haplotypes

Summary

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 The use of inferred haplotypes in downstream analyses
    D Y Lin
    Am J Hum Genet 80:577-9. 2007
  2. 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
  3. doi 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 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
  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 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
  8. 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
  9. 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
  10. doi 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

Detail Information

Publications321 found, 100 shown here

  1. pmc The use of inferred haplotypes in downstream analyses
    D Y Lin
    Am J Hum Genet 80:577-9. 2007
  2. 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...
  3. doi 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 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...
  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 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...
  8. 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...
  9. 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...
  10. doi 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...
  11. 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...
  12. 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 ..
  13. 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...
  14. 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...
  15. 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...
  16. 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...
  17. doi 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...
  18. doi 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)...
  19. 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...
  20. 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...
  21. 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...
  22. 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...
  23. 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...
  24. 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...
  25. doi 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...
  26. 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...
  27. doi 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...
  28. 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...
  29. 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...
  30. 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...
  31. 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
    ....
  32. 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
    ....
  33. 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...
  34. 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...
  35. doi 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...
  36. 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
    ....
  37. 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
    ....
  38. 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 ..
  39. 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...
  40. 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...
  41. 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...
  42. doi 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...
  43. 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
    ....
  44. 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...
  45. 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...
  46. 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...
  47. doi 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...
  48. doi 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...
  49. 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...
  50. 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...
  51. 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 ..
  52. 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 ..
  53. 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...
  54. 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...
  55. 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
    ....
  56. 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...
  57. 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...
  58. 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...
  59. 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...
  60. 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...
  61. 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...
  62. doi 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.
  63. 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...
  64. 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...
  65. 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...
  66. 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...
  67. 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...
  68. doi 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
    ....
  69. 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
    ....
  70. 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...
  71. 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...
  72. 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
    ....
  73. 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...
  74. 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...
  75. 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 ..
  76. doi 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...
  77. 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...
  78. 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
    ....
  79. 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...
  80. 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 ..
  81. pmc Clinical expression of Leber hereditary optic neuropathy is affected by the mitochondrial DNA-haplogroup background
    Gavin Hudson
    Mitochondrial Research Group, Department of Ophthalmology and Institute of Human Genetics, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
    Am J Hum Genet 81:228-33. 2007
    ..Substitutions on MTCYB provide an explanation for these findings, which demonstrate that common genetic variants have a marked effect on the expression of an ostensibly monogenic mtDNA disorder...
  82. pmc Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms
    Toshio Yamamoto
    QTL Genomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
    BMC Genomics 11:267. 2010
    ..Finally, we applied this array to analyze historical representative rice cultivars to understand the dynamics of their genome composition...
  83. 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...
  84. pmc The role of geography in human adaptation
    Graham Coop
    Department of Human Genetics, University of Chicago, Chicago, IL, USA
    PLoS Genet 5:e1000500. 2009
