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Article: The impact of genotyping error on family-based analysis of quantitative traits

TitleThe impact of genotyping error on family-based analysis of quantitative traits
Authors
KeywordsAssociation analysis
Genotype error
Linkage analysis
QTL
SNP
Issue Date2001
PublisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/ejhg
Citation
European Journal Of Human Genetics, 2001, v. 9 n. 2, p. 130-134 How to Cite?
AbstractErrors in genotyping can substantially influence the power to detect linkage using affected sib-pairs, but it is not clear what effect such errors have on quantitative trait analyses. Here we use Monte Carlo simulation to examine the influence of genotyping error on multipoint vs two-point analysis, variable map density, locus effect size and allele frequency in quantitative trait linkage and association studies of sib-pairs. The analyses are conducted using variance components methods. We contrast the effects of error on quantitative trait analyses with those on the affected sib-pair design. The results indicate that genotyping error influences linkage studies of affected sib pairs more severely than studies of quantitative traits in unselected sibs. In situations of modest effect size, 5% genotyping error eliminates all supporting evidence for linkage to a true susceptibility locus in affected pairs, but may only result in a loss of 15% of linkage information in random pairs. Multipoint analysis does not suffer substantially more than two-point analysis; for moderate error rates (<5%), multipoint analysis with error is more powerful than two-point with no error. Map density does not appear to be an important factor for linkage analysis. QTL association analyses of common alleles are reasonably robust to genotyping error but power can be affected dramatically with rare alleles.
Persistent Identifierhttp://hdl.handle.net/10722/143641
ISSN
2015 Impact Factor: 4.58
2015 SCImago Journal Rankings: 2.077
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorAbecasis, GRen_HK
dc.contributor.authorCherny, SSen_HK
dc.contributor.authorCardon, LRen_HK
dc.date.accessioned2011-12-16T08:08:22Z-
dc.date.available2011-12-16T08:08:22Z-
dc.date.issued2001en_HK
dc.identifier.citationEuropean Journal Of Human Genetics, 2001, v. 9 n. 2, p. 130-134en_HK
dc.identifier.issn1018-4813en_HK
dc.identifier.urihttp://hdl.handle.net/10722/143641-
dc.description.abstractErrors in genotyping can substantially influence the power to detect linkage using affected sib-pairs, but it is not clear what effect such errors have on quantitative trait analyses. Here we use Monte Carlo simulation to examine the influence of genotyping error on multipoint vs two-point analysis, variable map density, locus effect size and allele frequency in quantitative trait linkage and association studies of sib-pairs. The analyses are conducted using variance components methods. We contrast the effects of error on quantitative trait analyses with those on the affected sib-pair design. The results indicate that genotyping error influences linkage studies of affected sib pairs more severely than studies of quantitative traits in unselected sibs. In situations of modest effect size, 5% genotyping error eliminates all supporting evidence for linkage to a true susceptibility locus in affected pairs, but may only result in a loss of 15% of linkage information in random pairs. Multipoint analysis does not suffer substantially more than two-point analysis; for moderate error rates (<5%), multipoint analysis with error is more powerful than two-point with no error. Map density does not appear to be an important factor for linkage analysis. QTL association analyses of common alleles are reasonably robust to genotyping error but power can be affected dramatically with rare alleles.en_HK
dc.publisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/ejhgen_HK
dc.relation.ispartofEuropean Journal of Human Geneticsen_HK
dc.subjectAssociation analysisen_HK
dc.subjectGenotype erroren_HK
dc.subjectLinkage analysisen_HK
dc.subjectQTLen_HK
dc.subjectSNPen_HK
dc.titleThe impact of genotyping error on family-based analysis of quantitative traitsen_HK
dc.typeArticleen_HK
dc.identifier.emailCherny, SS: cherny@hku.hken_HK
dc.identifier.authorityCherny, SS=rp00232en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.pmid11313746-
dc.identifier.scopuseid_2-s2.0-0035131982en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-0035131982&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume9en_HK
dc.identifier.issue2en_HK
dc.identifier.spage130en_HK
dc.identifier.epage134en_HK
dc.identifier.isiWOS:000167133600008-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.f10001001661-
dc.identifier.scopusauthoridAbecasis, GR=6604013253en_HK
dc.identifier.scopusauthoridCherny, SS=7004670001en_HK
dc.identifier.scopusauthoridCardon, LR=7005082964en_HK

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