Summary: The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.

Top Publications

  1. 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
  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 DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
    P Librado
    Departament de Genetica, Facultat de Biologia and Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
    Bioinformatics 25:1451-2. 2009
  4. ncbi Haploview: analysis and visualization of LD and haplotype maps
    J C Barrett
    Whitehead Institute for Biomedical Research Cambridge, MA 02142, USA
    Bioinformatics 21:263-5. 2005
  5. pmc Origins and functional impact of copy number variation in the human genome
    Donald F Conrad
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
    Nature 464:704-12. 2010
  6. pmc Prediction of total genetic value using genome-wide dense marker maps
    T H Meuwissen
    Research Institute of Animal Science and Health, 8200 AB Lelystad, The Netherlands
    Genetics 157:1819-29. 2001
  7. pmc A comparison of bayesian methods for haplotype reconstruction from population genotype data
    Matthew Stephens
    Department of Statistics, University of Washington, Seattle, WA 98195 4322, USA
    Am J Hum Genet 73:1162-9. 2003
  8. pmc A new statistical method for haplotype reconstruction from population data
    M Stephens
    Department of Statistics, University of Oxford
    Am J Hum Genet 68:978-89. 2001
  9. ncbi Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation
    Mannis van Oven
    Department of Forensic Molecular Biology, Erasmus University Medical Center Rotterdam, The Netherlands
    Hum Mutat 30:E386-94. 2009
  10. 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

Detail Information

Publications339 found, 100 shown here

  1. 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
    ..in each study, the effects of most common SNPs must be evaluated indirectly using either genotyped markers or haplotypes thereof as proxies...
  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
    ..These methods and public data will support the next phase of human genetic research...
  3. ncbi DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
    P Librado
    Departament de Genetica, Facultat de Biologia and Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
    Bioinformatics 25:1451-2. 2009
  4. ncbi Haploview: analysis and visualization of LD and haplotype maps
    J C Barrett
    Whitehead Institute for Biomedical Research Cambridge, MA 02142, USA
    Bioinformatics 21:263-5. 2005
    ..Haploview is a software package that provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data in a visually appealing and interactive interface...
  5. pmc Origins and functional impact of copy number variation in the human genome
    Donald F Conrad
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
    Nature 464:704-12. 2010
  6. pmc Prediction of total genetic value using genome-wide dense marker maps
    T H Meuwissen
    Research Institute of Animal Science and Health, 8200 AB Lelystad, The Netherlands
    Genetics 157:1819-29. 2001
    ..Here we attempted to estimate the effects of approximately 50,000 marker haplotypes simultaneously from a limited number of phenotypic records...
  7. pmc A comparison of bayesian methods for haplotype reconstruction from population genotype data
    Matthew Stephens
    Department of Statistics, University of Washington, Seattle, WA 98195 4322, USA
    Am J Hum Genet 73:1162-9. 2003
    In this report, we compare and contrast three previously published Bayesian methods for inferring haplotypes from genotype data in a population sample...
  8. pmc A new statistical method for haplotype reconstruction from population data
    M Stephens
    Department of Statistics, University of Oxford
    Am J Hum Genet 68:978-89. 2001
    ..b>Haplotypes can be obtained, at considerable cost, experimentally or (partially) through genotyping of additional family ..
  9. ncbi Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation
    Mannis van Oven
    Department of Forensic Molecular Biology, Erasmus University Medical Center Rotterdam, The Netherlands
    Hum Mutat 30:E386-94. 2009
    ..This complete mtDNA tree includes previously published as well as newly identified haplogroups, is easily navigable, will be continuously and regularly updated in the future, and is online available at http://www.phylotree.org...
  10. 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
    ..This model is based on the idea that, over short regions, haplotypes in a population tend to cluster into groups of similar haplotypes...
  11. pmc Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering
    Sharon R Browning
    Department of Statistics, The University of Auckland, Auckland, New Zealand
    Am J Hum Genet 81:1084-97. 2007
    ..1 days of computing time, with 99% of masked alleles imputed correctly. Our method is implemented in the Beagle software package, which is freely available...
  12. 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
    ..We present a useful measure of imputation accuracy, allelic R(2), and show that this measure can be estimated accurately from posterior genotype probabilities. Our methods are implemented in version 3.0 of the BEAGLE software package...
  13. ncbi Detecting recent positive selection in the human genome from haplotype structure
    Pardis C Sabeti
    Whitehead Institute MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 419:832-7. 2002
    ..we introduce a framework for detecting the genetic imprint of recent positive selection by analysing long-range haplotypes in human populations. We first identify haplotypes at a locus of interest (core haplotypes)...
  14. 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
    ..a powerful approach to disease gene mapping, based on the association between causal mutations and the ancestral haplotypes on which they arose...
  15. ncbi SHEsis, a powerful software platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci
    Yong Yong Shi
    Bio X Life Science Research Center, Shanghai Jiao Tong University, Shanghai, China
    Cell Res 15:97-8. 2005
    ..The platform has been well evaluated by several sets of real data...
  16. pmc Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci
    John B Harley
    Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, Oklahoma 73104, USA
    Nat Genet 40:204-10. 2008
    ..Our results show that numerous genes, some with known immune-related functions, predispose to SLE...
  17. 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
    ..Our approach makes ~1000 genes accessible to genetic studies of disease association...
  18. pmc A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other
    Dale R Nyholt
    Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
    Am J Hum Genet 74:765-9. 2004
    ..Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor "loadings" after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region...
  19. pmc Complement factor H polymorphism in age-related macular degeneration
    Robert J Klein
    Laboratory of Statistical Genetics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Science 308:385-9. 2005
    ..This polymorphism is in a region of CFH that binds heparin and C-reactive protein. The CFH gene is located on chromosome 1 in a region repeatedly linked to AMD in family-based studies...
  20. pmc Genome sequence, comparative analysis, and population genetics of the domestic horse
    C M Wade
    Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
    Science 326:865-7. 2009
    ..Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds...
  21. pmc Neuregulin 1 and susceptibility to schizophrenia
    Hreinn Stefansson
    deCODE Genetics, Reykjavik, Iceland
    Am J Hum Genet 71:877-92. 2002
    ..We also demonstrate that the behavioral phenotypes of the NRG1 hypomorphs are partially reversible with clozapine, an atypical antipsychotic drug used to treat schizophrenia...
  22. pmc New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree
    Tatiana M Karafet
    ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA
    Genome Res 18:830-8. 2008
    ..Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree...
