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Article: A second generation human haplotype map of over 3.1 million SNPs

TitleA second generation human haplotype map of over 3.1 million SNPs
Authors
Frazer, KABallinger, DGCox, DRHinds, DAStuve, LLGibbs, RABelmont, JWBoudreau, AHardenbol, PLeal, SMPasternak, SWheeler, DAWillis, TDYu, FYang, HZeng, CGao, YHu, HHu, WLi, CLin, WLiu, SPan, HTang, XWang, JWang, WYu, JZhang, BZhang, QZhao, HZhao, HZhou, JGabriel, SBBarry, RBlumenstiel, BCamargo, ADefelice, MFaggart, MGoyette, MGupta, SMoore, JNguyen, HOnofrio, RCParkin, MRoy, JStahl, EWinchester, EZiaugra, LAltshuler, DShen, YYao, ZHuang, WChu, XHe, YJin, LLiu, YShen, YSun, WWang, HWang, YWang, YXiong, XXu, LWaye, MMYTsui, SKWXue, HWong, JTFGalver, LMFan, JBGunderson, KMurray, SSOliphant, ARChee, MSMontpetit, AChagnon, FFerretti, VLeboeuf, MOlivier, JFPhillips, MSRoumy, SSallée, CVerner, AHudson, TJKwok, PYCai, DKoboldt, DCMiller, RDPawlikowska, LTaillonMiller, PXiao, MTsui, LCMak, WYou, QSTam, PKHNakamura, YKawaguchi, TKitamoto, TMorizono, TNagashima, AOhnishi, YSekine, ATanaka, TTsunoda, TDeloukas, PBird, CPDelgado, MDermitzakis, ETGwilliam, RHunt, SMorrison, JPowell, DStranger, BEWhittaker, PBentley, DRDaly, MJDe Bakker, PIWBarrett, JChretien, YRMaller, JMcCarroll, SPatterson, NPe'Er, IPrice, APurcell, SRichter, DJSabeti, PSaxena, RSchaffner, SFSham, PCVarilly, PStein, LDKrishnan, LSmith, AVTelloRuiz, MKThorisson, GAChakravarti, AChen, PECutler, DJKashuk, CSLin, SAbecasis, GRGuan, WLi, YMunro, HMQin, ZSThomas, DJMcVean, GAuton, ABottolo, LCardin, NEyheramendy, SFreeman, CMarchini, JMyers, SSpencer, CStephens, MDonnelly, PCardon, LRClarke, GEvans, DMMorris, APWeir, BSJohnson, TAMullikin, JCSherry, STFeolo, MSkol, AZhang, HMatsuda, IFukushima, YMacEr, DRSuda, ERotimi, CNAdebamowo, CAAjayi, IAniagwu, TMarshall, PANkwodimmah, CRoyal, CDMLeppert, MFDixon, MPeiffer, AQiu, RKent, AKato, KNiikawa, NAdewole, IFKnoppers, BMFoster, MWClayton, EWWatkin, JMuzny, DNazareth, LSodergren, EWeinstock, GMYakub, IBirren, BWWilson, RKFulton, LLRogers, JBurton, JCarter, NPClee, CMGriffiths, MJones, MCMcLay, KPlumb, RWRoss, MTSims, SKWilley, DLChen, ZHan, HKang, LGodbout, MWallenburg, JCL'Archevêque, PBellemare, GSaeki, KWang, HAn, DFu, HLi, QWang, ZWang, RHolden, ALBrooks, LDMcEwen, JEGuyer, MSWang, VOPeterson, JLShi, MSpiegel, JSung, LMZacharia, LFCollins, FSKennedy, KJamieson, RStewart, J
Issue Date2007
PublisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/nature
Citation
Nature, 2007, v. 449 n. 7164, p. 851-861 How to Cite?
AbstractWe 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 r 2 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 r 2 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. ©2007 Nature Publishing Group.
Persistent Identifierhttp://hdl.handle.net/10722/83344
ISSN
2023 Impact Factor: 50.5
2023 SCImago Journal Rankings: 18.509
PubMed Central ID
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorFrazer, KAen_HK
dc.contributor.authorBallinger, DGen_HK
dc.contributor.authorCox, DRen_HK
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dc.contributor.authorStuve, LLen_HK
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dc.date.accessioned2010-09-06T08:39:55Z-
dc.date.available2010-09-06T08:39:55Z-
dc.date.issued2007en_HK
dc.identifier.citationNature, 2007, v. 449 n. 7164, p. 851-861en_HK
dc.identifier.issn0028-0836en_HK
dc.identifier.urihttp://hdl.handle.net/10722/83344-
dc.description.abstractWe 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 r 2 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 r 2 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. ©2007 Nature Publishing Group.en_HK
dc.languageengen_HK
dc.publisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/natureen_HK
dc.relation.ispartofNatureen_HK
dc.titleA second generation human haplotype map of over 3.1 million SNPsen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0028-0836&volume=449&issue=7164&spage=851&epage=861&date=2007&atitle=A+second+generation+human+haplotype+map+of+over+3.1+million+SNPs+(Co-PI+of+Hong+Kong+Centre+which+responsible+2.5%+of+genome)en_HK
dc.identifier.emailTsui, LC: tsuilc@hkucc.hku.hken_HK
dc.identifier.emailYou, QS: songy@hku.hken_HK
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dc.identifier.doi10.1038/nature06258en_HK
dc.identifier.pmid17943122-
dc.identifier.pmcidPMC2689609-
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dc.identifier.citeulike1780948-
dc.identifier.issnl0028-0836-

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