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Conference Paper: Sampling among haplotype resolutions in a coalescent-based genealogy sampler

TitleSampling among haplotype resolutions in a coalescent-based genealogy sampler
Authors
Issue Date2000
PublisherJohn Wiley & Sons, Inc. The Journal's web site is located at http://www3.interscience.wiley.com/cgi-bin/jhome/35841
Citation
Genetic Epidemiology, 2000, v. 19 SUPPL. 1, p. S15-S21 How to Cite?
AbstractAnalysis of the coalescent structure of a population may provide information useful in mapping disease loci. Current coalescent-based genealogy samplers require haplotyped data, but haplotypes are not always available, and it is not practical to sum over all haplotype assignments for large data sets. We describe a method of adding haplotype re-evaluation to the sampler, so that it samples not only among genealogies explaining a given haplotype configuration, but also among different haplotype configurations. Several different haplotype-rearrangement strategies are considered, but the simplest - inverting the phase of a single site in a single individual - appears to be the most successful. The straightforward haplotype sampler does not mix well; heating approaches can greatly improve its performance. (C) 2000 Wiley-Liss, Inc.
Persistent Identifierhttp://hdl.handle.net/10722/176090
ISSN
2015 Impact Factor: 2.553
2015 SCImago Journal Rankings: 2.101
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorSham, PCen_US
dc.contributor.authorZhao, JHen_US
dc.contributor.authorCherny, SSen_US
dc.contributor.authorHewitt, JKen_US
dc.date.accessioned2012-11-26T09:05:33Z-
dc.date.available2012-11-26T09:05:33Z-
dc.date.issued2000en_US
dc.identifier.citationGenetic Epidemiology, 2000, v. 19 SUPPL. 1, p. S15-S21en_US
dc.identifier.issn0741-0395en_US
dc.identifier.urihttp://hdl.handle.net/10722/176090-
dc.description.abstractAnalysis of the coalescent structure of a population may provide information useful in mapping disease loci. Current coalescent-based genealogy samplers require haplotyped data, but haplotypes are not always available, and it is not practical to sum over all haplotype assignments for large data sets. We describe a method of adding haplotype re-evaluation to the sampler, so that it samples not only among genealogies explaining a given haplotype configuration, but also among different haplotype configurations. Several different haplotype-rearrangement strategies are considered, but the simplest - inverting the phase of a single site in a single individual - appears to be the most successful. The straightforward haplotype sampler does not mix well; heating approaches can greatly improve its performance. (C) 2000 Wiley-Liss, Inc.en_US
dc.languageengen_US
dc.publisherJohn Wiley & Sons, Inc. The Journal's web site is located at http://www3.interscience.wiley.com/cgi-bin/jhome/35841en_US
dc.relation.ispartofGenetic Epidemiologyen_US
dc.subject.meshComputer Simulationen_US
dc.subject.meshHaplotypesen_US
dc.subject.meshPedigreeen_US
dc.subject.meshSampling Studiesen_US
dc.subject.meshSoftwareen_US
dc.titleSampling among haplotype resolutions in a coalescent-based genealogy sampleren_US
dc.typeConference_Paperen_US
dc.identifier.emailSham, PC: pcsham@hku.hken_US
dc.identifier.emailCherny, SS: cherny@hku.hken_US
dc.identifier.authoritySham, PC=rp00459en_US
dc.identifier.authorityCherny, SS=rp00232en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1002/1098-2272(2000)19:1+<::AID-GEPI3>3.0.CO;2-Ven_US
dc.identifier.pmid11055365-
dc.identifier.scopuseid_2-s2.0-0033809986en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-0033809986&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume19en_US
dc.identifier.issueSUPPL. 1en_US
dc.identifier.spageS15en_US
dc.identifier.epageS21en_US
dc.identifier.isiWOS:000089683700004-
dc.publisher.placeUnited Statesen_US
dc.identifier.scopusauthoridSham, PC=34573429300en_US
dc.identifier.scopusauthoridZhao, JH=7410311266en_US
dc.identifier.scopusauthoridCherny, SS=7004670001en_US
dc.identifier.scopusauthoridHewitt, JK=7202713286en_US

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