  23. ncbi Distinctive Paleo-Indian migration routes from Beringia marked by two rare mtDNA haplogroups
    Ugo A Perego
    Dipartimento di Genetica e Microbiologia, Universita di Pavia, 27100 Pavia, Italy
    Curr Biol 19:1-8. 2009
    ..In this study, we have instead identified and analyzed mtDNAs belonging to two rare Native American haplogroups named D4h3 and X2a...
  24. ncbi Worldwide human relationships inferred from genome-wide patterns of variation
    Jun Z Li
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 5120, USA
    Science 319:1100-4. 2008
    ..This data set allows the most comprehensive characterization to date of human genetic variation...
  25. pmc Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations
    Faviel F Gonzalez-Galarza
    Institute of Infection and Global Health, University of Liverpool, Royal Liverpool and Broadgreen University Hospital, Liverpool, UK
    Nucleic Acids Res 39:D913-9. 2011
    ..Demographic information, frequency data and searching tools can be freely accessed through the website...
  26. pmc A "Copernican" reassessment of the human mitochondrial DNA tree from its root
    Doron M Behar
    Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
    Am J Hum Genet 90:675-84. 2012
  27. pmc Subspecific origin and haplotype diversity in the laboratory mouse
    Hyuna Yang
    The Jackson Laboratory, Bar Harbor, Maine, USA
    Nat Genet 43:648-55. 2011
    ..The subspecific origin, haplotype diversity and identity by descent maps can be visualized using the Mouse Phylogeny Viewer (see URLs)...
  28. pmc Haplotype phasing: existing methods and new developments
    Sharon R Browning
    Department of Biostatistics, University of Washington, Seattle, Washington 98195, USA
    Nat Rev Genet 12:703-14. 2011
    ..We also describe recent developments that may transform this field, particularly the use of identity-by-descent for computational phasing...
  29. ncbi Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure
    A G Nackley
    Center for Neurosensory Disorders, University of North Carolina, Chapel Hill, NC 27599, USA
    Science 314:1930-3. 2006
    ..Three common haplotypes of the human COMT gene, divergent in two synonymous and one nonsynonymous position, code for differences in COMT ..
  30. pmc Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data
    Bingshan Li
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Am J Hum Genet 83:311-21. 2008
    ..The CMC method can be applied to either candidate-gene or whole-genome sequence data...
  31. ncbi Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum
    John C Wootton
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 6075, USA
    Nature 418:320-3. 2002
    ..The presence of linkage disequilibrium provides a basis for mapping genes under drug selection in P. falciparum...
  32. pmc Genome-wide detection and characterization of positive selection in human populations
    Pardis C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Nature 449:913-8. 2007
  33. ncbi A composite of multiple signals distinguishes causal variants in regions of positive selection
    Sharon R Grossman
    Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Science 327:883-6. 2010
    ..CMS can not just identify individual loci but implicates precise variants selected by evolution...
  34. ncbi Merlin--rapid analysis of dense genetic maps using sparse gene flow trees
    Goncalo R Abecasis
    The Wellcome Trust Center for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
    Nat Genet 30:97-101. 2002
  35. pmc A second generation human haplotype map of over 3.1 million SNPs
    Kelly A Frazer
    The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA
    Nature 449:851-61. 2007
    ..Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations...
  36. pmc Association of trypanolytic ApoL1 variants with kidney disease in African Americans
    Giulio Genovese
    Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
    Science 329:841-5. 2010
    ..APOL1 variants are common in African chromosomes but absent from European chromosomes, and both reside within haplotypes that harbor signatures of positive selection...
  37. ncbi Complement factor H variant increases the risk of age-related macular degeneration
    Jonathan L Haines
    Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
    Science 308:419-21. 2005
    ..45 and 5.57. This common variant likely explains approximately 43% of AMD in older adults...
  38. pmc Parental origin of sequence variants associated with complex diseases
    Augustine Kong
    deCODE Genetics, Sturlugata 8, 101 Reykjavik, Iceland
    Nature 462:868-74. 2009
    ..We identified a differentially methylated CTCF-binding site at 11p15 and demonstrated correlation of rs2334499 with decreased methylation of that site...
  39. pmc A whole-genome association study of major determinants for host control of HIV-1
    Jacques Fellay
    Center for Population Genomics and Pharmacogenetics, Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
    Science 317:944-7. 2007
    ..These findings emphasize the importance of studying human genetic variation as a guide to combating infectious agents...
  40. pmc Relative impact of nucleotide and copy number variation on gene expression phenotypes
    Barbara E Stranger
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Science 315:848-53. 2007
    ..Interrogation of the genome for both types of variants may be an effective way to elucidate the causes of complex phenotypes and disease in humans...
  41. ncbi Genome sequence, comparative analysis and haplotype structure of the domestic dog
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 438:803-19. 2005
    ..Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds...
  42. pmc Targeted capture and massively parallel sequencing of 12 human exomes
    Sarah B Ng
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Nature 461:272-6. 2009
    ..This strategy may be extendable to diseases with more complex genetics through larger sample sizes and appropriate weighting of non-synonymous variants by predicted functional impact...
  43. ncbi SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans
    Rebecca L Lamason
    Jake Gittlen Cancer Research Foundation, Department of Pathology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
    Science 310:1782-6. 2005
  44. pmc The Arabian cradle: mitochondrial relicts of the first steps along the southern route out of Africa
    Veronica Fernandes
    Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
    Am J Hum Genet 90:347-55. 2012
    ..This pattern suggests that Arabia was indeed the first staging post in the spread of modern humans around the world...
  45. pmc The history of African gene flow into Southern Europeans, Levantines, and Jews
    Priya Moorjani
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 7:e1001373. 2011
    ..For the Jewish admixture, we obtain an average estimated date of about 72 generations. This may reflect descent of these groups from a common ancestral population that already had some African ancestry prior to the Jewish Diasporas...
  46. pmc Genomic scans for selective sweeps using SNP data
    Rasmus Nielsen
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genome Res 15:1566-75. 2005
    ..Evidence for selective sweeps is also found in many other regions, including genes known to be associated with disease risk such as DPP10 and COL4A3...
  47. ncbi A unifying genetic model for facioscapulohumeral muscular dystrophy
    Richard J L F Lemmers
    Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
    Science 329:1650-3. 2010
    ..These findings suggest that FSHD arises through a toxic gain of function attributable to the stabilized distal DUX4 transcript...
