Science.gov

Sample records for genome program contractor-grantee

  1. DOE Human Genome Program contractor-grantee workshop

    SciTech Connect

    1996-01-01

    This volume contains the proceedings for the DOE Human Genome Program`s Contractor-Grantee Workshop V held in Sante Fe, New Mexico January 28, February 1, 1996. Presentations were divided into sessions entitled Sequencing; Mapping; Informatics; Ethical, Legal, and Social Issues; and Infrastructure. Reports of individual projects described herein are separately indexed and abstracted for the database.

  2. DOE Human Genome Program: Contractor-Grantee Workshop IV, November 13--17, 1994, Santa Fe, New Mexico

    SciTech Connect

    Not Available

    1994-10-01

    This volume contains the proceedings of the fourth Contractor-Grantee Workshop for the Department of Energy (DOE) Human Genome Program. Of the 204 abstracts in this book, some 200 describe the genome research of DOE-funded grantees and contractors located at the multidisciplinary centers at Lawrence Berkeley Laboratory, Lawrence Livermore National Laboratory, and Los Alamos National Laboratory; other DOE-supported laboratories; and more than 54 universities, research organizations, and companies in the United States and abroad. Included are 16 abstracts from ongoing projects in the Ethical, Legal, and Social Issues (ELSI) component, an area that continues to attract considerable attention from a wide variety of interested parties. Three abstracts summarize work in the new Microbial Genome Initiative launched this year by the Office of Health and Environmental Research (OHER) to provide genome sequence and mapping data on industrially important microorganisms and those that live under extreme conditions. Many of the projects will be discussed at plenary sessions held throughout the workshop, and all are represented in the poster sessions.

  3. Genomics:GTL Contractor-Grantee Workshop IV and Metabolic Engineering Working Group Inter-Agency Conference on Metabolic Engineering 2006

    SciTech Connect

    Mansfield, Betty Kay; Martin, Sheryl A

    2006-02-01

    Welcome to the 2006 joint meeting of the fourth Genomics:GTL Contractor-Grantee Workshop and the six Metabolic Engineering Working Group Inter-Agency Conference. The vision and scope of the Genomics:GTL program continue to expand and encompass research and technology issues from diverse scientific disciplines, attracting broad interest and support from researchers at universities, DOE national laboratories, and industry. Metabolic engineering's vision is the targeted and purposeful alteration of metabolic pathways to improve the understanding and use of cellular pathways for chemical transformation, energy transduction, and supramolecular assembly. These two programs have much complementarity in both vision and technological approaches, as reflected in this joint workshop. GLT's challenge to the scientific community remains the further development and use of a broad array of innovative technologies and computational tools to systematically leverage the knowledge and capabilities brought to us by DNA sequencing projects. The goal is to seek a broad and predictive understanding of the functioning and control of complex systems--individual microbes, microbial communities, and plants. GTL's prominent position at the interface of the physical, computational, and biological sciences is both a strength and challenge. Microbes remain GTL's principal biological focus. In the complex 'simplicity' of microbes, they find capabilities needed by DOE and the nation for clean and secure energy, cleanup of environmental contamination, and sequestration of atmospheric carbon dioxide that contributes to global warming. An ongoing challenge for the entire GTL community is to demonstrate that the fundamental science conducted in each of your research projects brings us a step closer to biology-based solutions for these important national energy and environmental needs.

  4. JGI Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  5. Epidemiology & Genomics Research Program

    Cancer.gov

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  6. Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  7. Human Genome Program

    SciTech Connect

    Not Available

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  8. Programs | Office of Cancer Genomics

    Cancer.gov

    OCG facilitates cancer genomics research through a series of highly-focused programs. These programs generate and disseminate genomic data for use by the cancer research community. OCG programs also promote advances in technology-based infrastructure and create valuable experimental reagents and tools. OCG programs encourage collaboration by interconnecting with other genomics and cancer projects in order to accelerate translation of findings into the clinic. Below are OCG’s current, completed, and initiated programs:

  9. Human genome. 1993 Program report

    SciTech Connect

    Not Available

    1994-03-01

    The purpose of this report is to update the Human Genome 1991-92 Program Report and provide new information on the DOE genome program to researchers, program managers, other government agencies, and the interested public. This FY 1993 supplement includes abstracts of 60 new or renewed projects and listings of 112 continuing and 28 completed projects. These two reports, taken together, present the most complete published view of the DOE Human Genome Program through FY 1993. Research is progressing rapidly toward 15-year goals of mapping and sequencing the DNA of each of the 24 different human chromosomes.

  10. Human Genome Education Program

    SciTech Connect

    Richard Myers; Lane Conn

    2000-05-01

    The funds from the DOE Human Genome Program, for the project period 2/1/96 through 1/31/98, have provided major support for the curriculum development and field testing efforts for two high school level instructional units: Unit 1, ''Exploring Genetic Conditions: Genes, Culture and Choices''; and Unit 2, ''DNA Snapshots: Peaking at Your DNA''. In the original proposal, they requested DOE support for the partial salary and benefits of a Field Test Coordinator position to: (1) complete the field testing and revision of two high school curriculum units, and (2) initiate the education of teachers using these units. During the project period of this two-year DOE grant, a part-time Field-Test Coordinator was hired (Ms. Geraldine Horsma) and significant progress has been made in both of the original proposal objectives. Field testing for Unit 1 has occurred in over 12 schools (local and non-local sites with diverse student populations). Field testing for Unit 2 has occurred in over 15 schools (local and non-local sites) and will continue in 12-15 schools during the 96-97 school year. For both curricula, field-test sites and site teachers were selected for their interest in genetics education and in hands-on science education. Many of the site teachers had no previous experience with HGEP or the unit under development. Both of these first-year biology curriculum units, which contain genetics, biotechnology, societal, ethical and cultural issues related to HGP, are being implemented in many local and non-local schools (SF Bay Area, Southern California, Nebraska, Hawaii, and Texas) and in programs for teachers. These units will reach over 10,000 students in the SF Bay Area and continues to receive support from local corporate and private philanthropic organizations. Although HGEP unit development is nearing completion for both units, data is still being gathered and analyzed on unit effectiveness and student learning. The final field testing result from this analysis will

  11. Mating programs including genomic relationships

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Computer mating programs have helped breeders minimize pedigree inbreeding and avoid recessive defects by mating animals with parents that have fewer common ancestors. With genomic selection, breed associations, AI organizations, and on-farm software providers could use new programs to minimize geno...

  12. Human Genome Program Image Gallery (from genomics.energy.gov)

    DOE Data Explorer

    This collection contains approximately 240 images from the genome programs of DOE's Office of Science. The images are divided into galleries related to biofuels research, systems biology, and basic genomics. Each image has a title, a basic citation, and a credit or source. Most of the images are original graphics created by the Genome Management Information System (GMIS). GMIS images are recognizable by their credit line. Permission to use these graphics is not needed, but please credit the U.S. Department of Energy Genome Programs and provide the website http://genomics.energy.gov. Other images were provided by third parties and not created by the U.S. Department of Energy. Users must contact the person listed in the credit line before using those images. The high-resolution images can be downloaded.

  13. Pseudo Boolean Programming for Partially Ordered Genomes

    NASA Astrophysics Data System (ADS)

    Angibaud, Sébastien; Fertin, Guillaume; Thévenin, Annelyse; Vialette, Stéphane

    Comparing genomes of different species is a crucial problem in comparative genomics. Different measures have been proposed to compare two genomes: number of common intervals, number of adjacencies, number of reversals, etc. These measures are classically used between two totally ordered genomes. However, genetic mapping techniques often give rise to different maps with some unordered genes. Starting from a partial order between genes of a genome, one method to find a total order consists in optimizing a given measure between a linear extension of this partial order and a given total order of a close and well-known genome. However, for most common measures, the problem turns out to be NP-hard. In this paper, we propose a (0,1)-linear programming approach to compute a linear extension of one genome that maximizes the number of common intervals (resp. the number of adjacencies) between this linear extension and a given total order. Next, we propose an algorithm to find linear extensions of two partial orders that maximize the number of adjacencies.

  14. Programmed genome rearrangements in the ciliate Oxytricha

    PubMed Central

    Yerlici, V. Talya; Landweber, Laura F.

    2015-01-01

    The ciliate Oxytricha is a microbial eukaryote with two genomes, one of which experiences extensive genome remodeling during development. Each round of conjugation initiates a cascade of events that construct a transcriptionally active somatic genome from a scrambled germline genome, with considerable help from both long and small noncoding RNAs. This process of genome remodeling entails massive DNA deletion and reshuffling of remaining DNA segments to form functional genes from their interrupted and scrambled germline precursors. The use of Oxytricha as a model system provides an opportunity to study an exaggerated form of programmed genome rearrangement. Furthermore, studying the mechanisms that maintain nuclear dimorphism and mediate genome rearrangement has demonstrated a surprising plasticity and diversity of non-coding RNA pathways, with new roles that go beyond conventional gene silencing. Another aspect of ciliate genetics is their unorthodox patterns of RNA-mediated, epigenetic inheritance, that rival Mendelian inheritance. This review takes the reader through the key experiments in a model eukaryote that led to fundamental discoveries in RNA biology and pushes the biological limits of DNA processing. PMID:26104449

  15. Mating programs including genomic relationships and dominance effects

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Breed associations, artificial-insemination organizations, and on-farm software providers need new computerized mating programs for genomic selection so that genomic inbreeding could be minimized by comparing genotypes of potential mates. Efficient methods for transferring elements of the genomic re...

  16. Dairy cattle genomics evaluation program update

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Implementation of genomic evaluation has caused profound changes in dairy cattle breeding. All young bulls bought by major artificial-insemination organizations now are selected based on these evaluation. Evaluation reliability can reach ~75% for yield traits, which is adequate for marketing semen o...

  17. Mating programs including genomic relationships and dominance effects

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Computer mating programs have helped breeders minimize pedigree inbreeding and avoid recessive defects by mating animals with parents that have fewer common ancestors. With genomic selection, breed associations, AI organizations, and on-farm software providers could use new programs to minimize geno...

  18. Human Genome Program Report. Part 1, Overview and Progress

    DOE R&D Accomplishments Database

    1997-11-01

    This report contains Part 1 of a two-part report to reflect research and progress in the U.S. Department of Energy Human Genome Program from 1994 through 1996, with specified updates made just before publication. Part 1 consists of the program overview and report on progress.

  19. Human genome program report. Part 1, overview and progress

    SciTech Connect

    1997-11-01

    This report contains Part 1 of a two-part report to reflect research and progress in the U.S. Department of Energy Human Genome Program from 1994 through 1996, with specified updates made just before publication. Part 1 consists of the program overview and report on progress.

  20. Primer on Molecular Genetics; DOE Human Genome Program

    DOE R&D Accomplishments Database

    1992-04-01

    This report is taken from the April 1992 draft of the DOE Human Genome 1991--1992 Program Report, which is expected to be published in May 1992. The primer is intended to be an introduction to basic principles of molecular genetics pertaining to the genome project. The material contained herein is not final and may be incomplete. Techniques of genetic mapping and DNA sequencing are described.

  1. Primer on molecular genetics. DOE Human Genome Program

    SciTech Connect

    Not Available

    1992-04-01

    This report is taken from the April 1992 draft of the DOE Human Genome 1991--1992 Program Report, which is expected to be published in May 1992. The primer is intended to be an introduction to basic principles of molecular genetics pertaining to the genome project. The material contained herein is not final and may be incomplete. Techniques of genetic mapping and DNA sequencing are described.

  2. Human Genome Program Report. Part 2, 1996 Research Abstracts

    DOE R&D Accomplishments Database

    1997-11-01

    This report contains Part 2 of a two-part report to reflect research and progress in the US Department of Energy Human Genome Program from 1994 through 1996, with specified updates made just before publication. Part 2 consists of 1996 research abstracts. Attention is focused on the following: sequencing; mapping; informatics; ethical, legal, and social issues; infrastructure; and small business innovation research.

  3. Integrating genomics into applied tropical fruit breeding programs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The plant genetics group at the SHRS is divided into three CRIS projects. All three are in the thematic National Program (NP) 301, Plant Microbial and Insect Genetic Resources, Genomics and Genetic Improvement. A major germplasm/breeding CRIS was established in 1998 for improving and preserving orna...

  4. Human genome program report. Part 2, 1996 research abstracts

    SciTech Connect

    1997-11-01

    This report contains Part 2 of a two-part report to reflect research and progress in the US Department of Energy Human Genome Program from 1994 through 1996, with specified updates made just before publication. Part 2 consists of 1996 research abstracts. Attention is focused on the following: sequencing; mapping; informatics; ethical, legal, and social issues; infrastructure; and small business innovation research.

  5. Genomic Tools in Groundnut Breeding Program: Status and Perspectives

    PubMed Central

    Janila, P.; Variath, Murali T.; Pandey, Manish K.; Desmae, Haile; Motagi, Babu N.; Okori, Patrick; Manohar, Surendra S.; Rathnakumar, A. L.; Radhakrishnan, T.; Liao, Boshou; Varshney, Rajeev K.

    2016-01-01

    Groundnut, a nutrient-rich food legume, is cultivated world over. It is valued for its good quality cooking oil, energy and protein rich food, and nutrient-rich fodder. Globally, groundnut improvement programs have developed varieties to meet the preferences of farmers, traders, processors, and consumers. Enhanced yield, tolerance to biotic and abiotic stresses and quality parameters have been the target traits. Spurt in genetic information of groundnut was facilitated by development of molecular markers, genetic, and physical maps, generation of expressed sequence tags (EST), discovery of genes, and identification of quantitative trait loci (QTL) for some important biotic and abiotic stresses and quality traits. The first groundnut variety developed using marker assisted breeding (MAB) was registered in 2003. Since then, USA, China, Japan, and India have begun to use genomic tools in routine groundnut improvement programs. Introgression lines that combine foliar fungal disease resistance and early maturity were developed using MAB. Establishment of marker-trait associations (MTA) paved way to integrate genomic tools in groundnut breeding for accelerated genetic gain. Genomic Selection (GS) tools are employed to improve drought tolerance and pod yield, governed by several minor effect QTLs. Draft genome sequence and low cost genotyping tools such as genotyping by sequencing (GBS) are expected to accelerate use of genomic tools to enhance genetic gains for target traits in groundnut. PMID:27014312

  6. Genomic Tools in Groundnut Breeding Program: Status and Perspectives.

    PubMed

    Janila, P; Variath, Murali T; Pandey, Manish K; Desmae, Haile; Motagi, Babu N; Okori, Patrick; Manohar, Surendra S; Rathnakumar, A L; Radhakrishnan, T; Liao, Boshou; Varshney, Rajeev K

    2016-01-01

    Groundnut, a nutrient-rich food legume, is cultivated world over. It is valued for its good quality cooking oil, energy and protein rich food, and nutrient-rich fodder. Globally, groundnut improvement programs have developed varieties to meet the preferences of farmers, traders, processors, and consumers. Enhanced yield, tolerance to biotic and abiotic stresses and quality parameters have been the target traits. Spurt in genetic information of groundnut was facilitated by development of molecular markers, genetic, and physical maps, generation of expressed sequence tags (EST), discovery of genes, and identification of quantitative trait loci (QTL) for some important biotic and abiotic stresses and quality traits. The first groundnut variety developed using marker assisted breeding (MAB) was registered in 2003. Since then, USA, China, Japan, and India have begun to use genomic tools in routine groundnut improvement programs. Introgression lines that combine foliar fungal disease resistance and early maturity were developed using MAB. Establishment of marker-trait associations (MTA) paved way to integrate genomic tools in groundnut breeding for accelerated genetic gain. Genomic Selection (GS) tools are employed to improve drought tolerance and pod yield, governed by several minor effect QTLs. Draft genome sequence and low cost genotyping tools such as genotyping by sequencing (GBS) are expected to accelerate use of genomic tools to enhance genetic gains for target traits in groundnut. PMID:27014312

  7. Survey of university programs in remote sensing funded under grants from the NASA University-Space Applications program

    NASA Technical Reports Server (NTRS)

    Madigan, J. A.; Earhart, R. W.

    1978-01-01

    NASA's Office of Space and Terrestrial Applications (OSTA) is currently assessing approaches to transferring NASA technology to both the public and private sectors. As part of this assessment, NASA is evaluating the effectiveness of an ongoing program in remote sensing technology transfer conducted by 20 university contractors/grantees, each supported totally or partially by NASA funds. The University-Space Applications program has as its objective the demonstration of practical benefits from the use of remote sensing technology to a broad spectrum of new users, principally in state and local governments. To evaluate the University-Space Applications program, NASA has a near-term requirement for data on each university effort including total funding, funding sources, length of program, program description, and effectiveness measures.

  8. Genomic prediction in CIMMYT maize and wheat breeding programs

    PubMed Central

    Crossa, J; Pérez, P; Hickey, J; Burgueño, J; Ornella, L; Cerón-Rojas, J; Zhang, X; Dreisigacker, S; Babu, R; Li, Y; Bonnett, D; Mathews, K

    2014-01-01

    Genomic selection (GS) has been implemented in animal and plant species, and is regarded as a useful tool for accelerating genetic gains. Varying levels of genomic prediction accuracy have been obtained in plants, depending on the prediction problem assessed and on several other factors, such as trait heritability, the relationship between the individuals to be predicted and those used to train the models for prediction, number of markers, sample size and genotype × environment interaction (GE). The main objective of this article is to describe the results of genomic prediction in International Maize and Wheat Improvement Center's (CIMMYT's) maize and wheat breeding programs, from the initial assessment of the predictive ability of different models using pedigree and marker information to the present, when methods for implementing GS in practical global maize and wheat breeding programs are being studied and investigated. Results show that pedigree (population structure) accounts for a sizeable proportion of the prediction accuracy when a global population is the prediction problem to be assessed. However, when the prediction uses unrelated populations to train the prediction equations, prediction accuracy becomes negligible. When genomic prediction includes modeling GE, an increase in prediction accuracy can be achieved by borrowing information from correlated environments. Several questions on how to incorporate GS into CIMMYT's maize and wheat programs remain unanswered and subject to further investigation, for example, prediction within and between related bi-parental crosses. Further research on the quantification of breeding value components for GS in plant breeding populations is required. PMID:23572121

  9. Genomic prediction in CIMMYT maize and wheat breeding programs.

    PubMed

    Crossa, J; Pérez, P; Hickey, J; Burgueño, J; Ornella, L; Cerón-Rojas, J; Zhang, X; Dreisigacker, S; Babu, R; Li, Y; Bonnett, D; Mathews, K

    2014-01-01

    Genomic selection (GS) has been implemented in animal and plant species, and is regarded as a useful tool for accelerating genetic gains. Varying levels of genomic prediction accuracy have been obtained in plants, depending on the prediction problem assessed and on several other factors, such as trait heritability, the relationship between the individuals to be predicted and those used to train the models for prediction, number of markers, sample size and genotype × environment interaction (GE). The main objective of this article is to describe the results of genomic prediction in International Maize and Wheat Improvement Center's (CIMMYT's) maize and wheat breeding programs, from the initial assessment of the predictive ability of different models using pedigree and marker information to the present, when methods for implementing GS in practical global maize and wheat breeding programs are being studied and investigated. Results show that pedigree (population structure) accounts for a sizeable proportion of the prediction accuracy when a global population is the prediction problem to be assessed. However, when the prediction uses unrelated populations to train the prediction equations, prediction accuracy becomes negligible. When genomic prediction includes modeling GE, an increase in prediction accuracy can be achieved by borrowing information from correlated environments. Several questions on how to incorporate GS into CIMMYT's maize and wheat programs remain unanswered and subject to further investigation, for example, prediction within and between related bi-parental crosses. Further research on the quantification of breeding value components for GS in plant breeding populations is required. PMID:23572121

  10. Genome research in Austria--a program of the future.

    PubMed

    Pasterk, Markus G

    2002-11-01

    Genome research is a central area both for progress in scientific findings in life sciences and for the innovative capacity in medical science, and the pharmaceutical and biotech industries. The research findings obtained by interdisciplinary cooperation are of paramount epistemological importance. They will establish a new understanding of biology. In this context, there will be revolutionary opportunities for new medical therapies, for instance, or for keeping plants and animals healthy. Austria will participate in this science and innovation field and will use the resulting opportunities for scientific and economic development as well as for overall social prosperity. For this purpose, [corrected] Austria has developed the 'Austrian Genome Research Programme', a 'programme of the future' for Austria. This program will be based on the good foundations that genome research has already established in Austria. PMID:12437484

  11. Optimization of Swine Breeding Programs Using Genomic Selection with ZPLAN.

    PubMed

    Lopez, B M; Kang, H S; Kim, T H; Viterbo, V S; Kim, H S; Na, C S; Seo, K S

    2016-05-01

    The objective of this study was to evaluate the present conventional selection program of a swine nucleus farm and compare it with a new selection strategy employing genomic enhanced breeding value (GEBV) as the selection criteria. The ZPLAN+ software was employed to calculate and compare the genetic gain, total cost, return and profit of each selection strategy. The first strategy reflected the current conventional breeding program, which was a progeny test system (CS). The second strategy was a selection scheme based strictly on genomic information (GS1). The third scenario was the same as GS1, but the selection by GEBV was further supplemented by the performance test (GS2). The last scenario was a mixture of genomic information and progeny tests (GS3). The results showed that the accuracy of the selection index of young boars of GS1 was 26% higher than that of CS. On the other hand, both GS2 and GS3 gave 31% higher accuracy than CS for young boars. The annual monetary genetic gain of GS1, GS2 and GS3 was 10%, 12%, and 11% higher, respectively, than that of CS. As expected, the discounted costs of genomic selection strategies were higher than those of CS. The costs of GS1, GS2 and GS3 were 35%, 73%, and 89% higher than those of CS, respectively, assuming a genotyping cost of $120. As a result, the discounted profit per animal of GS1 and GS2 was 8% and 2% higher, respectively, than that of CS while GS3 was 6% lower. Comparison among genomic breeding scenarios revealed that GS1 was more profitable than GS2 and GS3. The genomic selection schemes, especially GS1 and GS2, were clearly superior to the conventional scheme in terms of monetary genetic gain and profit. PMID:26954222

  12. Optimization of Swine Breeding Programs Using Genomic Selection with ZPLAN+

    PubMed Central

    Lopez, B. M.; Kang, H. S.; Kim, T. H.; Viterbo, V. S.; Kim, H. S.; Na, C. S.; Seo, K. S.

    2016-01-01

    The objective of this study was to evaluate the present conventional selection program of a swine nucleus farm and compare it with a new selection strategy employing genomic enhanced breeding value (GEBV) as the selection criteria. The ZPLAN+ software was employed to calculate and compare the genetic gain, total cost, return and profit of each selection strategy. The first strategy reflected the current conventional breeding program, which was a progeny test system (CS). The second strategy was a selection scheme based strictly on genomic information (GS1). The third scenario was the same as GS1, but the selection by GEBV was further supplemented by the performance test (GS2). The last scenario was a mixture of genomic information and progeny tests (GS3). The results showed that the accuracy of the selection index of young boars of GS1 was 26% higher than that of CS. On the other hand, both GS2 and GS3 gave 31% higher accuracy than CS for young boars. The annual monetary genetic gain of GS1, GS2 and GS3 was 10%, 12%, and 11% higher, respectively, than that of CS. As expected, the discounted costs of genomic selection strategies were higher than those of CS. The costs of GS1, GS2 and GS3 were 35%, 73%, and 89% higher than those of CS, respectively, assuming a genotyping cost of $120. As a result, the discounted profit per animal of GS1 and GS2 was 8% and 2% higher, respectively, than that of CS while GS3 was 6% lower. Comparison among genomic breeding scenarios revealed that GS1 was more profitable than GS2 and GS3. The genomic selection schemes, especially GS1 and GS2, were clearly superior to the conventional scheme in terms of monetary genetic gain and profit. PMID:26954222

  13. Genomic resources in mungbean for future breeding programs

    PubMed Central

    Kim, Sue K.; Nair, Ramakrishnan M.; Lee, Jayern; Lee, Suk-Ha

    2015-01-01

    Among the legume family, mungbean (Vigna radiata) has become one of the important crops in Asia, showing a steady increase in global production. It provides a good source of protein and contains most notably folate and iron. Beyond the nutritional value of mungbean, certain features make it a well-suited model organism among legume plants because of its small genome size, short life-cycle, self-pollinating, and close genetic relationship to other legumes. In the past, there have been several efforts to develop molecular markers and linkage maps associated with agronomic traits for the genetic improvement of mungbean and, ultimately, breeding for cultivar development to increase the average yields of mungbean. The recent release of a reference genome of the cultivated mungbean (V. radiata var. radiata VC1973A) and an additional de novo sequencing of a wild relative mungbean (V. radiata var. sublobata) has provided a framework for mungbean genetic and genome research, that can further be used for genome-wide association and functional studies to identify genes related to specific agronomic traits. Moreover, the diverse gene pool of wild mungbean comprises valuable genetic resources of beneficial genes that may be helpful in widening the genetic diversity of cultivated mungbean. This review paper covers the research progress on molecular and genomics approaches and the current status of breeding programs that have developed to move toward the ultimate goal of mungbean improvement. PMID:26322067

  14. Post-Genome Era Pedagogy: How a BS Biotechnology Program Benefits the Liberal Arts Institution

    ERIC Educational Resources Information Center

    Eden, Peter

    2005-01-01

    Genomics profoundly affects society, because genome sequence information is widely used in such areas as genetic testing, genomic medicine/vaccine development, and so forth. Therefore, a responsibility to modernize science curricula exists for "post-genome era" educators. At my university, we developed a BS biotechnology program within a liberal…

  15. [Strategies of the study on herb genome program].

