A second generation human haplotype map of over 3.1 million SNPs

Kelly A. Frazer;Dennis G. Ballinger;David R. Cox;David A. Hinds;Laura L. Stuve;Richard A. Gibbs;John W. Belmont;Andrew Boudreau;Paul Hardenbol;Suzanne M. Leal;Shiran Pasternak;David A. Wheeler;Thomas D. Willis;Fuli Yu;焕明 杨;长青 曾;Yang Gao;Haoran Hu;Weitao Hu;Chaohua Li;Wei Lin;Siqi Liu;Hao Pan;Xiaoli Tang;Jian Wang;Wei Wang;军 于;Bo Zhang;Qingrun Zhang;Hongbin Zhao;Hui Zhao;Jun Zhou;Stacey B. Gabriel;Rachel Barry;Brendan Blumenstiel;Amy Camargo;Matthew Defelice;Maura Faggart;Mary Goyette;Supriya Gupta;Jamie Moore;Huy Nguyen;Robert C. Onofrio;Melissa Parkin;Jessica Roy;Erich Stahl;Ellen Winchester;Liuda Ziaugra;David Altshuler;岩 沈;Zhijian Yao;Wei Huang;Xun Chu;Yungang He;力 金;Yangfan Liu;Yayun Shen;Weiwei Sun;Haifeng Wang;Yi Wang;Ying Wang;Xiaoyan Xiong;Liang Xu;Mary M.Y. Waye;Stephen K.W. Tsui;Hong Xue;J. Tze Fei Wong;Luana M. Galver;Jian Bing Fan;Kevin Gunderson;Sarah S. Murray;Arnold R. Oliphant;Mark S. Chee;Alexandre Montpetit;Fanny Chagnon;Vincent Ferretti;Martin Leboeuf;Jean François Olivier;Michael S. Phillips;Stéphanie Roumy;Clémentine Sallée;Andrei Verner;Thomas J. Hudson;Pui Yan Kwok;Dongmei Cai;Daniel C. Koboldt;Raymond D. Miller;Ludmila Pawlikowska;Patricia Taillon-Miller;Ming Xiao;立之 徐;William Mak;Qiang Song You;Paul K.H. Tam;Yusuke Nakamura;Takahisa Kawaguchi;Takuya Kitamoto;Takashi Morizono;Atsushi Nagashima;Yozo Ohnishi;Akihiro Sekine;Toshihiro Tanaka;Tatsuhiko Tsunoda;Panos Deloukas;Christine P. Bird;Marcos Delgado;Emmanouil T. Dermitzakis;Rhian Gwilliam;Sarah Hunt;Jonathan Morrison;Don Powell;Barbara E. Stranger;Pamela Whittaker;David R. Bentley;Mark J. Daly;Paul I.W. De Bakker;Jeff Barrett;Yves R. Chretien;Julian Maller;Steve McCarroll;Nick Patterson;Itsik Pe'Er;Alkes Price;Shaun Purcell;Daniel J. Richter;Pardis Sabeti;Richa Saxena;Stephen F. Schaffner;Pak C. Sham;Patrick Varilly;Lincoln D. Stein;Lalitha Krishnan;Albert Vernon Smith;Marcela K. Tello-Ruiz;Gudmundur A. Thorisson;Aravinda Chakravarti;Peter E. Chen;David J. Cutler;Carl S. Kashuk;Shin Lin;Gonçalo R. Abecasis;Weihua Guan;Yun Li;Heather M. Munro;Zhaohui Steve Qin;Daryl J. Thomas;Gilean McVean;Adam Auton;Leonardo Bottolo;Niall Cardin;Susana Eyheramendy;Colin Freeman;Jonathan Marchini;Simon Myers;Chris Spencer;Matthew Stephens;Peter Donnelly;Lon R. Cardon;Geraldine Clarke;David M. Evans;Andrew P. Morris;Bruce S. Weir;Todd A. Johnson;James C. Mullikin;Stephen T. Sherry;Michael Feolo;Andrew Skol;Houcan Zhang;Ichiro Matsuda;Yoshimitsu Fukushima;Darryl R. MacEr;Eiko Suda;Charles N. Rotimi;Clement A. Adebamowo;Ike Ajayi;Toyin Aniagwu;Patricia A. Marshall;Chibuzor Nkwodimmah;Charmaine D.M. Royal;Mark F. Leppert;Missy Dixon;Andy Peiffer;Renzong Qiu;Alastair Kent;Kazuto Kato;Norio Niikawa;Isaac F. Adewole;Bartha M. Knoppers;Morris W. Foster;Ellen Wright Clayton;Jessica Watkin;Donna Muzny;Lynne Nazareth;Erica Sodergren;George M. Weinstock;Imtaz Yakub;Bruce W. Birren;Richard K. Wilson;Lucinda L. Fulton;Jane Rogers;John Burton;Nigel P. Carter;Christopher M. Clee;Mark Griffiths;Matthew C. Jones;Kirsten McLay;Robert W. Plumb;Mark T. Ross;Sarah K. Sims;David L. Willey;竺 陈;Hua Han;乐 康;Martin Godbout;John C. Wallenburg;Paul L'Archevêque;Guy Bellemare;Koji Saeki;Hongguang Wang;Daochang An;Hongbo Fu;Qing Li;Zhen Wang;Renwu Wang;Arthur L. Holden;Lisa D. Brooks;Jean E. McEwen;Mark S. Guyer;Vivian Ota Wang;Jane L. Peterson;Michael Shi;Jack Spiegel;Lawrence M. Sung;Lynn F. Zacharia;Francis S. Collins;Karen Kennedy;Ruth Jamieson;John Stewart

