Article

Nature 437, 1299-1320 (27 October 2005) | doi:10.1038/nature04226; Received 11 August 2005; Accepted 12 September 2005

A haplotype map of the human genome

The International HapMap Consortium64

  1. Affiliations for participants: Baylor College of Medicine, Human Genome Sequencing Center, Department of Molecular and Human Genetics, 1 Baylor Plaza, Houston, Texas 77030, USA
  2. ParAllele Bioscience, Inc., 7300 Shoreline Court, South San Francisco, California 94080, USA
  3. Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 100300, China
  4. The Broad Institute of Harvard and Massachusetts Institute of Technology, 1 Kendall Square, Cambridge, Massachusetts 02139, USA
  5. Massachusetts General Hospital and Harvard Medical School, Simches Research Center, 185 Cambridge Street, Boston, Massachusetts 02114, USA
  6. Chinese National Human Genome Center at Beijing, 3-707 N. Yongchang Road, Beijing Economic-Technological Development Area, 100176, China
  7. Chinese National Human Genome Center at Shanghai, 250 Bi Bo Road, Shanghai 201203, China
  8. The Chinese University of Hong Kong, Department of Biochemistry, The Croucher Laboratory for Human Genomics, 6/F Mong Man Wai Building, Shatin, Hong Kong
  9. Hong Kong University of Science and Technology, Department of Biochemistry, Clear Water Bay, Kowloon, Hong Kong
  10. Illumina, 9885 Towne Centre Drive, San Diego, California 92121, USA
  11. 15518 Markar Road, Poway, California 92064, USA
  12. Prognosys Biosciences, Inc., 4215 Sorrento Valley Boulevard, Suite 105, San Diego, California 92121, USA
  13. McGill University and Génome Québec Innovation Centre, 740 Drive Penfield Avnue, Montréal, Québec H3A 1A4, Canada
  14. University of Montréal, The Public Law Research Centre (CRDP), P.O. Box 6128, Downtown Station, Montréal, Québec H3C 3J7, Canada
  15. Perlegen Sciences, Inc., 2021 Stierlin Court, Mountain View, California 94043, USA
  16. University of California, San Francisco, Cardiovascular Research Institute, 513 Parnassus Avenue, Box 0793, San Francisco, California 94143, USA
  17. Washington University School of Medicine, Department of Genetics, 660 S. Euclid Avenue, Box 8232, St Louis, Missouri 63110, USA
  18. University of Hong Kong, Genome Research Centre, 6/F, Laboratory Block, 21 Sassoon Road, Pokfulam, Hong Kong
  19. University of Tokyo, Institute of Medical Science, 4-6-1 Sirokanedai, Minato-ku, Tokyo 108-8639, Japan
  20. RIKEN SNP Research Center, 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama, Kanagawa 230-0045, Japan
  21. Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
  22. Solexa Ltd, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK
  23. Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
  24. Johns Hopkins University School of Medicine, McKusick-Nathans Institute of Genetic Medicine, Broadway Research Building, Suite 579, 733 N. Broadway, Baltimore, Maryland 21205, USA
  25. University of Michigan, Center for Statistical Genetics, Department of Biostatistics, 1420 Washington Heights, Ann Arbor, Michigan 48109, USA
  26. Center for Biomolecular Science and Engineering, Engineering 2, Suite 501, Mail Stop CBSE/ITI, UC Santa Cruz, Santa Cruz, California 95064, USA
  27. University of Oxford, Department of Statistics, 1 South Parks Road, Oxford OX1 3TG, UK
  28. University of Washington, Department of Statistics, Box 354322, Seattle, Washington 98195, USA
  29. University of Oxford/Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
  30. North Carolina State University, Bioinformatics Research Center, Campus Box 7566, Raleigh, North Carolina 27695, USA
  31. US National Institutes of Health, National Human Genome Research Institute, 50 South Drive, Bethesda, Maryland 20892, USA
  32. US National Institutes of Health, National Library of Medicine, National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