    PubMed

    Chen, Shi-lin; Sun, Yong-zhen; Xu, Jiang; Luo, Hong-mei; Sun, Chao; He, Liu; Cheng, Xiang-lin; Zhang, Bo-li; Xiao, Pei-gen

    2010-07-01

    Herb Genome Program (HerbGP) includes a series of projects on whole genome sequencing (WGS) and post-genomics research of medicinal plants with unique secondary metabolism pathways or/and those of great medical and pharmaceutical importance. In this paper, we systematically discussed the strategy of HerbGP, from species selection, whole-genome sequencing, assembly and bioinformatics analysis, to postgenomics research. HerbGP will push study on Chinese traditional medicines into the front field of life science, by selecting a series of plants with unique secondary metabolism pathways as models and introducing "omics" methods into the research of these medicinal plants. HerbGP will provide great opportunities for China to be the leader in the basic research field of traditional Chinese medicine. HerbGP shall also have significant impacts on the R&D of natural medicines and the development of medicinal farming by analysis of secondary metabolic pathways and selection of cultivars with good agricultural traits. PMID:20931775

  16. An Introduction to the China Rice Functional Genomics Program

    PubMed Central

    Xu, Zhihong

    2002-01-01

    The China Rice Functional Genomics Program (CRFGP) was initiated in 1999 by the Ministry of Science and Technology of China under the National Basic Sciences Initiative and was expected to last for an initial period of five years. The CRFGP involves 20 research groups from the Chinese Academy of Sciences and some major universities and focuses on the identification of genes controlling flowering, plant architecture, fertility, reproduction, metabolic controls and stress responses in rice through a combinatorial approach based on genetics, molecular biology and functional genomics as well as the generation of intellectual properties related to crop breeding and improvements. We will briefly describe the mission of the CRFGP as well as its recent progress. PMID:18628891

  17. 78 FR 18680 - Genomic Medicine Program Advisory Committee, Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-27

    ... AFFAIRS Genomic Medicine Program Advisory Committee, Notice of Meeting The Department of Veterans Affairs... Medicine Program Advisory Committee will meet on April 11, 2013, in Suite 1000 at the United States Access... Million Veteran Program, as well as the clinical Genomic Medicine Service. The emerging implications...

  18. 75 FR 26846 - Genomic Medicine Program Advisory Committee; Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-12

    ... AFFAIRS Genomic Medicine Program Advisory Committee; Notice of Meeting The Department of Veterans Affairs (VA) gives notice under Public Law 92-463 (Federal Advisory Committee Act) that the Genomic Medicine... protecting the privacy of Veterans; presentations on genomic medicine delivery within VHA and proof...

  19. 76 FR 65563 - Genomic Medicine Program Advisory Committee; Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-21

    ... AFFAIRS Genomic Medicine Program Advisory Committee; Notice of Meeting The Department of Veterans Affairs (VA) gives notice under Public Law 92-463 (Federal Advisory Committee Act) that the Genomic Medicine... continue discussions on the potential impact of whole genome data on clinical decisionmaking. The...

  20. GENOMEPOP: A program to simulate genomes in populations

    PubMed Central

    Carvajal-Rodríguez, Antonio

    2008-01-01

    Background There are several situations in population biology research where simulating DNA sequences is useful. Simulation of biological populations under different evolutionary genetic models can be undertaken using backward or forward strategies. Backward simulations, also called coalescent-based simulations, are computationally efficient. The reason is that they are based on the history of lineages with surviving offspring in the current population. On the contrary, forward simulations are less efficient because the entire population is simulated from past to present. However, the coalescent framework imposes some limitations that forward simulation does not. Hence, there is an increasing interest in forward population genetic simulation and efficient new tools have been developed recently. Software tools that allow efficient simulation of large DNA fragments under complex evolutionary models will be very helpful when trying to better understand the trace left on the DNA by the different interacting evolutionary forces. Here I will introduce GenomePop, a forward simulation program that fulfills the above requirements. The use of the program is demonstrated by studying the impact of intracodon recombination on global and site-specific dN/dS estimation. Results I have developed algorithms and written software to efficiently simulate, forward in time, different Markovian nucleotide or codon models of DNA mutation. Such models can be combined with recombination, at inter and intra codon levels, fitness-based selection and complex demographic scenarios. Conclusion GenomePop has many interesting characteristics for simulating SNPs or DNA sequences under complex evolutionary and demographic models. These features make it unique with respect to other simulation tools. Namely, the possibility of forward simulation under General Time Reversible (GTR) mutation or GTR×MG94 codon models with intra-codon recombination, arbitrary, user-defined, migration patterns, diploid or

  1. Genomic Tools in Cowpea Breeding Programs: Status and Perspectives.

    PubMed

    Boukar, Ousmane; Fatokun, Christian A; Huynh, Bao-Lam; Roberts, Philip A; Close, Timothy J

    2016-01-01

    Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA). It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds, and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids, and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP) genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS)-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS), promises an increase in the number of improved

  2. Genomic Tools in Cowpea Breeding Programs: Status and Perspectives

    PubMed Central

    Boukar, Ousmane; Fatokun, Christian A.; Huynh, Bao-Lam; Roberts, Philip A.; Close, Timothy J.

    2016-01-01

    Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA). It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds, and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids, and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP) genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS)-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS), promises an increase in the number of improved

  3. GIANT API: an application programming interface for functional genomics

    PubMed Central

    Roberts, Andrew M.; Wong, Aaron K.; Fisk, Ian; Troyanskaya, Olga G.

    2016-01-01

    GIANT API provides biomedical researchers programmatic access to tissue-specific and global networks in humans and model organisms, and associated tools, which includes functional re-prioritization of existing genome-wide association study (GWAS) data. Using tissue-specific interaction networks, researchers are able to predict relationships between genes specific to a tissue or cell lineage, identify the changing roles of genes across tissues and uncover disease-gene associations. Additionally, GIANT API enables computational tools like NetWAS, which leverages tissue-specific networks for re-prioritization of GWAS results. The web services covered by the API include 144 tissue-specific functional gene networks in human, global functional networks for human and six common model organisms and the NetWAS method. GIANT API conforms to the REST architecture, which makes it stateless, cacheable and highly scalable. It can be used by a diverse range of clients including web browsers, command terminals, programming languages and standalone apps for data analysis and visualization. The API is freely available for use at http://giant-api.princeton.edu. PMID:27098035

  4. GIANT API: an application programming interface for functional genomics.

    PubMed

    Roberts, Andrew M; Wong, Aaron K; Fisk, Ian; Troyanskaya, Olga G

    2016-07-01

    GIANT API provides biomedical researchers programmatic access to tissue-specific and global networks in humans and model organisms, and associated tools, which includes functional re-prioritization of existing genome-wide association study (GWAS) data. Using tissue-specific interaction networks, researchers are able to predict relationships between genes specific to a tissue or cell lineage, identify the changing roles of genes across tissues and uncover disease-gene associations. Additionally, GIANT API enables computational tools like NetWAS, which leverages tissue-specific networks for re-prioritization of GWAS results. The web services covered by the API include 144 tissue-specific functional gene networks in human, global functional networks for human and six common model organisms and the NetWAS method. GIANT API conforms to the REST architecture, which makes it stateless, cacheable and highly scalable. It can be used by a diverse range of clients including web browsers, command terminals, programming languages and standalone apps for data analysis and visualization. The API is freely available for use at http://giant-api.princeton.edu. PMID:27098035

  5. 77 FR 16898 - Genomic Medicine Program Advisory Committee, Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-22

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF VETERANS AFFAIRS Genomic Medicine Program Advisory Committee, Notice of Meeting The Department of Veterans Affairs (VA) gives notice under Public Law 92-463 (Federal Advisory Committee Act) that the Genomic...

  6. Genomic selection accuracy using multi-family prediction models in a wheat breeding program

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic selection (GS) uses genome-wide molecular marker data to predict the genetic value of selection candidates in breeding programs. In plant breeding, the ability to produce large numbers of progeny per cross allows GS to be conducted within each family. However, this approach requires phenotyp...

  7. 76 FR 24573 - Genomic Medicine Program Advisory Committee; Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-02

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF VETERANS AFFAIRS Genomic Medicine Program Advisory Committee; Notice of Meeting The Department of Veterans Affairs (VA) gives notice under Public Law 92-463 (Federal Advisory Committee Act) that the Genomic...

  8. 77 FR 58913 - Genomic Medicine Program Advisory Committee, Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-24

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF VETERANS AFFAIRS Genomic Medicine Program Advisory Committee, Notice of Meeting The Department of Veterans Affairs (VA) gives notice under Public Law 92-463 (Federal Advisory Committee Act) that the Genomic...

  9. 75 FR 61861 - Genomic Medicine Program Advisory Committee; Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-06

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF VETERANS AFFAIRS Genomic Medicine Program Advisory Committee; Notice of Meeting The Department of Veterans Affairs (VA) gives notice under Public Law 92-463 (Federal Advisory Committee Act) that the Genomic...

  10. 78 FR 58612 - Genomic Medicine Program Advisory Committee, Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-24

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF VETERANS AFFAIRS Genomic Medicine Program Advisory Committee, Notice of Meeting The Department of Veterans Affairs (VA) gives notice under the Federal Advisory Committee Act, 5 U.S.C. App. 2, that the Genomic...

  11. The NSF Plant Genome Research Outreach Program for American Indians at Iowa State University

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The involvement of Native American students and researchers in plant genome research is minimal. In an effort to increase their representation in the research community, a summer program to mentor Native American/American Indian undergraduates in plant genomics research has begun on the Iowa State U...

  12. RNA-Mediated Epigenetic Programming of Genome Rearrangements

    PubMed Central

    Nowacki, Mariusz; Shetty, Keerthi; Landweber, Laura F.

    2012-01-01

    RNA, normally thought of as a conduit in gene expression, has a novel mode of action in ciliated protozoa. Maternal RNA templates provide both an organizing guide for DNA rearrangements and a template that can transport somatic mutations to the next generation. This opportunity for RNA-mediated genome rearrangement and DNA repair is profound in the ciliate Oxytricha, which deletes 95% of its germline genome during development in a process that severely fragments its chromosomes and then sorts and reorders the hundreds of thousands of pieces remaining. Oxytricha’s somatic nuclear genome is therefore an epigenome formed through RNA templates and signals arising from the previous generation. Furthermore, this mechanism of RNA-mediated epigenetic inheritance can function across multiple generations, and the discovery of maternal template RNA molecules has revealed new biological roles for RNA and has hinted at the power of RNA molecules to sculpt genomic information in cells. PMID:21801022

  13. Programmed genome rearrangements: in lampreys, all cells are not equal.

    PubMed

    Sémon, Marie; Schubert, Michael; Laudet, Vincent

    2012-08-21

    How can organisms silence deleterious gene loci? A recent study has shed light on a very brute mechanism in a jawless vertebrate: the irreversible deletion of massive chunks of genomic DNA. PMID:22917513

  14. Genomic selection needs to be carefully assessed to meet specific requirements in livestock breeding programs

    PubMed Central

    Jonas, Elisabeth; de Koning, Dirk-Jan

    2015-01-01

    Genomic selection is a promising development in agriculture, aiming improved production by exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. It opens opportunities for research, as novel algorithms and lab methodologies are developed. Genomic selection can be applied in many breeds and species. Further research on the implementation of genomic selection (GS) in breeding programs is highly desirable not only for the common good, but also the private sector (breeding companies). It has been projected that this approach will improve selection routines, especially in species with long reproduction cycles, late or sex-limited or expensive trait recording and for complex traits. The task of integrating GS into existing breeding programs is, however, not straightforward. Despite successful integration into breeding programs for dairy cattle, it has yet to be shown how much emphasis can be given to the genomic information and how much additional phenotypic information is needed from new selection candidates. Genomic selection is already part of future planning in many breeding companies of pigs and beef cattle among others, but further research is needed to fully estimate how effective the use of genomic information will be for the prediction of the performance of future breeding stock. Genomic prediction of production in crossbreeding and across-breed schemes, costs and choice of individuals for genotyping are reasons for a reluctance to fully rely on genomic information for selection decisions. Breeding objectives are highly dependent on the industry and the additional gain when using genomic information has to be considered carefully. This review synthesizes some of the suggested approaches in selected livestock species including cattle, pig, chicken, and fish. It outlines tasks to help understanding possible consequences when applying genomic information in breeding scenarios. PMID

  15. Genomic selection needs to be carefully assessed to meet specific requirements in livestock breeding programs.

    PubMed

    Jonas, Elisabeth; de Koning, Dirk-Jan

    2015-01-01

    Genomic selection is a promising development in agriculture, aiming improved production by exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. It opens opportunities for research, as novel algorithms and lab methodologies are developed. Genomic selection can be applied in many breeds and species. Further research on the implementation of genomic selection (GS) in breeding programs is highly desirable not only for the common good, but also the private sector (breeding companies). It has been projected that this approach will improve selection routines, especially in species with long reproduction cycles, late or sex-limited or expensive trait recording and for complex traits. The task of integrating GS into existing breeding programs is, however, not straightforward. Despite successful integration into breeding programs for dairy cattle, it has yet to be shown how much emphasis can be given to the genomic information and how much additional phenotypic information is needed from new selection candidates. Genomic selection is already part of future planning in many breeding companies of pigs and beef cattle among others, but further research is needed to fully estimate how effective the use of genomic information will be for the prediction of the performance of future breeding stock. Genomic prediction of production in crossbreeding and across-breed schemes, costs and choice of individuals for genotyping are reasons for a reluctance to fully rely on genomic information for selection decisions. Breeding objectives are highly dependent on the industry and the additional gain when using genomic information has to be considered carefully. This review synthesizes some of the suggested approaches in selected livestock species including cattle, pig, chicken, and fish. It outlines tasks to help understanding possible consequences when applying genomic information in breeding scenarios. PMID

  16. Complexity, Post-genomic Biology and Gene Expression Programs

    NASA Astrophysics Data System (ADS)

    Williams, Rohan B. H.; Luo, Oscar Junhong

    Gene expression represents the fundamental phenomenon by which information encoded in a genome is utilised for the overall biological objectives of the organism. Understanding this level of information transfer is therefore essential for dissecting the mechanistic basis of form and function of organisms. We survey recent developments in the methodology of the life sciences that is relevant for understanding the organisation and function of the genome and review our current understanding of the regulation of gene expression, and finally, outline some new approaches that may be useful in understanding the organisation of gene regulatory systems.

  17. Genomic Tools in Pea Breeding Programs: Status and Perspectives.

    PubMed

    Tayeh, Nadim; Aubert, Grégoire; Pilet-Nayel, Marie-Laure; Lejeune-Hénaut, Isabelle; Warkentin, Thomas D; Burstin, Judith

    2015-01-01

    Pea (Pisum sativum L.) is an annual cool-season legume and one of the oldest domesticated crops. Dry pea seeds contain 22-25% protein, complex starch and fiber constituents, and a rich array of vitamins, minerals, and phytochemicals which make them a valuable source for human consumption and livestock feed. Dry pea ranks third to common bean and chickpea as the most widely grown pulse in the world with more than 11 million tons produced in 2013. Pea breeding has achieved great success since the time of Mendel's experiments in the mid-1800s. However, several traits still require significant improvement for better yield stability in a larger growing area. Key breeding objectives in pea include improving biotic and abiotic stress resistance and enhancing yield components and seed quality. Taking advantage of the diversity present in the pea genepool, many mapping populations have been constructed in the last decades and efforts have been deployed to identify loci involved in the control of target traits and further introgress them into elite breeding materials. Pea now benefits from next-generation sequencing and high-throughput genotyping technologies that are paving the way for genome-wide association studies and genomic selection approaches. This review covers the significant development and deployment of genomic tools for pea breeding in recent years. Future prospects are discussed especially in light of current progress toward deciphering the pea genome. PMID:26640470

  18. Genomic Tools in Pea Breeding Programs: Status and Perspectives

    PubMed Central

    Tayeh, Nadim; Aubert, Grégoire; Pilet-Nayel, Marie-Laure; Lejeune-Hénaut, Isabelle; Warkentin, Thomas D.; Burstin, Judith

    2015-01-01

    Pea (Pisum sativum L.) is an annual cool-season legume and one of the oldest domesticated crops. Dry pea seeds contain 22–25% protein, complex starch and fiber constituents, and a rich array of vitamins, minerals, and phytochemicals which make them a valuable source for human consumption and livestock feed. Dry pea ranks third to common bean and chickpea as the most widely grown pulse in the world with more than 11 million tons produced in 2013. Pea breeding has achieved great success since the time of Mendel's experiments in the mid-1800s. However, several traits still require significant improvement for better yield stability in a larger growing area. Key breeding objectives in pea include improving biotic and abiotic stress resistance and enhancing yield components and seed quality. Taking advantage of the diversity present in the pea genepool, many mapping populations have been constructed in the last decades and efforts have been deployed to identify loci involved in the control of target traits and further introgress them into elite breeding materials. Pea now benefits from next-generation sequencing and high-throughput genotyping technologies that are paving the way for genome-wide association studies and genomic selection approaches. This review covers the significant development and deployment of genomic tools for pea breeding in recent years. Future prospects are discussed especially in light of current progress toward deciphering the pea genome. PMID:26640470

  19. Office of Cancer Genomics launches new program | Office of Cancer Genomics

    Cancer.gov

    The NCI Office of Cancer Genomics, along with Cancer Research UK, foundation Hubrecht Organoid Technology, and Wellcome Trust Sanger Institute, launched the Human Cancer Models Initiative (HCMI). The international collaboration will generate approximately 1,000 new cancer models that are representative of human tumors. These models will allow the research community to better study cancer initiation, development, and progression.

  20. Flexible approaches for teaching computational genomics in a health information management program.

    PubMed

    Zhou, Leming; Watzlaf, Valerie; Abdelhak, Mervat

    2013-01-01

    The astonishing improvement of high-throughput biotechnologies in recent years makes it possible to access a huge amount of genomic data. The association between genomic data and genetic disease has already been and will continue to be applied to personalized healthcare. Health information management (HIM) professionals are the ones who will handle personal genetic information and provide solid evidence to support physicians' diagnoses and personalized treatment strategies, and therefore they will need to have the knowledge and skills to process genomic data. In this paper, we describe flexible approaches for teaching a computational genomics course in the HIM program at the University of Pittsburgh. HIM programs at other universities may choose an appropriate approach to fit into their own curriculum. PMID:23861672

  1. Genome image programs: visualization and interpretation of Escherichia coli microarray experiments.

    PubMed Central

    Zimmer, Daniel P; Paliy, Oleg; Thomas, Brian; Gyaneshwar, Prasad; Kustu, Sydney

    2004-01-01

    We have developed programs to facilitate analysis of microarray data in Escherichia coli. They fall into two categories: manipulation of microarray images and identification of known biological relationships among lists of genes. A program in the first category arranges spots from glass-slide DNA microarrays according to their position in the E. coli genome and displays them compactly in genome order. The resulting genome image is presented in a web browser with an image map that allows the user to identify genes in the reordered image. Another program in the first category aligns genome images from two or more experiments. These images assist in visualizing regions of the genome with common transcriptional control. Such regions include multigene operons and clusters of operons, which are easily identified as strings of adjacent, similarly colored spots. The images are also useful for assessing the overall quality of experiments. The second category of programs includes a database and a number of tools for displaying biological information about many E. coli genes simultaneously rather than one gene at a time, which facilitates identifying relationships among them. These programs have accelerated and enhanced our interpretation of results from E. coli DNA microarray experiments. Examples are given. PMID:15342544

  2. Mechanisms of Programmed DNA Lesions and Genomic Instability in the Immune System

    PubMed Central

    Alt, Frederick W.; Zhang, Yu; Meng, Fei-Long; Guo, Chunguang; Schwer, Bjoern

    2015-01-01

    Chromosomal translocations involving antigen receptor loci are common in lymphoid malignancies. Translocations require DNA double-strand breaks (DSBs) at two chromosomal sites, their physical juxtaposition, and their fusion by end joining. Ability of lymphocytes to generate diverse repertoires of antigen receptors and effector antibodies derives from programmed genomic alterations that produce DSBs. We discuss these lymphocyte-specific processes, with a focus on mechanisms that provide requisite DSB target specificity and mechanisms that suppress DSB translocation. We also discuss recent work that provides new insights into DSB repair pathways and influences of three-dimensional genome organization on physiological processes and cancer genomes. PMID:23374339

  3. CHALLENGES FOR IMPLEMENTING A PTSD PREVENTIVE GENOMIC SEQUENCING PROGRAM IN THE U.S. MILITARY

    PubMed Central

    Lázaro-Muñoz, Gabriel; Juengst, Eric T.

    2015-01-01

    There is growing interest in using the quickly developing field of genomics to contribute to military readiness and effectiveness. Specifically, influential military advisory panels have recommended that the U.S. military apply genomics to help treat, prevent, or minimize the risk for post-traumatic stress disorder (PTSD) among service members. This article highlights some important scientific, legal, and ethical challenges regarding the development and deployment of a preventive genomic sequencing (PGS) program to predict the risk of PTSD among military service members. PMID:26401056

  4. Genome-wide alterations of the DNA replication program during tumor progression

    NASA Astrophysics Data System (ADS)

    Arneodo, A.; Goldar, A.; Argoul, F.; Hyrien, O.; Audit, B.

    2016-08-01

    Oncogenic stress is a major driving force in the early stages of cancer development. Recent experimental findings reveal that, in precancerous lesions and cancers, activated oncogenes may induce stalling and dissociation of DNA replication forks resulting in DNA damage. Replication timing is emerging as an important epigenetic feature that recapitulates several genomic, epigenetic and functional specificities of even closely related cell types. There is increasing evidence that chromosome rearrangements, the hallmark of many cancer genomes, are intimately associated with the DNA replication program and that epigenetic replication timing changes often precede chromosomic rearrangements. The recent development of a novel methodology to map replication fork polarity using deep sequencing of Okazaki fragments has provided new and complementary genome-wide replication profiling data. We review the results of a wavelet-based multi-scale analysis of genomic and epigenetic data including replication profiles along human chromosomes. These results provide new insight into the spatio-temporal replication program and its dynamics during differentiation. Here our goal is to bring to cancer research, the experimental protocols and computational methodologies for replication program profiling, and also the modeling of the spatio-temporal replication program. To illustrate our purpose, we report very preliminary results obtained for the chronic myelogeneous leukemia, the archetype model of cancer. Finally, we discuss promising perspectives on using genome-wide DNA replication profiling as a novel efficient tool for cancer diagnosis, prognosis and personalized treatment.

  5. Cancer Therapy Evaluation Program | Office of Cancer Genomics

    Cancer.gov

    The Cancer Therapy Evaluation Program (CTEP) seeks to improve the lives of cancer patients by finding better treatments, control mechanisms, and cures for cancer. CTEP funds a national program of cancer research, sponsoring clinical trials to evaluate new anti-cancer agents.

  6. Genomic Selection and its Effects on Dairy Cattle Breeding Programs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The availability of high-throughput assays for genotyping single nucleotide polymorphisms (SNP) has led to the genotyping of thousands of dairy cattle, mostly progeny tested bulls in artificial insemination programs or young bulls that are candidates for such programs, using the BovineSNP50 BeadChip...