  48. ncbi An apolipoprotein influencing triglycerides in humans and mice revealed by comparative sequencing
    L A Pennacchio
    Genome Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Science 294:169-73. 2001
    ..These findings indicate that APOAV is an important determinant of plasma triglyceride levels, a major risk factor for coronary artery disease...
  49. pmc Classic selective sweeps were rare in recent human evolution
    Ryan D Hernandez
    Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Science 331:920-4. 2011
    ..These findings indicate that classic sweeps were not a dominant mode of human adaptation over the past ~250,000 years...
  50. ncbi Glacial refugia: hotspots but not melting pots of genetic diversity
    Remy J Petit
    Institut National de la Recherche Agronomique, UMR Biodiversité, Génes et Ecosystémes, F 33612 Cestas, France
    Science 300:1563-5. 2003
    ..However, the genetically most diverse populations were not located in the south but at intermediate latitudes, a likely consequence of the admixture of divergent lineages colonizing the continent from separate refugia...
  51. pmc Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies
    Osvaldo Zagordi
    Department of Biosystems Sciences and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Germany
    Nucleic Acids Res 38:7400-9. 2010
    ..We conclude that pyrosequencing can be used to investigate genetically diverse samples with high accuracy if technical errors are properly treated...
  52. ncbi Efficient mapping of mendelian traits in dogs through genome-wide association
    Elinor K Karlsson
    Broad Institute of Harvard and Massachusetts Institute of Technology MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Genet 39:1321-8. 2007
    ..Complete sequencing of the white and solid haplotypes identifies candidate regulatory mutations in the melanocyte-specific promoter of MITF...
  53. pmc Runs of homozygosity in European populations
    Ruth McQuillan
    Public Health Sciences, University of Edinburgh Medical School, Edinburgh EH8 9AG, UK
    Am J Hum Genet 83:359-72. 2008
  54. ncbi Accelerated species inventory on Madagascar using coalescent-based models of species delineation
    Michael T Monaghan
    Entomology Department, Natural History Museum, London, UK
    Syst Biol 58:298-311. 2009
    ..Local endemism was pronounced in all 5 insect groups. Most species (60-91%) and haplotypes (88-99%) were found at only 1 of the 5 study sites (40-1000 km apart)...
  55. ncbi A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians
    Yoichiro Kamatani
    Human Genome Center, Institute of Medical Science, The University of Tokyo, Japan
    Nat Genet 41:591-5. 2009
    ..34 x 10(-39) and 2.31 x 10(-38), OR = 0.57 and 0.56, respectively). Subsequent analyses revealed risk haplotypes (HLA-DPA1(*)0202-DPB1(*)0501 and HLA-DPA1(*)0202-DPB1(*)0301, OR = 1.45 and 2...
  56. ncbi A "silent" polymorphism in the MDR1 gene changes substrate specificity
    Chava Kimchi-Sarfaty
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
    Science 315:525-8. 2007
  57. ncbi LIAN 3.0: detecting linkage disequilibrium in multilocus data. Linkage Analysis
    B Haubold
    Max Planck Institut für Chemische Okologie, Carl Zeiss Promenade 10, D 07745 Jena, Germany
    Bioinformatics 16:847-8. 2000
    ..LIAN incorporates both a Monte Carlo method as well as a novel algebraic method to carry out the hypothesis test. The program further returns the genetic diversity of the sample and the pairwise distances between its members...
  58. pmc A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies
    Molly E McCue
    College of Veterinary Medicine, University of Minnesota, St Paul, MN, USA
    PLoS Genet 8:e1002451. 2012
    ..These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species...
  59. pmc Whole population, genome-wide mapping of hidden relatedness
    Alexander Gusev
    Department of Computer Science, Columbia University, New York, New York 10027, USA
    Genome Res 19:318-26. 2009
    ..Our approach is based on a dictionary of haplotypes that is used to efficiently discover short exact matches between individuals...
  60. ncbi HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups
    Anita Kloss-Brandstätter
    Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Austria
    Hum Mutat 32:25-32. 2011
    ..HaploGrep can be accessed freely at http://haplogrep.uibk.ac.at...
  61. ncbi Efficiency and power in genetic association studies
    Paul I W de Bakker
    Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge Street, CPZN 6818, Boston, Massachusetts 02114 2790, USA
    Nat Genet 37:1217-23. 2005
    ..Examining all observed haplotypes for association, rather than just those that are proxies for known SNPs, increases power to detect rare causal ..
  62. pmc mtDNA data indicate a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves
    Jun feng Pang
    State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
    Mol Biol Evol 26:2849-64. 2009
    ..The mean sequence distance to ancestral haplotypes indicates an origin 5,400-16,300 years ago (ya) from at least 51 female wolf founders...
  63. pmc Genomic ancestry of North Africans supports back-to-Africa migrations
    Brenna M Henn
    Department of Genetics, Stanford University, Stanford, CA, USA
    PLoS Genet 8:e1002397. 2012
    ..In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations...
  64. pmc Y-chromosomal variation in sub-Saharan Africa: insights into the history of Niger-Congo groups
    Cesare de Filippo
    Max Planck Research Group on Comparative Population Linguistics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
    Mol Biol Evol 28:1255-69. 2011
    ..genotypes were inferred from published data using linear discriminant analysis on short tandem repeat (STR) haplotypes. No reduction in STR diversity levels was found across the Bantu groups, suggesting the absence of serial ..
  65. ncbi Genetics and biology of vitamin D receptor polymorphisms
    Andre G Uitterlinden
    Genetic Laboratory, Room Ee575, Department of Internal Medicine, Erasmus MC, Dr Molewaterplein 50, PO Box 1738, NL 3000 DR Rotterdam, The Netherlands
    Gene 338:143-56. 2004
    ..Substantial progress has been made that will deepen our understanding of variability in the vitamin D endocrine system and might find applications in risk assessment of disease and in predicting response-to-treatment...
  66. ncbi Complement factor H polymorphism and age-related macular degeneration
    Albert O Edwards
    Department of Ophthalmology and McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center UTSWMC, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
    Science 308:421-4. 2005
    ..Possession of at least one histidine at amino acid position 402 increased the risk of AMD 2.7-fold and may account for 50% of the attributable risk of AMD...
  67. pmc A fast, powerful method for detecting identity by descent
    Brian L Browning
    Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98105, USA
    Am J Hum Genet 88:173-82. 2011
    ..This is useful for estimation of relationship and for adjusting for relatedness in association studies. FastIBD is incorporated in the freely available Beagle software package...