  33. Beijing Normal University, 19 Xinjiekouwai Street, Beijing 100875, China
  34. Health Sciences University of Hokkaido, Ishikari Tobetsu Machi 1757, Hokkaido 061-0293, Japan
  35. Shinshu University School of Medicine, Department of Medical Genetics, Matsumoto 390-8621, Japan
  36. United Nations Educational, Scientific and Cultural Organization (UNESCO Bangkok), 920 Sukhumwit Road, Prakanong, Bangkok 10110, Thailand
  37. University of Tsukuba, Eubios Ethics Institute, P.O. Box 125, Tsukuba Science City 305-8691, Japan
  38. Howard University, National Human Genome Center, 2216 6th Street, NW, Washington DC 20059, USA
  39. University of Ibadan College of Medicine, Ibadan, Oyo State, Nigeria
  40. Case Western Reserve University School of Medicine, Department of Bioethics, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
  41. University of Utah, Eccles Institute of Human Genetics, Department of Human Genetics, 15 North 2030 East, Salt Lake City, Utah 84112, USA
  42. Chinese Academy of Social Sciences, Center for Applied Ethics, 2121, Building 9, Caoqiao Xinyuan 3 Qu, Beijing 100054, China
  43. Genetic Interest Group, 4D Leroy House, 436 Essex Road, London N1 3QP, UK
  44. Kyoto University, Institute for Research in Humanities and Graduate School of Biostudies, Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
  45. Nagasaki University Graduate School of Biomedical Sciences, Department of Human Genetics, Sakamoto 1-12-4, Nagasaki 852-8523, Japan
  46. University of Oklahoma, Department of Anthropology, 455 W. Lindsey Street, Norman, Oklahoma 73019, USA
  47. Vanderbilt University, Center for Genetics and Health Policy, 507 Light Hall, Nashville, Tennessee 37232-0165, USA
  48. Wellcome Trust, 215 Euston Road, London NW1 2BE, UK
  49. Washington University School of Medicine, Genome Sequencing Center, Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
  50. Chinese Academy of Sciences, 52 Sanlihe Road, Beijing 100864, China
  51. Genome Canada, 150 Metcalfe Street, Suite 2100, Ottawa, Ontario K2P 1P1, Canada
  52. McGill University, Office of Technology Transfer, 3550 University Street, Montréal, Québec H3A 2A7, Canada
  53. Génome Québec, 630, boulevard René-Lévesque Ouest, Montréal, Québec H3B 1S6, Canada
  54. Ministry of Education, Culture, Sports, Science, and Technology, 3-2-2 Kasumigaseki, Chiyodaku, Tokyo 100-8959, Japan
  55. Ministry of Science and Technology of the People's Republic of China, 15 B. Fuxing Road, Beijing 100862, China
  56. The Human Genetic Resource Administration of China, b7, Zaojunmiao, Haidian District, Beijing 100081, China
  57. The SNP Consortium, 3 Parkway North, Deerfield, Illinois 60015, USA
  58. US National Institutes of Health, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, Bethesda, Maryland 20892, USA
  59. Novartis Pharmaceuticals Corporation, Biomarker Development, One Health Plaza, East Hanover, New Jersey 07936, USA
  60. US National Institutes of Health, Office of Technology Transfer, 6011 Executive Boulevard, Rockville, Maryland 20852, USA
  61. University of Maryland School of Law, 500 W. Baltimore Street, Baltimore, Maryland 21201, USA
  62. Frost & Sullivan, 2400 Geng Road, Suite 201, Palo Alto, California 94303, USA
  63. US National Institutes of Health, National Human Genome Research Institute, 31 Center Drive, Bethesda, Maryland 20892, USA
  64. *Lists of participants and affiliations appear at the end of the paper

Correspondence to: Correspondence and requests for materials should be addressed to D.A. (Email: altshuler@molbio.mgh.harvard.edu) or P.D. (Email: donnelly@stats.ox.ac.uk).

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Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution.

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