  7. Efficiency of genomic selection in an established commercial layer breeding program

    PubMed Central

    2013-01-01

    Background In breeding programs for layers, selection of hens and cocks is based on recording phenotypic data from hens in different housing systems. Genomic information can provide additional information for selection and/or allow for a strong reduction in the generation interval. In this study, a typical conventional layer breeding program using a four-line cross was modeled and the expected genetic progress was derived deterministically with the software ZPLAN+. This non-genomic reference scenario was compared to two genomic breeding programs to determine the best strategy for implementing genomic information in layer breeding programs. Results In scenario I, genomic information was used in addition to all other information available in the conventional breeding program, so the generation interval was the same as in the reference scenario, i.e. 14.5 months. Here, we assumed that either only young cocks or young cocks and hens were genotyped as selection candidates. In scenario II, we assumed that breeders of both sexes were used at the biologically earliest possible age, so that at the time of selection only performance data of the parent generation and genomic information of the selection candidates were available. In this case, the generation interval was reduced to eight months. In both scenarios, the number of genotyped male selection candidates was varied between 800 and 4800 males and two sizes of the calibration set (500 or 2000 animals) were considered. All genomic scenarios increased the expected genetic gain and the economic profit of the breeding program. In scenario II, the increase was much more pronounced and even in the most conservative implementation led to a 60% improvement in genetic gain and economic profit. This increase was in all cases associated with higher breeding costs. Conclusions While genomic selection is shown to have the potential to improve genetic gain in layer breeding programs, its implementation remains a business decision of

  8. Introduction to Metagenomics at DOE JGI: Program Overview and Program Informatics (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    SciTech Connect

    Tringe, Susannah

    2011-10-12

    Susannah Tringe of the DOE Joint Genome Institute talks about the Program Overview and Program Informatics at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  9. Introduction to Metagenomics at DOE JGI: Program Overview and Program Informatics (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Tringe, Susannah [DOE JGI

    2013-01-22

    Susannah Tringe of the DOE Joint Genome Institute talks about the Program Overview and Program Informatics at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  10. The effect of genomic information on optimal contribution selection in livestock breeding programs

    PubMed Central

    2013-01-01

    Background Long-term benefits in animal breeding programs require that increases in genetic merit be balanced with the need to maintain diversity (lost due to inbreeding). This can be achieved by using optimal contribution selection. The availability of high-density DNA marker information enables the incorporation of genomic data into optimal contribution selection but this raises the question about how this information affects the balance between genetic merit and diversity. Methods The effect of using genomic information in optimal contribution selection was examined based on simulated and real data on dairy bulls. We compared the genetic merit of selected animals at various levels of co-ancestry restrictions when using estimated breeding values based on parent average, genomic or progeny test information. Furthermore, we estimated the proportion of variation in estimated breeding values that is due to within-family differences. Results Optimal selection on genomic estimated breeding values increased genetic gain. Genetic merit was further increased using genomic rather than pedigree-based measures of co-ancestry under an inbreeding restriction policy. Using genomic instead of pedigree relationships to restrict inbreeding had a significant effect only when the population consisted of many large full-sib families; with a half-sib family structure, no difference was observed. In real data from dairy bulls, optimal contribution selection based on genomic estimated breeding values allowed for additional improvements in genetic merit at low to moderate inbreeding levels. Genomic estimated breeding values were more accurate and showed more within-family variation than parent average breeding values; for genomic estimated breeding values, 30 to 40% of the variation was due to within-family differences. Finally, there was no difference between constraining inbreeding via pedigree or genomic relationships in the real data. Conclusions The use of genomic estimated breeding

  11. Strategies, Actions, and Outcomes of Pilot State Programs in Public Health Genomics, 2003–2008

    PubMed Central

    St. Pierre, Jeanette; Bach, Janice; Duquette, Debra; Oehlke, Kristen; Nystrom, Robert; Silvey, Kerry; Zlot, Amy; Giles, Rebecca; Johnson, Jenny; Anders, H. Mack; Gwinn, Marta; Khoury, Muin J.

    2014-01-01

    State health departments in Michigan, Minnesota, Oregon, and Utah explored the use of genomic information, including family health history, in chronic disease prevention programs. To support these explorations, the Office of Public Health Genomics at the Centers for Disease Control and Prevention provided cooperative agreement funds from 2003 through 2008. The 4 states’ chronic disease programs identified advocates, formed partnerships, and assessed public data; they integrated genomics into existing state plans for genetics and chronic disease prevention; they developed projects focused on prevention of asthma, cancer, cardiovascular disease, diabetes, and other chronic conditions; and they created educational curricula and materials for health workers, policymakers, and the public. Each state’s program was different because of the need to adapt to existing culture, infrastructure, and resources, yet all were able to enhance their chronic disease prevention programs with the use of family health history, a low-tech “genomic tool.” Additional states are drawing on the experience of these 4 states to develop their own approaches. PMID:24921900

  12. Guide to Accessing Program Data | Office of Cancer Genomics

    Cancer.gov

    Visit the Guide to Accessing TARGET Data page for a visual and interactive guide on how to access OCG program data. Although this guide uses TARGET as an example, it is also applicable to CGCI data. 

  13. Development of Structural Neurobiology and Genomics Programs in the Neurogenetic Institute

    SciTech Connect

    Henderson, Brian E., M.D.

    2006-11-10

    The purpose of the DOE equipment-only grant was to purchase instrumentation in support of structural biology and genomics core facilities in the Zilkha Neurogenetic Institute (ZNI). The ZNI, a new laboratory facility (125,000 GSF) and a center of excellence at the Keck School of Medicine of USC, was opened in 2003. The goal of the ZNI is to recruit upwards of 30 new faculty investigators engaged in interdisciplinary research programs that will add breadth and depth to existing school strengths in neuroscience, epidemiology and genetics. Many of these faculty, and other faculty researchers at the Keck School will access structural biology and genomics facilities developed in the ZNI.

  14. Data Standards for the Genomes to Life Program

    SciTech Connect

    Arkin, Adam; Ambrosiano, John; Babnigg, Gyorgy; Frank, Ed; Geist,Al; Giometti, Carol; Jacobsen, Janet; Samatova, Nagiza; Slater, Nancy; Taylor, Ron

    2004-01-31

    Existing GTL Projects already have produced volumes of dataand, over the course of the next five years, will produce an estimatedhundreds, or possibly thousands, of terabytes of data from hundreds ofexperiments conducted at dozens of laboratories in National Labs anduniversities across the nation. These data will be the basis forpublications by individual researchers, research groups, andmulti-institutional collaborations, and the basis for future DOEdecisions on funding further research in bioremediation. The short-termand long-term value of the data to project participants, to the DOE, andto the nation depends, however, on being able to access the data and onhow, or whether, the data are archived. The ability to access data is thestarting point for data analysis and interpretation, data integration,data mining, and development of data-driven models. Limited orinefficient data access means that less data are analyzed in acost-effective and timely manner. Data production in the GTL Program willlikely outstrip, or may have already outstripped, the ability to analyzethe data. Being able to access data depends on two key factors: datastandards and implementation of the data standards. For the purpose ofthis proposal, a data standard is defined as a standard, documented wayin which data and information about the data are describe. The attributesof the experiment in which the data were collected need to be known andthe measurements corresponding to the data collected need to bedescribed. In general terms, a data standard could be a form (electronicor paper) that is completed by a researcher or a document that prescribeshow a protocol or experiment should be described in writing.Datastandards are critical to data access because they provide a frameworkfor organizing and managing data. Researchers spend significant amountsof time managing data and information about experiments using labnotebooks, computer files, Excel spreadsheets, etc. In addition, dataoutput format

  15. Reproductive technologies combine well with genomic selection in dairy breeding programs.

    PubMed

    Thomasen, J R; Willam, A; Egger-Danner, C; Sørensen, A C

    2016-02-01

    The objective of the present study was to examine whether genomic selection of females interacts with the use of reproductive technologies (RT) to increase annual monetary genetic gain (AMGG). This was tested using a factorial design with 3 factors: genomic selection of females (0 or 2,000 genotyped heifers per year), RT (0 or 50 donors selected at 14 mo of age for producing 10 offspring), and 2 reliabilities of genomic prediction. In addition, different strategies for use of RT and how strategies interact with the reliability of genomic prediction were investigated using stochastic simulation by varying (1) number of donors (25, 50, 100, 200), (2) number of calves born per donor (10 or 20), (3) age of donor (2 or 14 mo), and (4) number of sires (25, 50, 100, 200). In total, 72 different breeding schemes were investigated. The profitability of the different breeding strategies was evaluated by deterministic simulation by varying the costs of a born calf with reproductive technologies at levels of €500, €1,000, and €1,500. The results confirm our hypothesis that combining genomic selection of females with use of RT increases AMGG more than in a reference scheme without genomic selection in females. When the reliability of genomic prediction is high, the effect on rate of inbreeding (ΔF) is small. The study also demonstrates favorable interaction effects between the components of the breeder's equation (selection intensity, selection accuracy, generation interval) for the bull dam donor path, leading to higher AMGG. Increasing the donor program and number of born calves to achieve higher AMGG is associated with the undesirable effect of increased ΔF. This can be alleviated, however, by increasing the numbers of sires without compromising AMGG remarkably. For the major part of the investigated donor schemes, the investment in RT is profitable in dairy cattle populations, even at high levels of costs for RT. PMID:26686703

  16. Economic evaluation of genomic selection in small ruminants: a sheep meat breeding program.

    PubMed

    Shumbusho, F; Raoul, J; Astruc, J M; Palhiere, I; Lemarié, S; Fugeray-Scarbel, A; Elsen, J M

    2016-06-01

    Recent genomic evaluation studies using real data and predicting genetic gain by modeling breeding programs have reported moderate expected benefits from the replacement of classic selection schemes by genomic selection (GS) in small ruminants. The objectives of this study were to compare the cost, monetary genetic gain and economic efficiency of classic selection and GS schemes in the meat sheep industry. Deterministic methods were used to model selection based on multi-trait indices from a sheep meat breeding program. Decisional variables related to male selection candidates and progeny testing were optimized to maximize the annual monetary genetic gain (AMGG), that is, a weighted sum of meat and maternal traits annual genetic gains. For GS, a reference population of 2000 individuals was assumed and genomic information was available for evaluation of male candidates only. In the classic selection scheme, males breeding values were estimated from own and offspring phenotypes. In GS, different scenarios were considered, differing by the information used to select males (genomic only, genomic+own performance, genomic+offspring phenotypes). The results showed that all GS scenarios were associated with higher total variable costs than classic selection (if the cost of genotyping was 123 euros/animal). In terms of AMGG and economic returns, GS scenarios were found to be superior to classic selection only if genomic information was combined with their own meat phenotypes (GS-Pheno) or with their progeny test information. The predicted economic efficiency, defined as returns (proportional to number of expressions of AMGG in the nucleus and commercial flocks) minus total variable costs, showed that the best GS scenario (GS-Pheno) was up to 15% more efficient than classic selection. For all selection scenarios, optimization increased the overall AMGG, returns and economic efficiency. As a conclusion, our study shows that some forms of GS strategies are more advantageous

  17. Design and Implementation of a Genomics Field Trip Program Aimed at Secondary School Students

    PubMed Central

    Fox, Joanne A.

    2012-01-01

    With the rapid pace of advancements in biological research brought about by the application of computer science and information technology, we believe the time is right for introducing genomics and bioinformatics tools and concepts to secondary school students. Our approach has been to offer a full-day field trip in our research facility where secondary school students carry out experiments at the laboratory bench and on a laptop computer. This experience offers benefits for students, teachers, and field trip instructors. In delivering a wide variety of science outreach and education programs, we have learned that a number of factors contribute to designing a successful experience for secondary school students. First, it is important to engage students with authentic and fun activities that are linked to real-world applications and/or research questions. Second, connecting with a local high school teacher to pilot programs and linking to curricula taught in secondary schools will enrich the field trip experience. Whether or not programs are linked directly to local teachers, it is important to be flexible and build in mechanisms for collecting feedback in field trip programs. Finally, graduate students can be very powerful mentors for students and should be encouraged to share their enthusiasm for science and to talk about career paths. Our experiences suggest a real need for effective science outreach programs at the secondary school level and that genomics and bioinformatics are ideal areas to explore. PMID:22956895

  18. Cellular and Molecular Features of Developmentally Programmed Genome Rearrangement in a Vertebrate (Sea Lamprey: Petromyzon marinus)

    PubMed Central

    Timoshevskiy, Vladimir A.; Herdy, Joseph R.; Keinath, Melissa C.; Smith, Jeramiah J.

    2016-01-01

    The sea lamprey (Petromyzon marinus) represents one of the few vertebrate species known to undergo large-scale programmatic elimination of genomic DNA over the course of its normal development. Programmed genome rearrangements (PGRs) result in the reproducible loss of ~20% of the genome from somatic cell lineages during early embryogenesis. Studies of PGR hold the potential to provide novel insights related to the maintenance of genome stability during the cell cycle and coordination between mechanisms responsible for the accurate distribution of chromosomes into daughter cells, yet little is known regarding the mechanistic basis or cellular context of PGR in this or any other vertebrate lineage. Here we identify epigenetic silencing events that are associated with the programmed elimination of DNA and describe the spatiotemporal dynamics of PGR during lamprey embryogenesis. In situ analyses reveal that the earliest DNA methylation (and to some extent H3K9 trimethylation) events are limited to specific extranuclear structures (micronuclei) containing eliminated DNA. During early embryogenesis a majority of micronuclei (~60%) show strong enrichment for repressive chromatin modifications (H3K9me3 and 5meC). These analyses also led to the discovery that eliminated DNA is packaged into chromatin that does not migrate with somatically retained chromosomes during anaphase, a condition that is superficially similar to lagging chromosomes observed in some cancer subtypes. Closer examination of “lagging” chromatin revealed distributions of repetitive elements, cytoskeletal contacts and chromatin contacts that provide new insights into the cellular mechanisms underlying the programmed loss of these segments. Our analyses provide additional perspective on the cellular and molecular context of PGR, identify new structures associated with elimination of DNA and reveal that PGR is completed over the course of several successive cell divisions. PMID:27341395

  19. Prokaryotic Super Program Advisory Committee DOE Joint Genome Institute, Walnut Creek, CA, March 27, 2013

    PubMed Central

    Garrity, George M.; Banfield, Jill; Eisen, Jonathan; van der Lelie, Niels; McMahon, Trina; Rusch, Doug; DeLong, Edward; Moran, Mary Ann; Currie, Cameron; Furhman, Jed; Hallam, Steve; Hugenholtz, Phil; Moran, Nancy; Nelson, Karen; Roberts, Richard; Stepanauskas, Ramunas

    2013-01-01

    The Prokaryotic Super Program Advisory Committee met on March 27, 2013 for their annual review the Prokaryotic Super Program at the DOE Joint Genome Institute. As is the case with any site visit or program review, the objective is to evaluate progress in meeting organizational objectives, provide feedback to from the user-community and to assist the JGI in formulating plans for the coming year. The advisors want to commend the JGI for its central role in developing new technologies and capabilities, and for catalyzing the formation of new collaborative user communities. Highlights of the post-meeting exchanges among the advisors focused on the importance of programmatic initiatives including: • GEBA, which serves as a phylogenetic “base-map” on which our knowledge of functional diversity can be layered. • FEBA, which promises to provide new insights into the physiological capabilities of prokaryotes under highly standardized conditions. • Single-cell genomics technology, which is seen to significantly enhance our ability to interpret genomic and metagenomic data and broaden the scope of the GEBA program to encompass at least a part of the microbial “dark-matter”. • IMG, which is seen to play a central role in JGI programs and is viewed as a strategically important asset in the JGI portfolio. On this latter point, the committee encourages the formation of a strategic relationship between IMG and the Kbase to ensure that the intelligence, deep knowledge and experience captured in the former is not lost. The committee strongly urges the DOE to continue its support for maintaining this critical resource. PMID:24501639

  20. Prokaryotic Super Program Advisory Committee DOE Joint Genome Institute, Walnut Creek, CA, March 27, 2013.

    PubMed

    Garrity, George M; Banfield, Jill; Eisen, Jonathan; van der Lelie, Niels; McMahon, Trina; Rusch, Doug; Delong, Edward; Moran, Mary Ann; Currie, Cameron; Furhman, Jed; Hallam, Steve; Hugenholtz, Phil; Moran, Nancy; Nelson, Karen; Roberts, Richard; Stepanauskas, Ramunas

    2013-07-30

    The Prokaryotic Super Program Advisory Committee met on March 27, 2013 for their annual review the Prokaryotic Super Program at the DOE Joint Genome Institute. As is the case with any site visit or program review, the objective is to evaluate progress in meeting organizational objectives, provide feedback to from the user-community and to assist the JGI in formulating plans for the coming year. The advisors want to commend the JGI for its central role in developing new technologies and capabilities, and for catalyzing the formation of new collaborative user communities. Highlights of the post-meeting exchanges among the advisors focused on the importance of programmatic initiatives including: • GEBA, which serves as a phylogenetic "base-map" on which our knowledge of functional diversity can be layered. • FEBA, which promises to provide new insights into the physiological capabilities of prokaryotes under highly standardized conditions. • Single-cell genomics technology, which is seen to significantly enhance our ability to interpret genomic and metagenomic data and broaden the scope of the GEBA program to encompass at least a part of the microbial "dark-matter". • IMG, which is seen to play a central role in JGI programs and is viewed as a strategically important asset in the JGI portfolio. On this latter point, the committee encourages the formation of a strategic relationship between IMG and the Kbase to ensure that the intelligence, deep knowledge and experience captured in the former is not lost. The committee strongly urges the DOE to continue its support for maintaining this critical resource. PMID:24501639

  1. Report on the Imaging Workshop for the Genomes to Life Program

    SciTech Connect

    Colson, Steven; Sudar, Damir

    2002-11-01

    DOE's Genomes to Life program seeks to understand the composition and function of biochemical networks and pathways that carry out the essential processes of living organisms. Such understanding is critical for DOE to more effectively address its missions-clean energy, carbon management, bioremediation, and mitigation of bioterrorism. Imaging of living organisms links the genome to function and recognizes many of the steps along the way to understanding how cell function changes with time and environmental challenges. Innovations in imaging, coupled with computational advances, will accelerate scientific discovery and enable biological solutions to energy challenges. GTL has four main goals: (1) Identify and characterize the molecular machines of life-multiprotein complexes that execute cellular functions and govern cell form. (2) Characterize gene regulatory networks. (3) Characterize the functional repertoire of complex microbial communities in their natural environments at the molecular level. (4) Develop computational methods and capabilities to advance understanding of complex biological systems and predict their behavior.

  2. A genome resource to address mechanisms of developmental programming: determination of the fetal sheep heart transcriptome

    PubMed Central

    Cox, Laura A; Glenn, Jeremy P; Spradling, Kimberly D; Nijland, Mark J; Garcia, Roy; Nathanielsz, Peter W; Ford, Stephen P

    2012-01-01

    The pregnant sheep has provided seminal insights into reproduction related to animal and human development (ovarian function, fertility, implantation, fetal growth, parturition and lactation). Fetal sheep physiology has been extensively studied since 1950, contributing significantly to the basis for our understanding of many aspects of fetal development and behaviour that remain in use in clinical practice today. Understanding mechanisms requires the combination of systems approaches uniquely available in fetal sheep with the power of genomic studies. Absence of the full range of sheep genomic resources has limited the full realization of the power of this model, impeding progress in emerging areas of pregnancy biology such as developmental programming. We have examined the expressed fetal sheep heart transcriptome using high-throughput sequencing technologies. In so doing we identified 36,737 novel transcripts and describe genes, gene variants and pathways relevant to fundamental developmental mechanisms. Genes with the highest expression levels and with novel exons in the fetal heart transcriptome are known to play central roles in muscle development. We show that high-throughput sequencing methods can generate extensive transcriptome information in the absence of an assembled and annotated genome for that species. The gene sequence data obtained provide a unique genomic resource for sheep specific genetic technology development and, combined with the polymorphism data, augment annotation and assembly of the sheep genome. In addition, identification and pathway analysis of novel fetal sheep heart transcriptome splice variants is a first step towards revealing mechanisms of genetic variation and gene environment interactions during fetal heart development. PMID:22508961

  3. Integration of genomic information into sport horse breeding programs for optimization of accuracy of selection.

    PubMed

    Haberland, A M; König von Borstel, U; Simianer, H; König, S

    2012-09-01

    Reliable selection criteria are required for young riding horses to increase genetic gain by increasing accuracy of selection and decreasing generation intervals. In this study, selection strategies incorporating genomic breeding values (GEBVs) were evaluated. Relevant stages of selection in sport horse breeding programs were analyzed by applying selection index theory. Results in terms of accuracies of indices (r(TI) ) and relative selection response indicated that information on single nucleotide polymorphism (SNP) genotypes considerably increases the accuracy of breeding values estimated for young horses without own or progeny performance. In a first scenario, the correlation between the breeding value estimated from the SNP genotype and the true breeding value (= accuracy of GEBV) was fixed to a relatively low value of r(mg) = 0.5. For a low heritability trait (h(2) = 0.15), and an index for a young horse based only on information from both parents, additional genomic information doubles r(TI) from 0.27 to 0.54. Including the conventional information source 'own performance' into the before mentioned index, additional SNP information increases r(TI) by 40%. Thus, particularly with regard to traits of low heritability, genomic information can provide a tool for well-founded selection decisions early in life. In a further approach, different sources of breeding values (e.g. GEBV and estimated breeding values (EBVs) from different countries) were combined into an overall index when altering accuracies of EBVs and correlations between traits. In summary, we showed that genomic selection strategies have the potential to contribute to a substantial reduction in generation intervals in horse breeding programs. PMID:23031511

  4. Report on the Imaging Workshop for the Genomes to Life Program, April 16-18, 2002

    SciTech Connect

    Colson, STEVEN

    2003-08-04

    This report is a result of the Imaging Workshop for the Genomes to Life (GTL) program held April 16-19, 2002, in Charlotte, North Carolina. The meeting was sponsored by the Office of Biological and Environmental Research and the Office of Advanced Scientific Computing Research of the U.S. Department of Energy's (DOE) Office of Science. The purpose of the workshop was to project a broad vision for future needs and determine the value of imaging to GTL program research. The workshop included four technical sessions with plenary lectures on biology and technology perspectives and technical presentations on needs and approaches as they related to the following areas of the GTL program: (1) Molecular machines (protein complexes); (2) Intracellular and cellular structure, function, and processes; (3) Multicellular: Monoclonal and heterogeneous multicellular systems, cell-cell signaling, and model systems; and (4) Cells in situ and in vivo: Bacteria in the natural environment, microenvironment, and in vivo systems.

  5. The Human Genome Project and Mental Retardation: An Educational Program. Final Progress Report

    SciTech Connect

    Davis, Sharon

    1999-05-03

    The Arc, a national organization on mental retardation, conducted an educational program for members, many of whom have a family member with a genetic condition causing mental retardation. The project informed members about the Human Genome scientific efforts, conducted training regarding ethical, legal and social implications and involved members in issue discussions. Short reports and fact sheets on genetic and ELSI topics were disseminated to 2,200 of the Arc's leaders across the country and to other interested individuals. Materials produced by the project can e found on the Arc's web site, TheArc.org.

  6. Whole-Genome Screening of Newborns? The Constitutional Boundaries of State Newborn Screening Programs

    PubMed Central

    King, Jaime S.; Smith, Monica E.

