genotype

Summary

Summary: The genetic constitution of the individual; the characterization of the genes.

Top Publications

  1. pmc Inference of population structure using multilocus genotype data
    J K Pritchard
    Department of Statistics, University of Oxford, United Kingdom
    Genetics 155:945-59. 2000
  2. pmc A map of human genome variation from population-scale sequencing
    Richard M Durbin
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
    Nature 467:1061-73. 2010
  3. ncbi Principal components analysis corrects for stratification in genome-wide association studies
    Alkes L Price
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 38:904-9. 2006
  4. pmc A flexible and accurate genotype imputation method for the next generation of genome-wide association studies
    Bryan N Howie
    Department of Statistics, University of Oxford, Oxford, UK
    PLoS Genet 5:e1000529. 2009
  5. pmc Common SNPs explain a large proportion of the heritability for human height
    Jian Yang
    Queensland Institute of Medical Research, Brisbane, Queensland, Australia
    Nat Genet 42:565-9. 2010
  6. pmc Biological, clinical and population relevance of 95 loci for blood lipids
    Tanya M Teslovich
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
    Nature 466:707-13. 2010
  7. pmc MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes
    Yun Li
    Department of Genetics, Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, USA
    Genet Epidemiol 34:816-34. 2010
  8. pmc The Drosophila melanogaster Genetic Reference Panel
    Trudy F C Mackay
    Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
    Nature 482:173-8. 2012
  9. pmc PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
    Kai Wang
    Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Res 17:1665-74. 2007
  10. ncbi Peginterferon alfa-2a plus ribavirin for chronic hepatitis C virus infection
    Michael W Fried
    University of North Carolina, Chapel Hill 27599, USA
    N Engl J Med 347:975-82. 2002

Detail Information

Publications273 found, 100 shown here

  1. pmc Inference of population structure using multilocus genotype data
    J K Pritchard
    Department of Statistics, University of Oxford, United Kingdom
    Genetics 155:945-59. 2000
    We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations...
  2. pmc A map of human genome variation from population-scale sequencing
    Richard M Durbin
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
    Nature 467:1061-73. 2010
    ..characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype...
  3. ncbi Principal components analysis corrects for stratification in genome-wide association studies
    Alkes L Price
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 38:904-9. 2006
    ..Our simple, efficient approach can easily be applied to disease studies with hundreds of thousands of markers...
  4. pmc A flexible and accurate genotype imputation method for the next generation of genome-wide association studies
    Bryan N Howie
    Department of Statistics, University of Oxford, Oxford, UK
    PLoS Genet 5:e1000529. 2009
    b>Genotype imputation methods are now being widely used in the analysis of genome-wide association studies...
  5. pmc Common SNPs explain a large proportion of the heritability for human height
    Jian Yang
    Queensland Institute of Medical Research, Brisbane, Queensland, Australia
    Nat Genet 42:565-9. 2010
    ..using a linear model analysis, and validated the estimation method with simulations based on the observed genotype data. We show that 45% of variance can be explained by considering all SNPs simultaneously...
  6. pmc Biological, clinical and population relevance of 95 loci for blood lipids
    Tanya M Teslovich
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
    Nature 466:707-13. 2010
    ..Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD...
  7. pmc MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes
    Yun Li
    Department of Genetics, Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, USA
    Genet Epidemiol 34:816-34. 2010
    ..We have previously implemented a computationally efficient Markov Chain framework for genotype imputation and haplotyping in the freely available MaCH software package...
  8. pmc The Drosophila melanogaster Genetic Reference Panel
    Trudy F C Mackay
    Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
    Nature 482:173-8. 2012
    ..Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information...
  9. pmc PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
    Kai Wang
    Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Res 17:1665-74. 2007
    ..3%. Our results demonstrate the feasibility of whole-genome fine-mapping of CNVs via high-density SNP genotyping...
  10. ncbi Peginterferon alfa-2a plus ribavirin for chronic hepatitis C virus infection
    Michael W Fried
    University of North Carolina, Chapel Hill 27599, USA
    N Engl J Med 347:975-82. 2002
    ..We compared the efficacy and safety of peginterferon alfa-2a plus ribavirin, interferon alfa-2b plus ribavirin, and peginterferon alfa-2a alone in the initial treatment of chronic hepatitis C...
  11. pmc SNP detection for massively parallel whole-genome resequencing
    Ruiqiang Li
    Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China
    Genome Res 19:1124-32. 2009
    ..Our analyses demonstrate that our method has a very low false call rate at any sequencing depth and excellent genome coverage at a high sequencing depth...
  12. pmc A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species
    Robert J Elshire
    Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
    PLoS ONE 6:e19379. 2011
    ....
  13. pmc A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase
    Paul Scheet
    Department of Statistics, University of Washington, Seattle, 98195 4322, USA
    Am J Hum Genet 78:629-44. 2006
    ..We illustrate the utility of the model by applying it to dense single-nucleotide-polymorphism genotype data for the tasks of imputing missing genotypes and estimating haplotypic phase...
  14. pmc Mapping copy number variation by population-scale genome sequencing
    Ryan E Mills
    Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, USA
    Nature 470:59-65. 2011
    ..Our analytical framework and SV map serves as a resource for sequencing-based association studies...
  15. ncbi CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure
    Mattias Jakobsson
    Center for Computational Medicine and Biology, Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
    Bioinformatics 23:1801-6. 2007
    ....
  16. pmc Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
    Daniel Falush
    Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, Schumann Strasse 21 22, 10117 Berlin, Germany
    Genetics 164:1567-87. 2003
    We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci...
  17. pmc Missing heritability and strategies for finding the underlying causes of complex disease
    Evan E Eichler
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195 5065, USA
    Nat Rev Genet 11:446-50. 2010
    ....
  18. pmc Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes
    Jeffrey C Barrett
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
    Nat Genet 41:703-7. 2009
    ..01; overall P < 5 × 10(-8)) and 4 additional regions provided nominal evidence of replication (P < 0.05). The many new candidate genes suggested by these results include IL10, IL19, IL20, GLIS3, CD69 and IL27...
  19. pmc Rapid SNP discovery and genetic mapping using sequenced RAD markers
    Nathan A Baird
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
    PLoS ONE 3:e3376. 2008
    ..Sequencing of RAD markers is an integrated platform for SNP discovery and genotyping. This approach should be widely applicable to genetic mapping in a variety of organisms...
  20. pmc Common variants conferring risk of schizophrenia
    Hreinn Stefansson
    deCODE Genetics, Sturlugata 8, IS 101 Reykjavik, Iceland
    Nature 460:744-7. 2009
    ..2. Our findings implicating the MHC region are consistent with an immune component to schizophrenia risk, whereas the association with NRGN and TCF4 points to perturbation of pathways involved in brain development, memory and cognition...
