management, perceived less ambiguity in cancer prevention recommendations, and lower cancer prevention fatalism. Conclusions We identified several novel psychosocial correlates of sharing genetic information. Health professionals may use this information to identify patients less likely to share information with at-risk family members. PMID:25427996

  7. Defining a genetic ideotype for crop improvement.

    PubMed

    Trethowan, Richard M

    2014-01-01

    While plant breeders traditionally base selection on phenotype, the development of genetic ideotypes can help focus the selection process. This chapter provides a road map for the establishment of a refined genetic ideotype. The first step is an accurate definition of the target environment including the underlying constraints, their probability of occurrence, and impact on phenotype. Once the environmental constraints are established, the wealth of information on plant physiological responses to stresses, known gene information, and knowledge of genotype ×environment and gene × environment interaction help refine the target ideotype and form a basis for cross prediction.Once a genetic ideotype is defined the challenge remains to build the ideotype in a plant breeding program. A number of strategies including marker-assisted recurrent selection and genomic selection can be used that also provide valuable information for the optimization of genetic ideotype. However, the informatics required to underpin the realization of the genetic ideotype then becomes crucial. The reduced cost of genotyping and the need to combine pedigree, phenotypic, and genetic data in a structured way for analysis and interpretation often become the rate-limiting steps, thus reducing genetic gain. Systems for managing these data and an example of ideotype construction for a defined environment type are discussed. PMID:24816655

  8. Effect of ethnicity, gender and drug use history on achieving high rates of affirmative informed consent for genetics research: impact of sharing with a national repository

    PubMed Central

    Ray, Brenda; Jackson, Colin; Ducat, Elizabeth; Ho, Ann; Hamon, Sara; Kreek, Mary Jeanne

    2013-01-01

    Aim Genetic research representative of the population is crucial to understanding the underlying causes of many diseases. In a prospective evaluation of informed consent we assessed the willingness of individuals of different ethnicities, gender and drug dependence history to participate in genetic studies in which their genetic sample could be shared with a repository at the National Institutes of Health. Methods Potential subjects were recruited from the general population through the use of flyers and referrals from previous participants and clinicians with knowledge of our study. They could consent to 11 separate choices so that they could specify how and with whom their genetic sample could be shared. Rates of affirmative consent were then analysed by gender, ethnicity and drug dependence history. Results Of 1416 volunteers enrolled, 99.7% gave affirmative informed consent for studies of addiction conducted in our laboratory. No significant difference was found for participation in genetic studies conducted in our laboratory by gender, ethnicity or drug dependence history. Over all 11 questions, individuals with a history of drug use were more likely to agree to consent to participate in our study than were healthy volunteers. Conclusion A high percentage of each category of gender, ethnicity and drug history, gave affirmative consent at all levels. The level of detail in and the amount of time spent reviewing the informed consent, and a relationship of trust with the clinical investigator may contribute to this outcome. PMID:21266386

  9. Examining the genetic and environmental influences on self-control and delinquency: results from a genetically informative analysis of sibling pairs.

    PubMed

    Connolly, Eric J; Beaver, Kevin M

    2014-03-01

    The Child and Young Adult Supplement of the National Longitudinal Survey of Youth (CNLSY) has been used extensively within criminology. A significant amount of criminological research, for example, has explored various issues related to the correlates, causes, and consequences associated with levels of self-control and delinquent involvement. The overwhelming majority of these CNLSY studies, however, have not accounted for the potential effects of genetic factors on these two widely studied criminological variables and thus the findings generated from previous empirical work may be inaccurate due to genetic confounding. The current study partially addresses this possibility by analyzing a sample of kinship pairs nested within the CNLSY. Analyses of these data revealed that genetic factors accounted for between 51% and 92% of the variance in levels of self-control and between 30% and 41% of the variance in delinquency. We discuss the implications of these results for interpreting findings from the large body of existing research using the CNLSY. PMID:24142448

  10. Harvey Sarcoma Virus: A Second Murine Type C Sarcoma Virus with Rat Genetic Information

    PubMed Central

    Scolnick, Edward M.; Parks, Wade P.

    1974-01-01

    The nucleic acid sequences found in the Harvey strain of murine sarcoma virus have been analyzed by RNA·[3H]DNA and [3H]RNA·DNA hybridization techniques. The Harvey strain of murine sarcoma virus has been found to possess at least two sets of nucleic acid sequences. One set of sequences is contained in the Moloney strain of mouse type-C virus, and the other set is contained in DNA transcripts synthesized in endogenous reactions containing rat type-C virus(es). The nucleic acid sequences that are detected in the Harvey sarcoma virus with the DNA probes synthesized from the rat type-C virus(es) are related to the rat sequences detected in the Kirsten strain of murine sarcoma virus. The results support the model that both Kirsten and Harvey sarcoma viruses arose through a process of recombination or reassortment between mouse type-C viruses and sequences in rat cells and suggest that the information for transformation of fibroblasts may be contained in the rat type-C or cellular genome. PMID:4364897

  11. 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...

  12. 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...

  13. 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. PMID:23476971

  14. Availability of genotypic data for USDA-ARS National Plant Germplasm System accessions using the Genetic Resources Information Network (GRIN) database

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The National Plant Germplasm System (NPGS) provides critical genetic resources to researchers and breeders world wide. Users of the NPGS materials need access to both genotypic and phenotypic data for accessions. Descriptor records at the accession level within the Germplasm Resources Information ...

  15. 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?

  16. A genetic algorithm encoded with the structural information of amino acids and dipeptides for efficient conformational searches of oligopeptides.

    PubMed

    Ru, Xiao; Song, Ce; Lin, Zijing

    2016-05-15

    The genetic algorithm (GA) is an intelligent approach for finding minima in a highly dimensional parametric space. However, the success of GA searches for low energy conformations of biomolecules is rather limited so far. Herein an improved GA scheme is proposed for the conformational search of oligopeptides. A systematic analysis of the backbone dihedral angles of conformations of amino acids (AAs) and dipeptides is performed. The structural information is used to design a new encoding scheme to improve the efficiency of GA search. Local geometry optimizations based on the energy calculations by the density functional theory are employed to safeguard the quality and reliability of the GA structures. The GA scheme is applied to the conformational searches of Lys, Arg, Met-Gly, Lys-Gly, and Phe-Gly-Gly representative of AAs, dipeptides, and tripeptides with complicated side chains. Comparison with the best literature results shows that the new GA method is both highly efficient and reliable by providing the most complete set of the low energy conformations. Moreover, the computational cost of the GA method increases only moderately with the complexity of the molecule. The GA scheme is valuable for the study of the conformations and properties of oligopeptides. © 2016 Wiley Periodicals, Inc. PMID:26833761

  17. Genetic test reporting enhances understanding of risk information and acceptance of prevention recommendations compared to family history-based counseling alone.

    PubMed

    Taber, Jennifer M; Aspinwall, Lisa G; Stump, Tammy K; Kohlmann, Wendy; Champine, Marjan; Leachman, Sancy A

    2015-10-01

    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 1 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 1 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

  18. 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.

  19. 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... to develop the GTR, as outlined in this RFI, may submit comments by e-mail to GTR@od.nih.gov or...

  20. Genetic counseling.

    PubMed

    Fraser, F C

    1974-09-01

    A workshop was sponsored by the National Genetics Foundation to evaluate and make recommendations about the status of genetic counseling, its goals, nature, achievements, and needs. The process of genetic workup and counseling is divided into 5 stages: validation of the diagnosis; obtaining family history; estimation of the risk of recurrence; helping the family make a decision and take appropriate action; and extending counseling to other members of the family. Counseling can be directed at individuals or at special groups with the potential of carrying such diseases as sickle cell amenia or Tay-Sachs. No consensus exists on an optimal counseling approach. Genetic counseling is regarded as a team effort, requiring, in addition to the counselor, laboratory facilities and a variety of specialists. The source of payment for genetic counseling services is regarded as a problem of increasing concern. Generally, the fee paid rarely covers the cost of the many procedures and it is suggested that the cost, like that of other public health services, should be subsidized by the state. Considerable argument exists over whether a genetic counselor must have a M.D. degree or whether a Ph. D. in medical genetics is suitable enough. The quality of much genetic counseling, which is often done in the office of doctors unskilled in the field, would be increased if better training in genetics were offered to medical students and if physicians were informed of the existence of counseling centers. Further, there is a growing feeling that some sort of accreditation of genetic counselors is desirable. PMID:4609197

  1. How to accurately bypass damage

    PubMed Central

    Broyde, Suse; Patel, Dinshaw J.

    2016-01-01

    Ultraviolet radiation can cause cancer through DNA damage — specifically, by linking adjacent thymine bases. Crystal structures show how the enzyme DNA polymerase η accurately bypasses such lesions, offering protection. PMID:20577203

  2. Accurate Evaluation of Quantum Integrals

    NASA Technical Reports Server (NTRS)

    Galant, David C.; Goorvitch, D.