    2016-01-01

    State newborn screening (NBS) programs routinely screen nearly all of the 4 million newborns in the United States each year for ~30 primary conditions and a number of secondary conditions. NBS could be on the cusp of an unprecedented expansion as a result of advances in whole-genome sequencing (WGS). As WGS becomes cheaper and easier and as our knowledge and understanding of human genetics expand, the question of whether WGS has a role to play in state NBS programs becomes increasingly relevant and complex. As geneticists and state public health officials begin to contemplate the technical and procedural details of whether WGS could benefit existing NBS programs, this is an opportune time to revisit the legal framework of state NBS programs. In this article, we examine the constitutional underpinnings of state-mandated NBS and explore the range of current state statutes and regulations that govern the programs. We consider the legal refinements that will be needed to keep state NBS programs within constitutional bounds, focusing on 2 areas of concern: consent procedures and the criteria used to select new conditions for NBS panels. We conclude by providing options for states to consider when contemplating the use of WGS for NBS. PMID:26729704

  7. FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences

    PubMed Central

    Schiex, Thomas; Gouzy, Jérôme; Moisan, Annick; de Oliveira, Yannick

    2003-01-01

    We describe FrameD, a program that predicts coding regions in prokaryotic and matured eukaryotic sequences. Initially targeted at gene prediction in bacterial GC rich genomes, the gene model used in FrameD also allows to predict genes in the presence of frameshifts and partially undetermined sequences which makes it also very suitable for gene prediction and frameshift correction in unfinished sequences such as EST and EST cluster sequences. Like recent eukaryotic gene prediction programs, FrameD also includes the ability to take into account protein similarity information both in its prediction and its graphical output. Its performances are evaluated on different bacterial genomes. The web site (http://genopole.toulouse.inra.fr/bioinfo/FrameD/FD) allows direct prediction, sequence correction and translation and the ability to learn new models for new organisms. PMID:12824407

  8. FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences.

    PubMed

    Schiex, Thomas; Gouzy, Jérôme; Moisan, Annick; de Oliveira, Yannick

    2003-07-01

    We describe FrameD, a program that predicts coding regions in prokaryotic and matured eukaryotic sequences. Initially targeted at gene prediction in bacterial GC rich genomes, the gene model used in FrameD also allows to predict genes in the presence of frameshifts and partially undetermined sequences which makes it also very suitable for gene prediction and frameshift correction in unfinished sequences such as EST and EST cluster sequences. Like recent eukaryotic gene prediction programs, FrameD also includes the ability to take into account protein similarity information both in its prediction and its graphical output. Its performances are evaluated on different bacterial genomes. The web site (http://genopole.toulouse.inra.fr/bioinfo/FrameD/FD) allows direct prediction, sequence correction and translation and the ability to learn new models for new organisms. PMID:12824407

  9. An Innovative Plant Genomics and Gene Annotation Program for High School, Community College, and University Faculty

    ERIC Educational Resources Information Center

    Hacisalihoglu, Gokhan; Hilgert, Uwe; Nash, E. Bruce; Micklos, David A.

    2008-01-01

    Today's biology educators face the challenge of training their students in modern molecular biology techniques including genomics and bioinformatics. The Dolan DNA Learning Center (DNALC) of Cold Spring Harbor Laboratory has developed and disseminated a bench- and computer-based plant genomics curriculum for biology faculty. In 2007, a five-day…

  10. Extension of Type 2 Diabetes Genome-Wide Association Scan Results in the Diabetes Prevention Program

    PubMed Central

    Moore, Allan F.; Jablonski, Kathleen A.; McAteer, Jarred B.; Saxena, Richa; Pollin, Toni I.; Franks, Paul W.; Hanson, Robert L.; Shuldiner, Alan R.; Knowler, William C.; Altshuler, David; Florez, Jose C.

    2008-01-01

    OBJECTIVE— Genome-wide association scans (GWASs) have identified novel diabetes-associated genes. We evaluated how these variants impact diabetes incidence, quantitative glycemic traits, and response to preventive interventions in 3,548 subjects at high risk of type 2 diabetes enrolled in the Diabetes Prevention Program (DPP), which examined the effects of lifestyle intervention, metformin, and troglitazone versus placebo. RESEARCH DESIGN AND METHODS— We genotyped selected single nucleotide polymorphisms (SNPs) in or near diabetes-associated loci, including EXT2, CDKAL1, CDKN2A/B, IGF2BP2, HHEX, LOC387761, and SLC30A8 in DPP participants and performed Cox regression analyses using genotype, intervention, and their interactions as predictors of diabetes incidence. We evaluated their effect on insulin resistance and secretion at 1 year. RESULTS— None of the selected SNPs were associated with increased diabetes incidence in this population. After adjustments for ethnicity, baseline insulin secretion was lower in subjects with the risk genotype at HHEX rs1111875 (P = 0.01); there were no significant differences in baseline insulin sensitivity. Both at baseline and at 1 year, subjects with the risk genotype at LOC387761 had paradoxically increased insulin secretion; adjustment for self-reported ethnicity abolished these differences. In ethnicity-adjusted analyses, we noted a nominal differential improvement in β-cell function for carriers of the protective genotype at CDKN2A/B after 1 year of troglitazone treatment (P = 0.01) and possibly lifestyle modification (P = 0.05). CONCLUSIONS— We were unable to replicate the GWAS findings regarding diabetes risk in the DPP. We did observe genotype associations with differences in baseline insulin secretion at the HHEX locus and a possible pharmacogenetic interaction at CDKNA2/B. PMID:18544707

  11. Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations

    PubMed Central

    Lund, Eivind; Oldenburg, Anja R.; Collas, Philippe

    2014-01-01

    Nuclear lamins contact the genome at the nuclear periphery through large domains and are involved in chromatin organization. Among broad peak calling algorithms available to date, none are suited for mapping lamin–genome interactions genome wide. We disclose a novel algorithm, enriched domain detector (EDD), for analysis of broad enrichment domains from chromatin immunoprecipitation (ChIP)-seq data. EDD enables discovery of genomic domains interacting with broadly distributed proteins, such as A- and B-type lamins affinity isolated by ChIP. The advantages of EDD over existing broad peak callers are sensitivity to domain width rather than enrichment strength at a particular site, and robustness against local variations. PMID:24782521

  12. Genomic selection in a pig population including information from slaughtered full sibs of boars within a sib-testing program.

    PubMed

    Samorè, A B; Buttazzoni, L; Gallo, M; Russo, V; Fontanesi, L

    2015-05-01

    Genomic selection is becoming a common practise in dairy cattle, but only few works have studied its introduction in pig selection programs. Results described for this species are highly dependent on the considered traits and the specific population structure. This paper aims to simulate the impact of genomic selection in a pig population with a training cohort of performance-tested and slaughtered full sibs. This population is selected for performance, carcass and meat quality traits by full-sib testing of boars. Data were simulated using a forward-in-time simulation process that modeled around 60K single nucleotide polymorphisms and several quantitative trait loci distributed across the 18 porcine autosomes. Data were edited to obtain, for each cycle, 200 sires mated with 800 dams to produce 800 litters of 4 piglets each, two males and two females (needed for the sib test), for a total of 3200 newborns. At each cycle, a subset of 200 litters were sib tested, and 60 boars and 160 sows were selected to replace the same number of culled male and female parents. Simulated selection of boars based on performance test data of their full sibs (one castrated brother and two sisters per boar in 200 litters) lasted for 15 cycles. Genotyping and phenotyping of the three tested sibs (training population) and genotyping of the candidate boars (prediction population) were assumed. Breeding values were calculated for traits with two heritability levels (h 2=0.40, carcass traits, and h 2=0.10, meat quality parameters) on simulated pedigrees, phenotypes and genotypes. Genomic breeding values, estimated by various models (GBLUP from raw phenotype or using breeding values and single-step models), were compared with the classical BLUP Animal Model predictions in terms of predictive ability. Results obtained for traits with moderate heritability (h 2=0.40), similar to the heritability of traits commonly measured within a sib-testing program, did not show any benefit from the

  13. The Human Genome Initiative: Implications for the Comprehensive School Health Program.

    ERIC Educational Resources Information Center

    James, Delores C. S.

    1994-01-01

    The Human Genome Initiative (HGI) constructs common resources for studying human genetics. Early identification of people at risk for genetic disorders allows for early education and counseling. HGI research will create inexpensive, reliable genetic tests and diagnoses to help teachers and school staff assess, compare, and channel students. (SM)

  14. Democratizing Human Genome Project Information: A Model Program for Education, Information and Debate in Public Libraries.

    ERIC Educational Resources Information Center

    Pollack, Miriam

    The "Mapping the Human Genome" project demonstrated that librarians can help whomever they serve in accessing information resources in the areas of biological and health information, whether it is the scientists who are developing the information or a member of the public who is using the information. Public libraries can guide library users…

  15. Recurrent parent genome recovery analysis in a marker-assisted backcrossing program of rice (Oryza sativa L.).

    PubMed

    Miah, Gous; Rafii, Mohd Y; Ismail, Mohd R; Puteh, Adam B; Rahim, Harun A; Latif, Mohammad A

    2015-02-01

    Backcross breeding is the most commonly used method for incorporating a blast resistance gene into a rice cultivar. Linkage between the resistance gene and undesirable units can persist for many generations of backcrossing. Marker-assisted backcrossing (MABC) along with marker-assisted selection (MAS) contributes immensely to overcome the main limitation of the conventional breeding and accelerates recurrent parent genome (RPG) recovery. The MABC approach was employed to incorporate (a) blast resistance gene(s) from the donor parent Pongsu Seribu 1, the blast-resistant local variety in Malaysia, into the genetic background of MR219, a popular high-yielding rice variety that is blast susceptible, to develop a blast-resistant MR219 improved variety. In this perspective, the recurrent parent genome recovery was analyzed in early generations of backcrossing using simple sequence repeat (SSR) markers. Out of 375 SSR markers, 70 markers were found polymorphic between the parents, and these markers were used to evaluate the plants in subsequent generations. Background analysis revealed that the extent of RPG recovery ranged from 75.40% to 91.3% and from 80.40% to 96.70% in BC1F1 and BC2F1 generations, respectively. In this study, the recurrent parent genome content in the selected BC2F2 lines ranged from 92.7% to 97.7%. The average proportion of the recurrent parent in the selected improved line was 95.98%. MAS allowed identification of the plants that are more similar to the recurrent parent for the loci evaluated in backcross generations. The application of MAS with the MABC breeding program accelerated the recovery of the RP genome, reducing the number of generations and the time for incorporating resistance against rice blast. PMID:25553855

  16. EXONSAMPLER: a computer program for genome-wide and candidate gene exon sampling for targeted next-generation sequencing.

    PubMed

    Cosart, Ted; Beja-Pereira, Albano; Luikart, Gordon

    2014-11-01

    The computer program EXONSAMPLER automates the sampling of thousands of exon sequences from publicly available reference genome sequences and gene annotation databases. It was designed to provide exon sequences for the efficient, next-generation gene sequencing method called exon capture. The exon sequences can be sampled by a list of gene name abbreviations (e.g. IFNG, TLR1), or by sampling exons from genes spaced evenly across chromosomes. It provides a list of genomic coordinates (a bed file), as well as a set of sequences in fasta format. User-adjustable parameters for collecting exon sequences include a minimum and maximum acceptable exon length, maximum number of exonic base pairs (bp) to sample per gene, and maximum total bp for the entire collection. It allows for partial sampling of very large exons. It can preferentially sample upstream (5 prime) exons, downstream (3 prime) exons, both external exons, or all internal exons. It is written in the Python programming language using its free libraries. We describe the use of EXONSAMPLER to collect exon sequences from the domestic cow (Bos taurus) genome for the design of an exon-capture microarray to sequence exons from related species, including the zebu cow and wild bison. We collected ~10% of the exome (~3 million bp), including 155 candidate genes, and ~16,000 exons evenly spaced genomewide. We prioritized the collection of 5 prime exons to facilitate discovery and genotyping of SNPs near upstream gene regulatory DNA sequences, which control gene expression and are often under natural selection. PMID:24751285

  17. Proceedings of the relevance of mass spectrometry to DNA sequence determination: Research needs for the Human Genome Program

    SciTech Connect

    Edmonds, C.G.; Smith, R.D. ); Smith, L.M. )

    1990-11-01

    A workshop was sponsored for the US Department of Energy (DOE), Office of Health and Environmental Research by Pacific Northwest Laboratory, April 4--5, 1990, in Seattle, Washington, to examine the potential role of mass spectrometry in the joint DOE/National Institutes of Health (NIH) Human Genome Program. The workshop was occasioned by recent developments in mass spectrometry that are providing new levels for selectivity, sensitivity, and, in particular, new methods of ionization appropriate for large biopolymers such as DNA. During discussions, three general mass spectrometric approaches to the determination of DNA sequence were considered: (1) the mass spectrometric detection of isotopic labels from DNA sequencing mixtures separated using gel electrophoresis, (2) the direct mass spectrometric analysis from direct ionization of unfractionated sequencing mixtures where the measured mass of the constituents functions to identify and order the base sequence (replacing separation by gel electrophoresis), and (3) an approach in which a single highly charged molecular ion of a large DNA segment produced is rapidly sequenced in an ion cyclotron resonance ion trap. The consensus of the workshop was that, on the basis of the new developments, mass spectrometry has the potential to provide the substantial increases in sequencing speed required for the Human Genome Program. 66 refs., 3 tabs.

  18. Cytokine-induced megakaryocytic differentiation is regulated by genome-wide loss of a uSTAT transcriptional program.

    PubMed

    Park, Hyun Jung; Li, Juan; Hannah, Rebecca; Biddie, Simon; Leal-Cervantes, Ana I; Kirschner, Kristina; Flores Santa Cruz, David; Sexl, Veronika; Göttgens, Berthold; Green, Anthony R

    2016-03-15

    Metazoan development is regulated by transcriptional networks, which must respond to extracellular cues including cytokines. The JAK/STAT pathway is a highly conserved regulatory module, activated by many cytokines, in which tyrosine-phosphorylated STATs (pSTATs) function as transcription factors. However, the mechanisms by which STAT activation modulates lineage-affiliated transcriptional programs are unclear. We demonstrate that in the absence of thrombopoietin (TPO), tyrosine-unphosphorylated STAT5 (uSTAT5) is present in the nucleus where it colocalizes with CTCF and represses a megakaryocytic transcriptional program. TPO-mediated phosphorylation of STAT5 triggers its genome-wide relocation to STAT consensus sites with two distinct transcriptional consequences, loss of a uSTAT5 program that restrains megakaryocytic differentiation and activation of a canonical pSTAT5-driven program which includes regulators of apoptosis and proliferation. Transcriptional repression by uSTAT5 reflects restricted access of the megakaryocytic transcription factor ERG to target genes. These results identify a previously unrecognized mechanism of cytokine-mediated differentiation. PMID:26702099

  19. Multimedia Presentations on the Human Genome: Implementation and Assessment of a Teaching Program for the Introduction to Genome Science Using a Poster and Animations

    ERIC Educational Resources Information Center

    Kano, Kei; Yahata, Saiko; Muroi, Kaori; Kawakami, Masahiro; Tomoda, Mari; Miyaki, Koichi; Nakayama, Takeo; Kosugi, Shinji; Kato, Kazuto

    2008-01-01

    Genome science, including topics such as gene recombination, cloning, genetic tests, and gene therapy, is now an established part of our daily lives; thus we need to learn genome science to better equip ourselves for the present day. Learning from topics directly related to the human has been suggested to be more effective than learning from…

  20. Genome-wide analysis of genetic and epigenetic control of programmed DNA deletion.

    PubMed

    Swart, Estienne C; Wilkes, Cyril Denby; Sandoval, Pamela Y; Arambasic, Miroslav; Sperling, Linda; Nowacki, Mariusz

    2014-08-01

    During the development of the somatic genome from the Paramecium germline genome the bulk of the copies of ∼45 000 unique, internal eliminated sequences (IESs) are deleted. IES targeting is facilitated by two small RNA (sRNA) classes: scnRNAs, which relay epigenetic information from the parental nucleus to the developing nucleus, and iesRNAs, which are produced and used in the developing nucleus. Why only certain IESs require sRNAs for their removal has been enigmatic. By analyzing the silencing effects of three genes: PGM (responsible for DNA excision), DCL2/3 (scnRNA production) and DCL5 (iesRNA production), we identify key properties required for IES elimination. Based on these results, we propose that, depending on the exact combination of their lengths and end bases, some IESs are less efficiently recognized or excised and have a greater requirement for targeting by scnRNAs and iesRNAs. We suggest that the variation in IES retention following silencing of DCL2/3 is not primarily due to scnRNA density, which is comparatively uniform relative to IES retention, but rather the genetic properties of IESs. Taken together, our analyses demonstrate that in Paramecium the underlying genetic properties of developmentally deleted DNA sequences are essential in determining the sensitivity of these sequences to epigenetic control. PMID:25016527

  1. [Genome-cohort studies for the development of personalized cancer prevention programs in Japan].

    PubMed

    Tanaka, Hideo

    2015-05-01

    One of the most important roles of molecular epidemiology is to investigate gene-environment interactions in order to provide data for personalized risk modification. A case-control study conducted in Aichi showed that an aldehyde dehydrogenase- 2(ALDH2)polymorphism together with cigarette smoking significantly affects the risk of lung cancer. The main purpose of this large-scale genome-cohort study of healthy individuals is to confirm that these factors are associated with the development of diseases and to set optimal thresholds for the environmental factors. The Japan Multi-Institutional Collaborative Cohort(J-MICC)Study was launched in 2005. It has recruited 100,600 healthy participants up to the end of 2014, and plans to follow them until 2025. Although Japanese genome-cohort studies, including the J-MICC Study, the Japan Public Health Center-based Prospective(JPHC)Study, and the Tohoku Medical Megabank Organization Study, consist of different research teams with different financial resources, collaboration to standardize the data collection format for successful pooled analysis is being discussed. PMID:25981648

  2. Genome-wide analysis of p53 transcriptional programs in B cells upon exposure to genotoxic stress in vivo

    PubMed Central

    Tonelli, Claudia; Morelli, Marco J.; Bianchi, Salvatore; Rotta, Luca; Capra, Thelma; Sabò, Arianna; Campaner, Stefano; Amati, Bruno

    2015-01-01

    The tumor suppressor p53 is a transcription factor that coordinates the cellular response to DNA damage. Here we provide an integrated analysis of p53 genomic occupancy and p53-dependent gene regulation in the splenic B and non-B cell compartments of mice exposed to whole-body ionizing radiation, providing insight into general principles of p53 activity in vivo. In unstressed conditions, p53 bound few genomic targets; induction of p53 by ionizing radiation increased the number of p53 bound sites, leading to highly overlapping profiles in the different cell types. Comparison of these profiles with chromatin features in unstressed B cells revealed that, upon activation, p53 localized at active promoters, distal enhancers, and a smaller set of unmarked distal regions. At promoters, recognition of the canonical p53 motif as well as binding strength were associated with p53-dependent transcriptional activation, but not repression, indicating that the latter was most likely indirect. p53-activated targets constituted the core of a cell type-independent response, superimposed onto a cell type-specific program. Core response genes included most of the known p53-regulated genes, as well as many new ones. Our data represent a unique characterization of the p53-regulated response to ionizing radiation in vivo. PMID:26372730

  3. Genomes to Life''Center for Molecular and Cellular Systems'': A research program for identification and characterization of protein complexes.

    SciTech Connect

    Buchanan, M V.; Larimer, Frank; Wiley, H S.; Kennel, S J.; Squier, Thomas C.; Ramsey, John M.; Rodland, Karin D.; Hurst, G B.; Smith, Richard D.; Xu, Ying; Dixon, David A.; Doktycz, M J.; Colson, Steve D.; Gesteland, R; Giometti, Carol S.; Young, Mark E.; Giddings, Ralph M.

    2002-02-01

    Goal 1 of Department of Energy's Genomes to Life (GTL) program seeks to identify and characterize the complete set of protein complexes within a cell. Goal 1 forms the foundation necessary to accomplish the other objectives of the GTL program, which focus on gene regulatory networks and molecular level characterization of interactions in microbial communities. Together this information would allow cells and their components to be understood in sufficient detail to predict, test, and understand the responses of a biological system to its environment. The Center for Molecular and Cellular Systems has been established to identify and characterize protein complexes using high through-put analytical technologies. A dynamic research program is being developed that supports the goals of the Center by focusing on the development of new capabilities for sample preparation and complex separations, molecular level identification of the protein complexes by mass spectrometry, characterization of the complexes in living cells by imaging techniques, and bioinformatics and computational tools for the collection and interpretation of data and formation of databases and tools to allow the data to be shared by the biological community.

  4. GENETICS AND GENOMICS - INTEGRATION OF MOLECULAR GENETICS INTO A BREEDING PROGRAM FOR RAINBOW TROUT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    At the National Center for Cool and Cold Water Aquaculture (US Department of Agriculture, Ag. Research Service) in Leetown, WV, we have a broodstock development program now entering the 2nd generation of family based selective breeding using expected breeding values (EBVs). Our major breeding objec...

  5. Genome-wide view of TGFβ/Foxh1 regulation of the early mesendoderm program

    PubMed Central

    Chiu, William T.; Charney Le, Rebekah; Blitz, Ira L.; Fish, Margaret B.; Li, Yi; Biesinger, Jacob; Xie, Xiaohui; Cho, Ken W. Y.

    2014-01-01

    Nodal/TGFβ signaling regulates diverse biological responses. By combining RNA-seq on Foxh1 and Nodal signaling loss-of-function embryos with ChIP-seq of Foxh1 and Smad2/3, we report a comprehensive genome-wide interaction between Foxh1 and Smad2/3 in mediating Nodal signaling during vertebrate mesendoderm development. This study significantly increases the total number of Nodal target genes regulated by Foxh1 and Smad2/3, and reinforces the notion that Foxh1-Smad2/3-mediated Nodal signaling directly coordinates the expression of a cohort of genes involved in the control of gene transcription, signaling pathway modulation and tissue morphogenesis during gastrulation. We also show that Foxh1 may function independently of Nodal signaling, in addition to its role as a transcription factor mediating Nodal signaling via Smad2/3. Finally, we propose an evolutionarily conserved interaction between Foxh1 and PouV, a mechanism observed in Pou5f1-mediated regulation of pluripotency in human embryonic stem and epiblast cells. PMID:25359723

  6. mlRho - a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes.

    PubMed

    Haubold, Bernhard; Pfaffelhuber, Peter; Lynch, Michael

    2010-03-01

    Improvements in sequencing technology over the past 5 years are leading to routine application of shotgun sequencing in the fields of ecology and evolution. However, the theory to estimate evolutionary parameters from these data is still being worked out. Here we present an extension and implementation of part of this theory, mlRho. This program can efficiently compute the following three maximum likelihood estimators based on shotgun sequence data obtained from single diploid individuals: the population mutation rate (4N(e)mu), the sequencing error rate, and the population recombination rate (4N(e)c). We demonstrate the accuracy of mlRho by applying it to simulated data sets. In addition, we analyse the genomes of the sea squirt Ciona intestinalis and the water flea Daphnia pulex. Ciona intestinalis is an obligate outcrosser, while D. pulex is a cyclic parthenogen, and we discuss how these contrasting life histories are reflected in our parameter estimates. The program mlRho is freely available from http://guanine.evolbio.mpg.de/mlRho. PMID:20331786

  7. mlRho – a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes

    PubMed Central

    HAUBOLD, BERNHARD; PFAFFELHUBER, PETER; LYNCH, MICHAEL

    2016-01-01

    Improvements in sequencing technology over the past 5 years are leading to routine application of shotgun sequencing in the fields of ecology and evolution. However, the theory to estimate evolutionary parameters from these data is still being worked out. Here we present an extension and implementation of part of this theory, mlRho. This program can efficiently compute the following three maximum likelihood estimators based on shotgun sequence data obtained from single diploid individuals: the population mutation rate (4Neμ), the sequencing error rate, and the population recombination rate (4Nec). We demonstrate the accuracy of mlRho by applying it to simulated data sets. In addition, we analyse the genomes of the sea squirt Ciona intestinalis and the water flea Daphnia pulex. Ciona intestinalis is an obligate outcrosser, while D. pulex is a cyclic parthenogen, and we discuss how these contrasting life histories are reflected in our parameter estimates. The program mlRho is freely available from http://guanine.evolbio.mpg.de/mlRho. PMID:20331786

  8. Cultural differences define diagnosis and genomic medicine practice: implications for undiagnosed diseases program in China

    PubMed Central

    Duan, Xiaohong; Markello, Thomas; Adams, David; Toro, Camilo; Tifft, Cynthia; Gahl, William A.; Boerkoel, Cornelius F.

    2013-01-01

    Despite the current acceleration and increasing leadership of Chinese genetics research, genetics and its clinical application have largely been imported to China from the Occident. Neither genetics nor the scientific reductionism underpinning its clinical application is integral to the traditional Chinese worldview. Given that disease concepts and their incumbent diagnoses are historically derived and culturally meaningful, we hypothesize that the cultural expectations of genetic diagnoses and medical genetics practice differs between the Occident and China. Specifically, we suggest that an undiagnosed diseases program in China will differ from the recently established Undiagnosed Diseases Program at the United States National Institutes of Health; a culturally sensitive concept will integrate traditional Chinese understanding of disease with the scientific reductionism of Occidental medicine. PMID:23856975

  9. Cultural differences define diagnosis and genomic medicine practice: implications for undiagnosed diseases program in China.

