A second generation human haplotype map of over 3.1 million SNPs

Nature - Tập 449 Số 7164 - Trang 851-861 - 2007
Kelly A. Frazer1, Dennis G. Ballinger, David R. Cox, David A. Hinds, Laura L. Stuvé, Richard A. Gibbs2, John W. Belmont2, Andrew Boudreau, Paul Hardenbol3, Suzanne M. Leal2, Shiran Pasternak, David A. Wheeler2, T. D. Willis, Fuli Yu4, Huanming Yang5, Changqing Zeng5, Yang Gao5, Haoran Hu5, Weitao Hu5, Chaohua Li5, Wei Lin5, Siqi Liu5, Hao Pan5, Xiaoli Tang5, Jun Wang5, Wei Wang5, Jun Yu5, Bo Zhang5, Qingrun Zhang5, Hongbin Zhao5, Hui Zhao5, Jun Zhou5, Stacey Gabriel4, Rachel Barry4, Brendan Blumenstiel4, Amy L. Camargo4, Matthew DeFelice4, Maura Faggart4, Mary Goyette4, Supriya Gupta4, Jamie Moore4, Huy Nguyen4, Robert C. Onofrio4, Melissa Parkin4, Jessica Roy4, Erich Stahl4, Ellen Winchester4, Liuda Ziaugra4, David Green6, Yan Shen, Zhijian Yao, Wei Huang, Xun Chu, Yungang He, Jin Li7, Yangfan Liu, Yayun Shen, Weiwei Sun, Haifeng Wang, Yi Wang, Ying Wang, Xiaoyan Xiong, Lang Xu, Mary Miu Yee Waye8, Stephen Kwok‐Wing Tsui8, Hong Xue9, J. Tze‐Fei Wong9, Luana Galver10, Jian-Bing Fan10, Kevin L. Gunderson10, Sarah S. Murray1, Arnold Oliphant, Mark S. Chee, Alexandre Montpetit11, Fanny Chagnon11, Vincent Ferretti11, Martin Leboeuf11, Jean François Olivier, Michael Phillips11, Stéphanie Roumy10, Clémentine Sallée12, Andrei Verner11, Thomas J. Hudson13, Pui‐Yan Kwok14, Dongmei Cai14, Daniel C. Koboldt15, Raymond D. Miller15, Ludmila Pawlikowska14, Patricia Taillon‐Miller15, Ming Xiao14, L.-C. Tsui16, William Mak16, You‐Qiang Song16, Paul Kwong Hang Tam16, Yusuke Nakamura, Takahisa Kawaguchi, Takuya Kitamoto, Takashi Morizono, Atsushi Nagashima, Yozo Ohnishi, Akihiro Sekine, Toshihiro Tanaka, Tatsuhiko Tsunoda, Panos Deloukas, Christine Bird, Marcos Delgado, Emmanouil T. Dermitzakis, Sarah Hunt, Jonathan J. Morrison17, Don Powell, Barbara E. Stranger, Pamela Whittaker, David Bentley, Mark J. Daly6, Paul I. W. de Bakker6, Jeff Barrett6, Yves Chrétien4, Julian Maller6, Steven A. McCarroll6, Hon‐Cheong So4, Itsik Pe’er18, Alkes L. Price4, Shaun Purcell6, Daniel J. Richter4, Pardis C. Sabeti4, Richa Saxena6, S. F. Schaffner4, Pak C. Sham16, Patrick Varilly4, Lincoln D. Stein, Lalitha Krishnan, Albert Hofman, Aravinda Chakravarti19, Peter E. Chen20, David J. Cutler20, Carl Kashuk20, Shin Lin20, Gonçalo R. Abecasis21, Yun Li21, Heather M. Munro, Zhaohui Qin21, Gil McVean22, Adam Auton22, Leonardo Bottolo22, Susana Eyheramendy22, S. Eyheramendy22, Jonathan Marchini22, Simon Myers22, Stephen B. Montgomery23, Peter Humburg22, Peter Donnelly24, Geraldine M Clarke22, David M. Evans22, Bruce S. Weir25, Todd A. Johnson, James C. Mullikin26, S Sherry26, Andrew D. Skol23, Houcan Zhang27, Ichiro Matsuda28, Yoshimitsu Fukushima29, Darryl Macer, Charles N. Rotimi30, IkeOluwapo O. Ajayi31, Alan Christoffels31, Clement Adebamowo32, Charmaine Royal30, Mark Leppert33, Missy