    1994-01-01

    Combining an appropriate finite difference method with Richardson's extrapolation results in a simple, highly accurate numerical method for solving a Schr\\"{o}dinger's equation. Important results are that error estimates are provided, and that one can extrapolate expectation values rather than the wavefunctions to obtain highly accurate expectation values. We discuss the eigenvalues, the error growth in repeated Richardson's extrapolation, and show that the expectation values calculated on a crude mesh can be extrapolated to obtain expectation values of high accuracy.

  3. 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.

  4. 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 ...

  5. 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 ...

  6. Genetic Screening

    PubMed Central

    Burke, Wylie; Tarini, Beth; Press, Nancy A.; Evans, James P.

    2011-01-01

    Current approaches to genetic screening include newborn screening to identify infants who would benefit from early treatment, reproductive genetic screening to assist reproductive decision making, and family history assessment to identify individuals who would benefit from additional prevention measures. Although the traditional goal of screening is to identify early disease or risk in order to implement preventive therapy, genetic screening has always included an atypical element—information relevant to reproductive decisions. New technologies offer increasingly comprehensive identification of genetic conditions and susceptibilities. Tests based on these technologies are generating a different approach to screening that seeks to inform individuals about all of their genetic traits and susceptibilities for purposes that incorporate rapid diagnosis, family planning, and expediting of research, as well as the traditional screening goal of improving prevention. Use of these tests in population screening will increase the challenges already encountered in genetic screening programs, including false-positive and ambiguous test results, overdiagnosis, and incidental findings. Whether this approach is desirable requires further empiric research, but it also requires careful deliberation on the part of all concerned, including genomic researchers, clinicians, public health officials, health care payers, and especially those who will be the recipients of this novel screening approach. PMID:21709145

  7. 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

  8. 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. PMID:12747164

  9. Genetic screening

    PubMed Central

    Andermann, Anne; Blancquaert, Ingeborg

    2010-01-01

    Abstract OBJECTIVE To provide a primer for primary care professionals who are increasingly called upon to discuss the growing number of genetic screening services available and to help patients make informed decisions about whether to participate in genetic screening, how to interpret results, and which interventions are most appropriate. QUALITY OF EVIDENCE As part of a larger research program, a wide literature relating to genetic screening was reviewed. PubMed and Internet searches were conducted using broad search terms. Effort was also made to identify the gray literature. MAIN MESSAGE Genetic screening is a type of public health program that is systematically offered to a specified population of asymptomatic individuals with the aim of providing those identified as high risk with prevention, early treatment, or reproductive options. Ensuring an added benefit from screening, as compared with standard clinical care, and preventing unintended harms, such as undue anxiety or stigmatization, depends on the design and implementation of screening programs, including the recruitment methods, education and counseling provided, timing of screening, predictive value of tests, interventions available, and presence of oversight mechanisms and safeguards. There is therefore growing apprehension that economic interests might lead to a market-driven approach to introducing and expanding screening before program effectiveness, acceptability, and feasibility have been demonstrated. As with any medical intervention, there is a moral imperative for genetic screening to do more good than harm, not only from the perspective of individuals and families, but also for the target population and society as a whole. CONCLUSION Primary care professionals have an important role to play in helping their patients navigate the rapidly changing terrain of genetic screening services by informing them about the benefits and risks of new genetic and genomic technologies and empowering them to

  10. Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent

    PubMed Central

    Browning, Sharon R.; Browning, Brian L.

    2015-01-01

    Existing methods for estimating historical effective population size from genetic data have been unable to accurately estimate effective population size during the most recent past. We present a non-parametric method for accurately estimating recent effective population size by using inferred long segments of identity by descent (IBD). We found that inferred segments of IBD contain information about effective population size from around 4 generations to around 50 generations ago for SNP array data and to over 200 generations ago for sequence data. In human populations that we examined, the estimates of effective size were approximately one-third of the census size. We estimate the effective population size of European-ancestry individuals in the UK four generations ago to be eight million and the effective population size of Finland four generations ago to be 0.7 million. Our method is implemented in the open-source IBDNe software package. PMID:26299365

  11. 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 ...

  12. 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

  13. Accuracy of recall of information about a cancer-predisposing BRCA1/2 gene mutation among patients and relatives

    PubMed Central

    Jacobs, Chris; Dancyger, Caroline; Smith, Jonathan A; Michie, Susan

    2015-01-01

    This observational study aimed to (i) compare the accuracy of information recalled by patients and relatives following genetic counselling about a newly identified BRCA1/2 mutation, (ii) identify differences in accuracy of information about genetics and hereditary cancer and (iii) investigate whether accuracy among relatives improved when information was provided directly by genetics health professionals. Semistructured interviews following results from consultations with 10 breast/ovarian cancer patients and 22 relatives were audio-recorded and transcribed. Information provided by the genetics health professional was tracked through the families and coded for accuracy. Accuracy was analysed using the Wilcoxon Signed-Ranks test. Sources of information were tested using Spearman's rank-order correlation coefficient. Fifty-three percent of the information recalled by patients was accurate. Accuracy of recall among relatives was significantly lower than that among patients (P=0.017). Both groups recalled a lower proportion of information about hereditary cancer than about genetics (P=0.005). Relatives who learnt the information from the patient alone recalled significantly less accurate information than those informed directly by genetics health professionals (P=0.001). Following genetic counselling about a BRCA1/2 mutation, accuracy of recall was low among patients and relatives, particularly about hereditary cancer. Multiple sources of information, including direct contact with genetics health professionals, may improve the accuracy of information among relatives. PMID:24848747

  14. 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

  15. 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

  16. 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.

  17. 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

  18. Genetics of familial hypercholesterolemia.

    PubMed

    Brautbar, Ariel; Leary, Emili; Rasmussen, Kristen; Wilson, Don P; Steiner, Robert D; Virani, Salim

    2015-04-01

    Familial hypercholesterolemia (FH) is a genetic disorder characterized by elevated low-density lipoprotein (LDL) cholesterol and premature cardiovascular disease, with a prevalence of approximately 1 in 200-500 for heterozygotes in North America and Europe. Monogenic FH is largely attributed to mutations in the LDLR, APOB, and PCSK9 genes. Differential diagnosis is critical to distinguish FH from conditions with phenotypically similar presentations to ensure appropriate therapeutic management and genetic counseling. Accurate diagnosis requires careful phenotyping based on clinical and biochemical presentation, validated by genetic testing. Recent investigations to discover additional genetic loci associated with extreme hypercholesterolemia using known FH families and population studies have met with limited success. Here, we provide a brief overview of the genetic determinants, differential diagnosis, genetic testing, and counseling of FH genetics. PMID:25712136

  19. 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) ...

  20. Influence of Genetic Risk Information on Parental Role Identity in Adolescent Girls and Young Women from Families with Fragile X Syndrome

    PubMed Central

    Heise, Elizabeth Melvin; Spiridigliozzi, Gail A.

    2012-01-01

    Using a multi-group cross-sectional design, we explored self-concept related to parental role salience and enactment in 53 young women (14 to 24 years) with knowledge they were either carriers, non-carriers, or could be a carrier of fragile X syndrome (FXS). Parental role salience included the participants’ desire “to be a mother” and the importance they placed on this role. Enactment focused on the participants’ views regarding ways to become a mother (reproductive options), parenting a child affected by FXS, and the development of partner relationships (marriage). Participants completed the FXS Adolescent Interview and the FX-Visual Analog Scale. Participants’ knowledge of their genetic risk status appears to have influenced both salience and enactment of the parental role, and the effect varied based on carrier status. For many, knowledge of genetic risk appears to have led to reappraisal, redefinition, and re-engagement with the goal of becoming a parent. This process was prominent in those who were carriers and less so in those who were at-risk, and it did not typically occur in those who were non-carriers. Findings offer valuable insight into the impact of genetic risk information on developing perceptions of the parental role and offer new directions for genetic counseling with adolescents and young women with a family history of FXS. PMID:21826579

  1. Effective utilization of genetic information for athletes and coaches: focus on ACTN3 R577X polymorphism

    PubMed Central

    Kikuchi, Naoki; Nakazato, Koichi

    2015-01-01

    Training variants (type, intensity, and duration of exercise) can be selected according to individual aims and fitness assessment. Recently, various methods of resistance and endurance training have been used for muscle hypertrophy and VO2max improvement. Although several genetic variants are associated with elite athletic performance and muscle phenotypes, genetic background has not been used as variant for physical training. ACTN3 R577X is a well-studied genetic polymorphism. It is the only genotype associated with elite athletic performance in multiple cohorts. This association is strongly supported by mechanistic data from an Actn3-knockout mouse model. In this review, possible guidelines are discussed for effective utilization of ACTN3 R577X polymorphism for physical training. PMID:26526670

  2. Effective utilization of genetic information for athletes and coaches: focus on ACTN3 R577X polymorphism.

    PubMed

    Kikuchi, Naoki; Nakazato, Koichi

    2015-09-01

    Training variants (type, intensity, and duration of exercise) can be selected according to individual aims and fitness assessment. Recently, various methods of resistance and endurance training have been used for muscle hypertrophy and VO2max improvement. Although several genetic variants are associated with elite athletic performance and muscle phenotypes, genetic background has not been used as variant for physical training. ACTN3 R577X is a well-studied genetic polymorphism. It is the only genotype associated with elite athletic performance in multiple cohorts. This association is strongly supported by mechanistic data from an Actn3-knockout mouse model. In this review, possible guidelines are discussed for effective utilization of ACTN3 R577X polymorphism for physical training. PMID:26526670

  3. Associations between reading achievement and independent reading in early elementary school: A genetically-informative cross-lagged study

    PubMed Central

    Harlaar, Nicole; Deater-Deckard, Kirby; Thompson, Lee A.; DeThorne, Laura S.; Petrill, Stephen A.