Scripps Research Institute;Perlegen Sciences; Inc.;Baylor College of Medicine;Thermo Fisher Scientific;Pacific Biosciences;Cold Spring Harbor Laboratory;Massachusetts Institute of Technology;Chinese Academy of Sciences;Harvard University;Chinese National Human Genome Center;Fudan University;Chinese University of Hong Kong;Hong Kong University of Science and Technology;Illumina;Complete Genomics;Prognosys Biosciences; Inc.;McGill University;University of Montreal;Ontario Institute for Cancer Research;University of California at San Francisco;Washington University St. Louis;The University of Hong Kong;The University of Tokyo;RIKEN;Wellcome Trust;University of Cambridge;Solexa Ltd.;Columbia University;University of Leicester;Johns Hopkins University;University of Michigan; Ann Arbor;International Epidemiology Institute;University of California at Santa Cruz;University of Oxford;The University of Chicago;Fred Hutchinson Cancer Research Center;University of Washington;National Institutes of Health;Beijing Normal University;Health Sciences University of Hokkaido;Shinshu University;Scientific and Cultural Organization (UNESCO Bangkok);University of Tsukuba;Howard University;Department of Medicine;Case Western Reserve University;University of Utah;Chinese Academy of Social Sciences;Genetic Interest Group;Kyoto University;Nagasaki University;University of Oklahoma;Vanderbilt University;Genome Canada;Génome Québec;Min. of Educ.; Science; and Culture;Ministry of Science and Technology of the People's Republic of China;Human Genetic Resource Administration of China;Novartis;University of Maryland; Baltimore

发表时间:2007-10-18

期 刊:Nature

语 言:English

U R L: http://www.scopus.com/inward/record.url?scp=35348983887&partnerID=8YFLogxK

摘要

We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. 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.

被引量

期刊度量

Scopus度量

年份 CiteScore SJR SNIP
1996
1997
1998
1999 15.599 7.187
2000 11.917 6.857
2001 9.874 6.767
2002 10.114 7.184
2003 11.384 7.492
2004 11.222 7.538
2005 10.333 7.199
2006 9.702 7.156
2007 10.344 7.097
2008 13.17 7.307
2009 15.185 8.234
2010 16.465 8.204
2011 53.1 17.598 8.667
2012 51 17.546 8.409
2013 50.9 19.69 8.511
2014 49.9 18.78 7.918
2015 51.6 19.669 8.08
2016 49.2 18.389 7.901
2017 53.7 17.875 8.679
2018 55.7 16.345 9.448
2019 51 14.047 8.546
2020 56.9 15.993 9.249
2021 56

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