    ..These patterns suggest that selection is often weak enough that neutral processes -- especially population history, migration, and drift -- exert powerful influences over the fate and geographic distribution of selected alleles...
  85. doi EMPOP--a forensic mtDNA database
    Walther Parson
    Institute of Legal Medicine, Innsbruck Medical University Müllerstreet 44, 6020 Innsbruck, Austria
    Forensic Sci Int Genet 1:88-92. 2007
    ..EMPOP has been launched on 16 October 2006 and is since then available at http://www.empop.org...
  86. 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)...
  87. pmc Mitochondrial DNA haplogroups M7b1'2 and M8a affect clinical expression of leber hereditary optic neuropathy in Chinese families with the m.11778G-->a mutation
    Yanli Ji
    State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat Sen University, Guangzhou, China
    Am J Hum Genet 83:760-8. 2008
    ..These findings will assist in further understanding the pathogenesis of LHON and guide future genetic counseling in East Asian patients with m.11778G-->A...
  88. pmc High-throughput sequencing of complete human mtDNA genomes from the Philippines
    Ellen D Gunnarsdóttir
    Max Planck Institute for Evolutionary Anthropology, D 04103 Leipzig, Germany
    Genome Res 21:1-11. 2011
    ..Our results clearly demonstrate that the high-throughput sequencing platforms are the methodology of choice for generating complete mtDNA genome sequences...
  89. doi Whole-genome molecular haplotyping of single cells
    H Christina Fan
    Department of Bioengineering, Stanford University, Stanford, California, USA
    Nat Biotechnol 29:51-7. 2011
    ..SNP) array analysis of amplified DNA enabled us to achieve completely deterministic, whole-genome, personal haplotypes of four individuals, including a HapMap trio with European ancestry (CEU) and an unrelated European individual...
  90. ncbi Collaborative analysis of alpha-synuclein gene promoter variability and Parkinson disease
    Demetrius M Maraganore
    Department of Neurology, Mayo Clinic College of Medicine, Rochester, Minn 55905, USA
    JAMA 296:661-70. 2006
    ..Alpha-synuclein (SNCA) has been one of the most promising susceptibility genes, but large-scale studies have been lacking...
  91. pmc Japanese population structure, based on SNP genotypes from 7003 individuals compared to other ethnic groups: effects on population-based association studies
    Yumi Yamaguchi-Kabata
    Laboratory for Statistical Analysis, Center for Genomic Medicine, The Institute of Physical and Chemical Research RIKEN, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Am J Hum Genet 83:445-56. 2008
    ..Simulation studies showed that the inclusion of different proportions of individuals from different regions of Japan in case and control groups can lead to an inflated rate of false-positive results when the sample sizes are large...
  92. pmc Plasmodium knowlesi: reservoir hosts and tracking the emergence in humans and macaques
    Kim Sung Lee
    Malaria Research Centre, Faculty of Medicine and Health Sciences, University Malaysia Sarawak, Kuching, Sarawak, Malaysia
    PLoS Pathog 7:e1002015. 2011
    ..knowlesi csp gene and certain mtDNA haplotypes were shared between both hosts...
  93. pmc Major histocompatibility complex (MHC) class II alleles, haplotypes and epitopes which confer susceptibility or protection in systemic sclerosis: analyses in 1300 Caucasian, African-American and Hispanic cases and 1000 controls
    Frank C Arnett
    Division of Rheumatology, Department of Internal Medicine, The University of Texas Health Science Center at Houston UTHSC H, 6431 Fannin Street, MSB 5 270, Houston, TX 77030, USA
    Ann Rheum Dis 69:822-7. 2010
    To determine human leucocyte antigen-class II (HLA-class II) (DRB1, DQB1, DQA1 and DPB1) alleles, haplotypes and shared epitopes associated with scleroderma (systemic sclerosis (SSc)) and its subphenotypes in a large multi-ethnic US ..
  94. pmc Updating phylogeny of mitochondrial DNA macrohaplogroup m in India: dispersal of modern human in South Asian corridor
    Adimoolam Chandrasekar
    Anthropological Survey of India, Southern Regional Centre, Bogadi, Mysore, India
    PLoS ONE 4:e7447. 2009
    ..Northeast Indian mtDNA pool harbors region specific lineages, other Indian lineages and East Asian lineages. We also suggest the establishment of an East Asian gene in North East India through admixture rather than replacement...
  95. pmc Paternal genetic affinity between Western Austronesians and Daic populations
    Hui Li
    MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes for Biomedical Sciences, Fudan University, Shanghai 200433, China
    BMC Evol Biol 8:146. 2008
    ....
  96. pmc A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe
    Natalie M Myres
    Sorenson Molecular Genealogy Foundation, Salt Lake City, UT, USA
    Eur J Hum Genet 19:95-101. 2011
    ....
  97. doi Forensic and phylogeographic characterization of mtDNA lineages from northern Thailand (Chiang Mai)
    Bettina Zimmermann
    Institute of Legal Medicine, Innsbruck Medical University, Mullerstrasse 44, Innsbruck, Austria
    Int J Legal Med 123:495-501. 2009
    ..This necessitates establishing regional databases, especially for forensic applications. The population data have been submitted to the EMPOP database (www.empop.org) and will be available on publication...
  98. doi The HLA DRB1*1501-DQB1*0602-DPB1*0501 haplotype is a risk factor for toluene diisocyanate-induced occupational asthma
    Jeong Hee Choi
    Department of Internal Medicine, Hallym University, Anyang, Korea
    Int Arch Allergy Immunol 150:156-63. 2009
    ....
  99. ncbi The APOA5 locus is a strong determinant of plasma triglyceride concentrations across ethnic groups in Singapore
    Chao Qiang Lai
    Nutrition and Genomics Laboratory, JM USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
    J Lipid Res 44:2365-73. 2003
    ..These data suggest that APOA5 plays a role in the ethnic differences observed for plasma TG and HDL cholesterol concentrations...
  100. ncbi SNAP: Combine and Map modules for multilocus population genetic analysis
    David L Aylor
    Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
    Bioinformatics 22:1399-401. 2006
    ..SNAP Map collapses DNA sequence data into unique haplotypes, extracts variable sites and manipulates output into multiple formats for input into existing software packages ..
  101. pmc Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1
    Christopher I Amos
    Department of Epidemiology, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
    Nat Genet 40:616-22. 2008
    ..Haplotype analysis was consistent with there being a single risk variant in this region. We conclude that variation in a region of 15q25.1 containing nicotinic acetylcholine receptors genes contributes to lung cancer risk...