  21. pmc Genotype imputation
    Yun Li
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109 2029, USA
    Annu Rev Genomics Hum Genet 10:387-406. 2009
    b>Genotype imputation is now an essential tool in the analysis of genome-wide association scans. This technique allows geneticists to accurately evaluate the evidence for association at genetic markers that are not directly genotyped...
  22. pmc Fast model-based estimation of ancestry in unrelated individuals
    David H Alexander
    Department of Biomathematics, University of California at Los Angeles, Los Angeles, California 90095, USA
    Genome Res 19:1655-64. 2009
    ..Estimated ancestries, derived from multi-locus genotype data, can be used to perform a statistical correction for population stratification...
  23. ncbi Peginterferon-alpha2a and ribavirin combination therapy in chronic hepatitis C: a randomized study of treatment duration and ribavirin dose
    Stephanos J Hadziyannis
    Department of Medicine and Hepatology, Henry Dunant Hospital, Athens, Greece
    Ann Intern Med 140:346-55. 2004
    ..Treatment with pegylated interferon (peginterferon) and ribavirin for 48 weeks is more effective than conventional interferon and ribavirin in patients with chronic hepatitis C...
  24. ncbi R/qtl: QTL mapping in experimental crosses
    Karl W Broman
    Department of Biostatistics, Johns Hopkins University, 615 N Wolfe St, Baltimore, MD 21205, USA
    Bioinformatics 19:889-90. 2003
    ....
  25. pmc Autism genome-wide copy number variation reveals ubiquitin and neuronal genes
    Joseph T Glessner
    Center for Applied Genomics, Children s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
    Nature 459:569-73. 2009
    ....
  26. pmc Fast and accurate genotype imputation in genome-wide association studies through pre-phasing
    Bryan Howie
    Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
    Nat Genet 44:955-9. 2012
    ..sequencing efforts are producing large collections of haplotypes that can be used as reference panels for genotype imputation in genome-wide association studies (GWAS)...
  27. doi Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance
    Dongliang Ge
    Institute for Genome Sciences and Policy, Center for Human Genome Variation, Duke University, Durham, North Carolina 27708, USA
    Nature 461:399-401. 2009
    ..06 x 10(-25)) and African-Americans (P = 2.06 x 10(-3)). Because the genotype leading to better response is in substantially greater frequency in European than African populations, this ..
  28. pmc Accurate whole human genome sequencing using reversible terminator chemistry
    David R Bentley
    Illumina Cambridge Ltd Formerly Solexa Ltd, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK
    Nature 456:53-9. 2008
    ..Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications...
  29. ncbi Peginterferon alfa-2b plus ribavirin compared with interferon alfa-2b plus ribavirin for initial treatment of chronic hepatitis C: a randomised trial
    M P Manns
    Division of Gastroenterology and Hepatology, Medical School of Hannover, Hannover, Germany
    Lancet 358:958-65. 2001
    ..In this randomised trial, peginterferon alfa-2b plus ribavirin was compared with interferon alfa-2b plus ribavirin...
  30. pmc A simple and robust statistical test for detecting the presence of recombination
    Trevor C Bruen
    McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
    Genetics 172:2665-81. 2006
    ..The results suggest that phi(w) is one of the best approaches to distinguish recurrent mutation from recombination in a wide variety of circumstances...
  31. doi Telaprevir with peginterferon and ribavirin for chronic HCV genotype 1 infection
    John G McHutchison
    Duke Clinical Research Institute and Duke University, Durham, NC 27715, USA
    N Engl J Med 360:1827-38. 2009
    ..therapy for chronic hepatitis C virus (HCV) infection is effective in less than 50% of patients infected with HCV genotype 1...
  32. pmc Rare variants create synthetic genome-wide associations
    Samuel P Dickson
    Institute for Genome Sciences and Policy, Center for Human Genome Variation, Duke University, Durham, North Carolina, USA
    PLoS Biol 8:e1000294. 2010
    ..In conclusion, uncommon or rare genetic variants can easily create synthetic associations that are credited to common variants, and this possibility requires careful consideration in the interpretation and follow up of GWAS signals...
  33. ncbi Association of anxiety-related traits with a polymorphism in the serotonin transporter gene regulatory region
    K P Lesch
    Department of Psychiatry, University of Wurzburg, Fuchsleinstrasse 15, 97080 Wurzburg, Germany
    Science 274:1527-31. 1996
    ....
  34. pmc Genome-wide association analysis of metabolic traits in a birth cohort from a founder population
    Chiara Sabatti
    Department of Human Genetics and Los Angeles, Los Angeles, California 90095, USA
    Nat Genet 41:35-46. 2009
    ..The association observed between low-density lipoprotein and an infrequent variant in AR suggests the potential of such a cohort for identifying associations with both common, low-impact and rarer, high-impact quantitative trait loci...
  35. ncbi The structure of haplotype blocks in the human genome
    Stacey B Gabriel
    Whitehead MIT Center for Genome Research, Cambridge, MA 02139, USA
    Science 296:2225-9. 2002
    ..Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease...
  36. pmc SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap
    Andrew D Johnson
    The Framingham Heart Study of the National Heart, Lung, and Blood Institute of the National Institutes of Health, USA
    Bioinformatics 24:2938-9. 2008
    ....
  37. pmc Genome-wide association study identifies five new breast cancer susceptibility loci
    Clare Turnbull
    Section of Cancer Genetics, The Institute of Cancer Research, Sutton, Surrey, UK
    Nat Genet 42:504-7. 2010
    ....
  38. pmc The genetic structure and history of Africans and African Americans
    Sarah A Tishkoff
    Department of Biology, University of Maryland, College Park, MD 20742, USA
    Science 324:1035-44. 2009
    ..This study helps tease apart the complex evolutionary history of Africans and African Americans, aiding both anthropological and genetic epidemiologic studies...
  39. pmc Common regulatory variation impacts gene expression in a cell type-dependent manner
    Antigone S Dimas
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1HH, Cambridge, UK
    Science 325:1246-50. 2009
    ..These data suggest that the complete regulatory variant repertoire can only be uncovered in the context of cell-type specificity...
  40. pmc Boceprevir for untreated chronic HCV genotype 1 infection
    Fred Poordad
    Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
    N Engl J Med 364:1195-206. 2011
    ..The rate of sustained virologic response has been below 50% in cases of HCV genotype 1 infection...
  41. pmc Reconstructing Indian population history
    David Reich
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 461:489-94. 2009
    ..We therefore predict that there will be an excess of recessive diseases in India, which should be possible to screen and map genetically...
  42. ncbi A new multipoint method for genome-wide association studies by imputation of genotypes
    Jonathan Marchini
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    Nat Genet 39:906-13. 2007
    ..A notable future use of our method will be to boost power by combining data from genome-wide scans that use different SNP sets...
  43. pmc Genes mirror geography within Europe
    John Novembre
    Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics, University of California Los Angeles, Los Angeles, California 90095, USA
    Nature 456:98-101. 2008
    ..In addition, the results are relevant to the prospects of genetic ancestry testing; an individual's DNA can be used to infer their geographic origin with surprising accuracy-often to within a few hundred kilometres...
