Dataset Information

A second generation human haplotype map of over 3.1 million SNPs.

ABSTRACT: 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.

SUBMITTER: International HapMap Consortium

PROVIDER: S-EPMC2689609 | biostudies-literature | 2007 Oct

REPOSITORIES: biostudies-literature

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A second generation human haplotype map of over 3.1 million SNPs.

Frazer Kelly A KA Ballinger Dennis G DG Cox David R DR Hinds David A DA Stuve Laura L LL Gibbs Richard A RA Belmont John W JW Boudreau Andrew A Hardenbol Paul P Leal Suzanne M SM Pasternak Shiran S Wheeler David A DA Willis Thomas D TD Yu Fuli F Yang Huanming H Zeng Changqing C Gao Yang Y Hu Haoran H Hu Weitao W Li Chaohua C Lin Wei W Liu Siqi S Pan Hao H Tang Xiaoli X Wang Jian J Wang Wei W Yu Jun J Zhang Bo B Zhang Qingrun Q Zhao Hongbin H Zhao Hui H Zhou Jun J Gabriel Stacey B SB Barry Rachel R Blumenstiel Brendan B Camargo Amy A Defelice Matthew M Faggart Maura M Goyette Mary M Gupta Supriya S Moore Jamie J Nguyen Huy H Onofrio Robert C RC Parkin Melissa M Roy Jessica J Stahl Erich E Winchester Ellen E Ziaugra Liuda L Altshuler David D Shen Yan Y Yao Zhijian Z Huang Wei W Chu Xun X He Yungang Y Jin Li L Liu Yangfan Y Shen Yayun Y Sun Weiwei W Wang Haifeng H Wang Yi Y Wang Ying Y Xiong Xiaoyan X Xu Liang L Waye Mary M Y MM Tsui Stephen K W SK Xue Hong H Wong J Tze-Fei JT Galver Luana M LM Fan Jian-Bing JB Gunderson Kevin K Murray Sarah S SS Oliphant Arnold R AR Chee Mark S MS Montpetit Alexandre A Chagnon Fanny F Ferretti Vincent V Leboeuf Martin M Olivier Jean-François JF Phillips Michael S MS Roumy Stéphanie S Sallée Clémentine C Verner Andrei A Hudson Thomas J TJ Kwok Pui-Yan PY Cai Dongmei D Koboldt Daniel C DC Miller Raymond D RD Pawlikowska Ludmila L Taillon-Miller Patricia P Xiao Ming M Tsui Lap-Chee LC Mak William W Song You Qiang YQ Tam Paul K H PK Nakamura Yusuke Y Kawaguchi Takahisa T Kitamoto Takuya T Morizono Takashi T Nagashima Atsushi A Ohnishi Yozo Y Sekine Akihiro A Tanaka Toshihiro T Tsunoda Tatsuhiko T Deloukas Panos P Bird Christine P CP Delgado Marcos M Dermitzakis Emmanouil T ET Gwilliam Rhian R Hunt Sarah S Morrison Jonathan J Powell Don D Stranger Barbara E BE Whittaker Pamela P Bentley David R DR Daly Mark J MJ de Bakker Paul I W PI Barrett Jeff J Chretien Yves R YR Maller Julian J McCarroll Steve S Patterson Nick N Pe'er Itsik I Price Alkes A Purcell Shaun S Richter Daniel J DJ Sabeti Pardis P Saxena Richa R Schaffner Stephen F SF Sham Pak C PC Varilly Patrick P Altshuler David D Stein Lincoln D LD Krishnan Lalitha L Smith Albert Vernon AV Tello-Ruiz Marcela K MK Thorisson Gudmundur A GA Chakravarti Aravinda A Chen Peter E PE Cutler David J DJ Kashuk Carl S CS Lin Shin S Abecasis Gonçalo R GR Guan Weihua W Li Yun Y Munro Heather M HM Qin Zhaohui Steve ZS Thomas Daryl J DJ McVean Gilean G Auton Adam A Bottolo Leonardo L Cardin Niall N Eyheramendy Susana S Freeman Colin C Marchini Jonathan J Myers Simon S Spencer Chris C Stephens Matthew M Donnelly Peter P Cardon Lon R LR Clarke Geraldine G Evans David M DM Morris Andrew P AP Weir Bruce S BS Tsunoda Tatsuhiko T Mullikin James C JC Sherry Stephen T ST Feolo Michael M Skol Andrew A Zhang Houcan H Zeng Changqing C Zhao Hui H Matsuda Ichiro I Fukushima Yoshimitsu Y Macer Darryl R DR Suda Eiko E Rotimi Charles N CN Adebamowo Clement A CA Ajayi Ike I Aniagwu Toyin T Marshall Patricia A PA Nkwodimmah Chibuzor C Royal Charmaine D M CD Leppert Mark F MF Dixon Missy M Peiffer Andy A Qiu Renzong R Kent Alastair A Kato Kazuto K Niikawa Norio N Adewole Isaac F IF Knoppers Bartha M BM Foster Morris W MW Clayton Ellen Wright EW Watkin Jessica J Gibbs Richard A RA Belmont John W JW Muzny Donna D Nazareth Lynne L Sodergren Erica E Weinstock George M GM Wheeler David A DA Yakub Imtaz I Gabriel Stacey B SB Onofrio Robert C RC Richter Daniel J DJ Ziaugra Liuda L Birren Bruce W BW Daly Mark J MJ Altshuler David D Wilson Richard K RK Fulton Lucinda L LL Rogers Jane J Burton John J Carter Nigel P NP Clee Christopher M CM Griffiths Mark M Jones Matthew C MC McLay Kirsten K Plumb Robert W RW Ross Mark T MT Sims Sarah K SK Willey David L DL Chen Zhu Z Han Hua H Kang Le L Godbout Martin M Wallenburg John C JC L'Archevêque Paul P Bellemare Guy G Saeki Koji K Wang Hongguang H An Daochang D Fu Hongbo H Li Qing Q Wang Zhen Z Wang Renwu R Holden Arthur L AL Brooks Lisa D LD McEwen Jean E JE Guyer Mark S MS Wang Vivian Ota VO Peterson Jane L JL Shi Michael M Spiegel Jack J Sung Lawrence M LM Zacharia Lynn F LF Collins Francis S FS Kennedy Karen K Jamieson Ruth R Stewart John J