  68. pmc Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers
    Jianbing Yan
    Genetic Resources Program, International Maize and Wheat Improvement Center, Mexico City, Mexico
    PLoS ONE 4:e8451. 2009
    ..A total of 1229 informative SNPs and 1749 haplotypes within 327 loci was used to estimate the genetic diversity, population structure, and familial relatedness...
  69. ncbi Genetic variation increases during biological invasion by a Cuban lizard
    Jason J Kolbe
    Department of Biology, Campus Box 1137, Washington University, Saint Louis, Missouri 63130 4899, USA
    Nature 431:177-81. 2004
    ..If these costs are to be mitigated, a greater understanding of the causes, progression and consequences of biological invasions is needed...
  70. ncbi Newly identified loci that influence lipid concentrations and risk of coronary artery disease
    Cristen J Willer
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, Michigan 48109, USA
    Nat Genet 40:161-9. 2008
    ..Notably, the 11 independent variants associated with increased LDL cholesterol concentrations in our study also showed increased frequency in a sample of coronary artery disease cases versus controls...
  71. pmc Different patterns of evolution in the centromeric and telomeric regions of group A and B haplotypes of the human killer cell Ig-like receptor locus
    Chul Woo Pyo
    Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS ONE 5:e15115. 2010
    ..Nucleotide sequences for 24 representative human KIR haplotypes were determined...
  72. pmc A single IGF1 allele is a major determinant of small size in dogs
    Nathan B Sutter
    National Human Genome Research Institute, Building 50, Room 5349, 50 South Drive MSC 8000, Bethesda, MD 20892 8000, USA
    Science 316:112-5. 2007
    ..A single IGF1 single-nucleotide polymorphism haplotype is common to all small breeds and nearly absent from giant breeds, suggesting that the same causal sequence variant is a major contributor to body size in all small dogs...
  73. pmc Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content
    Nathan M Springer
    Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, USA
    PLoS Genet 5:e1000734. 2009
    ..Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop...
  74. pmc A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation
    A R Templeton
    Department of Biology, Washington University, St Louis, Missouri 63130
    Genetics 132:619-33. 1992
    We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypic deviations...
  75. ncbi The same sequence variant on 9p21 associates with myocardial infarction, abdominal aortic aneurysm and intracranial aneurysm
    Anna Helgadottir
    deCODE Genetics, Sturlugata 8, IS 101 Reykjavik, Iceland
    Nat Genet 40:217-24. 2008
    ..These findings extend our insight into the role of the sequence variant tagged by rs10757278-G and show that it is not confined to atherosclerotic diseases...
  76. ncbi Genome-wide analysis of transcript isoform variation in humans
    Tony Kwan
    Department of Human Genetics, McGill University, 740 Dr Penfield, Room 7210, Montreal, Quebec H3A 1A4, Canada
    Nat Genet 40:225-31. 2008
    ..This extra layer of molecular diversity may account for natural phenotypic variation and disease susceptibility...
  77. ncbi Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe
    Pontus Skoglund
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
    Science 336:466-9. 2012
    ..Our results suggest that migration from southern Europe catalyzed the spread of agriculture and that admixture in the wake of this expansion eventually shaped the genomic landscape of modern-day Europe...
  78. ncbi Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9
    Jonathan Cohen
    Donald W Reynolds Cardiovascular Clinical Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines, Dallas, Texas 75390 9046, USA
    Nat Genet 37:161-5. 2005
    ..1%) and were associated with a 40% reduction in plasma levels of LDL cholesterol. These data indicate that common sequence variations have large effects on plasma cholesterol levels in selected populations...
  79. pmc Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication
    Bridgett M VonHoldt
    Department of Ecology and Evolutionary Biology, 621 Charles E Young Drive South, University of California, Los Angeles, California 90095, USA
    Nature 464:898-902. 2010
    ..Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for ..
  80. pmc Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs
    Joshua M Korn
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Nat Genet 40:1253-60. 2008
    ..The Birdsuite software is applied here to data from the Affymetrix SNP 6.0 array. Additionally, we describe a method, implemented in PLINK, to utilize these combined SNP and CNV genotypes for association testing with a phenotype...
  81. ncbi Worldwide phylogeography of wild boar reveals multiple centers of pig domestication
    Greger Larson
    Henry Wellcome Ancient Biomolecules Centre, University of Oxford, Department of Zoology, South Parks Road OX1 3PS, UK
    Science 307:1618-21. 2005
    ..In contrast, new genetic data reveal multiple centers of domestication across Eurasia and that European, rather than Near Eastern, wild boar are the principal source of modern European domestic pigs...
  82. pmc Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping
    Amaury Vaysse
    Institut de Génétique et Développement de Rennes, CNRS UMR6061, Universite de Rennes 1, Rennes, France
    PLoS Genet 7:e1002316. 2011
    ..sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in ..
  83. pmc IRF5 haplotypes demonstrate diverse serological associations which predict serum interferon alpha activity and explain the majority of the genetic association with systemic lupus erythematosus
    Timothy B Niewold
    Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois 60637, USA
    Ann Rheum Dis 71:463-8. 2012
    ..Genetic variation in IRF5 is associated with SLE susceptibility; however, it is unclear how IRF5 functional genetic elements contribute to human disease...
  84. pmc Differential contributions of rare and common, coding and noncoding Ret mutations to multifactorial Hirschsprung disease liability
    Eileen Sproat Emison
    Center for Complex Disease Genomics, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Am J Hum Genet 87:60-74. 2010
    ..The RET allelic series, and its genotype-phenotype correlations, shows that success in variant identification in complex disorders may strongly depend on which patients are studied...
  85. pmc MYH9 is associated with nondiabetic end-stage renal disease in African Americans
    W H Linda Kao
    Department of Epidemiology, School of Medicine and Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21287, USA
    Nat Genet 40:1185-92. 2008
  86. pmc The landscape of recombination in African Americans
    Anjali G Hinch
    Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK
    Nature 476:170-5. 2011
    ..Sites of this motif are predicted to be risk loci for disease-causing genomic rearrangements in individuals carrying these alleles. More generally, this map provides a resource for research in human genetic variation and evolution...