    2013-01-01

    This study used a cross-lagged twin design to examine reading achievement and independent reading from 10 to 11 years (n = 436 twin pairs). Reading achievement at age 10 significantly predicted independent reading at age 11. The alternative path, from independent reading at age 10 to reading achievement at age 11, was not significant. Individual differences in reading achievement and independent reading at both ages were primarily due to genetic influences. Furthermore, individual differences in independent reading at age 11 partly reflected genetic influences on reading achievement at age 10. These findings suggest that genetic influences that contribute to individual differences in children’s reading abilities also influence the extent to which children actively seek out and create opportunities to read. PMID:22026450

  4. Force aggregation using genetic algortihms

    NASA Astrophysics Data System (ADS)

    Shea, Peter J.; Peterson, John; Alexander, Kathleen; Azevedo, Alcino

    2004-01-01

    A surveillance system needs to accurately locate and identify not only single targets, but also groups of targets engaged in a common activity. Most existing tracking systems are capable of tracking individual targets quite accurately; however, they fail to use information related to group behavior in order to improve these estimates. Furthermore, in wide area surveillance situations a military operator is required to sort through hundreds to thousands of individual targets in order to develop an understanding of the situation. Having the ability to collapse the behavior of individual targets into a common, coordinated motion can greatly enhance the productively and situational awareness of the operator. Our long-term approach to solving this problem is to develop an understanding of how to define a group and then to understand the inter-relationships between the various characteristics that describe a group. Then using this information, we will be able to partition the set of target into groups that can be aggregated over the entire military force hierarchy. This goal of this paper is to describe an approach that is based upon genetic algorithms for solving the military force hierarchy problem. This paper will describe the underlying genetic algorithm, scoring function, and some initial results.

  5. Force aggregation using genetic algortihms

    NASA Astrophysics Data System (ADS)

    Shea, Peter J.; Peterson, John; Alexander, Kathleen; Azevedo, Alcino

    2003-12-01

    A surveillance system needs to accurately locate and identify not only single targets, but also groups of targets engaged in a common activity. Most existing tracking systems are capable of tracking individual targets quite accurately; however, they fail to use information related to group behavior in order to improve these estimates. Furthermore, in wide area surveillance situations a military operator is required to sort through hundreds to thousands of individual targets in order to develop an understanding of the situation. Having the ability to collapse the behavior of individual targets into a common, coordinated motion can greatly enhance the productively and situational awareness of the operator. Our long-term approach to solving this problem is to develop an understanding of how to define a group and then to understand the inter-relationships between the various characteristics that describe a group. Then using this information, we will be able to partition the set of target into groups that can be aggregated over the entire military force hierarchy. This goal of this paper is to describe an approach that is based upon genetic algorithms for solving the military force hierarchy problem. This paper will describe the underlying genetic algorithm, scoring function, and some initial results.

  6. 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 ...

  7. 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

  8. 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

  9. 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. PMID:26914462

  10. Rater Biases in Genetically Informative Research Designs: Comment on Bartels, Boomsma, Hudziak, van Beijsterveldt, and van den Oord (2007)

    ERIC Educational Resources Information Center

    Hoyt, William T.

    2007-01-01

    Rater biases are of interest to behavior genetic researchers, who often use ratings data as a basis for studying heritability. Inclusion of multiple raters for each sibling pair (M. Bartels, D. I. Boomsma, J. J. Hudziak, T. C. E. M. van Beijsterveldt, & E. J. C. G. van den Oord, 2007) is a promising strategy for controlling bias variance and may…

  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. 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…

  13. 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…

  14. Nature-Nurture Interplay: Genetically Informative Designs Contribute to Understanding the Effects of Trauma and Interpersonal Violence

    ERIC Educational Resources Information Center

    Koenen, Karestan C.

    2005-01-01

    The past two decades have seen an explosion in research in the fields of violence and trauma and behavior genetics. These two fields came into direct conflict when Lisabeth Fisher DiLalla and Irving I. Gottesman outlined a fundamental conceptual limitation of trauma and violence research: that rather than being causal, the well-documented…

  15. Diabetes Pathology and Risk of Primary Open-Angle Glaucoma: Evaluating Causal Mechanisms by Using Genetic Information.

    PubMed

    Shen, Ling; Walter, Stefan; Melles, Ronald B; Glymour, M Maria; Jorgenson, Eric

    2016-01-15

    Although type 2 diabetes (T2D) predicts glaucoma, the potential for unmeasured confounding has hampered causal conclusions. We performed separate sample genetic instrumental variable analyses using the Genetic Epidemiology Research Study on Adult Health and Aging cohort (n = 69,685; 1995-2013) to estimate effects of T2D on primary open-angle glaucoma (POAG; 3,554 cases). Genetic instrumental variables for overall and mechanism-specific (i.e., linked to T2D via influences on adiposity, β-cell function, insulin regulation, or other metabolic processes) T2D risk were constructed by using 39 genetic polymorphisms established to predict T2D in other samples. Instrumental variable estimates indicated that T2D increased POAG risk (odds ratio = 2.53, 95% confidence interval: 1.04, 6.11). The instrumental variable for β-cell dysregulation also significantly predicted POAG (odds ratioβ-cell = 5.26, 95% confidence interval: 1.75, 15.85), even among individuals without diagnosed T2D, suggesting that metabolic dysregulation may increase POAG risk prior to T2D diagnosis. The T2D risk variant in the melatonin receptor 1B gene (MTNR1B) predicted risk of POAG independently of T2D status, indicating possible pleiotropic physiological functions of melatonin, but instrumental variable effect estimates were significant even excluding MTNR1B variants. To our knowledge, this is the first genetic instrumental variable study of T2D and glaucoma, providing a novel approach to evaluating this hypothesized relationship. Our findings substantially bolster observational evidence that T2D increases POAG risk. PMID:26608880

  16. 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)

  17. 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

  18. 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 ...

  19. Introductory molecular genetics

    SciTech Connect

    Edwards-Moulds, J.

    1986-01-01

    This book begins with an overview of the current principles of genetics and molecular genetics. Over this foundation, it adds detailed and specialized information: a description of the translation, transcription, expression and regulation of DNA and RNA; a description of the manipulation of genetic material via promoters, enhancers, and gene splicing; and a description of cloning techniques, especially those for blood group genes. The last chapter looks to the impact of molecular genetics on transfusion medicine.

  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. 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 ...

  2. The thermodynamic cost of accurate sensory adaptation

    NASA Astrophysics Data System (ADS)

    Tu, Yuhai

    2015-03-01

    Living organisms need to obtain and process environment information accurately in order to make decisions critical for their survival. Much progress have been made in identifying key components responsible for various biological functions, however, major challenges remain to understand system-level behaviors from the molecular-level knowledge of biology and to unravel possible physical principles for the underlying biochemical circuits. In this talk, we will present some recent works in understanding the chemical sensory system of E. coli by combining theoretical approaches with quantitative experiments. We focus on addressing the questions on how cells process chemical information and adapt to varying environment, and what are the thermodynamic limits of key regulatory functions, such as adaptation.

  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. 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.

  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. 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...

  7. 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.

