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Article: Incorporating genotyping uncertainty in haplotype frequency estimation in pedigree studies

TitleIncorporating genotyping uncertainty in haplotype frequency estimation in pedigree studies
Authors
KeywordsGenoSpectrum
Genotyping error
GS-PEM
Haplotype frequency estimation
Issue Date2007
PublisherS Karger AG. The Journal's web site is located at http://www.karger.com/HHE
Citation
Human Heredity, 2007, v. 64 n. 3, p. 172-181 How to Cite?
AbstractAims: Haplotype frequency estimation is indispensable in studies of human genetics based on haplotypes since studies based on haplotypes are likely to yield more information than those based on single SNP marker. However, most existing algorithms estimate haplotype frequencies under the assumption that all of the genotype data sets are correct. To date, nearly all large genotype data sets have errors, and studies have demonstrated that even a small quantity of genotyping errors can have enormous impact on haplotype frequency estimation. Methods: Although the GenoSpectrum (GS)-EM algorithm which estimates haplotype frequencies incorporating genotyping uncertainty has been presented recently [1], it can only be suitable for independent individuals rather than dependent pedigree data. In this paper, we describe a new EM algorithm, called GS-PEM, that calculates maximum likelihood estimates (MLEs) of haplotype frequencies based on all possible multilocus genotypes (GenoSpectrum) of each member of the pedigrees through making use of the dependence information of relatives. Results and Conclusion: We evaluate the performance of the GS-PEM by simulation studies and find that our GS-PEM can reduce the impact induced by the genotyping errors in haplotype frequency estimation. Copyright © 2007 S. Karger AG.
Persistent Identifierhttp://hdl.handle.net/10722/82831
ISSN
2015 Impact Factor: 1.539
2015 SCImago Journal Rankings: 0.942
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorZhu, WSen_HK
dc.contributor.authorFung, WKen_HK
dc.contributor.authorGuo, Jen_HK
dc.date.accessioned2010-09-06T08:33:54Z-
dc.date.available2010-09-06T08:33:54Z-
dc.date.issued2007en_HK
dc.identifier.citationHuman Heredity, 2007, v. 64 n. 3, p. 172-181en_HK
dc.identifier.issn0001-5652en_HK
dc.identifier.urihttp://hdl.handle.net/10722/82831-
dc.description.abstractAims: Haplotype frequency estimation is indispensable in studies of human genetics based on haplotypes since studies based on haplotypes are likely to yield more information than those based on single SNP marker. However, most existing algorithms estimate haplotype frequencies under the assumption that all of the genotype data sets are correct. To date, nearly all large genotype data sets have errors, and studies have demonstrated that even a small quantity of genotyping errors can have enormous impact on haplotype frequency estimation. Methods: Although the GenoSpectrum (GS)-EM algorithm which estimates haplotype frequencies incorporating genotyping uncertainty has been presented recently [1], it can only be suitable for independent individuals rather than dependent pedigree data. In this paper, we describe a new EM algorithm, called GS-PEM, that calculates maximum likelihood estimates (MLEs) of haplotype frequencies based on all possible multilocus genotypes (GenoSpectrum) of each member of the pedigrees through making use of the dependence information of relatives. Results and Conclusion: We evaluate the performance of the GS-PEM by simulation studies and find that our GS-PEM can reduce the impact induced by the genotyping errors in haplotype frequency estimation. Copyright © 2007 S. Karger AG.en_HK
dc.languageengen_HK
dc.publisherS Karger AG. The Journal's web site is located at http://www.karger.com/HHEen_HK
dc.relation.ispartofHuman Heredityen_HK
dc.rightsHuman Heredity. Copyright © S Karger AG.en_HK
dc.subjectGenoSpectrumen_HK
dc.subjectGenotyping erroren_HK
dc.subjectGS-PEMen_HK
dc.subjectHaplotype frequency estimationen_HK
dc.titleIncorporating genotyping uncertainty in haplotype frequency estimation in pedigree studiesen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0001-5652&volume=64&spage=172&epage=181&date=2007&atitle=Incorporating+genotyping+uncertainty+in+haplotype+frequency+estimation+in+pedigree+studiesen_HK
dc.identifier.emailFung, WK: wingfung@hku.hken_HK
dc.identifier.authorityFung, WK=rp00696en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1159/000102990en_HK
dc.identifier.pmid17536211en_HK
dc.identifier.scopuseid_2-s2.0-34250751712en_HK
dc.identifier.hkuros149907en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-34250751712&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume64en_HK
dc.identifier.issue3en_HK
dc.identifier.spage172en_HK
dc.identifier.epage181en_HK
dc.identifier.isiWOS:000247435200003-
dc.publisher.placeSwitzerlanden_HK
dc.identifier.scopusauthoridZhu, WS=12647165500en_HK
dc.identifier.scopusauthoridFung, WK=13310399400en_HK
dc.identifier.scopusauthoridGuo, J=7404489563en_HK

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