  87. pmc Dissection of the genetics of Parkinson's disease identifies an additional association 5' of SNCA and multiple associated haplotypes at 17q21
    Chris C A Spencer
    Wellcome Trust Centre for Human Genetics, Oxford, UK
    Hum Mol Genet 20:345-53. 2011
    ..We found no support for the previously reported SNP association in 12q12/LRRK2. We also found an association of the two SNPs in 4q22/SNCA with the age of onset of the disease...
  88. ncbi Integrated detection and population-genetic analysis of SNPs and copy number variation
    Steven A McCarroll
    Program in Medical and Population Genetics and Genetic Analysis Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nat Genet 40:1166-74. 2008
    ..Most common, diallelic CNPs were in strong linkage disequilibrium with SNPs, and most low-frequency CNVs segregated on specific SNP haplotypes.
  89. ncbi The archaeogenetics of Europe
    Pedro Soares
    Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
    Curr Biol 20:R174-83. 2010
  90. pmc Analysis of human APOBEC3H haplotypes and anti-human immunodeficiency virus type 1 activity
    Xiaojun Wang
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824 4320, USA
    J Virol 85:3142-52. 2011
    ..Human A3H has five single amino acid polymorphisms (N15Δ, R18L, G105R, K121D, and E178D), and four haplotypes (I to IV) have previously been identified in various human populations...
  91. ncbi Recombination and linkage disequilibrium in Arabidopsis thaliana
    Sung Kim
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Nat Genet 39:1151-5. 2007
    ..LD also reflects the action of selection, and it is more extensive between nonsynonymous polymorphisms than between synonymous polymorphisms...
  92. pmc Colloquium paper: human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency
    Angela M Hancock
    Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 107:8924-30. 2010
  93. pmc A new approach for using genome scans to detect recent positive selection in the human genome
    Kun Tang
    Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
    PLoS Biol 5:e171. 2007
    ..Gene ontology analysis of the candidate regions revealed several new functional groups that might help explain some important interpopulation differences in phenotypic traits...
  94. pmc Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified
    Hojun Song
    Department of Biology, Brigham Young University, Provo, UT 84602, USA
    Proc Natl Acad Sci U S A 105:13486-91. 2008
  95. pmc GAB2 alleles modify Alzheimer's risk in APOE epsilon4 carriers
    Eric M Reiman
    Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
    Neuron 54:713-20. 2007
    ..Our findings suggest that GAB2 modifies LOAD risk in APOE epsilon4 carriers and influences Alzheimer's neuropathology...
  96. ncbi Unmasking the causes of multifactorial disorders: OXPHOS differences between mitochondrial haplogroups
    Aurora Gómez-Durán
    Departamento de Bioquimica, Biologia Molecular y Celular, Centro de INvestigaciones Biomédicas en Red de Enfermedades Raras, Instituto Aragones de Ciencias de la Salud, Universidad de Zaragoza, Zaragoza, Spain
    Hum Mol Genet 19:3343-53. 2010
    ..The existence of mtDNA-based OXPHOS differences opens possibilities for the existence of a new field, mitochondrial pharmacogenomics. New sequence accession nos: HM103354-HM103363...
  97. pmc Missense mutations in the APOL1 gene are highly associated with end stage kidney disease risk previously attributed to the MYH9 gene
    Shay Tzur
    Ruth and Bruce Rappaport Faculty of Medicine and Research Institute, Technion Israel Institute of Technology, Haifa, Israel
    Hum Genet 128:345-50. 2010
    ..mapping of MYH9 identified individual single nucleotide polymorphisms (SNPs) and sets of such SNPs grouped as haplotypes that were found to be highly associated with a large and important group of ESKD risk phenotypes, which as a ..
  98. ncbi Positive natural selection in the human lineage
    P C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, MA, USA
    Science 312:1614-20. 2006
  99. ncbi Genetic evidence for an East Asian origin of domestic dogs
    Peter Savolainen
    Department of Biotechnology, Royal Institute of Technology KTH, 10691 Stockholm, Sweden
    Science 298:1610-3. 2002
    ..A larger genetic variation in East Asia than in other regions and the pattern of phylogeographic variation suggest an East Asian origin for the domestic dog, approximately 15,000 years ago...
  100. pmc Score tests for association between traits and haplotypes when linkage phase is ambiguous
    Daniel J Schaid
    Department of Health Sciences Research, Mayo Clinic Foundation, Rochester, MN 55905, USA
    Am J Hum Genet 70:425-34. 2002
    ..the discovery of a gene related to a trait is the finding of an association between the trait and one or more haplotypes. Haplotype analyses can also provide critical information regarding the function of a gene; however, when ..
  101. pmc Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia
    Todd Lencz
    Department of Psychiatry Research, Zucker Hillside Hospital, North Shore Long Island Jewish Health System, 75 59 263rd Street, Glen Oaks, NY 11004, USA
    Proc Natl Acad Sci U S A 104:19942-7. 2007
    ..Properties of common ROHs in healthy subjects, including chromosomal location and presence of nonancestral haplotypes, converged with prior reports identifying regions under selective pressure...

Research Grants71

  1. Variation in M. tuberculosis in response to host selection
    Sarah Fortune; Fiscal Year: 2009
    ..model of disease chosen to create different immune pressures on the bacteria [unreadable]mice of different MHC haplotypes. In these studies, we expect to provide fundamental insights into the mechanisms and targets of diversifying ..
  2. Genetics and Haloperidol Response
    Robert J Hitzemann; Fiscal Year: 2012
    ..and to determine which genes within the intervals have non-synonymous coding SNPs that match the predicted QTL haplotypes. The SNP data will also be used to mask striatal gene expression databases to determine which genes (actually ..
  3. Anti-Inflammatory Glycosaminoglycan Ethers for Treatment of Periodontitis
    JUSTIN RODNEY SAVAGE; Fiscal Year: 2013
    ..Risk for gingivitis is universal, but subjects with haplotypes of IL-1B producing higher IL-1[unreadable] levels in crevicular fluid, diabetics and smokers all have a more ..
  4. Triggers of Abruptio Placentae - A Case Crossover Study of an Ischemic Placental
    Michelle A Williams; Fiscal Year: 2013
    ..nucleotide polymorphism (SNP) "1536-chip" on the 1st half of samples to scan maternal and infant SNPs and SNP haplotypes for association with AP...
  5. Impacts of surface receptors [Toll like receptor (TLRs) and Fc gamma receptors (F
    Collins Ouma; Fiscal Year: 2012
    ..in phenotypically well-defined cohorts of children will maximize our ability to successfully identify genotypes/haplotypes that condition susceptibility to SMA...