    PubMed

    Brendgen, Mara; Vitaro, Frank; Barker, Edward D; Girard, Alain; Dionne, Ginette; Tremblay, Richard E; Boivin, Michel

    2013-02-01

    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 were children's close friends. The sample comprised 197 monozygotic and same-sex dizygotic twin pairs reared together (95 female pairs) assessed in Grade 4. Each twin's victimization experiences and victimization experienced by his or her friends and other classmates were measured using individuals' reports about their own levels of peer victimization. Aggression was assessed using peer nominations, and depression was measured using self-reports. Indicative of a possible social-learning mechanism or the emotional contagion of anger, multilevel regressions showed that personal victimization experiences were related to especially high levels of aggression when close friends where also highly victimized, albeit only in boys. Moreover, in line with social comparison theory, the effect of frequent personal victimization experiences on depressive feelings was much weaker when close friends were also highly victimized than when close friends were not or were only rarely victimized. Finally, a high level of peer victimization experienced by other classmates was related to a lower level of aggression in girls and boys, possibly because of a heightened sense of threat in classrooms where many suffer attacks from bullies. All of these results were independent of children's genetic risk for aggression or depression. Theoretical and practical implications are discussed. PMID:21967566

  8. Challenges and strategies of the Genetics Home Reference

    PubMed Central

    Mitchell, Joyce A.; Fomous, Cathy; Fun, Jane

    2006-01-01

    Objective: This paper focuses on the first two years of operation of Genetics Home Reference (GHR), a Web-based resource for the general public that helps to explain the health implications of findings from the Human Genome Project. Methods and Findings: Key challenges of Web-based consumer health communication encountered in the growth and maintenance of GHR are discussed: prioritizing topics for GHR, streamlining the development process while keeping genetic information accurate, and designing a system that helps consumers navigate complex genetic relationships. Various strategies are used to address these challenges. Tying content development to topics of national priority and addressing topics requested by users makes the site increasingly important for both consumers and health professionals. Informatics methods are essential for quality control, particularly for genetic information that changes frequently. Indexing and hierarchical browsing features help to facilitate navigation. Conclusions: GHR is a credible, dynamic Website that uses lay language to explain the effects of genetic variation on human health. Informatics strategies are key to effective management of a large and expanding body of genetics information. Feedback from formal and informal sources indicates increasing usage and favorable acceptance of GHR. PMID:16888669

  9. Predict amine solution properties accurately

    SciTech Connect

    Cheng, S.; Meisen, A.; Chakma, A.

    1996-02-01

    Improved process design begins with using accurate physical property data. Especially in the preliminary design stage, physical property data such as density viscosity, thermal conductivity and specific heat can affect the overall performance of absorbers, heat exchangers, reboilers and pump. These properties can also influence temperature profiles in heat transfer equipment and thus control or affect the rate of amine breakdown. Aqueous-amine solution physical property data are available in graphical form. However, it is not convenient to use with computer-based calculations. Developed equations allow improved correlations of derived physical property estimates with published data. Expressions are given which can be used to estimate physical properties of methyldiethanolamine (MDEA), monoethanolamine (MEA) and diglycolamine (DGA) solutions.

  10. 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.

  11. 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…

  12. Bringing genetic background into focus.

    PubMed

    Chow, Clement Y

    2016-02-01

    Researchers should embrace differences in genetic background to build richer disease models that more accurately reflect the level of variation in the human population, posits Clement Chow. PMID:26659016

  13. 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

  14. 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

  15. Accurate ab Initio Spin Densities

    PubMed Central

    2012-01-01

    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of α and β electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740]. PMID:22707921

  16. 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

  17. The changing landscape of genetic testing and its impact on clinical and laboratory services and research in Europe.

    PubMed

    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

    2012-09-01

    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

  18. 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.

  19. Accurate wavelength calibration method for flat-field grating spectrometers.

    PubMed

    Du, Xuewei; Li, Chaoyang; Xu, Zhe; Wang, Qiuping

    2011-09-01

    A portable spectrometer prototype is built to study wavelength calibration for flat-field grating spectrometers. An accurate calibration method called parameter fitting is presented. Both optical and structural parameters of the spectrometer are included in the wavelength calibration model, which accurately describes the relationship between wavelength and pixel position. Along with higher calibration accuracy, the proposed calibration method can provide information about errors in the installation of the optical components, which will be helpful for spectrometer alignment. PMID:21929865

  20. Predicting substance use in emerging adulthood: A genetically informed study of developmental transactions between impulsivity and family conflict.

    PubMed

    Elam, Kit K; Wang, Frances L; Bountress, Kaitlin; Chassin, Laurie; Pandika, Danielle; Lemery-Chalfant, Kathryn

    2016-08-01

    Deviance proneness models propose a multilevel interplay in which transactions among genetic, individual, and family risk factors place children at increased risk for substance use. We examined bidirectional transactions between impulsivity and family conflict from middle childhood to adolescence and their contributions to substance use in adolescence and emerging adulthood (n = 380). Moreover, we examined children's, mothers', and fathers' polygenic risk scores for behavioral undercontrol, and mothers' and fathers' interparental conflict and substance disorder diagnoses as predictors of these transactions. The results support a developmental cascade model in which children's polygenic risk scores predicted greater impulsivity in middle childhood. Impulsivity in middle childhood predicted greater family conflict in late childhood, which in turn predicted greater impulsivity in late adolescence. Adolescent impulsivity subsequently predicted greater substance use in emerging adulthood. Results are discussed with respect to evocative genotype-environment correlations within developmental cascades and applications to prevention efforts. PMID:27427799

  1. 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

  2. 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 ...

  3. Genetics Home Reference: Fryns syndrome

    MedlinePlus

    ... nasal bridge , a thick nasal tip, a wide space between the nose and upper lip ( a long ... my family? What is the prognosis of a genetic condition? Genetic and Rare Diseases Information Center Frequency ...

  4. 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.

  5. How are parent-child conflict and childhood externalizing symptoms related over time? Results from a genetically informative cross-lagged study.

    PubMed

    Burt, S Alexandra; McGue, Matt; Krueger, Robert F; Iacono, William G

    2005-01-01

    The present study attempted to determine the direction and etiology of the robust relationship between childhood externalizing (EXT) symptoms and parent-child conflict using a genetically informative longitudinal model and data from the ongoing Minnesota Twin Family Study. Participants consisted of 1,506 same-sex twins assessed at ages 11 and 14, and their parents. The relationship between EXT and parent-child conflict from ages 11 to 14 was examined within a biometrical cross-lagged design. The results revealed three primary findings: first, the stability of conflict and externalizing over time is largely, although not solely, a result of genetic factors. Second, there appears to be a bidirectional relationship between conflict and EXT over time, such that both conflict and EXT at 11 independently predict the other 3 years later. Finally, the results are consistent with the notion that parent-child conflict partially results from parental responses to their child's heritable externalizing behavior, while simultaneously contributing to child externalizing via environmental mechanisms. These results suggest a "downward spiral" of interplay between parent-child conflict and EXT, and offer confirmation of a (partially) environmentally mediated effect of parenting on child behavior. PMID:15971764

  6. 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

  7. 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

  8. Accurate Inventories Of Irrigated Land

    NASA Technical Reports Server (NTRS)

    Wall, S.; Thomas, R.; Brown, C.

    1992-01-01

    System for taking land-use inventories overcomes two problems in estimating extent of irrigated land: only small portion of large state surveyed in given year, and aerial photographs made on 1 day out of year do not provide adequate picture of areas growing more than one crop per year. Developed for state of California as guide to controlling, protecting, conserving, and distributing water within state. Adapted to any large area in which large amounts of irrigation water needed for agriculture. Combination of satellite images, aerial photography, and ground surveys yields data for computer analysis. Analyst also consults agricultural statistics, current farm reports, weather reports, and maps. These information sources aid in interpreting patterns, colors, textures, and shapes on Landsat-images.

  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. Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis.

    PubMed

    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

  11. Information processing of genetically modified food messages under different motives: an adaptation of the multiple-motive heuristic-systematic model.

    PubMed

    Kim, Jooyoung; Paek, Hye-Jin

    2009-12-01

    Recent risk management research has noted the importance of understanding how the lay public processes and reacts to risk-related information. Guided by the multiple-motive heuristic-systematic model, this study examines (1) how individuals process messages in the context of genetically modified foods to change their attitudes and (2) how the persuasion process varies across types of motives. In the three treatment conditions of accuracy, defense, and impression motives, the respondents changed their attitudes through either the heuristic or the systematic mode, depending on their motives. The accuracy-motive group appeared to use the systematic processing mode, while the impression-motive group seemed to employ the heuristic processing mode. The empirical findings highlight the importance of incorporating motives to improve our understanding of the process of attitude change in risk management and communication contexts. PMID:19948001

  12. Gene technology: also a gender issue. Views of Dutch informed women on genetic screening and gene therapy.

    PubMed

    van Berkel, D; Klinge, I

    1997-05-01

    The reported research was conceived as a pilot study to explore the views of women on the implications of the analysis of the human genome. The data were gathered by interview and questionnaire from a group of Dutch women, most likely to have an informed opinion. However, even women who were assumed to be informed express a serious lack of knowledge. Nevertheless, they mention a whole range of problematic issues. Overall, women are likely to think that gene technology does affect them differently than it does men. They draw attention to the social reality of women's lives, mentioning the greater responsibility of mothers for the embryo and childbirth and pointing to the fact that women are subjected to more complicated and painful examinations. In the public debate attentional for gender implications of gene technology is lacking. A plea is made to improve the quality of the debate by integrating sex and gender specific issues. PMID:9197802

  13. 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

  14. 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.

  15. 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.

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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.

  2. Towards accurate and automatic morphing

    NASA Astrophysics Data System (ADS)

    Wang, Zhe; Sharkey, Paul M.