    PubMed

    Duan, Xiaohong; Markello, Thomas; Adams, David; Toro, Camilo; Tifft, Cynthia; Gahl, William A; Boerkoel, Cornelius F

    2013-09-01

    Despite the current acceleration and increasing leadership of Chinese genetics research, genetics and its clinical application have largely been imported to China from the Occident. Neither genetics nor the scientific reductionism underpinning its clinical application is integral to the traditional Chinese worldview. Given that disease concepts and their incumbent diagnoses are historically derived and culturally meaningful, we hypothesize that the cultural expectations of genetic diagnoses and medical genetics practice differ between the Occident and China. Specifically, we suggest that an undiagnosed diseases program in China will differ from the recently established Undiagnosed Diseases Program at the United States National Institutes of Health; a culturally sensitive concept will integrate traditional Chinese understanding of disease with the scientific reductionism of Occidental medicine. PMID:23856975

  10. The pea aphid (Acyrthosiphon pisum) genome encodes two divergent early developmental programs.

    PubMed

    Duncan, Elizabeth J; Leask, Megan P; Dearden, Peter K

    2013-05-01

    The pea aphid (Acyrthosiphon pisum) can reproduce either sexually or asexually (parthenogenetically), giving rise, in each case, to almost identical adults. These two modes of reproduction are accompanied by differences in ovarian morphology and the developmental environment of the offspring, with sexual forms producing eggs that are laid, whereas asexual development occurs within the mother. Here we examine the effect each mode of reproduction has on the expression of key maternal and axis patterning genes; orthodenticle (otd), hunchback (hb), caudal (cad) and nanos (nos). We show that three of these genes (Ap-hb, Ap-otd and Ap-cad) are expressed differently between the sexually and asexually produced oocytes and embryos of the pea aphid. We also show, using immunohistochemistry and cytoskeletal inhibitors, that Ap-hb RNA is localized differently between sexually and asexually produced oocytes, and that this is likely due to differences in the 3' untranslated regions of the RNA. Furthermore, Ap-hb and Ap-otd have extensive expression domains in early sexually produced embryos, but are not expressed at equivalent stages in asexually produced embryos. These differences in expression likely correspond with substantial changes in the gene regulatory networks controlling early development in the pea aphid. These data imply that in the evolution of parthenogenesis a new program has evolved to control the development of asexually produced embryos, whilst retaining the existing, sexual, developmental program. The patterns of modification of these developmental processes mirror the changes that we see in developmental processes between species, in that early acting pathways in development are less constrained, and evolve faster, than later ones. We suggest that the evolution of the novel asexual development pathway in aphids is not a simple modification of an ancestral system, but the evolution of two very different developmental mechanisms occurring within a single

  11. Genomic Encyclopedia of Fungi

    SciTech Connect

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  12. Integrating genomics and proteomics data to predict drug effects using binary linear programming.

    PubMed

    Ji, Zhiwei; Su, Jing; Liu, Chenglin; Wang, Hongyan; Huang, Deshuang; Zhou, Xiaobo

    2014-01-01

    The Library of Integrated Network-Based Cellular Signatures (LINCS) project aims to create a network-based understanding of biology by cataloging changes in gene expression and signal transduction that occur when cells are exposed to a variety of perturbations. It is helpful for understanding cell pathways and facilitating drug discovery. Here, we developed a novel approach to infer cell-specific pathways and identify a compound's effects using gene expression and phosphoproteomics data under treatments with different compounds. Gene expression data were employed to infer potential targets of compounds and create a generic pathway map. Binary linear programming (BLP) was then developed to optimize the generic pathway topology based on the mid-stage signaling response of phosphorylation. To demonstrate effectiveness of this approach, we built a generic pathway map for the MCF7 breast cancer cell line and inferred the cell-specific pathways by BLP. The first group of 11 compounds was utilized to optimize the generic pathways, and then 4 compounds were used to identify effects based on the inferred cell-specific pathways. Cross-validation indicated that the cell-specific pathways reliably predicted a compound's effects. Finally, we applied BLP to re-optimize the cell-specific pathways to predict the effects of 4 compounds (trichostatin A, MS-275, staurosporine, and digoxigenin) according to compound-induced topological alterations. Trichostatin A and MS-275 (both HDAC inhibitors) inhibited the downstream pathway of HDAC1 and caused cell growth arrest via activation of p53 and p21; the effects of digoxigenin were totally opposite. Staurosporine blocked the cell cycle via p53 and p21, but also promoted cell growth via activated HDAC1 and its downstream pathway. Our approach was also applied to the PC3 prostate cancer cell line, and the cross-validation analysis showed very good accuracy in predicting effects of 4 compounds. In summary, our computational model can be

  13. Genome Informatics

    PubMed Central

    Winslow, Raimond L.; Boguski, Mark S.

    2005-01-01

    This article reviews recent advances in genomics and informatics relevant to cardiovascular research. In particular, we review the status of (1) whole genome sequencing efforts in human, mouse, rat, zebrafish, and dog; (2) the development of data mining and analysis tools; (3) the launching of the National Heart, Lung, and Blood Institute Programs for Genomics Applications and Proteomics Initiative; (4) efforts to characterize the cardiac transcriptome and proteome; and (5) the current status of computational modeling of the cardiac myocyte. In each instance, we provide links to relevant sources of information on the World Wide Web and critical appraisals of the promises and the challenges of an expanding and diverse information landscape. PMID:12750305

  14. Phytozome Comparative Plant Genomics Portal

    SciTech Connect

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  15. Accuracy of genomic selection in barley breeding programs: a simulation study based on the real SNP data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The aim of this study was to compare the accuracy of genomic selection (i.e., selection based on genome-wide markers) to phenotypic selection through simulations based on real barley SNPs data (1325 SNPs x 863 breeding lines). We simulated 100 QTL at randomly selected SNPs, which were dropped from t...

  16. 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

  17. Genome Maps, a new generation genome browser

    PubMed Central

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-01-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  18. Genome Maps, a new generation genome browser.

    PubMed

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  19. Querying genomic databases

    SciTech Connect

    Baehr, A.; Hagstrom, R.; Joerg, D.; Overbeek, R.

    1991-09-01

    A natural-language interface has been developed that retrieves genomic information by using a simple subset of English. The interface spares the biologist from the task of learning database-specific query languages and computer programming. Currently, the interface deals with the E. coli genome. It can, however, be readily extended and shows promise as a means of easy access to other sequenced genomic databases as well.

  20. A genome-wide association study of malting quality across eight U.S. barley breeding programs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study leverages the breeding data of 1,862 breeding lines evaluated in 97 field trials for genome-wide association study of malting quality traits in barley. The breeding lines were six-row and two-row barley advanced breeding lines from eight barley breeding populations established at six pub...

  1. Microbial genome program report: Optical approaches for physical mapping and sequence assembly of the Deinococcus radiodurans chromosome

    SciTech Connect

    Schwartz, David C.

    1999-11-23

    Maps of genomic or cloned DNA are frequently constructed by analyzing the cleavage patterns produced by restriction enzymes. Restriction enzymes are remarkable reagents that faithfully cleave only at specific sequences of between 4 and 8 nucleotides, which vary according to the specific enzymes. Restriction enzymes are reliable, numerous, and easily obtainable and presently, there are approximately 250 different sequences represented among thousands of enzymes. Restriction maps characterize gene structure and even entire genomes. Furthermore, such maps provide a useful scaffold for the alignment and verification of sequence data. Restriction maps generated by computer and predicted from the sequence are aligned with the actual restriction map. Restriction enzyme action has traditionally been assayed by gel electrophoresis. This technique separates cleaved molecules on the basis of their nobilities under the influence of an applied electrical field, within a gel separation matrix (small fragments have a greater mobility than large ones). Although gel electrophoresis distinguishes different sized DNA fragments (known as a fingerprint), the original order of these fragments remains unknown. The subsequent task of determining the order of such fragments is a labor intensive task, especially when making restriction maps of whole genomes, and therefore despite its obvious utility to genome analysis, it is not widely used.

  2. Whole-Genome Sequences of Two Campylobacter coli Isolates from the Antimicrobial Resistance Monitoring Program in Colombia

    PubMed Central

    Bernal, Johan F.; Donado-Godoy, Pilar; Valencia, María Fernanda; León, Maribel; Gómez, Yolanda; Rodríguez, Fernando; Agarwala, Richa; Landsman, David

    2016-01-01

    Campylobacter coli, along with Campylobacter jejuni, is a major agent of gastroenteritis and acute enterocolitis in humans. We report the whole-genome sequences of two multidrug-resistance C. coli strains, isolated from the Colombian poultry chain. The isolates contain a variety of antimicrobial resistance genes for aminoglycosides, lincosamides, fluoroquinolones, and tetracycline. PMID:26988048

  3. Genotype by environment interaction and the use of unbalanced historical data for genomic selection in an international wheat breeding program

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic selection (GS) offers breeders the possibility of using historic data and unbalanced breeding trials to form training populations for predicting the performance of new lines. However, in using datasets that are unbalanced over time and space, there is increasing exposure to particular genoty...

  4. Assessing the impact of natural service bulls and genotype by environment interactions on genetic gain and inbreeding in organic dairy cattle genomic breeding programs.

    PubMed

    Yin, T; Wensch-Dorendorf, M; Simianer, H; Swalve, H H; König, S

    2014-06-01

    The objective of the present study was to compare genetic gain and inbreeding coefficients of dairy cattle in organic breeding program designs by applying stochastic simulations. Evaluated breeding strategies were: (i) selecting bulls from conventional breeding programs, and taking into account genotype by environment (G×E) interactions, (ii) selecting genotyped bulls within the organic environment for artificial insemination (AI) programs and (iii) selecting genotyped natural service bulls within organic herds. The simulated conventional population comprised 148 800 cows from 2976 herds with an average herd size of 50 cows per herd, and 1200 cows were assigned to 60 organic herds. In a young bull program, selection criteria of young bulls in both production systems (conventional and organic) were either 'conventional' estimated breeding values (EBV) or genomic estimated breeding values (GEBV) for two traits with low (h 2=0.05) and moderate heritability (h 2=0.30). GEBV were calculated for different accuracies (r mg), and G×E interactions were considered by modifying originally simulated true breeding values in the range from r g=0.5 to 1.0. For both traits (h 2=0.05 and 0.30) and r mg⩾0.8, genomic selection of bulls directly in the organic population and using selected bulls via AI revealed higher genetic gain than selecting young bulls in the larger conventional population based on EBV; also without the existence of G×E interactions. Only for pronounced G×E interactions (r g=0.5), and for highly accurate GEBV for natural service bulls (r mg>0.9), results suggests the use of genotyped organic natural service bulls instead of implementing an AI program. Inbreeding coefficients of selected bulls and their offspring were generally lower when basing selection decisions for young bulls on GEBV compared with selection strategies based on pedigree indices. PMID:24703184

  5. Program in Functional Genomics of Autoimmunity and Immunology of yhe University of Kentucky and the University of Alabama

    SciTech Connect

    Alan M Kaplan

    2012-10-12

    This grant will be used to augment the equipment infrastructure and core support at the University of Kentucky and the University of Alabama particularly in the areas of genomics/informatics, molecular analysis and cell separation. In addition, we will promote collaborative research interactions through scientific workshops and exchange of scientists, as well as joint exploration of the role of immune receptors as targets in autoimmunity and host defense, innate and adaptive immune responses, and mucosal immunity in host defense.

  6. Human Genome Project

    SciTech Connect

    Block, S.; Cornwall, J.; Dally, W.; Dyson, F.; Fortson, N.; Joyce, G.; Kimble, H. J.; Lewis, N.; Max, C.; Prince, T.; Schwitters, R.; Weinberger, P.; Woodin, W. H.

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  7. A Review on Genomics APIs

    PubMed Central

    Swaminathan, Rajeswari; Huang, Yungui; Moosavinasab, Soheil; Buckley, Ronald; Bartlett, Christopher W.; Lin, Simon M.

    2015-01-01

    The constant improvement and falling prices of whole human genome Next Generation Sequencing (NGS) has resulted in rapid adoption of genomic information at both clinics and research institutions. Considered together, the complexity of genomics data, due to its large volume and diversity along with the need for genomic data sharing, has resulted in the creation of Application Programming Interface (API) for secure, modular, interoperable access to genomic data from different applications, platforms, and even organizations. The Genomics APIs are a set of special protocols that assist software developers in dealing with multiple genomic data sources for building seamless, interoperable applications leading to the advancement of both genomic and clinical research. These APIs help define a standard for retrieval of genomic data from multiple sources as well as to better package genomic information for integration with Electronic Health Records. This review covers three currently available Genomics APIs: a) Google Genomics, b) SMART Genomics, and c) 23andMe. The functionalities, reference implementations (if available) and authentication protocols of each API are reviewed. A comparative analysis of the different features across the three APIs is provided in the Discussion section. Though Genomics APIs are still under active development and have yet to reach widespread adoption, they hold the promise to make building of complicated genomics applications easier with downstream constructive effects on healthcare. PMID:26702340

  8. MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

    PubMed Central

    Abby, Sophie S.; Néron, Bertrand; Ménager, Hervé; Touchon, Marie; Rocha, Eduardo P. C.

    2014-01-01

    Motivation Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a generic tool for this purpose. Results Macromolecular System Finder (MacSyFinder) provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway) including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include functional analogs, and the multiple uses of a same component by different systems. Models are used to search for molecular systems in complete genomes or in unstructured data like metagenomes. The components of the systems are searched by sequence similarity using Hidden Markov model (HMM) protein profiles. The assignment of hits to a given system is decided based on compliance with the content and organization of the system model. A graphical interface, MacSyView, facilitates the analysis of the results by showing overviews of component content and genomic context. To exemplify the use of MacSyFinder we built models to detect and class CRISPR-Cas systems following a previously established classification. We show that MacSyFinder allows to easily define an accurate “Cas-finder” using publicly available protein profiles. Availability and Implementation MacSyFinder is a standalone application implemented in Python. It requires Python 2.7, Hmmer and makeblastdb (version 2.2.28 or higher). It is freely available with its source code under a GPLv3 license at https://github.com/gem-pasteur/macsyfinder. It is compatible with all platforms supporting Python and Hmmer/makeblastdb. The “Cas-finder” (models and HMM profiles) is distributed as a compressed tarball archive as Supporting Information. PMID:25330359

  9. Genomic-Based Optimum Contribution in Conservation and Genetic Improvement Programs with Antagonistic Fitness and Productivity Traits

    PubMed Central

    Sánchez-Molano, Enrique; Pong-Wong, Ricardo; Banos, Georgios

    2016-01-01

    Animal selection for genetic improvement of productivity may lead to an increase in inbreeding through the use of techniques that enhance the reproductive capability of selected animals. Therefore, breeding strategies aim to balance maintaining genetic variability and acceptable fitness levels with increasing productivity. The present study demonstrates the effectiveness of genomic-based optimum contribution strategies at addressing this objective when fitness and productivity are genetically antagonistic traits. Strategies are evaluated in directional selection (increasing productivity) or conservation (maintaining fitness) scenarios. In the former case, substantial rates of genetic gain can be achieved while greatly constraining the rate of increase in inbreeding. Under a conservation approach, inbreeding depression can be effectively halted while also achieving a modest rate of genetic gain for productivity. Furthermore, the use of optimum contribution strategies when combined with a simple non-random mating scheme (minimum kinship method) showed an additional delay in the increase of inbreeding in the short term. In conclusion, genomic-based optimum contribution methods can be effectively used to control inbreeding and inbreeding depression, and still allow genetic gain for productivity traits even when fitness and productivity are antagonistically correlated. PMID:26941779

  10. GenomeVista

    SciTech Connect

    Poliakov, Alexander; Couronne, Olivier

    2002-11-04

    Aligning large vertebrate genomes that are structurally complex poses a variety of problems not encountered on smaller scales. Such genomes are rich in repetitive elements and contain multiple segmental duplications, which increases the difficulty of identifying true orthologous SNA segments in alignments. The sizes of the sequences make many alignment algorithms designed for comparing single proteins extremely inefficient when processing large genomic intervals. We integrated both local and global alignment tools and developed a suite of programs for automatically aligning large vertebrate genomes and identifying conserved non-coding regions in the alignments. Our method uses the BLAT local alignment program to find anchors on the base genome to identify regions of possible homology for a query sequence. These regions are postprocessed to find the best candidates which are then globally aligned using the AVID global alignment program. In the last step conserved non-coding segments are identified using VISTA. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. The GenomeVISTA software is a suite of Perl programs that is built on a MySQL database platform. The scheduler gets control data from the database, builds a queve of jobs, and dispatches them to a PC cluster for execution. The main program, running on each node of the cluster, processes individual sequences. A Perl library acts as an interface between the database and the above programs. The use of a separate library allows the programs to function independently of the database schema. The library also improves on the standard Perl MySQL database interfere package by providing auto-reconnect functionality and improved error handling.

  11. GenomeVista

    Energy Science and Technology Software Center (ESTSC)

    2002-11-04

    Aligning large vertebrate genomes that are structurally complex poses a variety of problems not encountered on smaller scales. Such genomes are rich in repetitive elements and contain multiple segmental duplications, which increases the difficulty of identifying true orthologous SNA segments in alignments. The sizes of the sequences make many alignment algorithms designed for comparing single proteins extremely inefficient when processing large genomic intervals. We integrated both local and global alignment tools and developed a suitemore » of programs for automatically aligning large vertebrate genomes and identifying conserved non-coding regions in the alignments. Our method uses the BLAT local alignment program to find anchors on the base genome to identify regions of possible homology for a query sequence. These regions are postprocessed to find the best candidates which are then globally aligned using the AVID global alignment program. In the last step conserved non-coding segments are identified using VISTA. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. The GenomeVISTA software is a suite of Perl programs that is built on a MySQL database platform. The scheduler gets control data from the database, builds a queve of jobs, and dispatches them to a PC cluster for execution. The main program, running on each node of the cluster, processes individual sequences. A Perl library acts as an interface between the database and the above programs. The use of a separate library allows the programs to function independently of the database schema. The library also improves on the standard Perl MySQL database interfere package by providing auto-reconnect functionality and improved error handling.« less

  12. Vita Genomics, Inc.

    PubMed

    Shih-Hsin Wu, Lawrence; Su, Chun-Lin; Chen, Ellson

    2007-06-01

    Vita Genomics, Inc., centered in Taiwan and China, aims to be a premier genomics-based biotechnological and biopharmaceutical company in the Asia-Pacific region. The company focuses on conducting pharmacogenomics research, in vitro diagnosis product development and specialty contract research services in both genomics and pharmacogenomics fields. We are now initiating a drug rescue program designed to resurrect drugs that have failed in the previous clinical trials owing to low efficacies. This program applies pharmacogenomics approaches using biomarkers to screen subsets of patients who may respond better or avoid adverse responses to the test drugs. Vita Genomics, Inc. has envisioned itself as an important player in the healthcare industry offering advanced molecular diagnostic products and services, revolutionizing thedrug-development process and providing pharmacogenomic solutions. PMID:17559355

  13. Programs.

    ERIC Educational Resources Information Center

    Community College Journal, 1996

    1996-01-01

    Includes a collection of eight short articles describing model community college programs. Discusses a literacy program, a mobile computer classroom, a support program for at-risk students, a timber-harvesting program, a multimedia presentation on successful women graduates, a career center, a collaboration with NASA, and an Israeli engineering…

  14. HIV-1 and M-PMV RNA Nuclear Export Elements Program Viral Genomes for Distinct Cytoplasmic Trafficking Behaviors.

    PubMed

    Pocock, Ginger M; Becker, Jordan T; Swanson, Chad M; Ahlquist, Paul; Sherer, Nathan M

    2016-04-01

    Retroviruses encode cis-acting RNA nuclear export elements that override nuclear retention of intron-containing viral mRNAs including the full-length, unspliced genomic RNAs (gRNAs) packaged into assembling virions. The HIV-1 Rev-response element (RRE) recruits the cellular nuclear export receptor CRM1 (also known as exportin-1/XPO1) using the viral protein Rev, while simple retroviruses encode constitutive transport elements (CTEs) that directly recruit components of the NXF1(Tap)/NXT1(p15) mRNA nuclear export machinery. How gRNA nuclear export is linked to trafficking machineries in the cytoplasm upstream of virus particle assembly is unknown. Here we used long-term (>24 h), multicolor live cell imaging to directly visualize HIV-1 gRNA nuclear export, translation, cytoplasmic trafficking, and virus particle production in single cells. We show that the HIV-1 RRE regulates unique, en masse, Rev- and CRM1-dependent "burst-like" transitions of mRNAs from the nucleus to flood the cytoplasm in a non-localized fashion. By contrast, the CTE derived from Mason-Pfizer monkey virus (M-PMV) links gRNAs to microtubules in the cytoplasm, driving them to cluster markedly to the centrosome that forms the pericentriolar core of the microtubule-organizing center (MTOC). Adding each export element to selected heterologous mRNAs was sufficient to confer each distinct export behavior, as was directing Rev/CRM1 or NXF1/NXT1 transport modules to mRNAs using a site-specific RNA tethering strategy. Moreover, multiple CTEs per transcript enhanced MTOC targeting, suggesting that a cooperative mechanism links NXF1/NXT1 to microtubules. Combined, these results reveal striking, unexpected features of retroviral gRNA nucleocytoplasmic transport and demonstrate roles for mRNA export elements that extend beyond nuclear pores to impact gRNA distribution in the cytoplasm. PMID:27070420

  15. HIV-1 and M-PMV RNA Nuclear Export Elements Program Viral Genomes for Distinct Cytoplasmic Trafficking Behaviors

    PubMed Central

    Pocock, Ginger M.; Becker, Jordan T.; Swanson, Chad M.; Ahlquist, Paul; Sherer, Nathan M.

    2016-01-01

    Retroviruses encode cis-acting RNA nuclear export elements that override nuclear retention of intron-containing viral mRNAs including the full-length, unspliced genomic RNAs (gRNAs) packaged into assembling virions. The HIV-1 Rev-response element (RRE) recruits the cellular nuclear export receptor CRM1 (also known as exportin-1/XPO1) using the viral protein Rev, while simple retroviruses encode constitutive transport elements (CTEs) that directly recruit components of the NXF1(Tap)/NXT1(p15) mRNA nuclear export machinery. How gRNA nuclear export is linked to trafficking machineries in the cytoplasm upstream of virus particle assembly is unknown. Here we used long-term (>24 h), multicolor live cell imaging to directly visualize HIV-1 gRNA nuclear export, translation, cytoplasmic trafficking, and virus particle production in single cells. We show that the HIV-1 RRE regulates unique, en masse, Rev- and CRM1-dependent “burst-like” transitions of mRNAs from the nucleus to flood the cytoplasm in a non-localized fashion. By contrast, the CTE derived from Mason-Pfizer monkey virus (M-PMV) links gRNAs to microtubules in the cytoplasm, driving them to cluster markedly to the centrosome that forms the pericentriolar core of the microtubule-organizing center (MTOC). Adding each export element to selected heterologous mRNAs was sufficient to confer each distinct export behavior, as was directing Rev/CRM1 or NXF1/NXT1 transport modules to mRNAs using a site-specific RNA tethering strategy. Moreover, multiple CTEs per transcript enhanced MTOC targeting, suggesting that a cooperative mechanism links NXF1/NXT1 to microtubules. Combined, these results reveal striking, unexpected features of retroviral gRNA nucleocytoplasmic transport and demonstrate roles for mRNA export elements that extend beyond nuclear pores to impact gRNA distribution in the cytoplasm. PMID:27070420

  16. Germ Line Transcripts Are Processed by a Dicer-Like Protein That Is Essential for Developmentally Programmed Genome Rearrangements of Tetrahymena thermophila

    PubMed Central

    Malone, Colin D.; Anderson, Alissa M.; Motl, Jason A.; Rexer, Charles H.; Chalker, Douglas L.