  44. doi Genotype imputation for genome-wide association studies
    Jonathan Marchini
    Department of Statistics, University of Oxford, Oxford, UK
    Nat Rev Genet 11:499-511. 2010
    ..b>Genotype imputation has been used widely in the analysis of GWA studies to boost power, fine-map associations and ..
  45. pmc Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
    Susanna Atwell
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Nature 465:627-31. 2010
    ..Our study demonstrates the feasibility of GWA studies in A. thaliana and suggests that the approach will be appropriate for many other organisms...
  46. pmc Mapping the genetic architecture of gene expression in human liver
    Eric E Schadt
    Rosetta Inpharmatics, Seattle, Washington, United States of America
    PLoS Biol 6:e107. 2008
    ..We also identify SORT1 and CELSR2 as candidate susceptibility genes for a locus recently associated with coronary artery disease and plasma low-density lipoprotein cholesterol levels in the process...
  47. pmc A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals
    Brian L Browning
    Department of Statistics, University of Auckland, Auckland 1142, New Zealand
    Am J Hum Genet 84:210-23. 2009
    ..particularly when imputing low-frequency variants, and that unphased reference panels can provide highly accurate genotype imputation...
  48. pmc Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG)
    Jelle Matthijnssens
    Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
    Arch Virol 156:1397-413. 2011
    ..This system assigns a specific genotype to each of the 11 genome segments of a particular RV strain according to established nucleotide percent cutoff ..
  49. ncbi An economic method for the fluorescent labeling of PCR fragments
    M Schuelke
    Department of Neuropediatrics, Charite University Hospital, Augustenburger Platz 1, D 13353 Berlin, Germany
    Nat Biotechnol 18:233-4. 2000
    ..A poor man's approach to genotyping for research and high-throughput diagnostics...
  50. pmc Population analysis of large copy number variants and hotspots of human genetic disease
    Andy Itsara
    Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA 98195, USA
    Am J Hum Genet 84:148-61. 2009
    ..g., 3q29, 16p12, and 15q25.2) for further investigation. This study provides one of the first analyses of large, rare (0.1%-1%) CNVs in the general population, with insights relevant to future analyses of genetic disease...
  51. doi Sofosbuvir for hepatitis C genotype 2 or 3 in patients without treatment options
    Ira M Jacobson
    Weill Cornell Medical College, New York, NY 10021, USA
    N Engl J Med 368:1867-77. 2013
    Patients chronically infected with hepatitis C virus (HCV) genotype 2 or 3 for whom treatment with peginterferon is not an option, or who have not had a response to prior interferon treatment, currently have no approved treatment options...
  52. ncbi Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families
    E H Corder
    Department of Medicine, Joseph and Kathleen Bryan Alzheimer s Disease Research Center, Duke University Medical Center, Durham, NC 27710
    Science 261:921-3. 1993
    ..Thus APOE-epsilon 4 gene dose is a major risk factor for late onset AD and, in these families, homozygosity for APOE-epsilon 4 was virtually sufficient to cause AD by age 80...
  53. pmc The architecture of gene regulatory variation across multiple human tissues: the MuTHER study
    Alexandra C Nica
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
    PLoS Genet 7:e1002003. 2011
    ..Our results underline the need to account for the complexity of eQTL tissue-specificity in an effort to assess consequences of such variants for complex traits...
  54. pmc The NCBI dbGaP database of genotypes and phenotypes
    Matthew D Mailman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892 6510, USA
    Nat Genet 39:1181-6. 2007
    ..for Biotechnology Information has created the dbGaP public repository for individual-level phenotype, exposure, genotype and sequence data and the associations between them...
  55. pmc Diversity of human copy number variation and multicopy genes
    Peter H Sudmant
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
    Science 330:641-6. 2010
    ..1 million "singly unique nucleotide" positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families...
  56. pmc Genetic sensitivity to the environment: the case of the serotonin transporter gene and its implications for studying complex diseases and traits
    Avshalom Caspi
    Department of Psychology, and Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Am J Psychiatry 167:509-27. 2010
    ....
  57. pmc Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis
    Philip Supply
    INSERM U629, Institut Pasteur de Lille, 1, Rue du Prof Calmette, F 59019 Lille cedex, France
    J Clin Microbiol 44:4498-510. 2006
    ..This 15-locus system is therefore proposed as the new standard for routine epidemiological discrimination of M. tuberculosis isolates and the 24-locus system as a high-resolution tool for phylogenetic studies...
  58. pmc Global variation in copy number in the human genome
    Richard Redon
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 444:444-54. 2006
    ..The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies...
  59. pmc Genotype and SNP calling from next-generation sequencing data
    Rasmus Nielsen
    Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
    Nat Rev Genet 12:443-51. 2011
    ..Recently developed statistical methods both improve and quantify the considerable uncertainty associated with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data...
  60. doi A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25
    Rayjean J Hung
    International Agency for Research on Cancer IARC, Lyon 69008, France
    Nature 452:633-7. 2008
    ..Our results provide compelling evidence of a locus at 15q25 predisposing to lung cancer, and reinforce interest in nicotinic acetylcholine receptors as potential disease candidates and chemopreventative targets...
  61. pmc Bioinformatics challenges for genome-wide association studies
    Jason H Moore
    Department of Genetics, Department of Community and Family Medicine, Dartmouth Medical School, Lebanon, NH 03756, USA
    Bioinformatics 26:445-55. 2010
    ..shift away from the biostatistical approach toward a more holistic approach that recognizes the complexity of the genotype-phenotype relationship that is characterized by significant heterogeneity and gene-gene and gene-environment ..
  62. doi Genome-wide genetic marker discovery and genotyping using next-generation sequencing
    John W Davey
    Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King s Buildings, West Mains Road, Edinburgh, EH9 3JT, UK
    Nat Rev Genet 12:499-510. 2011
    ....
  63. pmc Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS
    Mariely DeJesus-Hernandez
    Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
    Neuron 72:245-56. 2011
    ..Our findings indicate that repeat expansion in C9ORF72 is a major cause of both FTD and ALS...
  64. doi IL28B is associated with response to chronic hepatitis C interferon-alpha and ribavirin therapy
    Vijayaprakash Suppiah
    Storr Liver Unit, University of Sydney, Sydney, Australia
    Nat Genet 41:1100-4. 2009
    ..sustained virological response (SVR) to PEG-IFN-alpha/RBV combination therapy in 293 Australian individuals with genotype 1 chronic hepatitis C, with validation in an independent replication cohort consisting of 555 individuals...
  65. doi Human papillomavirus genotype attribution in invasive cervical cancer: a retrospective cross-sectional worldwide study
    Silvia de Sanjose
    IDIBELL, Institut Català d Oncologia Catalan Institute of Oncology, L Hospitalet de Llobregat, Barcelona, Spain
    Lancet Oncol 11:1048-56. 2010
    ..We aimed to provide novel and comprehensive data about the worldwide genotype distribution in patients with invasive cervical cancer.