Research Grants79

  1. Non-Human Primate Model of Gluten-Sensitive Enteropathy
    Karol Sestak; Fiscal Year: 2010
    ..Furthermore, we identified 2 DRB haplotypes and/or 4 DQ allelic pairs as candidate MHC II genes for immunogenetic association with gluten sensitivity in ..
  2. Non-Human Primate Model of Gluten-Sensitive Enteropathy
    Karol Sestak; Fiscal Year: 2009
    ..Furthermore, we identified 2 DRB haplotypes and/or 4 DQ allelic pairs as candidate MHC II genes for immunogenetic association with gluten sensitivity in ..
  3. 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...
  4. Role of HLA class II genes in demyelination
    Chella S David; Fiscal Year: 2010
    ..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...
  5. Molecular Epidemiology of DNA Repair in Head and Neck Cancer
    Qingyi Wei; Fiscal Year: 2010
    ..e., ERCC1, XPA, XPB, XPC, XPD, XPE, XPF, and XPG), to correlate the variant alleles/genotypes or haplotypes/diplotypes with three NER phenotypes (i.e...
  6. EMBRYO LETHAL GENES IN THE MHC AND T/T COMPLEXES
    Karen Artzt; Fiscal Year: 2001
    ..The tct mutation is common to all t haplotypes (which is a variant form of chromosome 17 consisting of multiple inversions spanning 15-20 centiMorgans of the ..
  7. Genetic and Immunological Impact of the HRES-1/Rab4 Locus in SLE
    Andras Perl; Fiscal Year: 2010
    ..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 ..
  8. ANTI-GLOMERULAR BASEMENT MEMBRANE DISEASE
    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...
  9. Insulin Clearance: Candidate and Positional Genetic Determinants
    MARK GOODARZI; Fiscal Year: 2011
    ..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) ..
  10. Insulin Clearance: Candidate and Positional Genetic Determinants
    MARK GOODARZI; Fiscal Year: 2009
    ..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) ..
  11. Insulin Clearance: Candidate and Positional Genetic Determinants
    MARK GOODARZI; Fiscal Year: 2010
    ..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) ..
  12. SEQUENCE AND POLYMORPHISM OF RHESUS MACAQUE MHC
    Daniel Geraghty; Fiscal Year: 2006
    ..indirect evidence exists that there may be as many as 3 class I B loci and 2 class I A loci on certain macaque haplotypes, but this has not been confirmed through direct genomic analysis...
  13. IMMUNOGENETICS OF COLLAGEN INDUCED ARTHRITIS
    Chella David; Fiscal Year: 2000
    ..By generating additional transgenic mice expressing HLA-DQ genes from RA linked and RA non-linked haplotypes, we will conform a role for DQ polymorphism in the predisposition to the disease...
  14. Genotypes, Haplotypes, and Blood Pressure Change from Childhood to Adulthood
    DAVID HALLMAN; Fiscal Year: 2009
    ..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 ..
  15. 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 ..
  16. IMMUNOGENETICS OF COLLAGEN INDUCED ARTHRITIS IN MICE
    Chella David; Fiscal Year: 2005
    ..Predisposition to RA has been linked to the MHC class II genes with haplotypes HLA-DQ8/DR4 showing the highest relative risk, and DQ6/DR2 being resistant...
  17. Beta2-Adrenergic Receptor Gene Variation and Cardiovascular Control in Humans
    John Eisenach; Fiscal Year: 2009
    ..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...
  18. Beta2-Adrenergic Receptor Gene Variation and Cardiovascular Control in Humans
    John H Eisenach; Fiscal Year: 2010
    ..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...
  19. Beta2-Adrenergic Receptor Gene Variation and Cardiovascular Control in Humans
    John Eisenach; Fiscal Year: 2009
    ..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...
  20. 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 ..
  21. Variation in Ara-C Pathway Genes and Treatment Outcomes in AML
    Rakesh Goyal; Fiscal Year: 2007
    ..and assess the impact of this variation on gene expression in vitro and in vivo; 2) to determine if specific haplotypes in patient ENT1, DCK, NT5C2 and CDA genes predict overall survival in children and adolescents undergoing ..