Dixon33, Andy Peiffer33, Renzong Qiu34, Alastair Kent, Kazuto Kato35, Norio Niikawa36, Isaac F. Adewole31, Morris W. Foster37, Ellen Wright Clayton38, Jessica Watkin39, Donna M. Muzny2, Erica Sodergren2, George M. Weinstock2, Imtiaz Yakub2, Bruce W. Birren4, Joan E. Bailey‐Wilson15, Lucinda Fulton15, John H. Burton, Nigel P. Carter, Christopher M. Clee, Mark Griffiths, Matthew Jones, Kirsten McLay, R. W. Plumb, Mark T. Ross, Sarah K. Sims, David Willey, Hua Han5, Le Kang5, Martin Godbout, John C. Wallenburg11, Paul L'Archevêque, Guy Bellemare, Keiichi Saeki, Hongguang Wang, Daochang An, Hongbo Fu, Qing Li, Zhen Wang, Rui Wang, Arthur L. Holden10, Jean McEwen26, Mark S. Guyer26, Vivian Ota Wang26, Jane L. Peterson26, Michael Shi40, Lawrence M. Sung41, Lynn F. Zacharia26, Francis S. Collins26, Karen Kennedy, Ruth Jamieson39, John Stewart39
1Scripps Research Institute, San Diego, United States
2Baylor College of Medicine, Houston, United States
3Pacific Biosciences (United States), Menlo Park, United States
4Broad Institute, Cambridge, United States
5Chinese Academy of Sciences, Beijing, China
6Harvard University, Cambridge, United States
7Fudan University, Shanghai, China
8Chinese University of Hong Kong, Hong Kong, China
9Hong Kong University of Science and Technology, Hong Kong, China
10Illumina (United States), San Diego, United States
11McGill University Montreal, Canada
12Université de Montréal, Montreal, Canada
13Ontario Institute for Cancer Research, Toronto, Canada
14University of California, San Francisco, San Francisco, United States
15Washington University in St Louis, St Louis, United States
16University of Hong Kong, Hong Kong, Hong Kong
17University of Cambridge, Cambridge, United Kingdom
18Columbia University, New York, United States
19University of Leicester, Leicester, United Kingdom
20Johns Hopkins University, Baltimore, United States
21University of Michigan–Ann Arbor, Ann Arbor, United States
22University of Oxford, Oxford, United Kingdom
23University of Chicago, Chicago, United States
24Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
25University of Washington, Seattle, United States
26National Institutes of Health, Bethesda, United States
27Beijing Normal University, Beijing, China
28Health Sciences University of Hokkaido, Tōbetsu, Japan
29Shinshu University, Matsumoto, Japan
30Howard University, Washington, United States
31University of Ibadan, Ibadan, Nigeria
32Case Western Reserve University, Cleveland, United States
33University of Utah, Salt Lake City, United States
34Chinese Academy of Social Sciences, Beijing, China
35Kyoto University, Kyoto, Japan
36Nagasaki University, Nagasaki, Japan
37University of Oklahoma, Norman, United States
38Vanderbilt University, Nashville, United States
39Wellcome Trust, London, United Kingdom
40Novartis (Switzerland), Basel, Switzerland
41University of Maryland, Baltimore, Baltimore, United States