  66. ncbi Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes
    Peter Simmonds
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, United Kingdom
    Hepatology 42:962-73. 2005
    ..Virus Database (Japan), euHCVdb (France), and Los Alamos (United States), met to re-examine the status of HCV genotype nomenclature, resolve conflicting genotype or subtype names among described variants of HCV, and draw up revised ..
  67. pmc DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines
    Jordana T Bell
    Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
    Genome Biol 12:R10. 2011
    ..Here we measured methylation levels at 22,290 CpG dinucleotides in lymphoblastoid cell lines from 77 HapMap Yoruba individuals, for which genome-wide gene expression and genotype data were also available.
  68. pmc Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism
    Stephan J Sanders
    Program on Neurogenetics, Yale University School of Medicine, 230 South Frontage Road, New Haven, CT 06520, USA
    Neuron 70:863-85. 2011
    ..4 × 10(-7)). We estimate there are 130-234 ASD-related CNV regions in the human genome and present compelling evidence, based on cumulative data, for association of rare de novo events at 7q11.23, 15q11.2-13.1, 16p11.2, and Neurexin 1...
  69. pmc Evaluation of next generation sequencing platforms for population targeted sequencing studies
    Olivier Harismendy
    Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
    Genome Biol 10:R32. 2009
    ..To evaluate these platforms for this application, we analyzed human sequence generated by the Roche 454, Illumina GA, and the ABI SOLiD technologies for the same 260 kb in four individuals...
  70. pmc CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
    Alexej Abyzov
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 21:974-84. 2011
    ..Finally, by combining discovery and genotyping, we identified six potential de novo CNVs in two family trios...
  71. pmc Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain
    J Raphael Gibbs
    Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Genet 6:e1000952. 2010
    ..We believe these data, which we have made publicly available, will provide a critical step toward understanding the biological effects of genetic variation...
  72. ncbi Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment
    Steven T Kalinowski
    Department of Ecology, Montana State University, Bozeman, MT 59717, USA
    Mol Ecol 16:1099-106. 2007
    ..0 and 2.0 of CERVUS to accommodate genotyping error miscalculate the probability of observing an erroneous genotype. Computer simulation and reanalysis of paternity in Rum red deer show that correcting this error increases ..
  73. ncbi Tumor stem cells derived from glioblastomas cultured in bFGF and EGF more closely mirror the phenotype and genotype of primary tumors than do serum-cultured cell lines
    Jeongwu Lee
    Neuro Oncology Branch, National Cancer Institute, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
    Cancer Cell 9:391-403. 2006
    ..from primary glioblastomas harbor extensive similarities to normal neural stem cells and recapitulate the genotype, gene expression patterns, and in vivo biology of human glioblastomas...
  74. pmc A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD
    Alan E Renton
    Neuromuscular Diseases Research Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
    Neuron 72:257-68. 2011
    ..The repeat expansion is also present in one-third of familial ALS cases of outbred European descent, making it the most common genetic cause of these fatal neurodegenerative diseases identified to date...
  75. doi Genetic variation in IL28B is associated with chronic hepatitis C and treatment failure: a genome-wide association study
    Andri Rauch
    University Clinic of Infectious Diseases, University Hospital Bern and University of Bern, Bern, Switzerland
    Gastroenterology 138:1338-45, 1345.e1-7. 2010
    ..We performed a genome-wide association study to screen for host genetic determinants of HCV persistence and response to therapy...
  76. ncbi High-resolution genotyping by amplicon melting analysis using LCGreen
    Carl T Wittwer
    Department of Pathology, University of Utah Medical School, Salt Lake City, UT 84132, USA
    Clin Chem 49:853-60. 2003
    ..Our aim was to develop a closed-tube system for genotyping and mutation scanning that did not require labeled oligonucleotides...
  77. pmc A variant associated with nicotine dependence, lung cancer and peripheral arterial disease
    Thorgeir E Thorgeirsson
    deCODE Genetics, 101 Reykjavik, Iceland
    Nature 452:638-42. 2008
    ..The findings provide a case study of a gene-environment interaction, highlighting the role of nicotine addiction in the pathology of other serious diseases...
  78. pmc Estimation of effect size distribution from genome-wide association studies and implications for future discoveries
    Ju Hyun Park
    Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Rockville, Maryland, USA
    Nat Genet 42:570-5. 2010
    ..However, for BPC cancers, which have modest familial aggregation, our analysis suggests that risk models based on common variants alone will have modest discriminatory power (63.5% area under curve), even with new discoveries...
  79. doi Invited review: reliability of genomic predictions for North American Holstein bulls
    P M Vanraden
    Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 2350, USA
    J Dairy Sci 92:16-24. 2009
    ..Reliability increased more by doubling the number of bulls genotyped than the number of markers genotyped. Genomic prediction improves reliability by tracing the inheritance of genes even with small effects...
  80. pmc Development and characterization of a high density SNP genotyping assay for cattle
    Lakshmi K Matukumalli
    Department of Bioinformatics and Computational Biology, George Mason University, Manassas, Virginia, United States of America
    PLoS ONE 4:e5350. 2009
    ..The BovineSNP50 assay described here is commercially available from Illumina and provides a robust platform for mapping disease genes and QTL in cattle...
  81. pmc Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach
    Jesse A Poland
    Hard Winter Wheat Genetics Research Unit, United States Department of Agriculture Agricultural Research Service, Manhattan, Kansas, United States of America
    PLoS ONE 7:e32253. 2012
    ..Finally, as a result of low per-sample costs, GBS will have broad application in genomics-assisted plant breeding programs...
  82. doi Telaprevir for retreatment of HCV infection
    Stefan Zeuzem
    Johann Wolfgang Goethe University Medical Center, Frankfurt am Main, Germany
    N Engl J Med 364:2417-28. 2011
    Up to 60% of patients with hepatitis C virus (HCV) genotype 1 infection do not have a sustained virologic response to therapy with peginterferon alfa plus ribavirin.
  83. pmc PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice
    F Baudat
    Institut de Genetique Humaine, UPR1142, CNRS, Montpellier, France
    Science 327:836-40. 2010
    ..Our results provide a molecular basis for the distribution of meiotic recombination in mammals, in which the binding of PRDM9 to specific DNA sequences targets the initiation of recombination at specific locations in the genome...
  84. doi SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
    Curtis P van Tassell
    Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA
    Nat Methods 5:247-52. 2008
    ..b>Genotype data for these 66 individuals validated 92% of 23,357 selected genome-wide SNPs, with a genotypic and sequence ..
  85. pmc Common genetic variation and the control of HIV-1 in humans
    Jacques Fellay
    Center for Human Genome Variation, Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, USA
    PLoS Genet 5:e1000791. 2009
    ..This study thus represents a comprehensive assessment of common human genetic variation in HIV-1 control in Caucasians...