    2005-10-01

    Image morphing has proved to be a powerful tool for generating compelling and pleasing visual effects and has been widely used in entertainment industry. However, traditional image morphing methods suffer from a number of drawbacks: feature specification between images is tedious and the reliance on 2D information ignores the possible advantages to be gained from 3D knowledge. In this paper, we utilize recent advantages of computer vision technologies to diminish these drawbacks. By analyzing multi view geometry theories, we propose a processing pipeline based on three reference images. We first seek a few seed correspondences using robust methods and then recover multi view geometries using the seeds, through bundle adjustment. Guided by the recovered two and three view geometries, a novel line matching algorithm across three views is then deduced, through edge growth, line fitting and two and three view geometry constraints. Corresponding lines on a novel image is then obtained by an image transfer method and finally matched lines are fed into the traditional morphing methods and novel images are generated. Novel images generated by this pipeline have advantages over traditional morphing methods: they have an inherent 3D foundation and are therefore physically close to real scenes; not only images located between the baseline connecting two reference image centers, but also extrapolated images away from the baseline are possible; and the whole processing can be either wholly automatic, or at least the tedious task of feature specification in traditional morphing methods can be greatly relieved.

  3. Synthetic Genetic Arrays: Automation of Yeast Genetics.

    PubMed

    Kuzmin, Elena; Costanzo, Michael; Andrews, Brenda; Boone, Charles

    2016-01-01

    Genome-sequencing efforts have led to great strides in the annotation of protein-coding genes and other genomic elements. The current challenge is to understand the functional role of each gene and how genes work together to modulate cellular processes. Genetic interactions define phenotypic relationships between genes and reveal the functional organization of a cell. Synthetic genetic array (SGA) methodology automates yeast genetics and enables large-scale and systematic mapping of genetic interaction networks in the budding yeast,Saccharomyces cerevisiae SGA facilitates construction of an output array of double mutants from an input array of single mutants through a series of replica pinning steps. Subsequent analysis of genetic interactions from SGA-derived mutants relies on accurate quantification of colony size, which serves as a proxy for fitness. Since its development, SGA has given rise to a variety of other experimental approaches for functional profiling of the yeast genome and has been applied in a multitude of other contexts, such as genome-wide screens for synthetic dosage lethality and integration with high-content screening for systematic assessment of morphology defects. SGA-like strategies can also be implemented similarly in a number of other cell types and organisms, includingSchizosaccharomyces pombe,Escherichia coli, Caenorhabditis elegans, and human cancer cell lines. The genetic networks emerging from these studies not only generate functional wiring diagrams but may also play a key role in our understanding of the complex relationship between genotype and phenotype. PMID:27037078

  4. 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.

  5. 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.

  6. 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 ...

  7. 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 ...

  8. 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

  9. New Genetics

    MedlinePlus

    ... human genome, behavioral genetics, pharmacogenetics, drug resistance, biofilms, computer modeling. » more Chapter 5: 21st-Century Genetics Covers systems biology, GFP, genetic testing, privacy concerns, DNA forensics, ...

  10. 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

  11. 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 ...

  12. 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 ( ...

  13. Genetics Home Reference: histidinemia

    MedlinePlus

    ... condition characterized by elevated blood levels of the amino acid histidine, a building block of most proteins. Histidinemia ... Additional Information & Resources MedlinePlus (2 links) Health Topic: Amino Acid Metabolism Disorders Health Topic: Newborn Screening Genetic and ...

  14. Genetics Home Reference: hyperlysinemia

    MedlinePlus

    ... condition characterized by elevated blood levels of the amino acid lysine, a building block of most proteins. Hyperlysinemia ... Additional Information & Resources MedlinePlus (2 links) Health Topic: Amino Acid Metabolism Disorders Health Topic: Newborn Screening Genetic and ...

  15. Genetics Home Reference: hypochondroplasia

    MedlinePlus

    ... Description Hypochondroplasia is a form of short-limbed dwarfism. This condition affects the conversion of cartilage into ... Resources MedlinePlus (2 links) Encyclopedia: Lordosis Health Topic: Dwarfism Genetic and Rare Diseases Information Center (1 link) ...

  16. Genetics Home Reference: sialidosis

    MedlinePlus

    ... syndrome Related Information How are genetic conditions and genes named? ... Morrone A. Type II sialidosis: review of the clinical spectrum and identification of a new splicing defect with chitotriosidase assessment in two patients. J ...

  17. Missing Genetic Information in Case-Control Family Data with General Semi-Parametric Shared Frailty Model

    PubMed Central

    Graber-Naidich, Anna; Malone, Kathleen E.; Hsu, Li

    2011-01-01

    Case-control family data are now widely used to examine the role of gene-environment interactions in the etiology of complex diseases. In these types of studies, exposure levels are obtained retrospectively and, frequently, information on most risk factors of interest is available on the probands but not on their relatives. In this work we consider correlated failure time data arising from population-based case-control family studies with missing genotypes of relatives. We present a new method for estimating the age-dependent marginalized hazard function. The proposed technique has two major advantages: (1) it is based on the pseudo full likelihood function rather than a pseudo composite likelihood function, which usually suffers from substantial efficiency loss; (2) the cumulative baseline hazard function is estimated using a two-stage estimator instead of an iterative process. We assess the performance of the proposed methodology with simulation studies, and illustrate its utility on a real data example. PMID:21153764

  18. 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

  19. Survey on genetic counseling and health management for symptomatic and asymptomatic female dystrophinopathy carriers in Japan today.

    PubMed

    Kobayashi, Michio; Ishizaki, Masatoshi; Adachi, Katsuhito; Yonemoto, Naohiro; Matsumura, Tsuyoshi; Toyoshima, Itaru; Kimura, En

    2016-06-22

    To clarify the current status of genetic counseling and health monitoring for symptomatic and asymptomatic female carriers of dystrophinopathy (Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD)), we sent out questionnaires to 104 member institutions of The Japan's National Liaison Council for Clinical Sections of Medical Genetics, and responses were received from 51 institutions. Between April 2013 and March 2014, 57 carriers at 21 institutions received genetic counseling, and 37 carriers at 15 institutions underwent genetic screening for DMD/BMD mutations. At the 23 institutions that gave genetic counseling, 20 (87%) informed carriers of possible health problems, 14 (61%) informed carriers of cardiomyopathy and heart failure, and 14 (61%) advised carriers about regular medical checkups. Evidence based on accurate and up-to-date epidemiological studies of female carriers is needed and should be widely shared with the families, medical providers, and society. PMID:27212674

  20. Measuring Fisher Information Accurately in Correlated Neural Populations

    PubMed Central

    Kohn, Adam; Pouget, Alexandre

    2015-01-01

    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. PMID:26030735

  1. Genetics Home Reference: Kallmann syndrome

    MedlinePlus

    ... Encyclopedia: Hypogonadotropic Hypogonadism Encyclopedia: Smell - Impaired Health Topic: Endocrine Diseases Health Topic: Taste and Smell Disorders Genetic and Rare Diseases Information Center (7 links) ...

  2. Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice.

    PubMed

    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

  3. 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

  4. 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

  5. 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

  6. Accurate lineshape spectroscopy and the Boltzmann constant.

    PubMed

    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

  7. WIPPER: an accurate and efficient field phenotyping platform for large-scale applications

    PubMed Central

    Utsushi, Hiroe; Abe, Akira; Tamiru, Muluneh; Ogasawara, Yumiko; Obara, Tsutomu; Sato, Emiko; Ochiai, Yusuke; Terauchi, Ryohei; Takagi, Hiroki

    2015-01-01

    More accurate, rapid, and easy phenotyping tools are required to match the recent advances in high-throughput genotyping for accelerating breeding and genetic analysis. The conventional data recording in field notebooks and then inputting data to computers for further analysis is inefficient, time-consuming, laborious, and prone to human error. Here, we report WIPPER (for Wireless Plant Phenotyper), a new phenotyping platform that combines field phenotyping and data recording with the aid of Bluetooth communication, thus saving time and labor not only for field data recoding but also for inputting data to computers. Additionally, it eliminates the risk of human error associated with phenotyping and inputting data. We applied WIPPER to 100 individuals of a rice recombinant inbred line (RIL) for measuring leaf width and relative chlorophyll content (SPAD value), and were able to record an accurate data in a significantly reduced time compared with the conventional method of data collection. We are currently using WIPPER for routine management of rice germplasm including recording and documenting information on phenotypic data, seeds, and DNA for their accelerated utilization in crop breeding. PMID:26175626

  8. Use of "Journal of Citation Reports" for Serials Management in Research Libraries: An Investigation of the Effect of Self-Citation on Journal Rankings in Library and Information Science and Genetics.

    ERIC Educational Resources Information Center

    Nisonger, Thomas E.