    2005-01-01

    Abundant ∼28-nucleotide RNAs that are thought to direct histone H3 lysine 9 (H3K9) methylation and promote the elimination of nearly 15 Mbp of DNA from the developing somatic genome are generated during Tetrahymena thermophila conjugation. To identify the protein(s) that generates these small RNAs, we studied three Dicer-related genes encoded within the Tetrahymena genome, two that contain both RNase III and RNA helicase motifs, Dicer 1 (DCR1) and DCR2, and a third that lacks the helicase domain, Dicer-like 1 (DCL1). DCL1 is expressed upon the initiation of conjugation, and the protein localizes to meiotic micronuclei when bidirectional germ line transcription occurs and small RNAs begin to accumulate. Cells in which we disrupted the DCL1 gene (ΔDCL1) grew normally and initiated conjugation as wild-type cells but arrested near the end of development and eventually died, unable to resume vegetative growth. These ΔDCL1 cells failed to generate the abundant small RNAs but instead accumulated germ line-limited transcripts. Together, our findings demonstrate that these transcripts are the precursors of the small RNAs and that DCL1 performs RNA processing within the micronucleus. Postconjugation ΔDCL1 cells die without eliminating the germ line-limited DNA sequences from their newly formed somatic macronuclei, a result that shows that this Dicer-related gene is required for programmed DNA rearrangements. Surprisingly, ΔDCL1 cells were not deficient in overall H3K9 methylation, but this modification was not enriched on germ line-limited sequences as it is in wild-type cells, which clearly demonstrates that these small RNAs are essential for its targeting to specific loci. PMID:16199890

  17. Prenatal stress-induced programming of genome-wide promoter DNA methylation in 5-HTT-deficient mice

    PubMed Central

    Schraut, K G; Jakob, S B; Weidner, M T; Schmitt, A G; Scholz, C J; Strekalova, T; El Hajj, N; Eijssen, L M T; Domschke, K; Reif, A; Haaf, T; Ortega, G; Steinbusch, H W M; Lesch, K P; Van den Hove, D L

    2014-01-01

    The serotonin transporter gene (5-HTT/SLC6A4)-linked polymorphic region has been suggested to have a modulatory role in mediating effects of early-life stress exposure on psychopathology rendering carriers of the low-expression short (s)-variant more vulnerable to environmental adversity in later life. The underlying molecular mechanisms of this gene-by-environment interaction are not well understood, but epigenetic regulation including differential DNA methylation has been postulated to have a critical role. Recently, we used a maternal restraint stress paradigm of prenatal stress (PS) in 5-HTT-deficient mice and showed that the effects on behavior and gene expression were particularly marked in the hippocampus of female 5-Htt+/− offspring. Here, we examined to which extent these effects are mediated by differential methylation of DNA. For this purpose, we performed a genome-wide hippocampal DNA methylation screening using methylated-DNA immunoprecipitation (MeDIP) on Affymetrix GeneChip Mouse Promoter 1.0 R arrays. Using hippocampal DNA from the same mice as assessed before enabled us to correlate gene-specific DNA methylation, mRNA expression and behavior. We found that 5-Htt genotype, PS and their interaction differentially affected the DNA methylation signature of numerous genes, a subset of which showed overlap with the expression profiles of the corresponding transcripts. For example, a differentially methylated region in the gene encoding myelin basic protein (Mbp) was associated with its expression in a 5-Htt-, PS- and 5-Htt × PS-dependent manner. Subsequent fine-mapping of this Mbp locus linked the methylation status of two specific CpG sites to Mbp expression and anxiety-related behavior. In conclusion, hippocampal DNA methylation patterns and expression profiles of female prenatally stressed 5-Htt+/− mice suggest that distinct molecular mechanisms, some of which are promoter methylation-dependent, contribute to the behavioral effects of the 5-Htt

  18. From genes to genome biology

    SciTech Connect

    Pennisi, E.

    1996-06-21

    This article describes a change in the approach to mapping genomes, from looking at one gene at a time, to other approaches. Strategies include everything from lab techniques to computer programs designed to analyze whole batches of genes at once. Also included is a update on the work on the human genome.

  19. Transgenic system for conditional induction and rescue of chronic myocardial hibernation provides insights into genomic programs of hibernation.

    PubMed

    May, Dalit; Gilon, Dan; Djonov, Valentin; Itin, Ahuva; Lazarus, Alon; Gordon, Oren; Rosenberger, Christian; Keshet, Eli

    2008-01-01

    A key energy-saving adaptation to chronic hypoxia that enables cardiomyocytes to withstand severe ischemic insults is hibernation, i.e., a reversible arrest of contractile function. Whereas hibernating cardiomyocytes represent the critical reserve of dysfunctional cells that can be potentially rescued, a lack of a suitable animal model has hampered insights on this medically important condition. We developed a transgenic mouse system for conditional induction of long-term hibernation and a system to rescue hibernating cardiomyocytes at will. Via myocardium-specific induction (and, in turn, deinduction) of a VEGF-sequestering soluble receptor, we show that VEGF is indispensable for adjusting the coronary vasculature to match increased oxygen consumption and exploit this finding to generate a hypoperfused heart. Importantly, ensuing ischemia is tunable to a level at which large cohorts of cardiomyocytes are driven to enter a hibernation mode, without cardiac cell death. Relieving the VEGF blockade even months later resulted in rapid revascularization and full recovery of contractile function. Furthermore, we show that left ventricular remodeling associated with hibernation is also fully reversible. The unique opportunity to uncouple hibernation from other ischemic heart phenotypes (e.g., infarction) was used to determine the genetic program of hibernation; uncovering hypoxia-inducible factor target genes associated with metabolic adjustments and induced expression of several cardioprotective genes. Autophagy, specifically self-digestion of mitochondria, was identified as a key prosurvival mechanism in hibernating cardiomyocytes. This system may lend itself for examining the potential utility of treatments to rescue dysfunctional cardiomyocytes and reverse maladaptive remodeling. PMID:18162550

  20. Genomic Resources for Cancer Epidemiology

    Cancer.gov

    This page provides links to research resources, complied by the Epidemiology and Genomics Research Program, that may be of interest to genetic epidemiologists conducting cancer research, but is not exhaustive.

  1. Collaborators | Office of Cancer Genomics

    Cancer.gov

    The TARGET initiative is jointly managed within the National Cancer Institute (NCI) by the Office of Cancer Genomics (OCG)Opens in a New Tab and the Cancer Therapy Evaluation Program (CTEP)Opens in a New Tab.

  2. Genome walking.

    PubMed

    Shapter, Frances M; Waters, Daniel L E

    2014-01-01

    Genome walking is a method for determining the DNA sequence of unknown genomic regions flanking a region of known DNA sequence. The Genome walking has the potential to capture 6-7 kb of sequence in a single round. Ideal for identifying gene promoter regions where only the coding region. Genome walking also has significant utility for capturing homologous genes in new species when there are areas in the target gene with strong sequence conservation to the characterized species. The increasing use of next-generation sequencing technologies will see the principles of genome walking adapted to in silico methods. However, for smaller projects, PCR-based genome walking will remain an efficient method of characterizing unknown flanking sequence. PMID:24243201

  3. Prophage Genomics

    PubMed Central

    Canchaya, Carlos; Proux, Caroline; Fournous, Ghislain; Bruttin, Anne; Brüssow, Harald

    2003-01-01

    The majority of the bacterial genome sequences deposited in the National Center for Biotechnology Information database contain prophage sequences. Analysis of the prophages suggested that after being integrated into bacterial genomes, they undergo a complex decay process consisting of inactivating point mutations, genome rearrangements, modular exchanges, invasion by further mobile DNA elements, and massive DNA deletion. We review the technical difficulties in defining such altered prophage sequences in bacterial genomes and discuss theoretical frameworks for the phage-bacterium interaction at the genomic level. The published genome sequences from three groups of eubacteria (low- and high-G+C gram-positive bacteria and γ-proteobacteria) were screened for prophage sequences. The prophages from Streptococcus pyogenes served as test case for theoretical predictions of the role of prophages in the evolution of pathogenic bacteria. The genomes from further human, animal, and plant pathogens, as well as commensal and free-living bacteria, were included in the analysis to see whether the same principles of prophage genomics apply for bacteria living in different ecological niches and coming from distinct phylogenetical affinities. The effect of selection pressure on the host bacterium is apparently an important force shaping the prophage genomes in low-G+C gram-positive bacteria and γ-proteobacteria. PMID:12794192

  4. A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence

    PubMed Central

    Theiss, Juliane Marie; Günther, Thomas; Alawi, Malik; Neumann, Friederike; Fischer, Nicole; Grundhoff, Adam

    2015-01-01

    Merkel cell polyomavirus (MCPyV) is considered the etiological agent of Merkel cell carcinoma and persists asymptomatically in the majority of its healthy hosts. Largely due to the lack of appropriate model systems, the mechanisms of viral replication and MCPyV persistence remain poorly understood. Using a semi-permissive replication system, we here report a comprehensive analysis of the role of the MCPyV-encoded microRNA (miRNA) mcv-miR-M1 during short and long-term replication of authentic MCPyV episomes. We demonstrate that cells harboring intact episomes express high levels of the viral miRNA, and that expression of mcv-miR-M1 limits DNA replication. Furthermore, we present RACE, RNA-seq and ChIP-seq studies which allow insight in the viral transcription program and mechanisms of miRNA expression. While our data suggest that mcv-miR-M1 can be expressed from canonical late strand transcripts, we also present evidence for the existence of an independent miRNA promoter that is embedded within early strand coding sequences. We also report that MCPyV genomes can establish episomal persistence in a small number of cells for several months, a time period during which viral DNA as well as LT-Ag and viral miRNA expression can be detected via western blotting, FISH, qPCR and southern blot analyses. Strikingly, despite enhanced replication in short term DNA replication assays, a mutant unable to express the viral miRNA was severely limited in its ability to establish long-term persistence. Our data suggest that MCPyV may have evolved strategies to enter a non- or low level vegetative stage of infection which could aid the virus in establishing and maintaining a lifelong persistence. PMID:26218535

  5. Glucose metabolism ontogenesis in rainbow trout (Oncorhynchus mykiss) in the light of the recently sequenced genome: new tools for intermediary metabolism programming.

    PubMed

    Marandel, Lucie; Véron, Vincent; Surget, Anne; Plagnes-Juan, Élisabeth; Panserat, Stéphane

    2016-03-01

    The rainbow trout (Oncorhynchus mykiss), a carnivorous fish species, displays a 'glucose-intolerant' phenotype when fed a high-carbohydrate diet. The importance of carbohydrate metabolism during embryogenesis and the timing of establishing this later phenotype are currently unclear. In addition, the mechanisms underlying the poor ability of carnivorous fish to use dietary carbohydrates as a major energy substrate are not well understood. It has recently been shown in trout that duplicated genes involved in glucose metabolism may participate in establishing the glucose-intolerant phenotype. The aim of this study was therefore to provide new understanding of glucose metabolism during ontogenesis and nutritional transition, taking into consideration the complexity of the trout genome. Trout were sampled at several stages of development from fertilization to hatching, and alevins were then fed a non-carbohydrate or a high-carbohydrate diet during first feeding. mRNA levels of all glucose metabolism-related genes increased in embryos during the setting up of the primitive liver. After the first meal, genes rapidly displayed expression patterns equivalent to those observed in the livers of juveniles. g6pcb2.a (a glucose 6-phosphatase-encoding gene) was up-regulated in alevins fed a high-carbohydrate diet, mimicking the expression pattern of gck genes. The g6pcb2.a gene may contribute to the non-inhibition of the last step of gluconeogenesis and thus to establishing the glucose-intolerant phenotype in trout fed a high-carbohydrate diet as early as first feeding. This information is crucial for nutritional programming investigations as it suggests that first feeding would be too late to programme glucose metabolism in the long term. PMID:26747908

  6. A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence.

    PubMed

    Theiss, Juliane Marie; Günther, Thomas; Alawi, Malik; Neumann, Friederike; Tessmer, Uwe; Fischer, Nicole; Grundhoff, Adam

    2015-07-01

    Merkel cell polyomavirus (MCPyV) is considered the etiological agent of Merkel cell carcinoma and persists asymptomatically in the majority of its healthy hosts. Largely due to the lack of appropriate model systems, the mechanisms of viral replication and MCPyV persistence remain poorly understood. Using a semi-permissive replication system, we here report a comprehensive analysis of the role of the MCPyV-encoded microRNA (miRNA) mcv-miR-M1 during short and long-term replication of authentic MCPyV episomes. We demonstrate that cells harboring intact episomes express high levels of the viral miRNA, and that expression of mcv-miR-M1 limits DNA replication. Furthermore, we present RACE, RNA-seq and ChIP-seq studies which allow insight in the viral transcription program and mechanisms of miRNA expression. While our data suggest that mcv-miR-M1 can be expressed from canonical late strand transcripts, we also present evidence for the existence of an independent miRNA promoter that is embedded within early strand coding sequences. We also report that MCPyV genomes can establish episomal persistence in a small number of cells for several months, a time period during which viral DNA as well as LT-Ag and viral miRNA expression can be detected via western blotting, FISH, qPCR and southern blot analyses. Strikingly, despite enhanced replication in short term DNA replication assays, a mutant unable to express the viral miRNA was severely limited in its ability to establish long-term persistence. Our data suggest that MCPyV may have evolved strategies to enter a non- or low level vegetative stage of infection which could aid the virus in establishing and maintaining a lifelong persistence. PMID:26218535

  7. Molluscan Evolutionary Genomics

    SciTech Connect

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  8. Aquaculture Genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genomics chapter covers the basics of genome mapping and sequencing and the current status of several relevant species. The chapter briefly describes the development and use of (cDNA, BAC, etc.) libraries for mapping and obtaining specific sequence information. Other topics include comparative ...

  9. Fungal genome sequencing: basic biology to biotechnology.

    PubMed

    Sharma, Krishna Kant

    2016-08-01

    The genome sequences provide a first glimpse into the genomic basis of the biological diversity of filamentous fungi and yeast. The genome sequence of the budding yeast, Saccharomyces cerevisiae, with a small genome size, unicellular growth, and rich history of genetic and molecular analyses was a milestone of early genomics in the 1990s. The subsequent completion of fission yeast, Schizosaccharomyces pombe and genetic model, Neurospora crassa initiated a revolution in the genomics of the fungal kingdom. In due course of time, a substantial number of fungal genomes have been sequenced and publicly released, representing the widest sampling of genomes from any eukaryotic kingdom. An ambitious genome-sequencing program provides a wealth of data on metabolic diversity within the fungal kingdom, thereby enhancing research into medical science, agriculture science, ecology, bioremediation, bioenergy, and the biotechnology industry. Fungal genomics have higher potential to positively affect human health, environmental health, and the planet's stored energy. With a significant increase in sequenced fungal genomes, the known diversity of genes encoding organic acids, antibiotics, enzymes, and their pathways has increased exponentially. Currently, over a hundred fungal genome sequences are publicly available; however, no inclusive review has been published. This review is an initiative to address the significance of the fungal genome-sequencing program and provides the road map for basic and applied research. PMID:25721271

  10. Antarctic Genomics

    PubMed Central

    Clarke, Andrew; Cockell, Charles S.; Convey, Peter; Detrich III, H. William; Fraser, Keiron P. P.; Johnston, Ian A.; Methe, Barbara A.; Murray, Alison E.; Peck, Lloyd S.; Römisch, Karin; Rogers, Alex D.

    2004-01-01

    With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies. PMID:18629155

  11. Genome Science: A Video Tour of the Washington University Genome Sequencing Center for High School and Undergraduate Students

    ERIC Educational Resources Information Center

    Flowers, Susan K.; Easter, Carla; Holmes, Andrea; Cohen, Brian; Bednarski, April E.; Mardis, Elaine R.; Wilson, Richard K.; Elgin, Sarah C. R.

    2005-01-01

    Sequencing of the human genome has ushered in a new era of biology. The technologies developed to facilitate the sequencing of the human genome are now being applied to the sequencing of other genomes. In 2004, a partnership was formed between Washington University School of Medicine Genome Sequencing Center's Outreach Program and Washington…

  12. Genomic Testing

    MedlinePlus

    ... Working Group Independent Web site Informing the effective integration of genomics into health practice—Lynch syndrome ACCE Model for Evaluating Genetic Tests Recommendations by the EGAPP Working Group Top of ... ...

  13. The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects.

    PubMed

    Papanicolaou, Alexie

    2016-01-01

    Many research programs on non-model species biology have been empowered by genomics. In turn, genomics is underpinned by a reference sequence and ancillary information created by so-called "genome projects". The most reliable genome projects are the ones created as part of an active research program and designed to address specific questions but their life extends past publication. In this opinion paper I outline four key insights that have facilitated maintaining genomic communities: the key role of computational capability, the iterative process of building genomic resources, the value of community participation and the importance of manual curation. Taken together, these ideas can and do ensure the longevity of genome projects and the growing non-model species community can use them to focus a discussion with regards to its future genomic infrastructure. PMID:27006757

  14. The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects

    PubMed Central

    Papanicolaou, Alexie

    2016-01-01

    Many research programs on non-model species biology have been empowered by genomics. In turn, genomics is underpinned by a reference sequence and ancillary information created by so-called “genome projects”. The most reliable genome projects are the ones created as part of an active research program and designed to address specific questions but their life extends past publication. In this opinion paper I outline four key insights that have facilitated maintaining genomic communities: the key role of computational capability, the iterative process of building genomic resources, the value of community participation and the importance of manual curation. Taken together, these ideas can and do ensure the longevity of genome projects and the growing non-model species community can use them to focus a discussion with regards to its future genomic infrastructure. PMID:27006757

  15. 78 FR 20933 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-08

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel Loan Repayment Program... applications. Place: National Human Genome Research Institute, Room 3055, 5635 Fishers Lane, Rockville,...

  16. 78 FR 68856 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-15

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... Review Officer, Scientific Review Branch, National Human Genome Research Institute, National Institutes... of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  17. Breeding nursery tissue collection for possible genomic analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenotyping is considered a major bottleneck in breeding programs. With new genomic technologies, high throughput genotype schemes are constantly being developed. However, every genomic technology requires phenotypic data to inform prediction models generated from the technology. Forage breeders con...

  18. Genotypes are useful for more than genomic evaluation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New services that provide pedigree discovery, breed composition, mating programs, genomic inbreeding, fertility defects, and inheritance tracking all are possible from low cost genotyping, in addition to genomic evaluation. Genetic markers let breeders select among sibs before their phenotypes becam...

  19. Endometrial and acute myeloid leukemia cancer genomes characterized

    Cancer.gov

    Two studies from The Cancer Genome Atlas (TCGA) program reveal details about the genomic landscapes of acute myeloid leukemia (AML) and endometrial cancer. Both provide new insights into the molecular underpinnings of these cancers with the potential to i

  20. N-Myc regulates a widespread euchromatic program in the human genome partially independent of its role as a classical transcription factor

    PubMed Central

    Cotterman, Rebecca; Jin, Victor X.; Krig, Sheryl R.; Lemen, Jessica M.; Wey, Alice; Farnham, Peggy J.; Knoepfler, Paul S.

    2009-01-01

    Myc proteins have long been modeled to operate strictly as classical gene specific transcription factors, however we find that N-Myc has a robust role in the human genome in regulating global cellular euchromatin including that of intergenic regions. Strikingly, 90–95% of the total genomic euchromatic marks histone H3 acetylated at lysine 9 and methylated at lysine 4 is N-Myc dependent. However, Myc regulation of transcription, even of genes it directly binds and at which it is required for maintenance of active chromatin, is generally weak. Thus, Myc has a much more potent ability to regulate large domains of euchromatin than to influence transcription of individual genes. Overall, Myc regulation of chromatin in the human genome includes both specific genes, but also expansive genomic domains that invoke functions independent of a classical transcription factor. These findings support a new dual model for Myc chromatin function with important implications for the role of Myc in cancer and stem cell biology, including that of induced pluripotent stem (iPS) cells. PMID:19047142

  1. Genome databases

    SciTech Connect

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  2. Genome Improvement at JGI-HAGSC

    SciTech Connect

    Grimwood, Jane; Schmutz, Jeremy J.; Myers, Richard M.

    2012-03-03

    Since the completion of the sequencing of the human genome, the Joint Genome Institute (JGI) has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence. For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes.

  3. Fungal Genomics for Energy and Environment

    SciTech Connect

    Grigoriev, Igor V.

    2013-03-11

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Sequencing Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 200 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  4. Listeria Genomics

    NASA Astrophysics Data System (ADS)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  5. Genome Radio Project: Quarterly report

    SciTech Connect

    1997-08-01

    The process of conducting background research for the programs of the Genome Radio Project is continuing. The most developed of the program ``backgrounders`` have been reviewed by series and program advisors from various fields. Preliminary and background interviews have been conducted with dozens of potential program participants and advisors. Structurally, efforts are being directed toward developing and formalizing the project and series advisor relationships so that the best use can be made of those experts who have offered to assist the project in its presentation of program content. The library of research materials has been expanded considerably, creating a useful resource library for the producers.

  6. Whither genomics?

    PubMed Central

    Murray, Andrew W

    2000-01-01

    The flood of data from genome-wide analysis is transforming biology. We need to develop new, interdisciplinary approaches to convert these data into information about the components and structures of individual biological pathways and to use the resulting information to yield knowledge about general principles that explain the functions and evolution of life. PMID:11104516

  7. Single genome amplification of proviral HIV-1 DNA from dried blood spot specimens collected during early infant screening programs in Lusaka, Zambia

    PubMed Central

    Seu, Lillian; Mwape, Innocent; Guffey, M. Bradford

    2014-01-01

    The ability to evaluate individual HIV-1 virions from the quasispecies of vertically infected infants was evaluated in a field setting at the Centre for Infectious Disease Research in Zambia. Infant heel-prick blood specimens were spotted onto dried blood spot (DBS) filter paper cards at government health clinics. Nucleic acid was extracted and used as a template for HIV-1 proviral DNA detection by a commercial Amplicor HIV-1 PCR test (Roche, version 1.5). On samples that tested positive by commercial diagnostic assay, amplification of DNA was performed using an in-house assay of the 5′ and 3′ region of the HIV-1 genome. Additionally, fragments covering 1200 nucleotides within pol (full length protease and partial reverse transcriptase) and 1400 nucleotides within env (variable 1-variable 5 region) were further analyzed by single genome amplification (SGA). In summary, we have demonstrated an in-house assay for amplifying the 5′ and 3′ proviral HIV-1 DNA as well as pol and env proviral DNA fragments from DBS cards collected and analyzed entirely in Zambia. In conclusion, this study shows the feasibility of utilizing DBS cards to amplify the whole proviral HIV-1 genome as well as perform SGA on key HIV-1 genes. PMID:24667303

  8. The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development

    PubMed Central

    Chen, Xiao; Bracht, John R.; Goldman, Aaron David; Dolzhenko, Egor; Clay, Derek M.; Swart, Estienne C.; Perlman, David H.; Doak, Thomas G.; Stuart, Andrew; Amemiya, Chris T.; Sebra, Robert P.; Landweber, Laura F.

    2014-01-01

    SUMMARY Programmed DNA rearrangements in the single-celled eukaryote Oxytricha trifallax completely rewire its germline into a somatic nucleus during development. This elaborate, RNA-mediated pathway eliminates noncoding DNA sequences that interrupt gene loci and reorganizes the remaining fragments by inversions and permutations to produce functional genes. Here, we report the Oxytricha germline genome and compare it to the somatic genome to present a global view of its massive scale of genome rearrangements. The remarkably encrypted genome architecture contains >3,500 scrambled genes, as well as >800 predicted germline-limited genes expressed, and some posttranslationally modified, during genome rearrangements. Gene segments for different somatic loci often interweave with each other. Single gene segments can contribute to multiple, distinct somatic loci. Terminal precursor segments from neighboring somatic loci map extremely close to each other, often overlapping. This genome assembly provides a draft of a scrambled genome and a powerful model for studies of genome rearrangement. PMID:25171416

  9. The Human Genome Initiative of the Department of Energy

    SciTech Connect

    1988-01-01

    The structural characterization of genes and elucidation of their encoded functions have become a cornerstone of modern health research, biology and biotechnology. A genome program is an organized effort to locate and identify the functions of all the genes of an organism. Beginning with the DOE-sponsored, 1986 human genome workshop at Santa Fe, the value of broadly organized efforts supporting total genome characterization became a subject of intensive study. There is now national recognition that benefits will rapidly accrue from an effective scientific infrastructure for total genome research. In the US genome research is now receiving dedicated funds. Several other nations are implementing genome programs. Supportive infrastructure is being improved through both national and international cooperation. The Human Genome Initiative of the Department of Energy (DOE) is a focused program of Resource and Technology Development, with objectives of speeding and bringing economies to the national human genome effort. This report relates the origins and progress of the Initiative. 34 refs.

  10. The Human Genome Initiative of the Department of Energy

    DOE R&D Accomplishments Database

    1988-01-01

    The structural characterization of genes and elucidation of their encoded functions have become a cornerstone of modern health research, biology and biotechnology. A genome program is an organized effort to locate and identify the functions of all the genes of an organism. Beginning with the DOE-sponsored, 1986 human genome workshop at Santa Fe, the value of broadly organized efforts supporting total genome characterization became a subject of intensive study. There is now national recognition that benefits will rapidly accrue from an effective scientific infrastructure for total genome research. In the US genome research is now receiving dedicated funds. Several other nations are implementing genome programs. Supportive infrastructure is being improved through both national and international cooperation. The Human Genome Initiative of the Department of Energy (DOE) is a focused program of Resource and Technology Development, with objectives of speeding and bringing economies to the national human genome effort. This report relates the origins and progress of the Initiative.