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The International HapMap Consortium. Integrating ethics and science in the International HapMap Project. Nature Rev. Genet. 5, 467–475 (2004)

The International HapMap Consortium. The International HapMap Project. Nature 426, 789–796 (2003)

The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299–1320 (2005)

Bowcock, A. M. Genomics: guilt by association. Nature 447, 645–646 (2007)

Altshuler, D. & Daly, M. Guilt beyond a reasonable doubt. Nature Genet. 39, 813–815 (2007)

Myers, S., Bottolo, L., Freeman, C., McVean, G. & Donnelly, P. A fine-scale map of recombination rates and hotspots across the human genome. Science 310, 321–324 (2005)

McCarroll, S. A. et al. Common deletion polymorphisms in the human genome. Nature Genet. 38, 86–92 (2006)

Conrad, D. F., Andrews, T. D., Carter, N. P., Hurles, M. E. & Pritchard, J. K. A high-resolution survey of deletion polymorphism in the human genome. Nature Genet. 38, 75–81 (2006)

Voight, B. F., Kudaravalli, S., Wen, X. & Pritchard, J. K. A map of recent positive selection in the human genome. PLoS Biol. 4, e72 (2006)

Redon, R. et al. Global variation in copy number in the human genome. Nature 444, 444–454 (2006)

de Bakker, P. I. et al. A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nature Genet. 38, 1166–1172 (2006)

Pastinen, T. et al. Mapping common regulatory variants to human haplotypes. Hum. Mol. Genet. 14, 3963–3971 (2005)

Stranger, B. E. et al. Genome-wide associations of gene expression variation in humans. PLoS Genet. 1, e78 (2005)

Cheung, V. G. et al. Mapping determinants of human gene expression by regional and genome-wide association. Nature 437, 1365–1369 (2005)

Hinds, D. A. et al. Whole-genome patterns of common DNA variation in three human populations. Science 307, 1072–1079 (2005)

de Bakker, P. I. et al. Efficiency and power in genetic association studies. Nature Genet. 37, 1217–1223 (2005)

Pe'er, I. et al. Evaluating and improving power in whole-genome association studies using fixed marker sets. Nature Genet. 38, 663–667 (2006)

Barrett, J. C. & Cardon, L. R. Evaluating coverage of genome-wide association studies. Nature Genet. 38, 659–662 (2006)

Burdick, J. T., Chen, W. M., Abecasis, G. R. & Cheung, V. G. In silico method for inferring genotypes in pedigrees. Nature Genet. 38, 1002–1004 (2006)

Servin, B. R. & Stephens, M. Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet. 3, e114 (2007)

The Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661–668 (2007)

Scott, L. J. et al. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 316, 1341–1345 (2007)

Marchini, J., Howie, B., Myers, S., McVean, G. & Donnelly, P. A new multipoint method for genome-wide association studies via imputation of genotypes. Nature Genet. 39, 906–913 (2007)

Chapman, J. M., Cooper, J. D., Todd, J. A. & Clayton, D. G. Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power. Hum. Hered. 56, 18–31 (2003)

Paabo, S. The mosaic that is our genome. Nature 421, 409–412 (2003)

McVean, G., Spencer, C. C. & Chaix, R. Perspectives on human genetic variation from the HapMap Project. PLoS Genet. 1, e54 (2005)

Purcell, S. et al. PLINK: a toolset for whole-genome association and population-based linkage analysis. Am. J. Hum. Genet. 81, 559–575 (2007)

Broman, K. W. & Weber, J. L. Long homozygous chromosomal segments in reference families from the centre d’Etude du polymorphisme humain. Am. J. Hum. Genet. 65, 1493–1500 (1999)

Gibson, J., Morton, N. E. & Collins, A. Extended tracts of homozygosity in outbred human populations. Hum. Mol. Genet. 15, 789–795 (2006)

Lander, E. S. & Botstein, D. Homozygosity mapping: a way to map human recessive traits with the DNA of inbred children. Science 236, 1567–1570 (1987)

Leutenegger, A. L. et al. Using genomic inbreeding coefficient estimates for homozygosity mapping of rare recessive traits: application to Taybi-Linder syndrome. Am. J. Hum. Genet. 79, 62–66 (2006)