    2000-01-01

    Explores the use of "Journal Citation Reports" (JCR) for journal management in academic libraries. Outlines the advantages and disadvantages of using JCR citation data and researches the impact of journal self-citation on JCR rankings of library and information science and genetics journals. (Contains 41 references.) (Author/LRW)

  9. Opportunities to Integrate New Approaches in Genetic Toxicology: An ILSI-HESI Workshop Report

    PubMed Central

    Zeiger, Errol; Gollapudi, Bhaskar; Aardema, Marilyn J.; Auerbach, Scott; Boverhof, Darrell; Custer, Laura; Dedon, Peter; Honma, Masamitsu; Ishida, Seiichi; Kasinski, Andrea L.; Kim, James H.; Manjanatha, Mugimane G.; Marlowe, Jennifer; Pfuhler, Stefan; Pogribny, Igor; Slikker, William; Stankowski, Leon F.; Tanir, Jennifer Y.; Tice, Raymond; van Benthem, Jan; White, Paul; Witt, Kristine L.; Thybaud, Véronique

    2015-01-01

    Genetic toxicity tests currently used to identify and characterize potential human mutagens and carcinogens rely on measurements of primary DNA damage, gene mutation, and chromosome damage in vitro and in rodents. The International Life Sciences Institute Health and Environmental Sciences Institute (ILSI-HESI) Committee on the Relevance and Follow-up of Positive Results in In Vitro Genetic Toxicity Testing held an April 2012 Workshop in Washington, DC, to consider the impact of new understanding of biology and new technologies on the identification and characterization of genotoxic substances, and to identify new approaches to inform more accurate human risk assessment for genetic and carcinogenic effects. Workshop organizers and speakers were from industry, academe, and government. The Workshop focused on biological effects and technologies that would potentially yield the most useful information for evaluating human risk of genetic damage. Also addressed was the impact that improved understanding of biology and availability of new techniques might have on genetic toxicology practices. Workshop topics included (1) alternative experimental models to improve genetic toxicity testing, (2) Biomarkers of epigenetic changes and their applicability to genetic toxicology, and (3) new technologies and approaches. The ability of these new tests and technologies to be developed into tests to identify and characterize genotoxic agents; to serve as a bridge between in vitro and in vivo rodent, or preferably human, data; or to be used to provide dose response information for quantitative risk assessment was also addressed. A summary of the workshop and links to the scientific presentations are provided. PMID:25482136

  10. The Synthesis Paradigm in Genetics

    PubMed Central

    Rice, William R.

    2014-01-01

    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. PMID:24496401

  11. Accurate Computation of Survival Statistics in Genome-Wide Studies

    PubMed Central

    Vandin, Fabio; Papoutsaki, Alexandra; Raphael, Benjamin J.; Upfal, Eli

    2015-01-01

    A key challenge in genomics is to identify genetic variants that distinguish patients with different survival time following diagnosis or treatment. While the log-rank test is widely used for this purpose, nearly all implementations of the log-rank test rely on an asymptotic approximation that is not appropriate in many genomics applications. This is because: the two populations determined by a genetic variant may have very different sizes; and the evaluation of many possible variants demands highly accurate computation of very small p-values. We demonstrate this problem for cancer genomics data where the standard log-rank test leads to many false positive associations between somatic mutations and survival time. We develop and analyze a novel algorithm, Exact Log-rank Test (ExaLT), that accurately computes the p-value of the log-rank statistic under an exact distribution that is appropriate for any size populations. We demonstrate the advantages of ExaLT on data from published cancer genomics studies, finding significant differences from the reported p-values. We analyze somatic mutations in six cancer types from The Cancer Genome Atlas (TCGA), finding mutations with known association to survival as well as several novel associations. In contrast, standard implementations of the log-rank test report dozens-hundreds of likely false positive associations as more significant than these known associations. PMID:25950620

  12. Examining the family-centred approach to genetic testing and counselling among UK Pakistanis: a community perspective.

    PubMed

    Darr, A; Small, N; Ahmad, W I U; Atkin, K; Corry, P; Benson, J; Morton, R; Modell, B

    2013-01-01

    WHO advice suggests a family-centred approach for managing the elevated risk of recessively inherited disorders in consanguineous communities, whilst emerging policy recommends community engagement as an integral component of genetic service development. This paper explores the feasibility of the family-centred approach in the UK Pakistani origin community. The study took place within a context of debate in the media, professional and lay circles about cousin marriage causing disability in children. Using qualitative methods, a total of six single-sex focus group discussions (n = 50) were conducted in three UK cities with a high settlement of people of Pakistani origin. Tape-recorded transcripts were analysed using framework analysis. Kinship networks within Pakistani origin communities are being sustained and marriage between close blood relatives continues to take place alongside other marriage options. Study participants were critical of what was perceived as a prevalent notion that cousin marriage causes disability in children. They were willing to discuss cousin marriage and disability, share genetic information and engage with genetic issues. A desire for accurate information and a public informed about genetic issues was articulated whilst ineffective communication of genetic risk information undermined professionals in their support role. This study suggests a community that is embracing change, one in which kinship networks are still active and genetic information exchange is taking place. At the community level, these are conditions supportive of the family-centred approach to genetic testing and counselling. PMID:23086468

  13. Genetic counseling and the pediatrician.

    PubMed

    Bartsocas, C S

    1978-01-01

    The assistance of the pediatrician, following diagnosis of a child with a genetic disorder, towards his family consists today in giving genetic counseling for prevention of recurrence in future pregnancies. The process of genetic counseling, once the right diagnosis is made, should not be difficult as concerns Mendelian inheritance. It is well known that several chromosomal disorders follow the rules of Mendelian inheritance. The theory of polygenic or multifactorial inheritance may create problems in the accurate estimation of risks. An effort is made to discover the mechanisms of genetic "predisposition" or the adverse environmental factors, in order to minimize the occurrence of such disorders. An important tool in prevention of several genetic disorders, which should be mentioned in genetic counseling, is prenatal diagnosis. PMID:155240

  14. Genetic Diagnostic Methods for Inherited Eye Diseases

    PubMed Central

    Gabriel, Luis A. R.; Traboulsi, Elias I.

    2011-01-01

    Accurate molecular diagnosis of genetic eye diseases has proven to be of great importance because of the prognostic and therapeutic value of an accurate ascertainment of the underlying genetic mutation. Efforts continue in diagnostic laboratories to develop strategies that allow the discovery of responsible gene/mutations in the individual patient using the least number of assays and economizing on the expenses and time involved in the process. Once the ophthalmologist has made the best possible clinical diagnosis, blood samples are obtained for genetic testing. In this paper we will review the basic laboratory methods utilized to identify the chromosomal or mutational etiology of genetic diseases that affect the eye. PMID:21572730

  15. Nonexposure accurate location K-anonymity algorithm in LBS.

    PubMed

    Jia, Jinying; Zhang, Fengli

    2014-01-01

    This paper tackles location privacy protection in current location-based services (LBS) where mobile users have to report their exact location information to an LBS provider in order to obtain their desired services. Location cloaking has been proposed and well studied to protect user privacy. It blurs the user's accurate coordinate and replaces it with a well-shaped cloaked region. However, to obtain such an anonymous spatial region (ASR), nearly all existent cloaking algorithms require knowing the accurate locations of all users. Therefore, location cloaking without exposing the user's accurate location to any party is urgently needed. In this paper, we present such two nonexposure accurate location cloaking algorithms. They are designed for K-anonymity, and cloaking is performed based on the identifications (IDs) of the grid areas which were reported by all the users, instead of directly on their accurate coordinates. Experimental results show that our algorithms are more secure than the existent cloaking algorithms, need not have all the users reporting their locations all the time, and can generate smaller ASR. PMID:24605060

  16. Nonexposure Accurate Location K-Anonymity Algorithm in LBS

    PubMed Central

    2014-01-01

    This paper tackles location privacy protection in current location-based services (LBS) where mobile users have to report their exact location information to an LBS provider in order to obtain their desired services. Location cloaking has been proposed and well studied to protect user privacy. It blurs the user's accurate coordinate and replaces it with a well-shaped cloaked region. However, to obtain such an anonymous spatial region (ASR), nearly all existent cloaking algorithms require knowing the accurate locations of all users. Therefore, location cloaking without exposing the user's accurate location to any party is urgently needed. In this paper, we present such two nonexposure accurate location cloaking algorithms. They are designed for K-anonymity, and cloaking is performed based on the identifications (IDs) of the grid areas which were reported by all the users, instead of directly on their accurate coordinates. Experimental results show that our algorithms are more secure than the existent cloaking algorithms, need not have all the users reporting their locations all the time, and can generate smaller ASR. PMID:24605060

  17. The Genetic Privacy Act and commentary

    SciTech Connect

    Annas, G.J.; Glantz, L.H.; Roche, P.A.

    1995-02-28

    The Genetic Privacy Act is a proposal for federal legislation. The Act is based on the premise that genetic information is different from other types of personal information in ways that require special protection. Therefore, to effectively protect genetic privacy unauthorized collection and analysis of individually identifiable DNA must be prohibited. As a result, the premise of the Act is that no stranger should have or control identifiable DNA samples or genetic information about an individual unless that individual specifically authorizes the collection of DNA samples for the purpose of genetic analysis, authorized the creation of that private information, and has access to and control over the dissemination of that information.