  11. Fueling the Future with Fungal Genomes

    SciTech Connect

    Grigoriev, Igor V.

    2014-10-27

    Genomes of fungi relevant to energy and environment are in focus of the JGI Fungal Genomic Program. One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts and pathogens) and biorefinery processes (cellulose degradation and sugar fermentation) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Science Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 400 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics will lead to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such ‘parts’ suggested by comparative genomics and functional analysis in these areas are presented here.

  12. Reannotation of Shewanella oneidensis genome.

    PubMed

    Daraselia, N; Dernovoy, D; Tian, Y; Borodovsky, M; Tatusov, R; Tatusova, T

    2003-01-01

    As more and more complete bacterial genome sequences become available, the genome annotation of previously sequenced genomes may become quickly outdated. This is primarily due to the discovery and functional characterization of new genes. We have reannotated the recently published genome of Shewanella oneidensis with the following results: 51 new genes have been identified, and functional annotation has been added to the 97 genes, including 15 new and 82 existing ones with previously unassigned function. The identification of new genes was achieved by predicting the protein coding regions using the HMM-based program GeneMark.hmm. Subsequent comparison of the predicted gene products to the non-redundant protein database using BLAST and the COG (Clusters of Orthologous Groups) database using COGNITOR provided for the functional annotation. PMID:14506846

  13. The Human Genome Project: Past, Present, and Future

    NASA Astrophysics Data System (ADS)

    Watson, James D.

    1990-04-01

    This article presents a short discussion of the development of the human genome program in the United States, a summary of the current status of the organization and administration of the National Institutes of Health component of the program, and some prospects for the future directions of the program and the applications of genome information.

  14. Aspergillus flavus Genomics for Controlling Aflatoxin Contamination

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The main objectives of the Aspergillus flavus genomics program are to identify genes and regulatory components involved in aflatoxin biosynthesis for solving aflatoxin contamination in agricultural crops. A. flavus Expressed Sequence Tags (EST), microarray and whole genome sequencing have been achi...

  15. Can genomics boost productivity of orphan crops?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Advances in genomics over the past 20 years have enhanced the precision and efficiency of breeding programs in many temperate cereal crops. One of the first applications of genomics-assisted breeding has been the introgression of loci for resistance to biotic stresses or major quantitative trait loc...

  16. Citrus Genomics

    PubMed Central

    Talon, Manuel; Gmitter Jr., Fred G.

    2008-01-01

    Citrus is one of the most widespread fruit crops globally, with great economic and health value. It is among the most difficult plants to improve through traditional breeding approaches. Currently, there is risk of devastation by diseases threatening to limit production and future availability to the human population. As technologies rapidly advance in genomic science, they are quickly adapted to address the biological challenges of the citrus plant system and the world's industries. The historical developments of linkage mapping, markers and breeding, EST projects, physical mapping, an international citrus genome sequencing project, and critical functional analysis are described. Despite the challenges of working with citrus, there has been substantial progress. Citrus researchers engaged in international collaborations provide optimism about future productivity and contributions to the benefit of citrus industries worldwide and to the human population who can rely on future widespread availability of this health-promoting and aesthetically pleasing fruit crop. PMID:18509486

  17. Ancient genomics

    PubMed Central

    Der Sarkissian, Clio; Allentoft, Morten E.; Ávila-Arcos, María C.; Barnett, Ross; Campos, Paula F.; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J.; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D.; Moreno-Mayar, J. Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M. Thomas P.; Willerslev, Eske; Orlando, Ludovic

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past. PMID:25487338

  18. Genomic Imprinting

    PubMed Central

    Bajrami, Emirjeta; Spiroski, Mirko

    2016-01-01

    BACKGROUND: Genomic imprinting is the inheritance out of Mendelian borders. Many of inherited diseases and human development violates Mendelian law of inheritance, this way of inheriting is studied by epigenetics. AIM: The aim of this review is to analyze current opinions and options regarding to this way of inheriting. RESULTS: Epigenetics shows that gene expression undergoes changes more complex than modifications in the DNA sequence; it includes the environmental influence on the gametes before conception. Humans inherit two alleles from mother and father, both are functional for the majority of the genes, but sometimes one is turned off or “stamped” and doesn’t show in offspring, that gene is imprinted. Imprinting means that that gene is silenced, and gene from other parent is expressed. The mechanisms for imprinting are still incompletely defined, but they involve epigenetic modifications that are erased and then reset during the creation of eggs and sperm. Genomic imprinting is a process of silencing genes through DNA methylation. The repressed allele is methylated, while the active allele is unmethylated. The most well-known conditions include Prader-Willi syndrome, and Angelman syndrome. Both of these syndromes can be caused by imprinting or other errors involving genes on the long arm of chromosome 15. CONCLUSIONS: Genomic imprinting and other epigenetic mechanisms such as environment is shown that plays role in offspring neurodevelopment and autism spectrum disorder. PMID:27275355

  19. The human genome project and international health

    SciTech Connect

    Watson, J.D.; Cook-Deegan, R.M. )

    1990-06-27

    The human genome project is designed to provide common resources for the study of human genetics, and to assist biomedical researchers in their assault on disease. The main benefit will be to provide several kinds of maps of the human genome, and those of other organisms, to permit rapid isolation of genes for further study about DNA structure and function. This article describes genome research programs in developed and developing countries, and the international efforts that have contributed to genome research programs. For example, the large-scale collaborations to study Duchenne's muscular dystrophy, Huntington's disease, Alzheimer's disease, cystic fibrosis involve collaborators from many nations and families spread throughout the world. In the USA, the US Department of Energy was first to start a dedicated genome research program in 1987. Since then, another major government program has begun at the National Center for Human Genome Research of the National Institutes of Health. Italy, China, Australia, France, Canada, and Japan have genome research programs also.

  20. Human genome protein function database.

    PubMed Central

    Sorenson, D. K.

    1991-01-01

    A database which focuses on the normal functions of the currently-known protein products of the Human Genome was constructed. Information is stored as text, figures, tables, and diagrams. The program contains built-in functions to modify, update, categorize, hypertext, search, create reports, and establish links to other databases. The semi-automated categorization feature of the database program was used to classify these proteins in terms of biomedical functions. PMID:1807638

  1. The development of genomics applied to dairy breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic selection (GS) has profoundly changed dairy cattle breeding in the last decade and can be defined as the use of genomic breeding values (GEBV) in selection programs. The GEBV is the sum of the effects of dense DNA markers across the whole genome, capturing all the quantitative trait loci (QT...

  2. Genomic selection in wheat using genotyping-by-sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic selection (GS) is a promising approach to accelerate gain in plant breeding programs. In GS, genome-wide molecular markers are used to predict total breeding values and make selections of individuals or breeding lines prior to phenotyping. One premise of applying GS is that low-cost genome...

  3. BACFinder: genomic localisation of large insert genomic clones based on restriction fingerprinting

    PubMed Central

    Crowe, Mark L.; Rana, Debashis; Fraser, Fiona; Bancroft, Ian; Trick, Martin

    2002-01-01

    We have developed software that allows the prediction of the genomic location of a bacterial artificial chromosome (BAC) clone, or other large genomic clone, based on a simple restriction digest of the BAC. The mapping is performed by comparing the experimentally derived restriction digest of the BAC DNA with a virtual restriction digest of the whole genome sequence. Our trials indicate that this program identified the genomic regions represented by BAC clones with a degree of accuracy comparable to that of end-sequencing, but at considerably less cost. Although the program has been developed principally for use with Arabidopsis BACs, it should align large insert genomic clones to any fully sequenced genome. PMID:12409477

  4. Computational Profiling of Microbial Genomes using Short Sequences

    NASA Astrophysics Data System (ADS)

    Doering, Dale; Tsukuda, Toyoko

    2001-03-01

    The genomes of a number of microbial species have now been completely sequenced. We have developed a program for the statistical analysis of the appearance frequency and location of short DNA segments within an entire microbial genome. Using this program, the genomes of Methanococcus jannischii (1.66 Mbase; 68radiodurans (3.28 Mbase; 66and compared to a randomly generated genomic pattern. The random sequence shows the expected statistical frequency distribution about the average that equals the genome size divided by the total number of N size short segments (4N). In contrast, the microbial genomes are radically skewed with a large number of segments that rarely occur and a few that are highly represented in the genome. The specific distribution profile of the segments is strongly dependent on the overall bias in the organism. The biased appearance frequency allows us to develop a genome signature of each microbial species.

  5. Teaching Residents Genomic Pathology: A Novel Approach for New Technology

    PubMed Central

    Haspel, Richard L.

    2013-01-01

    Genomics-based diagnostics have become part of patient care. As pathologists have the expertise in clinical laboratory testing as well as access to patient samples, all genomic medicine is genomic pathology. This article will review the evidence that there is a critical need for pathology resident training in genomics. Several individual program curricula are described as well as the progress of the Training Residents in Genomic (TRIG) Working Group. This group has made significant advances towards developing, implementing and evaluating a national curriculum in genomics for pathology residents. The novel approach of the TRIG Working Group can be used as a model for training pathology professionals in any new technology. PMID:23399798

  6. Building international genomics collaboration for global health security

    SciTech Connect

    Cui, Helen H.; Erkkila, Tracy; Chain, Patrick S. G.; Vuyisich, Momchilo

    2015-12-07

    Genome science and technologies are transforming life sciences globally in many ways and becoming a highly desirable area for international collaboration to strengthen global health. The Genome Science Program at the Los Alamos National Laboratory is leveraging a long history of expertise in genomics research to assist multiple partner nations in advancing their genomics and bioinformatics capabilities. The capability development objectives focus on providing a molecular genomics-based scientific approach for pathogen detection, characterization, and biosurveillance applications. The general approaches include introduction of basic principles in genomics technologies, training on laboratory methodologies and bioinformatic analysis of resulting data, procurement, and installation of next-generation sequencing instruments, establishing bioinformatics software capabilities, and exploring collaborative applications of the genomics capabilities in public health. Genome centers have been established with public health and research institutions in the Republic of Georgia, Kingdom of Jordan, Uganda, and Gabon; broader collaborations in genomics applications have also been developed with research institutions in many other countries.

  7. Building International Genomics Collaboration for Global Health Security

    PubMed Central

    Cui, Helen H.; Erkkila, Tracy; Chain, Patrick S. G.; Vuyisich, Momchilo

    2015-01-01

    Genome science and technologies are transforming life sciences globally in many ways and becoming a highly desirable area for international collaboration to strengthen global health. The Genome Science Program at the Los Alamos National Laboratory is leveraging a long history of expertise in genomics research to assist multiple partner nations in advancing their genomics and bioinformatics capabilities. The capability development objectives focus on providing a molecular genomics-based scientific approach for pathogen detection, characterization, and biosurveillance applications. The general approaches include introduction of basic principles in genomics technologies, training on laboratory methodologies and bioinformatic analysis of resulting data, procurement, and installation of next-generation sequencing instruments, establishing bioinformatics software capabilities, and exploring collaborative applications of the genomics capabilities in public health. Genome centers have been established with public health and research institutions in the Republic of Georgia, Kingdom of Jordan, Uganda, and Gabon; broader collaborations in genomics applications have also been developed with research institutions in many other countries. PMID:26697418

  8. Dissection of genomic correlation matrices using multivariate factor analysis in dairy and dual-purpose cattle breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    SNP effects estimated in genomic selection programs allow for the prediction of direct genomic values (DGV) both at genome-wide and chromosomal level. As a consequence, genome-wide (G_GW) or chromosomal (G_CHR) correlation matrices between genomic predictions for different traits can be calculated. ...

  9. Genomes on ice.

    PubMed

    Parkhill, Julian

    2016-03-01

    This month's Genome Watch discusses the analysis of a Helicobacter pylori genome from the preserved Copper-Age mummy known as the Iceman and how ancient genomes shed light on the history of bacterial pathogens. PMID:26853114

  10. Whole Genome Sequencing

    MedlinePlus

    ... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...

  11. Genomics screens for metastasis genes

    PubMed Central

    Yan, Jinchun; Huang, Qihong

    2014-01-01

    Metastasis is responsible for most cancer mortality. The process of metastasis is complex, requiring the coordinated expression and fine regulation of many genes in multiple pathways in both the tumor and host tissues. Identification and characterization of the genetic programs that regulate metastasis is critical to understanding the metastatic process and discovering molecular targets for the prevention and treatment of metastasis. Genomic approaches and functional genomic analyses can systemically discover metastasis genes. In this review, we summarize the genetic tools and methods that have been used to identify and characterize the genes that play critical roles in metastasis. PMID:22684367

  12. Ensembl genomes 2016: more genomes, more complexity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent...

  13. Ensembl Genomes 2016: more genomes, more complexity.

    PubMed

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-01

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. PMID:26578574

  14. Ensembl Genomes 2016: more genomes, more complexity

    PubMed Central

    Kersey, Paul Julian; Allen, James E.; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J.; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J.; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K.; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D.; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello–Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M.; Howe, Kevin L.; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M.

    2016-01-01

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. PMID:26578574

  15. 76 FR 3643 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group; Genome Research Review... Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: January...

  16. 75 FR 26762 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-12

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group; Genome Research Review... Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: May 3,...

  17. 75 FR 2148 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-14

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group, Genome Research Review... Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS)...

  18. 75 FR 52537 - National Human Genome Research Institute; Notice of Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-26

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group; Genome Research Review... Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS)...

  19. Transposable element junctions in marker development and genomic characterization of barley

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Barley is a model plant in genomic studies of Triticeae species. A complete barley genome sequence will facilitate not only barley breeding programs, but also those for related species. However, the large genome size and high repetitive sequence content complicate the barley genome assembly. The ma...

  20. PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

    PubMed Central

    Pfeifer, Bastian; Wittelsbürger, Ulrich; Ramos-Onsins, Sebastian E.; Lercher, Martin J.

    2014-01-01

    Although many computer programs can perform population genetics calculations, they are typically limited in the analyses and data input formats they offer; few applications can process the large data sets produced by whole-genome resequencing projects. Furthermore, there is no coherent framework for the easy integration of new statistics into existing pipelines, hindering the development and application of new population genetics and genomics approaches. Here, we present PopGenome, a population genomics package for the R software environment (a de facto standard for statistical analyses). PopGenome can efficiently process genome-scale data as well as large sets of individual loci. It reads DNA alignments and single-nucleotide polymorphism (SNP) data sets in most common formats, including those used by the HapMap, 1000 human genomes, and 1001 Arabidopsis genomes projects. PopGenome also reads associated annotation files in GFF format, enabling users to easily define regions or classify SNPs based on their annotation; all analyses can also be applied to sliding windows. PopGenome offers a wide range of diverse population genetics analyses, including neutrality tests as well as statistics for population differentiation, linkage disequilibrium, and recombination. PopGenome is linked to Hudson’s MS and Ewing’s MSMS programs to assess statistical significance based on coalescent simulations. PopGenome’s integration in R facilitates effortless and reproducible downstream analyses as well as the production of publication-quality graphics. Developers can easily incorporate new analyses methods into the PopGenome framework. PopGenome and R are freely available from CRAN (http://cran.r-project.org/) for all major operating systems under the GNU General Public License. PMID:24739305

  1. Funding Opportunity: Genomic Data Centers

    Cancer.gov

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  2. Recent developments of genomic research in soybean.

    PubMed

    Chan, Ching; Qi, Xinpeng; Li, Man-Wah; Wong, Fuk-Ling; Lam, Hon-Ming

    2012-07-20

    Soybean is an important cash crop with unique and important traits such as the high seed protein and oil contents, and the ability to perform symbiotic nitrogen fixation. A reference genome of cultivated soybeans was established in 2010, followed by whole-genome re-sequencing of wild and cultivated soybean accessions. These efforts revealed unique features of the soybean genome and helped to understand its evolution. Mapping of variations between wild and cultivated soybean genomes were performed. These genomic variations may be related to the process of domestication and human selection. Wild soybean germplasms exhibited high genomic diversity and hence may be an important source of novel genes/alleles. Accumulation of genomic data will help to refine genetic maps and expedite the identification of functional genes. In this review, we summarize the major findings from the whole-genome sequencing projects and discuss the possible impacts on soybean researches and breeding programs. Some emerging areas such as transcriptomic and epigenomic studies will be introduced. In addition, we also tabulated some useful bioinformatics tools that will help the mining of the soybean genomic data. PMID:22835978

  3. Scaffolder - software for manual genome scaffolding

    PubMed Central

    2012-01-01

    Background The assembly of next-generation short-read sequencing data can result in a fragmented non-contiguous set of genomic sequences. Therefore a common step in a genome project is to join neighbouring sequence regions together and fill gaps. This scaffolding step is non-trivial and requires manually editing large blocks of nucleotide sequence. Joining these sequences together also hides the source of each region in the final genome sequence. Taken together these considerations may make reproducing or editing an existing genome scaffold difficult. Methods The software outlined here, “Scaffolder,” is implemented in the Ruby programming language and can be installed via the RubyGems software management system. Genome scaffolds are defined using YAML - a data format which is both human and machine-readable. Command line binaries and extensive documentation are available. Results This software allows a genome build to be defined in terms of the constituent sequences using a relatively simple syntax. This syntax further allows unknown regions to be specified and additional sequence to be used to fill known gaps in the scaffold. Defining the genome construction in a file makes the scaffolding process reproducible and easier to edit compared with large FASTA nucleotide sequences. Conclusions Scaffolder is easy-to-use genome scaffolding software which promotes reproducibility and continuous development in a genome project. Scaffolder can be found at http://next.gs. PMID:22640820

  4. Enabling functional genomics with genome engineering

    PubMed Central

    Hilton, Isaac B.; Gersbach, Charles A.

    2015-01-01

    Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances. PMID:26430154

  5. Exploring Other Genomes: Bacteria.

    ERIC Educational Resources Information Center

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  6. Navigating yeast genome maintenance with functional genomics.

    PubMed

    Measday, Vivien; Stirling, Peter C

    2016-03-01

    Maintenance of genome integrity is a fundamental requirement of all organisms. To address this, organisms have evolved extremely faithful modes of replication, DNA repair and chromosome segregation to combat the deleterious effects of an unstable genome. Nonetheless, a small amount of genome instability is the driver of evolutionary change and adaptation, and thus a low level of instability is permitted in populations. While defects in genome maintenance almost invariably reduce fitness in the short term, they can create an environment where beneficial mutations are more likely to occur. The importance of this fact is clearest in the development of human cancer, where genome instability is a well-established enabling characteristic of carcinogenesis. This raises the crucial question: what are the cellular pathways that promote genome maintenance and what are their mechanisms? Work in model organisms, in particular the yeast Saccharomyces cerevisiae, has provided the global foundations of genome maintenance mechanisms in eukaryotes. The development of pioneering genomic tools inS. cerevisiae, such as the systematic creation of mutants in all nonessential and essential genes, has enabled whole-genome approaches to identifying genes with roles in genome maintenance. Here, we review the extensive whole-genome approaches taken in yeast, with an emphasis on functional genomic screens, to understand the genetic basis of genome instability, highlighting a range of genetic and cytological screening modalities. By revealing the biological pathways and processes regulating genome integrity, these analyses contribute to the systems-level map of the yeast cell and inform studies of human disease, especially cancer. PMID:26323482

  7. Teaching Genomic Counseling: Preparing the Genetic Counseling Workforce for the Genomic Era

    PubMed Central

    Hooker, Gillian W.; Ormond, Kelly E.; Sweet, Kevin; Biesecker, Barbara B.

    2014-01-01

    Genetic counselors have a long-standing history of working on the clinical forefront of implementing new genetic technology. Genomic sequencing is no exception. The rapid advancement of genomic sequencing technologies, including but not limited to next generation sequencing approaches, across all subspecialties of genetic counseling mandates attention to genetic counselor training at both the graduate and continuing education levels. The current era provides a tremendous opportunity for counselors to become actively involved in making genomics more accessible, engaging the population in decisions to undergo sequencing and effectively translating genomic information to promote health and well-being. In this commentary, we explore reasons why genomic sequencing warrants particular consideration and put forward strategies for training program curricula and continuing education programs to meet this need. PMID:24504939

  8. Genomic definition of species. Revision 2

    SciTech Connect

    Crkvenjakov, R.; Drmanac, R.

    1993-03-01

    A genome is the sum total of the DNA sequences in the cells of an individual organism. The common usage that species possess genomes comes naturally to biochemists, who have shown that all protein and nucleic acid molecules are at the same time species- and individual-specific, with minor individual variations being superimposed on a consensus sequence that is constant for a species. By extension, this property is attributed to the common features of DNA in the chromosomes of members of a given species and is called species genome. Our proposal for the definition of a biological species is as follows: A species comprises a group of actual and potential biological organisms built according to a unique genome program that is recorded, and at least in part expressed, in the structures of their genomic nucleic acid molecule(s), having intragroup sequence differences which can be fully interconverted in the process of organismal reproduction.

  9. Emerging issues in public health genomics

    PubMed Central

    Roberts, J. Scott

    2014-01-01

    This review highlights emerging areas of interest in public health genomics. First, recent advances in newborn screening (NBS) are described, with a focus on practice and policy implications of current and future efforts to expand NBS programs (e.g., via next-generation sequencing). Next, research findings from the rapidly progressing field of epigenetics and epigenomics are detailed, highlighting ways in which our emerging understanding in these areas could guide future intervention and research efforts in public health. We close by considering various ethical, legal and social issues posed by recent developments in public health genomics; these include policies to regulate access to personal genomic information; the need to enhance genetic literacy in both health professionals and the public; and challenges in ensuring that the benefits (and burdens) from genomic discoveries and applications are equitably distributed. Needs for future genomics research that integrates across basic and social sciences are also noted. PMID:25184533

  10. MycoCosm, an Integrated Fungal Genomics Resource

    SciTech Connect

    Shabalov, Igor; Grigoriev, Igor

    2012-03-16

    MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in response to an urgent call from the fungal community for integration of all fungal genomes and analytical tools in one place (Pan-fungal data resources meeting, Feb 21-22, 2010, Alexandria, VA). MycoCosm integrates genomics data and analysis tools to navigate through over 100 fungal genomes sequenced at JGI and elsewhere. This resource allows users to explore fungal genomes in the context of both genome-centric analysis and comparative genomics, and promotes user community participation in data submission, annotation and analysis. MycoCosm has over 4500 unique visitors/month or 35000+ visitors/year as well as hundreds of registered users contributing their data and expertise to this resource. Its scalable architecture allows significant expansion of the data expected from JGI Fungal Genomics Program, its users, and integration with external resources used by fungal community.

  11. MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data.

    PubMed

    Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu

    2015-01-01

    The microbial genome database for comparative analysis (MBGD) (available at http://mbgd.genome.ad.jp/) is a comprehensive ortholog database for flexible comparative analysis of microbial genomes, where the users are allowed to create an ortholog table among any specified set of organisms. Because of the rapid increase in microbial genome data owing to the next-generation sequencing technology, it becomes increasingly challenging to maintain high-quality orthology relationships while allowing the users to incorporate the latest genomic data available into an analysis. Because many of the recently accumulating genomic data are draft genome sequences for which some complete genome sequences of the same or closely related species are available, MBGD now stores draft genome data and allows the users to incorporate them into a user-specific ortholog database using the MyMBGD functionality. In this function, draft genome data are incorporated into an existing ortholog table created only from the complete genome data in an incremental manner to prevent low-quality draft data from affecting clustering results. In addition, to provide high-quality orthology relationships, the standard ortholog table containing all the representative genomes, which is first created by the rapid classification program DomClust, is now refined using DomRefine, a recently developed program for improving domain-level clustering using multiple sequence alignment information. PMID:25398900

  12. Accelerating Genome Sequencing 100X with FPGAs

    SciTech Connect

    Storaasli, Olaf O; Strenski, Dave

    2007-01-01

    The performance of two Cray XD1 systems with Virtex-II Pro 50 and Virtex-4 LX160 FPGAs was evaluated using the FASTA computational biology program for human genome (DNA and protein) sequence comparisons. FPGA speedups of 50X (Virtex-II Pro 50) and 100X (Virtex-4 LX160) over a 2.2 GHz Opteron were obtained. FPGA coding issues for human genome data are described.

  13. Algorithm to search for genomic rearrangements

    NASA Astrophysics Data System (ADS)

    Nałecz-Charkiewicz, Katarzyna; Nowak, Robert

    2013-10-01

    The aim of this article is to discuss the issue of comparing nucleotide sequences in order to detect chromosomal rearrangements (for example, in the study of genomes of two cucumber varieties, Polish and Chinese). Two basic algorithms for detecting rearrangements has been described: Smith-Waterman algorithm, as well as a new method of searching genetic markers in combination with Knuth-Morris-Pratt algorithm. The computer program in client-server architecture was developed. The algorithms properties were examined on genomes Escherichia coli and Arabidopsis thaliana genomes, and are prepared to compare two cucumber varieties, Polish and Chinese. The results are promising and further works are planned.