Te Meerman, G. J., Van der Meulen, M. A. & Sandkuijl, L. A. Perspectives of identity by descent (IBD) mapping in founder populations. Clin. Exp. Allergy 25 (Suppl 2). 97–102 (1995)

Houwen, R. H. et al. Genome screening by searching for shared segments: mapping a gene for benign recurrent intrahepatic cholestasis. Nature Genet. 8, 380–386 (1994)

Durham, L. K. & Feingold, E. Genome scanning for segments shared identical by descent among distant relatives in isolated populations. Am. J. Hum. Genet. 61, 830–842 (1997)

Jeffreys, A. J. & May, C. A. Intense and highly localized gene conversion activity in human meiotic crossover hot spots. Nature Genet. 36, 151–156 (2004)

McVean, G. A. et al. The fine-scale structure of recombination rate variation in the human genome. Science 304, 581–584 (2004)

Myers, S. et al. The distribution and causes of meiotic recombination in the human genome. Biochem. Soc. Trans. 34, 526–530 (2006)

Spencer, C. C. et al. The influence of recombination on human genetic diversity. PLoS Genet. 2, e148 (2006)

Petes, T. D. Meiotic recombination hot spots and cold spots. Nature Rev. Genet. 2, 360–369 (2001)

Smith, A. V., Thomas, D. J., Munro, H. M. & Abecasis, G. R. Sequence features in regions of weak and strong linkage disequilibrium. Genome Res. 15, 1519–1534 (2005)

Thomas, P. D. et al. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 13, 2129–2141 (2003)

Winckler, W. et al. Comparison of fine-scale recombination rates in humans and chimpanzees. Science 308, 107–111 (2005)

Ptak, S. E. et al. Fine-scale recombination patterns differ between chimpanzees and humans. Nature Genet. 37, 429–434 (2005)

Sabeti, P. C. et al. Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832–837 (2002)

Sabeti, P. C. et al. Genome-wide detection and characterization of positive selection in human populations. Nature doi:10.1038/nature06250 (this issue).

Bustamante, C. D. et al. Natural selection on protein-coding genes in the human genome. Nature 437, 1153–1157 (2005)

Cargill, M. et al. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nature Genet. 22, 231–238 (1999)

Akey, J. M., Zhang, G., Zhang, K., Jin, L. & Shriver, M. D. Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 12, 1805–1814 (2002)

Sabeti, P. C. et al. Positive natural selection in the human lineage. Science 312, 1614–1620 (2006)

de Bakker, P. I. et al. Transferability of tag SNPs in genetic association studies in multiple populations. Nature Genet. 38, 1298–1303 (2006)

Conrad, D. F. et al. A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nature Genet. 38, 1251–1260 (2006)

Service, S., Sabatti, C. & Freimer, N. Tag SNPs chosen from HapMap perform well in several population isolates. Genet. Epidemiol. 31, 189–194 (2007)

Lim, J. et al. Comparative study of the linkage disequilibrium of an ENCODE region, chromosome 7p15, in Korean, Japanese, and Han Chinese samples. Genomics 87, 392–398 (2006)

Rabbee, N. & Speed, T. P. A genotype calling algorithm for affymetrix SNP arrays. Bioinformatics 22, 7–12 (2006)

Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007)

Price, A. L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nature Genet. 38, 904–909 (2006)

Smith, R. A., Ho, P. J., Clegg, J. B., Kidd, J. R. & Thein, S. L. Recombination breakpoints in the human β-globin gene cluster. Blood 92, 4415–4421 (1998)

Holloway, K., Lawson, V. E. & Jeffreys, A. J. Allelic recombination and de novo deletions in sperm in the human β-globin gene region. Hum. Mol. Genet. 15, 1099–1111 (2006)

Weir, B. S. & Cockerham, C. C. Estimating F-statistics for the analysis of population structure. Evolution 38, 1358–1370 (1984)