  18. Fast and Accurate Construction of Confidence Intervals for Heritability.

    PubMed

    Schweiger, Regev; Kaufman, Shachar; Laaksonen, Reijo; Kleber, Marcus E; März, Winfried; Eskin, Eleazar; Rosset, Saharon; Halperin, Eran

    2016-06-01

    Estimation of heritability is fundamental in genetic studies. Recently, heritability estimation using linear mixed models (LMMs) has gained popularity because these estimates can be obtained from unrelated individuals collected in genome-wide association studies. Typically, heritability estimation under LMMs uses the restricted maximum likelihood (REML) approach. Existing methods for the construction of confidence intervals and estimators of SEs for REML rely on asymptotic properties. However, these assumptions are often violated because of the bounded parameter space, statistical dependencies, and limited sample size, leading to biased estimates and inflated or deflated confidence intervals. Here, we show that the estimation of confidence intervals by state-of-the-art methods is inaccurate, especially when the true heritability is relatively low or relatively high. We further show that these inaccuracies occur in datasets including thousands of individuals. Such biases are present, for example, in estimates of heritability of gene expression in the Genotype-Tissue Expression project and of lipid profiles in the Ludwigshafen Risk and Cardiovascular Health study. We also show that often the probability that the genetic component is estimated as 0 is high even when the true heritability is bounded away from 0, emphasizing the need for accurate confidence intervals. We propose a computationally efficient method, ALBI (accurate LMM-based heritability bootstrap confidence intervals), for estimating the distribution of the heritability estimator and for constructing accurate confidence intervals. Our method can be used as an add-on to existing methods for estimating heritability and variance components, such as GCTA, FaST-LMM, GEMMA, or EMMAX. PMID:27259052

  19. Evolutionary behavioral genetics

    PubMed Central

    Zietsch, Brendan P.; de Candia, Teresa R; Keller, Matthew C.

    2014-01-01

    We describe the scientific enterprise at the intersection of evolutionary psychology and behavioral genetics—a field that could be termed Evolutionary Behavioral Genetics—and how modern genetic data is revolutionizing our ability to test questions in this field. We first explain how genetically informative data and designs can be used to investigate questions about the evolution of human behavior, and describe some of the findings arising from these approaches. Second, we explain how evolutionary theory can be applied to the investigation of behavioral genetic variation. We give examples of how new data and methods provide insight into the genetic architecture of behavioral variation and what this tells us about the evolutionary processes that acted on the underlying causal genetic variants. PMID:25587556

  20. Informatics-based, highly accurate, noninvasive prenatal paternity testing

    PubMed Central

    Ryan, Allison; Baner, Johan; Demko, Zachary; Hill, Matthew; Sigurjonsson, Styrmir; Baird, Michael L.; Rabinowitz, Matthew

    2013-01-01

    Purpose: The aim of the study was to evaluate the diagnostic accuracy of an informatics-based, noninvasive, prenatal paternity test using array-based single-nucleotide polymorphism measurements of cell-free DNA isolated from maternal plasma. Methods: Blood samples were taken from 21 adult pregnant women (with gestational ages between 6 and 21 weeks), and a genetic sample was taken from the corresponding biological fathers. Paternity was confirmed by genetic testing of the infant, products of conception, control of fertilization, and/or preimplantation genetic diagnosis during in vitro fertilization. Parental DNA samples and maternal plasma cell-free DNA were amplified and analyzed using a HumanCytoSNP-12 array. An informatics-based method measured single-nucleotide polymorphism data, confirming or rejecting paternity. Each plasma sample with a sufficient fetal cell-free DNA fraction was independently tested against the confirmed father and 1,820 random, unrelated males. Results: One of the 21 samples had insufficient fetal cell-free DNA. The test correctly confirmed paternity for the remaining 20 samples (100%) when tested against the biological father, with P values of <10−4. For the 36,400 tests using an unrelated male as the alleged father, 99.95% (36,382) correctly excluded paternity and 0.05% (18) were indeterminate. There were no miscalls. Conclusion: A noninvasive paternity test using informatics-based analysis of single-nucleotide polymorphism array measurements accurately determined paternity early in pregnancy. PMID:23258349

  1. Genetics and Genetic Testing in Pancreatic Cancer.

    PubMed

    Whitcomb, David C; Shelton, Celeste A; Brand, Randall E

    2015-10-01

    Genetic testing of germline DNA is used in patients suspected of being at risk of pancreatic ductal adenocarcinoma (PDAC) to better define the individual's risk and to determine the mechanism of risk. A high genetic risk increases the pretest probability that a biomarker of early cancer is a true positive and warrants further investigation. The highest PDAC risk is generally associated with a hereditary predisposition. However, the majority of PDAC results from complex, progressive gene-environment interactions that currently fall outside the traditional risk models. Over many years, the combination of inflammation, exposure to DNA-damaging toxins, and failed DNA repair promote the accumulation of somatic mutations in pancreatic cells; PDAC risk is further increased by already present oncogenic germline mutations. Predictive models and new technologies are needed to classify patients into more accurate and mechanistic PDAC risk categories that can be linked to improved surveillance and preventative strategies. PMID:26255042

  2. Genetic Mapping

    MedlinePlus

    ... Genetic Education Resources for Teachers Genomic Careers National DNA Day Online Education Kit Online Genetics Education Resources ... prevalent. Using various laboratory techniques, the scientists isolate DNA from these samples and examine it for unique ...

  3. Genetic counseling

    MedlinePlus

    ... this page: //medlineplus.gov/ency/patientinstructions/000510.htm Genetic counseling To use the sharing features on this ... cystic fibrosis or Down syndrome. Who May Want Genetic Counseling? It is up to you whether or ...

  4. Genetic counseling

    MedlinePlus

    Genetics is the study of heredity, the process of a parent passing certain genes on to their ... certain diseases are also often determined by genes. Genetic counseling is the process where parents can learn ...

  5. Genetic Disorders

    MedlinePlus

    ... This can cause a medical condition called a genetic disorder. You can inherit a gene mutation from ... during your lifetime. There are three types of genetic disorders: Single-gene disorders, where a mutation affects ...

  6. Genetic modification and genetic determinism

    PubMed Central

    Resnik, David B; Vorhaus, Daniel B

    2006-01-01

    In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by ones propped up by false or misleading biological assumptions. PMID:16800884

  7. Mill profiler machines soft materials accurately

    NASA Technical Reports Server (NTRS)

    Rauschl, J. A.

    1966-01-01

    Mill profiler machines bevels, slots, and grooves in soft materials, such as styrofoam phenolic-filled cores, to any desired thickness. A single operator can accurately control cutting depths in contour or straight line work.

  8. Remote balance weighs accurately amid high radiation

    NASA Technical Reports Server (NTRS)

    Eggenberger, D. N.; Shuck, A. B.

    1969-01-01

    Commercial beam-type balance, modified and outfitted with electronic controls and digital readout, can be remotely controlled for use in high radiation environments. This allows accurate weighing of breeder-reactor fuel pieces when they are radioactively hot.

  9. Understanding the Code: keeping accurate records.

    PubMed

    Griffith, Richard

    2015-10-01

    In his continuing series looking at the legal and professional implications of the Nursing and Midwifery Council's revised Code of Conduct, Richard Griffith discusses the elements of accurate record keeping under Standard 10 of the Code. This article considers the importance of accurate record keeping for the safety of patients and protection of district nurses. The legal implications of records are explained along with how district nurses should write records to ensure these legal requirements are met. PMID:26418404

  10. Imaging Genetics

    ERIC Educational Resources Information Center

    Munoz, Karen E.; Hyde, Luke W.; Hariri, Ahmad R.

    2009-01-01

    Imaging genetics is an experimental strategy that integrates molecular genetics and neuroimaging technology to examine biological mechanisms that mediate differences in behavior and the risks for psychiatric disorder. The basic principles in imaging genetics and the development of the field are discussed.

  11. [The genetic language: grammar, semantics, evolution].

    PubMed

    Ratner, V A

    1993-05-01

    The genetic language is a collection of rules and regularities of genetic information coding for genetic texts. It is defined by alphabet, grammar, collection of punctuation marks and regulatory sites, semantics. There is a review of these general attributes of genetic language, including also the problems of synonymy and evolution. The main directions of theoretical investigations of genetic language and neighbouring questions are formulated: (1) cryptographic problems, (2) analysis of genetic texts, (3) theoretical-linguistic problems, (4) evolutionary linguistic questions. The problem of genetic language becomes one of the key ones of molecular genetics, molecular biology and gene engineering. PMID:8335231

  12. [Human genetics and ethics].