Nature 20071001 7164

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 ...[more]

PMID: 17943122

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Project description:BackgroundGenetic maps characterizing the inheritance patterns of traits and markers have been developed for a wide range of species and used to study questions in biomedicine, agriculture, ecology and evolutionary biology. The status of rainbow trout genetic maps has progressed significantly over the last decade due to interest in this species in aquaculture and sport fisheries, and as a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. We constructed a second generation genetic map for rainbow trout using microsatellite markers to facilitate the identification of quantitative trait loci for traits affecting aquaculture production efficiency and the extraction of comparative information from the genome sequences of model fish species.ResultsA genetic map ordering 1124 microsatellite loci spanning a sex-averaged distance of 2927.10 cM (Kosambi) and having 2.6 cM resolution was constructed by genotyping 10 parents and 150 offspring from the National Center for Cool and Cold Water Aquaculture (NCCCWA) reference family mapping panel. Microsatellite markers, representing pairs of loci resulting from an evolutionarily recent whole genome duplication event, identified 180 duplicated regions within the rainbow trout genome. Microsatellites associated with genes through expressed sequence tags or bacterial artificial chromosomes produced comparative assignments with tetraodon, zebrafish, fugu, and medaka resulting in assignments of homology for 199 loci.ConclusionThe second generation NCCCWA genetic map provides an increased microsatellite marker density and quantifies differences in recombination rate between the sexes in outbred populations. It has the potential to integrate with cytogenetic and other physical maps, identifying paralogous regions of the rainbow trout genome arising from the evolutionarily recent genome duplication event, and anchoring a comparative map with the zebrafish, medaka, tetraodon, and fugu genomes. This resource will facilitate the identification of genes affecting traits of interest through fine mapping and positional cloning of candidate genes.

Project description:BACKGROUND: Japanese flounder (Paralichthys olivaceus) is one of the most economically important marine species in Northeast Asia. Information on genetic markers associated with quantitative trait loci (QTL) can be used in breeding programs to identify and select individuals carrying desired traits. Commercial production of Japanese flounder could be increased by developing disease-resistant fish and improving commercially important traits. Previous maps have been constructed with AFLP markers and a limited number of microsatellite markers. In this study, improved genetic linkage maps are presented. In contrast with previous studies, these maps were built mainly with a large number of codominant markers so they can potentially be used to analyze different families and populations. RESULTS: Sex-specific genetic linkage maps were constructed for the Japanese flounder including a total of 1,375 markers [1,268 microsatellites, 105 single nucleotide polymorphisms (SNPs) and two genes]; 1,167 markers are linked to the male map and 1,067 markers are linked to the female map. The lengths of the male and female maps are 1,147.7 cM and 833.8 cM, respectively. Based on estimations of map lengths, the female and male maps covered 79 and 82% of the genome, respectively. Recombination ratio in the new maps revealed F:M of 1:0.7. All linkage groups in the maps presented large differences in the location of sex-specific recombination hot-spots. CONCLUSIONS: The improved genetic linkage maps are very useful for QTL analyses and marker-assisted selection (MAS) breeding programs for economically important traits in Japanese flounder. In addition, SNP flanking sequences were blasted against Tetraodon nigroviridis (puffer fish) and Danio rerio (zebrafish), and synteny analysis has been carried out. The ability to detect synteny among species or genera based on homology analysis of SNP flanking sequences may provide opportunities to complement initial QTL experiments with candidate gene approaches from homologous chromosomal locations identified in related model organisms.

Dataset Information

A second generation human haplotype map of over 3.1 million SNPs.

Publications

A second generation human haplotype map of over 3.1 million SNPs.

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