  6. Runx Proteins and Sex Steroid Signaling in Bone
    Baruch Frenkel; Fiscal Year: 2009
    ..In humans, Runx2 haplotypes contribute to variations in bone mass...
  7. Role of formyl peptide receptor variants in mucosal innate immune defense
    HEINI MARITA MIETTINEN; Fiscal Year: 2010
    ..six non-synonymous single nucleotide polymorphisms (SNPs) and four synonymous SNPs resulting in >40 different haplotypes in humans...
  8. Sex Steroids and Runx Signaling in Bone
    Baruch Frenkel; Fiscal Year: 2013
    ..In humans, Runx2 haplotypes contribute to variations in bone mass...
  9. Regulation of TSLP receptor expression and function in eczema in mice and man
    Steven F Ziegler; Fiscal Year: 2013
    ..Bioinformatics and luciferase reporter assays will then be used to identify and confirm promoter elements and haplotypes that enhance TSLPR gene activity...
    Anne M Delany; Fiscal Year: 2013
    ..determine the activity of human osteonectin 3'UTR haplotypes in vivo, using mice carrying knock-in mutations of the human UTR and 3...
  11. North Carolina Birth Defects Study To Evaluate Pregnancy Exposures (NC BD-STEPS)
    Andrew Olshan; Fiscal Year: 2013
    ..missing data, correlated exposures, pooled samples, approaches for the analysis of gene sets, multiple SNPs, haplotypes, GWAS and epigenetics;(5) Conduct innovative laboratory research to develop innovative methods for using dried ..
  12. Non-Human Primate Model of Gluten-Sensitive Enteropathy
    Karol Sestak; Fiscal Year: 2013
    ..Furthermore, we identified 2 DRB haplotypes and/or 4 DQ allelic pairs as candidate MHC II genes for immunogenetic association with gluten sensitivity in ..
  13. Prostacyclin Synthase and Receptors in Pulmonary Arterial Hypertension
    Mark W Geraci; Fiscal Year: 2011
    ..We will sequence the PGIS promoters from familial pulmonary hypertension, correlating specific haplotypes with disease on-set, severity, and morbidity...
  14. Functional impact of IL33 polymorphisms on asthma &other Th2-mediated diseases
    Kathleen C Barnes; Fiscal Year: 2013
    ..quantification of protein, and to test for association between IL-33 and sST2 concentrations and IL33 genotypes/haplotypes;(ii) characterize the effects of IL33 genetic variation on production of IL-33 and sST2, in response to Th2-..
  15. Mechanisms of Race-Based Differences in Factor VIII Immunogenicity in Hemophilia
    KATHLEEN PALMER PRATT; Fiscal Year: 2010
    ..A previous analysis of F8 haplotypes (Viel et al, NEJM 2009) will be expanded and refined...
  16. Insulin Clearance: Candidate and Positional Genetic Determinants
    MARK GOODARZI; Fiscal Year: 2012
    ..Insulin clearance is a highly heritable trait. Preliminary data show that haplotypes in the genes for adenosine monophosphate deaminase (AMPD1 and AMPD2) and the AMP-activated protein kinase (AMPK) ..
  17. Origins of Diversity at Human Classical MHC Class I Genes
    PETER R PARHAM; Fiscal Year: 2013
    ..A candidate human AL gene has been identified and associated with HLA haplotypes from non-caucasoid populations...
  18. Factors for Epigenetic Silencing of Lung Cancer Genes
    Steven A Belinsky; Fiscal Year: 2013
    ..Aim 1 will discover and validate gene sequence variations, copy number variants, and haplotypes that are determinants of gene promoter hypermethylation using a whole genome-wide association study (GWAS)...
  19. Investigating gene x environment interaction using human exposures to O3 & LPS
    David B Peden; Fiscal Year: 2010
    ..for nicotinamide adenine dinucleotide (phosphate) reduced:quinone oxidoreductase (NQO1), with the resulting haplotypes. Other common single nucleotide polymorphisms (SNPs) of interest exist in NF-E2, related factor 2 (NRF2), GSTP1, ..
  20. Beta2-Adrenergic Receptor Gene Variation and Cardiovascular Control in Humans
    John H Eisenach; Fiscal Year: 2012
    ..in combination, whereas the need exists to examine the functional relevance of the three, most common haplotypes in an ethnically homogenous cohort, thus controlling for variation in SNP's and race/ethnicity...
  21. A novel vaccine to prevent HCV infection and hence liver cancer
    Ellen S Vitetta; Fiscal Year: 2010
    ..Hence, T cell help will not be restricted to individuals with certain HLA haplotypes. We have already shown that peptoids conjugated to carrier proteins are highly immunogenic and that, in a model ..
  22. A Program of Research and Mentorship on Alcohol Use and Intimate Partner Violence
    Gregory L Stuart; Fiscal Year: 2013
    ..We will also examine whether GABRA2 polymorphisms and haplotypes are associated with IPV and alcohol treatment outcome...
  23. Pharmacogenomics of CVD risk Reduction
    ALAN SHULDINER; Fiscal Year: 2009
    ..variation and haplotype structure of 100 candidate genes and perform linkage and association analysis of SNPs/haplotypes with platelet function phenotypes;and (3) perform genome-wide linkage analysis to identify chromosome regions (..
  24. Human Population Diversity in Leukocyte Receptors
    PETER R PARHAM; Fiscal Year: 2013
    ..We have shown that KIR haplotypes exhibit high variability in gene content, which combines with allelic polymorphism to diversify human genotypes ..
  25. Models for?functional evaluation of?CHRN polymorphisms
    Beverly H Koller; Fiscal Year: 2012
    ..of loci for which disease association has been demonstrated, the mouse gene can be replaced with various human haplotypes, either those believed to be protective or those associated with increased vulnerability to addiction...
  26. Immunogenicity of the Type IV Secretin System
    WENDY CATHERINE BROWN; Fiscal Year: 2012
    ..By testing cattle that express a diverse repertoire of class II haplotypes, representative of the diversity of MHC class II expression in humans, the immunological consequence of these ..
  27. Discovering More Juvenile Myoclonic Epilepsy Genes by a Consortium
    Antonio V Delgado-Escueta; Fiscal Year: 2013
    ..2-21 to screen 14 other large 'DNA ready'JME families. We will then use constructed STS and tSNP haplotypes to screen 239 other medium-size 'DNA ready'families with JME and look for more recombinations...