    PubMed

    Zergollern, L

    1990-01-01

    Many new problems and dilemmas have occurred in the practice of medical geneticists with the development of human genetics and its subdisciplines--molecular genetics, ethic genetics and juridical genetics. Devoid of the possibility to get adequate education, genetic informer or better to say, counsellor, although a scientist and a professional who has already formed his ethic attitudes, often finds himself in a dilemma when he has to decide whether a procedure made possible by progress of science is ethical or not. Thus, due to different attitudes, same decision is ethical for some, while for the others it is not. Ethic committees are groups of moral and good people trying to find an objective approach to certain genetic and ethic problems. There are more and more ethically unanswered questions in modern human genetics, and particularly in medical genetics. Medical geneticist-ethicist still encounters numerous problems in his work. These are, for example, experiments with human gametes and embryos, possibilities of hybridization of human gametes with animal gametes, in vitro fertilization, detection of heterozygotes and homozygotes for monogene diseases. early detection of chromosomopathies, substitute mothers, homo and hetero insemination, transplantation of fetal and cadeveric organs, uncontrolled consumption of alcohol and drugs, environmental pollution, etc. It is almost impossible to create a single attitude which shall be shared by all those engaged in human health protection. Therefore, it is best to have a neutral eugenetic attitude which allows free ethical choice of each individual, in any case, for the well-being of man. PMID:2366624

  13. Leveraging Two Kinect Sensors for Accurate Full-Body Motion Capture

    PubMed Central

    Gao, Zhiquan; Yu, Yao; Zhou, Yu; Du, Sidan

    2015-01-01

    Accurate motion capture plays an important role in sports analysis, the medical field and virtual reality. Current methods for motion capture often suffer from occlusions, which limits the accuracy of their pose estimation. In this paper, we propose a complete system to measure the pose parameters of the human body accurately. Different from previous monocular depth camera systems, we leverage two Kinect sensors to acquire more information about human movements, which ensures that we can still get an accurate estimation even when significant occlusion occurs. Because human motion is temporally constant, we adopt a learning analysis to mine the temporal information across the posture variations. Using this information, we estimate human pose parameters accurately, regardless of rapid movement. Our experimental results show that our system can perform an accurate pose estimation of the human body with the constraint of information from the temporal domain. PMID:26402681

  14. Leveraging Two Kinect Sensors for Accurate Full-Body Motion Capture.

    PubMed

    Gao, Zhiquan; Yu, Yao; Zhou, Yu; Du, Sidan

    2015-01-01

    Accurate motion capture plays an important role in sports analysis, the medical field and virtual reality. Current methods for motion capture often suffer from occlusions, which limits the accuracy of their pose estimation. In this paper, we propose a complete system to measure the pose parameters of the human body accurately. Different from previous monocular depth camera systems, we leverage two Kinect sensors to acquire more information about human movements, which ensures that we can still get an accurate estimation even when significant occlusion occurs. Because human motion is temporally constant, we adopt a learning analysis to mine the temporal information across the posture variations. Using this information, we estimate human pose parameters accurately, regardless of rapid movement. Our experimental results show that our system can perform an accurate pose estimation of the human body with the constraint of information from the temporal domain. PMID:26402681

  15. A simple yet accurate correction for winner's curse can predict signals discovered in much larger genome scans

    PubMed Central

    Bigdeli, T. Bernard; Lee, Donghyung; Webb, Bradley Todd; Riley, Brien P.; Vladimirov, Vladimir I.; Fanous, Ayman H.; Kendler, Kenneth S.; Bacanu, Silviu-Alin

    2016-01-01

    Motivation: For genetic studies, statistically significant variants explain far less trait variance than ‘sub-threshold’ association signals. To dimension follow-up studies, researchers need to accurately estimate ‘true’ effect sizes at each SNP, e.g. the true mean of odds ratios (ORs)/regression coefficients (RRs) or Z-score noncentralities. Naïve estimates of effect sizes incur winner’s curse biases, which are reduced only by laborious winner’s curse adjustments (WCAs). Given that Z-scores estimates can be theoretically translated on other scales, we propose a simple method to compute WCA for Z-scores, i.e. their true means/noncentralities. Results:WCA of Z-scores shrinks these towards zero while, on P-value scale, multiple testing adjustment (MTA) shrinks P-values toward one, which corresponds to the zero Z-score value. Thus, WCA on Z-scores scale is a proxy for MTA on P-value scale. Therefore, to estimate Z-score noncentralities for all SNPs in genome scans, we propose FDR Inverse Quantile Transformation (FIQT). It (i) performs the simpler MTA of P-values using FDR and (ii) obtains noncentralities by back-transforming MTA P-values on Z-score scale. When compared to competitors, realistic simulations suggest that FIQT is more (i) accurate and (ii) computationally efficient by orders of magnitude. Practical application of FIQT to Psychiatric Genetic Consortium schizophrenia cohort predicts a non-trivial fraction of sub-threshold signals which become significant in much larger supersamples. Conclusions: FIQT is a simple, yet accurate, WCA method for Z-scores (and ORs/RRs, via simple transformations). Availability and Implementation: A 10 lines R function implementation is available at https://github.com/bacanusa/FIQT. Contact: sabacanu@vcu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27187203

  16. Finding Reliable Health Information Online

    MedlinePlus

    ... with your physician any articles that interest you. Internet Credibility Help from Genetic Alliance The Access To ... for people developing educational materials. Top of page Internet Resources Genetics Information Genetic Testing Registry www.ncbi. ...

  17. LGH: A Fast and Accurate Algorithm for Single Individual Haplotyping Based on a Two-Locus Linkage Graph.

    PubMed

    Xie, Minzhu; Wang, Jianxin; Chen, Xin

    2015-01-01

    Phased haplotype information is crucial in our complete understanding of differences between individuals at the genetic level. Given a collection of DNA fragments sequenced from a homologous pair of chromosomes, the problem of single individual haplotyping (SIH) aims to reconstruct a pair of haplotypes using a computer algorithm. In this paper, we encode the information of aligned DNA fragments into a two-locus linkage graph and approach the SIH problem by vertex labeling of the graph. In order to find a vertex labeling with the minimum sum of weights of incompatible edges, we develop a fast and accurate heuristic algorithm. It starts with detecting error-tolerant components by an adapted breadth-first search. A proper labeling of vertices is then identified for each component, with which sequencing errors are further corrected and edge weights are adjusted accordingly. After contracting each error-tolerant component into a single vertex, the above procedure is iterated on the resulting condensed linkage graph until error-tolerant components are no longer detected. The algorithm finally outputs a haplotype pair based on the vertex labeling. Extensive experiments on simulated and real data show that our algorithm is more accurate and faster than five existing algorithms for single individual haplotyping. PMID:26671798

  18. Are genetic self-tests dangerous? Assessing the commercialization of genetic testing in terms of personal autonomy.

    PubMed

    Beckman, Ludvig

    2004-01-01

    Should a growing market for genetic self-tests be welcomed or feared? From the point of view of personal autonomy the increasing availability of predictive health information seems promising. Yet it is frequently pointed out that genetic information about future health may cause anxiety, distress and even loss of "life-hopes." In this article the argument that genetic self-tests undermine personal autonomy is assessed and criticized. I contend that opportunities for autonomous choice are not reduced by genetic information but by misperceptions and misunderstandings of the results of genetic tests. Since the interpretation of genetic information is sometimes distorted by the information provided about the genetic products, more attention should be given to deceitful marketing that overblows the utility of genetic products. Yet personal autonomy is reduced neither by genetic tests nor by genetic information and there is consequently no compelling case for the conclusion that genetic self-tests should be prohibited. PMID:15690941

  19. Genetic professionals' views on genetic counsellors: a French survey.

    PubMed

    Cordier, Christophe; Taris, Nicolas; Moldovan, Ramona; Sobol, Hagay; Voelckel, Marie-Antoinette

    2016-01-01

    The genetic counselling profession was established in France in 2004. Eight years later, 122 genetic counsellors have graduated from the unique educational French program which awards the Professional Master Degree of Human Pathology, entitled "Master of Genetic Counselling and Predictive Medicine". As part of a global evaluation of this new profession by health genetic professionals, we undertook a national survey investigating various aspects such as employment, work responsibilities and integration. To our knowledge, this is the first study to investigate the views of genetic professionals on the genetic counsellors' role. Of 422 French professionals invited to take part in this study, 126 participated. The survey underlines that this profession is significantly recognized by physicians practicing within genetics departments. French genetic counsellors are allowed to manage consultations independently, without the necessary presence of a qualified medical geneticist but under his or her responsibility. Genetic counsellors participate in a wide range of consultations. They provide both information for relevant and for genetic testing and sometimes disclose the genetic test result to patient. Eventually, the role of genetic counsellors appears to be directly dependent from the relationship of trust between the two health professions. PMID:26280995

  20. A highly accurate interatomic potential for argon

    NASA Astrophysics Data System (ADS)

    Aziz, Ronald A.

    1993-09-01

    A modified potential based on the individually damped model of Douketis, Scoles, Marchetti, Zen, and Thakkar [J. Chem. Phys. 76, 3057 (1982)] is presented which fits, within experimental error, the accurate ultraviolet (UV) vibration-rotation spectrum of argon determined by UV laser absorption spectroscopy by Herman, LaRocque, and Stoicheff [J. Chem. Phys. 89, 4535 (1988)]. Other literature potentials fail to do so. The potential also is shown to predict a large number of other properties and is probably the most accurate characterization of the argon interaction constructed to date.