  86. pmc Genome structural variation discovery and genotyping
    Can Alkan
    Department of Genome Sciences, University of Washington School of Medicine, Foege S413C, 3720 15th Ave NE, Seattle, Washington, USA
    Nat Rev Genet 12:363-76. 2011
    ..We argue that the long-term goal should be routine, cost-effective and high quality de novo assembly of human genomes to comprehensively assess all classes of structural variation...
  87. doi A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits
    Yoon Shin Cho
    Center for Genome Science, National Institute of Health, Seoul, Korea
    Nat Genet 41:527-34. 2009
    ..2 x 10(-3), P = 1.4 x 10(-7) and P = 6.0 x 10(-4), respectively). This large-scale GWA analysis of well-characterized Korean population-based samples highlights previously unknown biological pathways...
  88. pmc The relationship of DNA methylation with age, gender and genotype in twins and healthy controls
    Marco P Boks
    Rudolf Magnus Institute of Neuroscience, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
    PLoS ONE 4:e6767. 2009
    ..The identification of CpG loci of which DNA methylation levels are under genetic control or are related to age or gender will facilitate further studies into the role of DNA methylation and disease...
  89. ncbi Effects of age, sex, and ethnicity on the association between apolipoprotein E genotype and Alzheimer disease. A meta-analysis. APOE and Alzheimer Disease Meta Analysis Consortium
    L A Farrer
    Department of Neurology, Boston University School of Medicine, Mass 02118, USA
    JAMA 278:1349-56. 1997
    To examine more closely the association between apolipoprotein E (APOE) genotype and Alzheimer disease (AD) by age and sex in populations of various ethnic and racial denominations.
  90. ncbi 'Mendelian randomization': can genetic epidemiology contribute to understanding environmental determinants of disease?
    George Davey Smith
    University of Bristol, Department of Social Medicine, Canynge Hall, Whiteladies Road, Bristol BS8 2PR, UK
    Int J Epidemiol 32:1-22. 2003
    ....
  91. doi Clinical risk factors, DNA variants, and the development of type 2 diabetes
    Valeriya Lyssenko
    Department of Clinical Sciences, Lund University, Malmo, Sweden
    N Engl J Med 359:2220-32. 2008
    ..Type 2 diabetes mellitus is thought to develop from an interaction between environmental and genetic factors. We examined whether clinical or genetic factors or both could predict progression to diabetes in two prospective cohorts...
  92. pmc Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology
    Antonio M Ramos
    Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands
    PLoS ONE 4:e6524. 2009
    ....
  93. ncbi Epidemiology of hepatitis C virus infection in Pakistan
    Nadeem Sajjad Raja
    Department of Medical Microbiology, Southend University Hospital NHS Foundation Trust, Essex, United Kingdom
    J Microbiol Immunol Infect 41:4-8. 2008
    ..Although at present a small proportion of those with chronic HCV infection develop liver failure or hepatocellular carcinoma, it is estimated that the incidence of these advanced disease complications will increase over the coming years...
  94. pmc Development and implementation of high-throughput SNP genotyping in barley
    Timothy J Close
    Department of Botany and Plant Sciences, University of California UCR, Riverside, CA, 92521, USA
    BMC Genomics 10:582. 2009
    ..maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear ..
  95. pmc Boceprevir for previously treated chronic HCV genotype 1 infection
    Bruce R Bacon
    Saint Louis University School of Medicine, St Louis, Mo 63110 0250, USA
    N Engl J Med 364:1207-17. 2011
    In patients with chronic infection with hepatitis C virus (HCV) genotype 1 who do not have a sustained response to therapy with peginterferon-ribavirin, outcomes after retreatment are suboptimal...
  96. pmc Dissection of genetically complex traits with extremely large pools of yeast segregants
    Ian M Ehrenreich
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA
    Nature 464:1039-42. 2010
    ..Our method should have broad applications in yeast and can be extended to other organisms...
  97. pmc GWAMA: software for genome-wide association meta-analysis
    Reedik Magi
    Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    BMC Bioinformatics 11:288. 2010
    ..Although statistical software analysis packages incorporate routines for meta-analysis, they are ill equipped to meet the challenges of the scale and complexity of data generated in genome-wide association studies...
  98. pmc Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing
    Magnus Manske
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Nature 487:375-9. 2012
    ..An open-access web application has been established for the exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome...
  99. ncbi An automated genotyping system for analysis of HIV-1 and other microbial sequences
    Tulio de Oliveira
    Evolution Group at the Zoology Department, University of Oxford, UK
    Bioinformatics 21:3797-800. 2005
    ..Here, we describe the development of an automated genotyping system that can be easily applied to HIV-1 and other rapidly evolving viral pathogens...
  100. pmc Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa
    Keyan Zhao
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
    Nat Commun 2:467. 2011
    ....
  101. doi Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays
    Radoje Drmanac
    Complete Genomics, Inc, 2071 Stierlin Court, Mountain View, CA 94043, USA
    Science 327:78-81. 2010
    ..The high accuracy, affordable cost of $4400 for sequencing consumables, and scalability of this platform enable complete human genome sequencing for the detection of rare variants in large-scale genetic studies...

Research Grants74

  1. STATISITICAL DESIGN, MONITORING &COORD. OF VISION CLINICAL TRIALS &EPIDEMIOLOGY
    Keri Hammel; Fiscal Year: 2013
    ..No treatment will be provided as part of this protocol. Title: Genotype-Phenotype Study of Patients with Plaquenil(Registered Trademark)-Induced Retinal Toxicity, with Evaluation of the ..
  2. STATISITICAL DESIGN, MONITORING &COORD. OF VISION CLINICAL TRIALS &EPIDEMIOLOGY
    Keri Hammel; Fiscal Year: 2012
    ..No treatment will be provided as part of this protocol. Title: Genotype-Phenotype Study of Patients with Plaquenil(Registered Trademark)-Induced Retinal Toxicity, with Evaluation of the ..
  3. Understanding/ Treating Neuropsychiatric Symptoms of Pediatric Physical Illness
    Eva Szigethy; Fiscal Year: 2009
    ..abstract_text> ..
  4. Genetic variation and regulatory networks: Mechanisms and complexity
    DANA PE ER; Fiscal Year: 2009
    ..We will develop computational algorithms that integrate genotype, gene expression and phenotype data to construct models that describe how sequence variation perturbs the ..
  5. Prevention of Complications in Thalassemia
    Elliott P Vichinsky; Fiscal Year: 2011
    ..of newborns who have undergone DNA and genetic modifier diagnosis has enabled us to better understand the genotype/phenotype correlations20-23...
  6. High Throughput Genotyping and DNA Sequencing for Studying the Genetic Contributi
    Sonia Dua; Fiscal Year: 2013
    ..and ensure that any data related to family structure, when available, are cross-referenced to any DNA samples and genotype data generated from the sample...