  14. TCGA's Pan-Cancer Efforts and Expansion to Include Whole Genome Sequence - TCGA

    Cancer.gov

    Carolyn Hutter, Ph.D., Program Director of NHGRI's Division of Genomic Medicine, discusses the expansion of TCGA's Pan-Cancer efforts to include the Pan-Cancer Analysis of Whole Genomes (PAWG) project.

  15. Genomics and Health Impact Update

    MedlinePlus

    ... Genomics in Practice Newborn Screening Pharmacogenomics Reproductive Health Tools and Databases About the Genomics & Health Impact Update The Office of Public Health Genomics provides updated and credible ...

  16. Integrating sequence, evolution and functional genomics in regulatory genomics

    PubMed Central

    Vingron, Martin; Brazma, Alvis; Coulson, Richard; van Helden, Jacques; Manke, Thomas; Palin, Kimmo; Sand, Olivier; Ukkonen, Esko

    2009-01-01

    With genome analysis expanding from the study of genes to the study of gene regulation, 'regulatory genomics' utilizes sequence information, evolution and functional genomics measurements to unravel how regulatory information is encoded in the genome. PMID:19226437

  17. Genome instability, cancer and aging

    PubMed Central

    Maslov, Alexander Y.; Vijg, Jan

    2015-01-01

    DNA damage-driven genome instability underlies the diversity of life forms generated by the evolutionary process but is detrimental to the somatic cells of individual organisms. The cellular response to DNA damage can be roughly divided in two parts. First, when damage is severe, programmed cell death may occur or, alternatively, temporary or permanent cell cycle arrest. This protects against cancer but can have negative effects on the long term, e.g., by depleting stem cell reservoirs. Second, damage can be repaired through one or more of the many sophisticated genome maintenance pathways. However, erroneous DNA repair and incomplete restoration of chromatin after damage is resolved, produce mutations and epimutations, respectively, both of which have been shown to accumulate with age. An increased burden of mutations and/or epimutations in aged tissues increases cancer risk and adversely affects gene transcriptional regulation, leading to progressive decline in organ function. Cellular degeneration and uncontrolled cell proliferation are both major hallmarks of aging. Despite the fact that one seems to exclude the other, they both may be driven by a common mechanism. Here, we review age related changes in the mammalian genome and their possible functional consequences, with special emphasis on genome instability in stem/progenitor cells. PMID:19344750

  18. Genomic Data Commons | Office of Cancer Genomics

    Cancer.gov

    The NCI’s Center for Cancer Genomics launches the Genomic Data Commons (GDC), a unified data sharing platform for the cancer research community. The mission of the GDC is to enable data sharing across the entire cancer research community, to ultimately support precision medicine in oncology.

  19. Harvesting rice's dispensable genome.

    PubMed

    Wing, Rod A

    2015-01-01

    A rapid and cost-effective approach has been developed to harvest and map the dispensable genome, that is, population-level natural sequence variation within a species that is not present in static genome assemblies. PMID:26429765

  20. Libraries for genomic SELEX.

    PubMed Central

    Singer, B S; Shtatland, T; Brown, D; Gold, L

    1997-01-01

    An increasing number of proteins are being identified that regulate gene expression by binding specific nucleic acidsin vivo. A method termed genomic SELEX facilitates the rapid identification of networks of protein-nucleic acid interactions by identifying within the genomic sequences of an organism the highest affinity sites for any protein of the organism. As with its progenitor, SELEX of random-sequence nucleic acids, genomic SELEX involves iterative binding, partitioning, and amplification of nucleic acids. The two methods differ in that the variable region of the nucleic acid library for genomic SELEX is derived from the genome of an organism. We have used a quick and simple method to construct Escherichia coli, Saccharomyces cerevisiae, and human genomic DNA PCR libraries that can be transcribed with T7 RNA polymerase. We present evidence that the libraries contain overlapping inserts starting at most of the positions within the genome, making these libraries suitable for genomic SELEX. PMID:9016629

  1. Genomic Data Commons launches

    Cancer.gov

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  2. GENOMICS AND ENVIRONMENTAL RESEARCH

    EPA Science Inventory

    The impact of recently developed and emerging genomics technologies on environmental sciences has significant implications for human and ecological risk assessment issues. The linkage of data generated from genomics, transcriptomics, proteomics, metabalomics, and ecology can be ...

  3. Exploiting the genome

    SciTech Connect

    Block, S.; Cornwall, J.; Dyson, F.; Koonin, S.; Lewis, N.; Schwitters, R.

    1998-09-11

    In 1997, JASON conducted a DOE-sponsored study of the human genome project with special emphasis on the areas of technology, quality assurance and quality control, and informatics. The present study has two aims: first, to update the 1997 Report in light of recent developments in genome sequencing technology, and second, to consider possible roles for the DOE in the ''post-genomic" era, following acquisition of the complete human genome sequence.

  4. Using CAVE technology for functional genomics studies.

    PubMed

    Sensen, Christoph W

    2002-01-01

    We have established the first Java 3D-enabled CAVE (CAVE automated virtual environment). The Java application programming interface allows the complete separation of the program development from the program execution, opening new application domains for the CAVE technology. Programs can be developed on any Java-enabled computer platform, including Windows, Macintosh, and Linux workstations, and executed in the CAVE without modification. The introduction of Java, one of the major programming environments for bioinformatics, into the CAVE environment allows the rapid development applications for genome research, especially for the analysis of the spatial and temporal data that are being produced by functional genomics experiments. The CAVE technology will play a major role in the modeling of biological systems that is necessary to understand how these systems are organized and how they function. PMID:12614491

  5. COMPARATIVE GENOMICS IN LEGUMES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The legume plant family will soon include three sequenced genomes. The majority of the gene-containing portions of the model legumes Medicago truncatula and Lotus japonicus have been sequenced in clone-by-clone projects, and the sequencing of the soybean genome is underway in a whole-genome shotgun ...

  6. Whole Genome Selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Whole genome selection (WGS) is an approach to using DNA markers that are distributed throughout the entire genome. Genes affecting most economically-important traits are distributed throughout the genome and there are relatively few that have large effects with many more genes with progressively sm...

  7. Genomics and functional genomics with haloarchaea.

    PubMed

    Soppa, J; Baumann, A; Brenneis, M; Dambeck, M; Hering, O; Lange, C

    2008-09-01

    The first haloarchaeal genome was published in 2000 and today five genome sequences are available. Transcriptome and proteome analyses have been established for two and three haloarchaeal species, respectively, and more than 20 studies using these functional genomic approaches have been published in the last two years. These studies gave global overviews of metabolic regulation (aerobic and anaerobic respiration, phototrophy, carbon source usage), stress response (UV, X-rays, transition metals, osmotic and temperature stress), cell cycle-dependent transcript level regulation, and transcript half-lives. The only translatome analysis available for any prokaryotic species revealed that 10 and 20% of all transcripts are translationally regulated in Haloferax volcanii and Halobacterium salinarum, respectively. Very effective methods for the construction of in frame deletion mutants have been established recently for haloarchaea and are intensively used to unravel the biological roles of genes in this group. Bioinformatic analyses include both cross-genome comparisons as well as integration of genomic data with experimental results. The first systems biology approaches have been performed that used experimental data to construct predictive models of gene expression and metabolism, respectively. In this contribution the current status of genomics, functional genomics, and molecular genetics of haloarchaea is summarized and selected examples are discussed. PMID:18493745

  8. Wheat Genomics: Present Status and Future Prospects

    PubMed Central

    Gupta, P. K.; Mir, R. R.; Mohan, A.; Kumar, J.

    2008-01-01

    Wheat (Triticum aestivum L.), with a large genome (16000 Mb) and high proportion (∼80%) of repetitive sequences, has been a difficult crop for genomics research. However, the availability of extensive cytogenetics stocks has been an asset, which facilitated significant progress in wheat genomic research in recent years. For instance, fairly dense molecular maps (both genetic and physical maps) and a large set of ESTs allowed genome-wide identification of gene-rich and gene-poor regions as well as QTL including eQTL. The availability of markers associated with major economic traits also allowed development of major programs on marker-assisted selection (MAS) in some countries, and facilitated map-based cloning of a number of genes/QTL. Resources for functional genomics including TILLING and RNA interference (RNAi) along with some new approaches like epigenetics and association mapping are also being successfully used for wheat genomics research. BAC/BIBAC libraries for the subgenome D and some individual chromosomes have also been prepared to facilitate sequencing of gene space. In this brief review, we discuss all these advances in some detail, and also describe briefly the available resources, which can be used for future genomics research in this important crop. PMID:18528518

  9. Chromium and Genomic Stability

    PubMed Central

    Wise, Sandra S.; Wise, John Pierce

    2014-01-01

    Many metals serve as micronutrients which protect against genomic instability. Chromium is most abundant in its trivalent and hexavalent forms. Trivalent chromium has historically been considered an essential element, though recent data indicate that while it can have pharmacological effects and value, it is not essential. There are no data indicating that trivalent chromium promotes genomic stability and, instead may promote genomic instability. Hexavalent chromium is widely accepted as highly toxic and carcinogenic with no nutritional value. Recent data indicate that it causes genomic instability and also has no role in promoting genomic stability. PMID:22192535

  10. The Genomic Medicine Game.

    PubMed

    Tran, Elvis; de Andrés-Galiana, Enrique J; Benitez, Sonia; Martin-Sanchez, Fernando; Lopez-Campos, Guillermo H

    2016-01-01

    With advancements in genomics technology, health care has been improving and new paradigms of medicine such as genomic medicine have evolved. The education of clinicians, researchers and students to face the challenges posed by these new approaches, however, has been often lagging behind. From this the Genomic Medicine Game, an educational tool, was created for the purpose of conceptualizing the key components of Genomic Medicine. A number of phenotype-genotype associations were found through a literature review, which was used to be a base for the concepts the Genomic Medicine Game would focus on. Built in Java, the game was successfully tested with promising results. PMID:27577486

  11. Unmet Challenges of Structural Genomics

    PubMed Central

    Chruszcz, Maksymilian; Domagalski, Marcin; Osinski, Tomasz; Wlodawer, Alexander; Minor, Wladek

    2010-01-01

    Summary Structural genomics (SG) programs have developed during the last decade many novel methodologies for faster and more accurate structure determination. These new tools and approaches led to determination of thousands of protein structures. The generation of enormous amounts of experimental data resulted in significant improvements in the understanding of many biological processes at molecular levels. However, the amount of data collected so far is so large that traditional analysis methods are limiting the rate of extraction of biological and biochemical information from 3-D models. This situation has prompted us to review the challenges that remain unmet by structural genomics, as well as the areas in which the potential impact of SG could exceed what has been achieved so far. PMID:20810277

  12. 10. international mouse genome conference

    SciTech Connect

    Meisler, M.H.

    1996-12-31

    Ten years after hosting the First International Mammalian Genome Conference in Paris in 1986, Dr. Jean-Louis Guenet presided over the Tenth Conference at the Pasteur Institute, October 7--10, 1996. The 1986 conference was a satellite to the Human Gene Mapping Workshop and had approximately 50 attendees. The 1996 meeting was attended by 300 scientists from around the world. In the interim, the number of mapped loci in the mouse increased from 1,000 to over 20,000. This report contains a listing of the program and its participants, and two articles that review the meeting and the role of the laboratory mouse in the Human Genome project. More than 200 papers were presented at the conference covering the following topics: International mouse chromosome committee meetings; Mutant generation and identification; Physical and genetic maps; New technology and resources; Chromatin structure and gene regulation; Rate and hamster genetic maps; Informatics and databases; and Quantitative trait analysis.

  13. Automated correction of genome sequence errors

    PubMed Central

    Gajer, Pawel; Schatz, Michael; Salzberg, Steven L.

    2004-01-01

    By using information from an assembly of a genome, a new program called AutoEditor significantly improves base calling accuracy over that achieved by previous algorithms. This in turn improves the overall accuracy of genome sequences and facilitates the use of these sequences for polymorphism discovery. We describe the algorithm and its application in a large set of recent genome sequencing projects. The number of erroneous base calls in these projects was reduced by 80%. In an analysis of over one million corrections, we found that AutoEditor made just one error per 8828 corrections. By substantially increasing the accuracy of base calling, AutoEditor can dramatically accelerate the process of finishing genomes, which involves closing all gaps and ensuring minimum quality standards for the final sequence. It also greatly improves our ability to discover single nucleotide polymorphisms (SNPs) between closely related strains and isolates of the same species. PMID:14744981

  14. Rhodopseudomonas palustris genome project. Final report

    SciTech Connect

    Harwood, Caroline S.

    2000-11-22

    Rhodopseudomonas palustris is a common soil and water bacterium that makes its living by converting sunlight to cellular energy and by absorbing atmospheric carbon dioxide and converting it to biomass. This microbe can also degrade and recycle components of the woody tissues of plants, wood being the most abundant polymer on earth. Because of its intimate involvement in carbon management and recycling, R. palustris was selected by the DOE Carbon Management Program to have its genome sequenced by the Joint Genome Institute (JGI). This award provided funds for the preparation of R. palustris genomic DNA which was then supplied to the JGI in sufficient amounts to enable the complete sequencing of the R. palustris genome. The PI also supplied the JGI with technical information about the molecular biology of R. palustris.

  15. The Bluejay genome browser.

    PubMed

    Soh, Jung; Gordon, Paul M K; Sensen, Christoph W

    2012-03-01

    The Bluejay genome browser is a stand-alone visualization tool for the multi-scale viewing of annotated genomes and other genomic elements. Bluejay allows users to customize display features to suit their needs, and produces publication-quality graphics. Bluejay provides a multitude of ways to interrelate biological data at the genome scale. Users can load gene expression data into a genome display for expression visualization in context. Multiple genomes can be compared concurrently, including time series expression data, based on Gene Ontology labels. External, context-sensitive biological Web Services are linked to the displayed genomic elements ad hoc for in-depth genomic data analysis and interpretation. Users can mark multiple points of interest in a genome by creating waypoints, and exploit them for easy navigation of single or multiple genomes. Using this comprehensive visual environment, users can study a gene not just in relation to its genome, but also its transcriptome and evolutionary origins. Written in Java, Bluejay is platform-independent and is freely available from http://bluejay.ucalgary.ca. PMID:22389011

  16. Microbial genomic taxonomy.

    PubMed

    Thompson, Cristiane C; Chimetto, Luciane; Edwards, Robert A; Swings, Jean; Stackebrandt, Erko; Thompson, Fabiano L

    2013-01-01

    A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, <10 in Karlin genomic signature, and > 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups. PMID:24365132

  17. Variations in genome mass.

    PubMed

    Wachtel, S S; Tiersch, T R

    1993-02-01

    1. Genome size varies considerably among vertebrates, ranging from less than 1 pg to more than 200 pg; the amount of DNA differing among individuals in a population can equal the amount in the entire structural gene complement. 2. Recent technological advances permit evaluation of genome size variation at several levels including sub-chromosomal, chromosomal and cellular. 3. Genome size variation may also be viewed from taxonomic levels, and across evolutionary time frames. 4. As sources of genome size variation are identified and studied, the conundrum of the C-value paradox (lack of correlations among genome size, genomic complexity and phylogenetic status of organisms) may prove to be more apparent than real. 5. For example, the limited and relatively constant genome size of avians may be related to the physiological constraints of flight. PMID:8462275

  18. Bacterial Genome Instability

    PubMed Central

    Darmon, Elise

    2014-01-01

    SUMMARY Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease. PMID:24600039

  19. UCSC genome browser tutorial.

    PubMed

    Zweig, Ann S; Karolchik, Donna; Kuhn, Robert M; Haussler, David; Kent, W James

    2008-08-01

    The University of California Santa Cruz (UCSC) Genome Bioinformatics website consists of a suite of free, open-source, on-line tools that can be used to browse, analyze, and query genomic data. These tools are available to anyone who has an Internet browser and an interest in genomics. The website provides a quick and easy-to-use visual display of genomic data. It places annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information. Many of the annotation tracks are submitted by scientists worldwide; the others are computed by the UCSC Genome Bioinformatics group from publicly available sequence data. It also allows users to upload and display their own experimental results or annotation sets by creating a custom track. The suite of tools, downloadable data files, and links to documentation and other information can be found at http://genome.ucsc.edu/. PMID:18514479

  20. Collaborative Research to Advance Precision Medicine in the Post-Genomic World | Office of Cancer Genomics

    Cancer.gov

    My name is Subhashini Jagu, and I am the Scientific Program Manager for the Cancer Target Discovery and Development (CTD2) Network at the Office of Cancer Genomics (OCG). In my new role, I help CTD2 work toward its mission, which is to develop new scientific approaches to accelerate the translation of genomic discoveries into new treatments. Collaborative efforts that bring together a variety of expertise and infrastructure are needed to understand and successfully treat cancer, a highly complex disease.

  1. Almost finished: the complete genome sequence of Mycosphaerella graminicola

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mycosphaerella graminicola causes septoria tritici blotch of wheat. An 8.9x shotgun sequence of bread wheat strain IPO323 was generated through the Community Sequencing Program of the U.S. Department of Energy’s Joint Genome Institute (JGI), and was finished at the Stanford Human Genome Center. The ...

  2. Towards a whole genome physical map in rainbow trout

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Over the last five years, tremendous genomic resources were developed in salmonids. In 2005, INRA joined formally the consortium for Genome Research on All Salmonids Program (cGRASP). This consortium (www.cgrasp.org) is the international collaborative structure for establishing needed pre- and post-...

  3. Global Implementation of Genomic Medicine: We Are Not Alone

    PubMed Central

    Manolio, Teri A.; Abramowicz, Marc; Al-Mulla, Fahd; Anderson, Warwick; Balling, Rudi; Berger, Adam C.; Bleyl, Steven; Chakravarti, Aravinda; Chantratita, Wasun; Chisholm, Rex L.; Dissanayake, Vajira H. W.; Dunn, Michael; Dzau, Victor J.; Han, Bok-Ghee; Hubbard, Tim; Kolbe, Anne; Korf, Bruce; Kubo, Michiaki; Lasko, Paul; Leego, Erkki; Mahasirimongkol, Surakameth; Majumdar, Partha P.; Matthijs, Gert; McLeod, Howard L.; Metspalu, Andres; Meulien, Pierre; Miyano, Satoru; Naparstek, Yaakov; O’Rourke, P. Pearl; Patrinos, George P.; Rehm, Heidi L.; Relling, Mary V.; Rennert, Gad; Rodriguez, Laura Lyman; Roden, Dan M.; Shuldiner, Alan R.; Sinha, Sukdev; Tan, Patrick; Ulfendahl, Mats; Ward, Robyn; Williams, Marc S.; Wong, John E.L.; Green, Eric D.; Ginsburg, Geoffrey S.

    2016-01-01

    Advances in high-throughput genomic technologies coupled with a growing number of genomic results potentially useful in clinical care have led to ground-breaking genomic medicine implementation programs in various nations. Many of these innovative programs capitalize on unique local capabilities arising from the structure of their health care systems or their cultural or political milieu, as well as from unusual burdens of disease or risk alleles. Many such programs are being conducted in relative isolation and might benefit from sharing of approaches and lessons learned in other nations. The National Human Genome Research Institute recently brought together 25 of these groups from around the world to describe and compare projects, examine the current state of implementation and desired near-term capabilities, and identify opportunities for collaboration to promote the responsible implementation of genomic medicine. The wide variety of nascent programs in diverse settings demonstrates that implementation of genomic medicine is expanding globally in varied and highly innovative ways. Opportunities for collaboration abound in the areas of evidence generation, health information technology, education, workforce development, pharmacogenomics, and policy and regulatory issues. Several international organizations that are already facilitating effective research collaborations should engage to ensure implementation proceeds collaboratively without potentially wasteful duplication. Efforts to coalesce these groups around concrete but compelling signature projects, such as global eradication of genetically-mediated drug reactions or developing a truly global genomic variant data resource across a wide number of ethnicities, would accelerate appropriate implementation of genomics to improve clinical care world-wide. PMID:26041702

  4. Genotypes are useful for more than genomic evaluation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New services that provide pedigree discovery, breed composition, mating programs, genomic inbreeding, fertility defects, and inheritance tracking all are possible from low-cost genotyping in addition to genomic evaluation. Genetic markers let breeders select among sibs before their phenotypes became...

  5. Multiple trait genomic selection methods increase genetic value prediction accuracy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic selection predicts genetic values with genome-wide markers. It is rapidly emerging in plant breeding and is widely implemented in animal breeding. Genetic correlations between quantitative traits are pervasive in many breeding programs. These correlations indicate that measurements of one tr...

  6. Intrauterine programming

    PubMed Central

    Sedaghat, Katayoun; Zahediasl, Saleh; Ghasemi, Asghar

    2015-01-01

    In mammals, the intrauterine condition has an important role in the development of fetal physiological systems in later life. Suboptimal maternal environment can alter the regulatory pathways that determine the normal development of the fetus in utero, which in post-natal life may render the individual more susceptible to cardiovascular or metabolic adult-life diseases. Changes in the intrauterine availability of nutrients, oxygen and hormones can change the fetal tissue developmental regulatory planning, which occurs genomically and non-genomically and can cause permanent structural and functional changes in the systems, leading to diseases in early years of life and those that particularly become overt in adulthood. In this review we take a brief look at the main elements which program the fetal system development and consequently induce a crucial impact on the cardiovascular, nervous and hormonal systems in adulthood. PMID:25945232

  7. Genomics to feed a switchgrass breeding program

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Development of improved cultivars is one of three pillars, along with sustainable production and efficient conversion, required for dedicated cellulosic bioenergy crops to succeed. Breeding new cultivars is a long, slow process requiring patience, dedication, and motivation to realize gains and adva...

  8. About the Epidemiology and Genomics Research Program

    Cancer.gov

    Epidemiology is the scientific study of the causes and distribution of disease in populations. NCI-funded epidemiology research is conducted through research at institutions in the United States and internationally.

  9. 2012 U.S. Department of Energy: Joint Genome Institute: Progress Report

    SciTech Connect

    Gilbert, David

    2013-01-01

    The mission of the U.S. Department of Energy Joint Genome Institute (DOE JGI) is to serve the diverse scientific community as a user facility, enabling the application of large-scale genomics and analysis of plants, microbes, and communities of microbes to address the DOE mission goals in bioenergy and the environment. The DOE JGI's sequencing efforts fall under the Eukaryote Super Program, which includes the Plant and Fungal Genomics Programs; and the Prokaryote Super Program, which includes the Microbial Genomics and Metagenomics Programs. In 2012, several projects made news for their contributions to energy and environment research.

  10. Methods of Genomic Competency Integration in Practice

    PubMed Central

    Jenkins, Jean; Calzone, Kathleen A.; Caskey, Sarah; Culp, Stacey; Weiner, Marsha; Badzek, Laurie

    2015-01-01

    Purpose Genomics is increasingly relevant to health care, necessitating support for nurses to incorporate genomic competencies into practice. The primary aim of this project was to develop, implement, and evaluate a year-long genomic education intervention that trained, supported, and supervised institutional administrator and educator champion dyads to increase nursing capacity to integrate genomics through assessments of program satisfaction and institutional achieved outcomes. Design Longitudinal study of 23 Magnet Recognition Program® Hospitals (21 intervention, 2 controls) participating in a 1-year new competency integration effort aimed at increasing genomic nursing competency and overcoming barriers to genomics integration in practice. Methods Champion dyads underwent genomic training consisting of one in-person kick-off training meeting followed by monthly education webinars. Champion dyads designed institution-specific action plans detailing objectives, methods or strategies used to engage and educate nursing staff, timeline for implementation, and outcomes achieved. Action plans focused on a minimum of seven genomic priority areas: champion dyad personal development; practice assessment; policy content assessment; staff knowledge needs assessment; staff development; plans for integration; and anticipated obstacles and challenges. Action plans were updated quarterly, outlining progress made as well as inclusion of new methods or strategies. Progress was validated through virtual site visits with the champion dyads and chief nursing officers. Descriptive data were collected on all strategies or methods utilized, and timeline for achievement. Descriptive data were analyzed using content analysis. Findings The complexity of the competency content and the uniqueness of social systems and infrastructure resulted in a significant variation of champion dyad interventions. Conclusions Nursing champions can facilitate change in genomic nursing capacity through