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Article: Detection of parent-of-origin effects using general pedigree data

TitleDetection of parent-of-origin effects using general pedigree data
Authors
Issue Date2010
PublisherJohn Wiley & Sons, Inc. The Journal's web site is located at http://www3.interscience.wiley.com/cgi-bin/jhome/35841
Citation
Genetic Epidemiology, 2010, v. 34 n. 2, p. 151-158 How to Cite?
AbstractGenomic imprinting is an important epigenetic factor in complex traits study, which has generally been examined by testing for parent-of-origin effects of alleles. For a diallelic marker locus, the parental-asymmetry test (PAT) based on case-parents trios and its extensions to incomplete nuclear families (1-PAT and C-PAT) are simple and powerful for detecting parent-oforigin effects. However, these methods are suitable only for nuclear families and thus are not amenable to general pedigree data. Use of data from extended pedigrees, if available, may lead to more powerful methods than randomly selecting one two-generation nuclear family from each pedigree. In this study, we extend PAT to accommodate general pedigree data by proposing the pedigree PAT (PPAT) statistic, which uses all informative family trios from pedigrees. To fully utilize pedigrees with some missing genotypes, we further develop the Monte Carlo (MC) PPAT (MCPPAT) statistic based on MC sampling and estimation. Extensive simulations were carried out to evaluate the performance of the proposed methods. Under the assumption that the pedigrees and their associated affection patterns are randomly drawn from a population of pedigrees with at least one affected offspring, we demonstrated that MCPPAT is a valid test for parent-of-origin effects in the presence of association. Further, MCPPAT is much more powerful compared to PAT for trios or even PPAT for all informative family trios from the same pedigrees if there is missing data. Application of the proposed methods to a rheumatoid arthritis dataset further demonstrates the advantage of MCPPAT. © 2009 Wiley-Liss, Inc.
Persistent Identifierhttp://hdl.handle.net/10722/172468
ISSN
2015 Impact Factor: 2.553
2015 SCImago Journal Rankings: 2.101
PubMed Central ID
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorZhou, JYen_US
dc.contributor.authorDing, Jen_US
dc.contributor.authorFung, WKen_US
dc.contributor.authorLin, Sen_US
dc.date.accessioned2012-10-30T06:22:41Z-
dc.date.available2012-10-30T06:22:41Z-
dc.date.issued2010en_US
dc.identifier.citationGenetic Epidemiology, 2010, v. 34 n. 2, p. 151-158en_US
dc.identifier.issn0741-0395en_US
dc.identifier.urihttp://hdl.handle.net/10722/172468-
dc.description.abstractGenomic imprinting is an important epigenetic factor in complex traits study, which has generally been examined by testing for parent-of-origin effects of alleles. For a diallelic marker locus, the parental-asymmetry test (PAT) based on case-parents trios and its extensions to incomplete nuclear families (1-PAT and C-PAT) are simple and powerful for detecting parent-oforigin effects. However, these methods are suitable only for nuclear families and thus are not amenable to general pedigree data. Use of data from extended pedigrees, if available, may lead to more powerful methods than randomly selecting one two-generation nuclear family from each pedigree. In this study, we extend PAT to accommodate general pedigree data by proposing the pedigree PAT (PPAT) statistic, which uses all informative family trios from pedigrees. To fully utilize pedigrees with some missing genotypes, we further develop the Monte Carlo (MC) PPAT (MCPPAT) statistic based on MC sampling and estimation. Extensive simulations were carried out to evaluate the performance of the proposed methods. Under the assumption that the pedigrees and their associated affection patterns are randomly drawn from a population of pedigrees with at least one affected offspring, we demonstrated that MCPPAT is a valid test for parent-of-origin effects in the presence of association. Further, MCPPAT is much more powerful compared to PAT for trios or even PPAT for all informative family trios from the same pedigrees if there is missing data. Application of the proposed methods to a rheumatoid arthritis dataset further demonstrates the advantage of MCPPAT. © 2009 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.meshAllelesen_US
dc.subject.meshArthritis, Rheumatoid - Geneticsen_US
dc.subject.meshComputer Simulationen_US
dc.subject.meshFemaleen_US
dc.subject.meshFounder Effecten_US
dc.subject.meshGenetic Predisposition To Disease - Geneticsen_US
dc.subject.meshGenomic Imprintingen_US
dc.subject.meshGenotypeen_US
dc.subject.meshHaplotypesen_US
dc.subject.meshHumansen_US
dc.subject.meshInheritance Patterns - Geneticsen_US
dc.subject.meshMaleen_US
dc.subject.meshModels, Geneticen_US
dc.subject.meshMonte Carlo Methoden_US
dc.subject.meshParentsen_US
dc.subject.meshPedigreeen_US
dc.titleDetection of parent-of-origin effects using general pedigree dataen_US
dc.typeArticleen_US
dc.identifier.emailFung, WK: wingfung@hku.hken_US
dc.identifier.authorityFung, WK=rp00696en_US
dc.description.naturelink_to_OA_fulltexten_US
dc.identifier.doi10.1002/gepi.20445en_US
dc.identifier.pmid19676055-
dc.identifier.pmcidPMC3011930-
dc.identifier.scopuseid_2-s2.0-76649131983en_US
dc.identifier.hkuros171330-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-76649131983&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume34en_US
dc.identifier.issue2en_US
dc.identifier.spage151en_US
dc.identifier.epage158en_US
dc.identifier.isiWOS:000274376800007-
dc.publisher.placeUnited Statesen_US
dc.identifier.scopusauthoridZhou, JY=16240300900en_US
dc.identifier.scopusauthoridDing, J=35236669400en_US
dc.identifier.scopusauthoridFung, WK=13310399400en_US
dc.identifier.scopusauthoridLin, S=7407613676en_US
dc.identifier.citeulike5435962-

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