  7. Brain Activation responses in adolescents with genetic predisposition to obesity
    Susan Carnell; Fiscal Year: 2011
    ..Buccal samples will be collected from 300 lean (BMI centile<85th) 14-18 yr olds, and used to genotype common obesity-associated variants (e.g., FTO)...
  8. Effects of Testosterone and Genetic Factors on Psychological and Motor Function i
    NICOLE RENEE TARTAGLIA; Fiscal Year: 2013
    ..research careers in psychology, outcomes in sex chromosomal abnormalities, endocrinology, clinical trials, genotype-phenotype studies, neurogenetic syndromes, developmental disabilities, bioethics, and molecular biology...
  9. Neurobehavioral Correlates of Familial/genetic obesity risk in adolescents
    Susan Carnell; Fiscal Year: 2013
    ..Buccal samples will be collected from 300 lean (BMI centile<85th) 14-18 yr olds, and used to genotype common obesity-associated variants (e.g., FTO)...
  10. Genetic and physiological causes of inherited Vascular and Metabolic Diseases
    Arya Mani; Fiscal Year: 2013
    ..In vitro studies have indicated that these mutations impair Wnt signaling. Genotype phenotype correlation showed that the mutations impact number of the metabolic phenotypes that are present in ..
  11. Role and Regulation of INrf2
    ANIL KUMAR JAISWAL; Fiscal Year: 2013
    ..In addition, compare the sensitivity of conditional INrf2 knockout mice expressing the null genotype with that of mice expressing INrf2, following carcinogen exposure, to develop skin and liver tumors...
  12. BIOCHEMISTRY OF PRE-MRNA SPLICING
    Adrian R Krainer; Fiscal Year: 2010
    ..counseling and phenotypic-risk assessment in the clinic, yet there is much room for improvement in predicting genotype-phenotype correlations that involve aberrant splicing or NMD...
  13. Functional Neuroimaging of Individual Differences in Affect and Motivation
    BRIAN JAMES MICKEY; Fiscal Year: 2013
    ..We propose to recruit 240 healthy participants and classify them by NPY genotype. We will characterize the effects of NPY variation on plasma NPY levels, motivated behavior, and emotional traits...
  14. The genetics and pathophysiology of impaired Wnt signaling in metabolic syndrome
    Arya Mani; Fiscal Year: 2012
    ..for mutations in LRP6, in order to identify the spectrum and prevalence of LRP6 mutation and establish genotype-phenotype correlations...
  15. Cell signaling as a leukemia biomarker
    JAMES WILLIAM JACOBBERGER; Fiscal Year: 2013
    ..To test this idea, we propose to correlate phenotype (signaling) and genotype, determined by high throughput sequencing...
  16. Impacts of surface receptors [Toll like receptor (TLRs) and Fc gamma receptors (F
    Collins Ouma; Fiscal Year: 2012
    ..Previous studies carried out in low malaria endemic areas demonstrated that Fc3RIIa- 131H/H genotype, in combination with Fc3RIIIb-NA2 allele, is associated with susceptibility to CM, while a recent study found no ..
  17. Dependency of O-3 Induced Lung Mucus Hypersecretion on NQ01
    W Michael Foster; Fiscal Year: 2010
    ..observations by us in a healthy cohort of non-smoking human subjects (n=135) demonstrates that a homozygotic genotype for a single nucleotide polymorphism of the quinone oxido-reductase enzyme, NQO1, protects from the acute ..
  18. Folate Status, Genomic Uracil, and the Balance of Base Excision Repair Activity
    Michael D Wyatt; Fiscal Year: 2011
    ..metabolism and BER should provide a better means devising better prevention and treatment strategies based on genotype. PUBLIC HEALTH RELEVANCE: Dietary folic acid is an important nutrient for human health, but there is concern that ..
  19. Insights from Comparative Genomics for the Treatment of Pneumococcal Infections
    Natalia Luisa Hiller; Fiscal Year: 2011
    ..induced otitis media and the development of a suite of bioinformatic tools for comparative genomics to identify genotype-phenotype correlations. Her work has exposed the very extensive genomic diversity among clinical S...
  20. Heat Shock Protein Synthesis Inhibitor Treatment of Hepatitis C Viral Infection
    SAMUEL WHEELER FRENCH; Fiscal Year: 2013
    ..70% of patients in the United States are infected with genotype 1 for which sustained virologic response (SVR) is only 42-46%...
  21. Epistasis in Steroidogenic Genes in the Prediction of Alzheimer's Disease
    CRAIG STEPHEN ATWOOD; Fiscal Year: 2013
    ..This grant therefore aims to perform genotype and hormone analyses in a larger sample size to gain greater confidence that these interactions are important ..
  22. Androgen Receptor Pathway and Risk of Hepatic Fibrosis in Hepatitis C
    DONNA LORRAINE WHITE; Fiscal Year: 2013
    ..chronic HCV to evaluate the association between the androgen mediated AR signaling pathway spanning from germline genotype to hepatic gene expression and the risk of cirrhosis in male veterans with chronic hepatitis C infection...
  23. Immune Development: Role of Milk Cell Transfer and Recipient Gender
    Ameae M Walker; Fiscal Year: 2013
    ..of DTH responsivity is the result of a change in the balance of T cell subsets, and 3) using the novel four core genotype mouse model, to determine whether the sex effect is caused by sex chromosome complement or by the testis-..
  24. Randomized trial of PEITC as a modifier of NNK metabolism in smokers
    Jian Min Yuan; Fiscal Year: 2012
    ..protective effect is confined to individuals with glutathione S-transferase (GST) M1 null-null or GSTT1 null-null genotype, and is particularly evident among those with the null genotypes of both GSTM1 and GSTT1...
  25. Role of Sex Chromosome Complement in the CNS during Autoimmune Disease
    Sienmi Du; Fiscal Year: 2013
    ..The XY*x genotype are females that essentially have 1 X chromosome (1X) and 0 Y chromosome (0Y), and thus can be used to compare ..
  26. Insights from Comparative Genomics for the Treatment of Pneumococcal Infections
    Natalia Luisa Hiller; Fiscal Year: 2013
    ..induced otitis media and the development of a suite of bioinformatic tools for comparative genomics to identify genotype-phenotype correlations. Her work has exposed the very extensive genomic diversity among clinical S...
  27. Irritable bowel syndrome-diarrhea: the role of gluten intolerance and HLA-DQ2
    MICHAEL L CAMILLERI; Fiscal Year: 2010
    ..we plan to determine the role of diet in the development of functional GI and motility disorders and how genotype contributes to the development of functional GI and motility disorders...
  28. Regulation of Human Papillomavirus Replication via Cell Signaling Pathways
    ANASTACIA GRIEGO; Fiscal Year: 2013
    ..HPVs are designated as oncogenic based on the ability of a specific viral genotype to cause transformation in the host cell...