  28. Complement Factor H Haplotypes and Smoking in Age-Related Macular Degeneration
    Baerbel Rohrer; Fiscal Year: 2011
  29. Genetics of Elevated High Density Lipoprotein Cholesterol
    DANIEL JAMES RADER; Fiscal Year: 2012
    ..In the family-based sample, we will test for association of HDL-C with SNP alleles and haplotypes using a quantitative trait analysis and the family-based association test (FBAT)...
  30. TNIP1 risk haplotypes and immune endophenotypes
    Peter K Gregersen; Fiscal Year: 2013
    ..of unique population resources to explore the functional effects of autoimmune disease associated TNIP1 risk haplotypes, with an emphasis on immune quantitative traits in B cells. Specific aim 1...
  31. Prospective evaluation of IGF and IL-6 Dysregulation and Multiple Myeloma
    Graham A Colditz; Fiscal Year: 2010
    ..Specific polymorphisms and haplotypes in the IGF-I, IGFBP-1,-2, and -3, IGF-I receptor (IGF-IR), and insulin receptor substrate (IRS)-1 and -2 genes ..
  32. Mouse models for the functional analysis of asthma-associated human polymorphisms
    Donata Vercelli; Fiscal Year: 2009
    ..modeled and dissected in BAC transgenic (TG) mice carrying WT or asthma/allergy-associated human IL13 haplotypes. More specifically, we propose: Specific Aim 1: To generate and validate [murine IL13-deficient] BAC TG mouse ..
  33. Developmental Pharmacology of cytosolic and mitochondrial GSTZ1-1/MAAI
    PETER WALLACE STACPOOLE; Fiscal Year: 2013
    ..Most adults clear repeated doses of DCA more slowly than most children. Persons with different GSTZ1-1 haplotypes appear to differ in their response to repeated doses of DCA...
  34. Thrombosis Genetics, MI and Stroke in Older Adults
    Alexander P Reiner; Fiscal Year: 2012
    ..and a flexible analytic approach that includes assessment of single- and multi-locus genotypes, haplotypes, gene-environment and gene-gene interaction...
  35. HLA and schizophrenia: a high-throughput sequencing study
    ..a large discovery sample and of samples from additional ethnic populations, to detect true signals (alleles and haplotypes) against diverse patterns of LD...
    Hong Wen Deng; Fiscal Year: 2013
    ..Aim I: To characterize the effects of individual potentially functional SNPs and haplotypes of HDC on gene expression and function, and their subsequent effects on osteoclastogenesis...
  37. Genetic determinants of total cholesterol levels in American Indians
    JOHANNA K DISTEFANO; Fiscal Year: 2013
    ..All QTL-associated SNP alleles and haplotypes will then be genotyped in 701 African American individuals from the Genetics of NIDDM (GENNID) study, in whom we ..
    Ashok Kumar; Fiscal Year: 2013
    ..In order to understand the role of glucocorticoids and IL-6 on transcription of -6A and -6G haplotypes of the hAGT gene and on the regulation of blood pressure in an in vivo situation, we have re-combineered 180 Kb ..
  39. The Role of Genome-Coded ME2 in Epilepsy
    David A Greenberg; Fiscal Year: 2010
    ..In this grant application, we will determine the different haplotypes of ME2 intron 1 based on our selected sample of cases for whom sequence data is available...
    TERRY FRANCIS DAVIES; Fiscal Year: 2013
    ..other susceptibility genes and epigenetic phenomena including the CTLA-4 and IL-23 receptor genes, the HLA DR-3 haplotypes and X chromosome inactivation (XCI)...
  41. Disparities in Breast Cancer: Development and Survival in Hispanic and NHW Women
    Martha L Slattery; Fiscal Year: 2013
    ..Breast cancer associations will be tested between genetic polymorphisms and haplotypes of these genes in Hispanic and NHW women and by proportion of American Indian ancestry...
  42. Dissecting the genetics of the Metabolic Syndrome on Chromosome 17 of the LH rat
    Anne E Kwitek; Fiscal Year: 2012
    ..2: Investigate interactions between trans-acting and cis-acting haplotypes on traits underlying the metabolic syndrome...
  43. Diet, Activity, and Lifestyle as a Risk Factor for Colorectal Cancer
    Martha L Slattery; Fiscal Year: 2012
    ..We examine known functional polymorphisms and evaluate haplotypes in candidate genes in an inflammation-related pathway (IL6, IL8, IL10, NFKB, TNF-A, IL4, IL1, ILIRA and IFNG) ..
  44. Familial Intracranial Aneurysm Study II (FIA II)
    JOSEPH PAUL BRODERICK; Fiscal Year: 2010
    ..Finally, we will use bioinformatics, statistical methods, and gene sequencing, to identify specific disease producing mutations and/or high risk haplotypes whose functional relevance will be subsequently explored.
  45. Nicotinic receptor genes & substance abuse: Functional studies of associated SNPs
    Jerry A Stitzel; Fiscal Year: 2010
    ..constituents were generated using our in vitro system containing different alleles for individual SNPs and haplotypes of SNPs...
  46. Interactions Between HLA Class I and Cytolytic Lymphocytes
    PETER R PARHAM; Fiscal Year: 2013
    ..A particular focus for study is to compare the influences on NK- cell receptor repertoire of the KIR A and B haplotypes that have been shown to differentially associate in numerous studies of human disease...
  47. Genetic and Immunological Impact of the HRES-1/Rab4 Locus in SLE
    Andras Perl; Fiscal Year: 2013
    ..and cloned the HRES-1 human endogenous retrovirus, mapped it to chromosome 1 at q42, newly identified six haplotypes in the long terminal repeat (LTR), and revealed an association of polymorphic HindIII653C-containing alleles ..
  48. Discovery of the 6p21.3 Reading Disability Gene
    Jeffrey R Gruen; Fiscal Year: 2010
    ..We will then test for association with single alleles and reconstructed haplotypes conditioned by the covariate modeling in AIM 1, define the attributable risks of RD for any child and for the ..
  49. Genetic Complexity and Modifiers of Hirschsprung Disease
    E Michelle Southard-Smith; Fiscal Year: 2011
    ..define Sox10[unreadable][unreadable]m phenotype variation across multiple inbred strains and identify shared haplotypes that alter aganglionosis by quantifying extent of enteric deficits in FT progeny derived from Sox10[unreadable]..