  29. Green Tea and Reduction of Breast Cancer Risk
    MINDY SUSAN KURZER; Fiscal Year: 2013
    ..with reduced breast cancer risk only in women with the low-activity catechol-O-methyltransferase (COMT) genotype. This is consistent with the understanding that COMT activity significantly influences catechin metabolism and ..
  30. GENETICS OF DELAYED PUBERTY
    Lawrence C Layman; Fiscal Year: 2013
    ..We will genotype individuals from families with mutations in either of these genes to characterize the segregation patterns and ..
  31. Oxidative stress and neurogenetic networks in Drosophila
    Robert R H Anholt; Fiscal Year: 2010
    ..Comparisons among the control and treatment condition will enable us to evaluate genotype by environment effects at the level of genetic networks and identify critical genes that drive the connectivity ..
  32. Anxiety development in 5-HT1A autoreceptor knockout mice, interaction with stress
    Rene Hen; Fiscal Year: 2010
    ..studies like those by Caspi et al demonstrating how early maltreatment interacts with the monoamine oxidase A genotype to yield antisocial behavior and how the 5-HTT transporter interacts with adverse early adult events to increase ..
  33. Zot, Zonulin, and Pathophysiology of Intestinal Tight Junctions
    Alessio Fasano; Fiscal Year: 2013
    ..e., the uncleaved product of HP2. The HP2- 2 genotype is more frequently encountered in immune-mediated conditions, including celiac disease, Crohn's disease, and ..
  34. MOUSE MODEL FOR DISEASES OF PROTEIN MISFOLDING
    P Michael Conn; Fiscal Year: 2012
    ..The two models to be used are available and have the predicted genotype and necessary phenotype...
  35. RRSS #08: Evaluating Prevalence HPV Infection Among Head and Neck Cancer Patients
    Dennis M Deapen; Fiscal Year: 2009
    ..16 alone was found to account for more than 90% of HPV-positive HNSCC and HPV type 18 is the second most common genotype, a variety of other high- and low-risk HPVs were also found to be present in HNSCC...
  36. Novel genetics, pathobiology &therapy of nephronophthisis-related ciliopathies
    Friedhelm Hildebrandt; Fiscal Year: 2013
    ..2. Functionally characterize novel ciliopathy genes and determine genotype-phenotype correlations. 3...
  37. Gender Bias in Lupus: Contribution of Sex Chromosomes
    Ram Raj Singh; Fiscal Year: 2012
    ..Finally, in Aim 3, we will generate mice of the XO genotype to determine if the sex chromosome effect on disease outcomes and immune measures in Aims 1 and 2 is attributable ..
  38. Identifying Key Structural Elements in the Activation of the Arp2/3 Complex
    Patricia A Khuu; Fiscal Year: 2013
    ..PCR and DNA sequencing will be used to genotype mutant strains, while Western blot will reveal expression levels of mutant genes...
  39. Adherent Escherichia coli and associated virulence genes in children with IBD
    Sandra C Kim; Fiscal Year: 2010
    ..their associated virulence genes in children and adolescents with IBD and correlating these findings with host genotype. PUBLIC HEALTH RELEVANCE: Completion of this proposal will identify specific dominant E...
  40. Contribution of Gstm1 to the severity of hypertension and chronic kidney disease
    Thu H Le; Fiscal Year: 2013
    ..Those with the GSTM1(0/0) genotype have increased risks of HTN...
  41. Genetic Vulnerability to Alcohol Withdrawal and Genetically Correlated Behaviors
    Kari J Buck; Fiscal Year: 2012
    ..2) Test the hypothesis that genotype- dependent differences in chronic ethanol withdrawal are related to oxidative stress and mitochondrial function...
  42. Functional Studies of Variants of the Bipolar Risk Gene CACNA1C in Human Neurons
    JEN PAN; Fiscal Year: 2013
    ..unique sequences in a genomic locus, introduces site-specific changes in the native genome, and helps elucidate genotype-phenotype relationships in an isogenic background...
  43. Arrhythmia Mechanisms in Sarcomeric Cardiomyopathies
    Bjorn C Knollmann; Fiscal Year: 2012
    ..While there is a rough relationship between prognosis and the degree of cardiac hypertrophy and fibrosis, this genotype/phenotype correlation is weak...
  44. Metabolic Pathways and Defects in Fructose Metabolism
    DEAN TOLAN; Fiscal Year: 2009
    ..Lack of knowledge about sites of fructose metabolism and about genotype-phenotype relationships still exists for this disease and reflects the incomplete understanding of normal ..
  45. Mouse Models of Non-Syndromic Cardiac Progeria
    Ali J Marian; Fiscal Year: 2012
    ..The models will genetically recapitulate the human genotype of Lmna mutations and also will enable analyzing involvement of multiple cardiac and non-cardiac cell types, ..
  46. OLFACTORY RECEPTOR COPY NUMBER ASSOCIATION WITH AGE AT ONSET OF ALZHEIMER DISEASE
    Kinga Szigeti; Fiscal Year: 2013
    ..The protocol will be amended with the olfactory phenotyping. We will correlate the olfactory genotype and phenotype using the aCGH and the University of Pennsylvania Smell Identification Test (UPSIT) measure...
  47. Interaction of fetal growth and bisphenol A in obesity
    Frederick S vom Saal; Fiscal Year: 2013
    ..novel model in two strains of mice with different sensitivities to estrogen to examine the interaction between genotype, rate of fetal growth, postnatal nutrition (by using high and low energy feeds), and BPA exposure at human ..
  48. Studying a Human Stem Cell Disease Using iPS Technology
    Steven E Artandi; Fiscal Year: 2010
    ..diseases by profiling reprogrammed induced pluripotent stem cells derived from affected individuals of defined genotype." The advent of induced pluripotent stem cell (iPS cell) technology offers new and profound opportunities to ..
  49. Classical and non-classical responses to vitamin D in children: the role of DBP g
    Thomas O Carpenter; Fiscal Year: 2010
    ..Moreover, our recent analysis of vitamin D status in these children reveals that vitamin D binding protein (DBP) genotype is a significant predictor of 25-OHD and 1,25 dihydroxyvitamin D [1,25 (OH)2D] levels...
  50. The role of satellite rasiRNA in the Segregation Distorter system of Drosophila
    AMANDA MARIE LARRACUENTE; Fiscal Year: 2013
    ..If SD affects Rsp rasiRNA production, then SD genotype will correlate with Rsp rasiRNA abundance in postmeiotic testis dissections.
  51. Control of liver autophagy by phosphatidic acid signaling
    GILBERT DIPAOLO; Fiscal Year: 2013
    ..as high fat diet and age, on the efficacy of macrolipophagy, with the prediction that they may further unmask genotype-specific differences in fat accumulation and lipid metabolism...
  52. Endemic maintenance of relapsing fever genotypes.
    Michael Bela Teglas; Fiscal Year: 2013
    ..goals for this discovery- driven research, we propose to complete the following specific aims: 1) Isolate and genotype relapsing fever strains from wild rodents at six established sites endemic for relapsing fever in California and ..
  53. Role of the Renin-Angiotensin system in placental insufficiency
    Eugenia Mata-Greenwood; Fiscal Year: 2013
    ..We will utilize the BN rat as a model of placental insufficiency linked to ACEhigh genotype (similar to the human ACE D/D genotype) and the Lou rat (L) as a model of normal pregnancy linked to ACElow ..
  54. Mutational Cloning in Familial Dementia and Alzheimers Disease
    Wendy H Raskind; Fiscal Year: 2010
    ..communities at large and to facilitate corroboration of our findings in other samples, we will deposit FD genotype and phenotype information into the on-line resources GeneTests and the NCBI Variation Databases (dbSNP and dbGaP)...
  55. Translating human PPARy binding regions to gene regulation and metabolic disease
    RAYMOND EDWARD SOCCIO; Fiscal Year: 2013
    ..revealing novel associations not found in the initial GWAS and by providing the missing mechanistic link between genotype and phenotype. We will assay allelic imbalance in PPAR binding as a first step linking SNP to disease...
  56. Characterizing Mitochondrial DNA Susceptibility to Breast, Colorectal, and Prosta
    Iona Cheng; Fiscal Year: 2012
    ..Next, we will genotype mtDNA variants identified from sequencing efforts in an independent multiethnic panel of 375 individuals for ..
  57. Diesel, Allergens and Gene Interaction and Child Atopy
    Grace LeMasters; Fiscal Year: 2009
    ..This revision proposes to genotype nicotine metabolism and oxidative stress related genes for both functional and tagging single nucleotide ..
  58. Longitudinal Study of Lipids and APOE in the Development of AD and AD Pathology
    Michelle M Mielke; Fiscal Year: 2013
    ..acids, cholesterol and cholesterol esters) reflect brain functioning and pathology, and may interact with ApoE genotype in the development of AD pathogenesis, warranting human studies...
  59. Neurotrophic Factors: Genetic Variation and Serum Levels in Brain Aging
    Sudha Seshadri; Fiscal Year: 2010
    ..We propose to genotype a comprehensive panel of NTF and NTF receptors and measure serum levels of three NTF: brain derived neurotrophic ..
  60. Fatty acid desaturase activity, fish oil and colorectal cancer chemoprevention
    Harvey J Murff; Fiscal Year: 2013
    ..Our first factor will be FADS1 genotype (GG, GT, and TT) and our second factor will be fish oil supplementation (fish oil versus placebo)...
  61. Using a MALDI-TOF System for SNP Analysis
    Nadereh Jafari; Fiscal Year: 2010
    ..investigate the genetic and structural determinants of heart failure and left ventricular hypertrophy, f)rapidly genotype the Y-chromosome and autosomal SNPs to assess the nature of the evolutionary relationships between prehistoric ..
  62. Response of Rhesus Sperm to Freezing: Recovery from Osmotic and Oxidative Stress
    Stuart A Meyers; Fiscal Year: 2010
    ..stem cells, somatic cell nuclear transfer, and transgenics where propagation of a specific individual's genotype is desired...
  63. Factors for Epigenetic Silencing of Lung Cancer Genes
    Steven Belinsky; Fiscal Year: 2009
    ..whether the effect of clinical risk factors that include smoking on methylation patterns vary as a function of genotype. Finally we will describe the gene-specific promoter hypermethylation patterns at study entry and at 18-month ..
  64. Towards Understanding the Morbidity of HEV Infection
    Mohamed Tarek Shata; Fiscal Year: 2007
    ..In the Indian subcontinent, and recently in outbreaks in Baghdad and in refugees in Darfur Sudan, the virulent genotype-1 strain of HEV was isolated from AVH cases. We reported HEV is endemic in rural villages in Egypt...
  65. Mitochondrial SOD & Breast Cancer Risk-Mechanism
    JAMES YAGER; Fiscal Year: 2003
    ..In contrast, the Ala/Ala genotype was associated with increased risk of breast cancer in premenopausal women...
  66. Role of epithelial HLA-G in lung transplantation
    Steven R White; Fiscal Year: 2010
    ..However, the role of HLA-G in lung transplant survival has never been studied, and the relationship between HLA-G genotype and expression of HLA protein of the transplanted lung and host in the development of BOS is completely unknown...
  67. In vivo phenotypic effects of naturally occuring sequence variations in WNV
    Robin M Moudy; Fiscal Year: 2010
    ..Recent work examining WNV evolution has identified a new genotype (WN02) that differs from the introduced genotype (NY99) by a single amino acid, a valine to alanine change at ..
  68. HCV TREATMENT IN AFRICAN AMERICANS VS NON HISPANIC WHIT*
    Lennox Jeffers; Fiscal Year: 2005
    ..of 40 kDa Pegylated interferon alfa-2a (Peginterferon alfa-2a) in combination with Ribavirin in the treatment of genotype-1 chronic hepatitis C (HCV, genotype-1) in African American men and women as compared to non-Hispanic whites...
  69. HETEROGENEITY OF ESTROGEN RECEPTOR STRUCTURE AND ACTION
    Beth Schachter; Fiscal Year: 1993
    ..Additional correlations with the variant genotype in the breast tumor samples include a lower estrogen receptor/progesterone receptor ratio and a higher ..
  70. GENETIC DISSECTION OF AGGRESSIVE BEHAVIOR OF HONEY BEES
    Greg Hunt; Fiscal Year: 2000
    ..This will allow an assessment of the interaction between colony genotype composition and genotype behavior, as well as the effect of colony size on genotypic behavior...
  71. DNA Probes for Acanthamoeba Genomics and Epidemiology
    Paul Fuerst; Fiscal Year: 2007
    ..Importantly, results indicated that the vast majority of AK cases are associated with a specific Acanthamoeba genotype: T4...
  72. Genotype and Metabolic Phenotype in Glioblastoma
    Elizabeth A Maher; Fiscal Year: 2010
    ..To address basic questions related to the genotype-metabolic phenotype connection in glioblastoma we have engaged a multidisciplinary team of physicians and ..
  73. Cell Culture System for Hepatitis C Virus Genotype 1a
    Adrian Di Bisceglie; Fiscal Year: 2009
    ..While recent success in HCV cell culture has been achieved using an "infectious clone" approach with a HCV genotype 2a strain (JFH1), this system has not been replicated with HCV strains other than JFH1, a strain which was ..
  74. COMT Genotype and Risky Decision Making in HIV and Methamphetamine Dependence
    Mariana Cherner; Fiscal Year: 2010
    ..DA-utilizing brain areas that subserve decision-making, these conditions may interact with the COMT Val158Met genotype to exacerbate risk-taking...