  50. Transcriptional Regulation of Angiotensinogen Gene
    Ashok Kumar; Fiscal Year: 2013
    ..with -532T, -793A, and -1074T and variants -217G, -532C, -793G, and -1074G always occur together forming two haplotypes. Since allele - 6A is the predominant allele (frequency 0...
  51. Molecular mechanism of omega-3 response
    JAMES T BRENNA; Fiscal Year: 2013
    ..g. FADS3 AT) of desaturation. Hypothesis 2: FADS AT modulation is related to SNPs and haplotypes via splicing factors. Specific Aim 1. Define the transcription start sites (TSS) and UTR of FADS CS and AT...
  52. Genes, Home Allergens and Asthma in Puerto Rican Children
    JUAN CARLOS CELEDON; Fiscal Year: 2010
    ..We will then test for association between SNPs and haplotypes in these candidate genes and a) asthma (in all subjects), b) lung function phenotypes (airway responsiveness, ..
  53. Mitochondrial associated CVD susceptibility in humans and mice
    Scott W Ballinger; Fiscal Year: 2010
    ..are provided that show: i) mice known to be resistant to CVD have genetically distinct mitochondrial DNA (mtDNA) haplotypes and function compared to those with increased CVD susceptibility;ii) CVD resistant mice have lower levels of ..
  54. Small RNA regulation of BDNF expression in schizophrenia
    Schahram Akbarian; Fiscal Year: 2012
    ..Aim #3 will use a population genetics-based approach to search for BDNF regulating microRNA haplotypes that (i) might confer genetic risk for schizophrenia and related disease or (ii) affect levels of microRNA ..
  55. H. pylori ancestral haplotype a gastric cancer risk determinant in Latin America
    Douglas Morgan; Fiscal Year: 2013
    ..Recent investigations suggest that the H. pylori phylogeographic origins, as determined by ancestral haplotypes with Multilocus sequence typing (MLST), may help delineate H...
  56. Diabetogenic Role of MHC Class I Alleles in NOD Mice
    David V Serreze; Fiscal Year: 2013
    ..to T cell mediated autoimmune type 1 diabetes (T1D) in both humans and NOD mice, but with particular MHC haplotypes providing the primary risk factor...
  57. Genetics of Nicotine Dependence
    Wade H Berrettini; Fiscal Year: 2013
    ..and protein will be assessed in post mortem human brain from individuals with the putative risk and protective haplotypes. CHRNA3 and CHRNA5 promoters sequences, from the risk and protective haplotypes, will be assessed in tissue ..
  58. Antioxidant Systems and Age-related Macular Degeneration
    Paul Sternberg; Fiscal Year: 2010
    ..recent results, performed with new collaborators at Vanderbilt, indicate that specific mitochondrial DNA haplotypes may be associated with an increased risk of AMD...
  59. Genes contributing for nicotine dependence in humans
    Kari Stefansson; Fiscal Year: 2013
    ..The pools will be enriched in samples from carriers of variants detected in GWA studies, and high-risk haplotypes detected by long-range phasing analysis with a focus on linkage regions...
  60. Role of HLA class II genes in demyelination
    Chella S David; Fiscal Year: 2013
    ..Among all the genetic factors associated with MS susceptibility, HLA-class II haplotypes such as DR2/DQ6, DR3/DQ2, DR4/DQ8, show the strongest association...
  61. Natural History of MYH9-Associated Nephropathy
    BARRY IRA FREEDMAN; Fiscal Year: 2012
    ..The rationale for this approach is based on the strong association of MYH9 risk haplotypes with Human Immunodeficiency Virus (HIV)-associated nephropathy (HIVAN) in African Americans...
  62. TGF-beta polymorphisms and breast cancer in families
    Boris Pasche; Fiscal Year: 2013
    ..We propose to assess the association between haplotypes of the 65 genes of the TGF-2 superfamily and breast cancer risk using a family-based association study...
  63. Pharmacogenetics and Cardiovascular Events
    Bruce Psaty; Fiscal Year: 2006
    ..is to assess interactions between selected cardiovascular medications and the major candidate-gene variants or haplotypes on the incidence of MI, stroke and AF...
    Sunil Ahuja; Fiscal Year: 1999
    ..In this Collaborative Study of the Mechanism of AIDS Pathogenesis we will: (1) identify CCR5 haplotypes that influence HIV transmission and disease progression; (2) determine whether CCR5 haplotypes produce race-..
    Raghu Kalluri; Fiscal Year: 2001
    ..that cross react with human Goodpasture autoantibodies, only a select few major histocompatibility complex haplotypes (MHC) developed inflammatory disease in organ tissues...
    CHESTER ALPER; Fiscal Year: 1999
    ..order, and the extent of deletions and insertions in the class III MHC regions of extended and non-extended MHC haplotypes. We have postulated that at least 30% of normal caucasian MHC haplotypes have fixed DNA at least over the HLA-B-..
    CHESTER ALPER; Fiscal Year: 1991
    Our previous work has provided evidence for extended major histocompatibility complex (MHC) haplotypes on caucasian chromosomes --specific alleles of HLA-B, DR, BF, C2, C4A, and C4B that occur as fixed sets with limited variation of ..
    Edmond Yunis; Fiscal Year: 1991
    ..6p and to better define the extent of non-random association (linkage disequilibrium) of genes in the extended haplotypes. As there is a fixity of alleles of the MHC in extended haplotypes, it is possible to predict the presence of ..
    Edmond Yunis; Fiscal Year: 1999
    ..0-A, HLA-B44, DR7 (DRB1*0701, DQB1*0202, DQB1*0201), HSP70 9.0-A. The haplotypes HLA-B8, DR3 (DRB1*0301, DQB1*0201, DQA1*0501, DPB1*0401), HSP70 8...
  70. Genotypes, Haplotypes, and Blood Pressure Change from Childhood to Adulthood
    DAVID MICHAEL HALLMAN; Fiscal Year: 2010
    ..We propose to investigate 3072 single-nucleotide polymorphisms (SNPs), both individually and as multilocus haplotypes (combinations of SNP alleles on a single chromosome), in 115 genes known or strongly suspected to affect blood ..
  71. Determinants of HbF Response to Hydroxyurea
    Martin Steinberg; Fiscal Year: 2005
    ..will use high throughput screening by mass spectrometry to: discover single nucleotide polymorphisms (SNPs) and haplotypes that predict the HbF level in sickle cell anemia patients taking hydroxyurea and discover SNPs and haplotypes ..