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Article: Detection of parent-of-origin effects based on complete and incomplete nuclear families with multiple affected children

TitleDetection of parent-of-origin effects based on complete and incomplete nuclear families with multiple affected children
Authors
KeywordsAssortative mating demographic model
Complete nuclear family
Genomic imprinting
Genotypic relative risk
Incomplete nuclear family
Missing parent
Parent-of-origin effects
Population stratification demographic model
Issue Date2008
PublisherS Karger AG. The Journal's web site is located at http://www.karger.com/HHE
Citation
Human Heredity, 2008, v. 67 n. 1, p. 1-12 How to Cite?
AbstractParent-of-origin effects are important in studying genetic traits. More than 1% of all mammalian genes are believed to show parent-of-origin effects. Some statistical methods may be ineffective or fail to detect linkage or association for a gene with parent-of-origin effects. Based on case-parents trios, the parental-asymmetry test (PAT) is simple and powerful in detecting parent-of-origin effects. However, it is common in practice to collect nuclear families with both parents as well as nuclear families with only one parent. In this paper, when only one parent is available for each family with an arbitrary number of affected children, we firstly develop a new test statistic 1-PAT to test for parent-of-origin effects in the presence of association between an allele at the marker locus under study and a disease gene. Then we extend the PAT to accommodate complete nuclear families each with one or more affected children. Combining families with both parents and families with only one parent, the C-PAT is proposed to detect parent-of-origin effects. The validity of the test statistics is verified by simulation in various scenarios of parameter values. A power study shows that using the additional information from incomplete nuclear families in the analysis greatly improves the power of the tests, compared to that based on only complete nuclear families. Also, utilizing all affected children in each family, the proposed tests have a higher power than when only one affected child from each family is selected. Additional power comparison also demonstrates that the C-PAT is more powerful than a number of other tests for detecting parent-of-origin effects. Copyright © 2008 S. Karger AG.
Persistent Identifierhttp://hdl.handle.net/10722/59873
ISSN
2015 Impact Factor: 1.539
2015 SCImago Journal Rankings: 0.942
ISI Accession Number ID
Funding AgencyGrant Number
Hong Kong RGC CERG ResearchHKU 702207P
National Natural Science Foundation of China10561008
Science Foundation of Southeast University9207011430
National Institute of Health5R01HG002657
Scientific Research Fund of Huaihua University
Funding Information:

We would like to thank two reviewers for their insightful and helpful suggestions which greatly improved our presentation. This work was partially supported by a Hong Kong RGC CERG Research Grant (HKU 702207P), the National Natural Science Foundation of China (10561008), the Science Foundation of Southeast University (9207011430), the National Institute of Health grant 5R01HG002657, and the Scientific Research Fund of Huaihua University.

References
Grants

 

DC FieldValueLanguage
dc.contributor.authorZhou, JYen_HK
dc.contributor.authorHu, YQen_HK
dc.contributor.authorLin, Sen_HK
dc.contributor.authorFung, WKen_HK
dc.date.accessioned2010-05-31T03:59:11Z-
dc.date.available2010-05-31T03:59:11Z-
dc.date.issued2008en_HK
dc.identifier.citationHuman Heredity, 2008, v. 67 n. 1, p. 1-12en_HK
dc.identifier.issn0001-5652en_HK
dc.identifier.urihttp://hdl.handle.net/10722/59873-
dc.description.abstractParent-of-origin effects are important in studying genetic traits. More than 1% of all mammalian genes are believed to show parent-of-origin effects. Some statistical methods may be ineffective or fail to detect linkage or association for a gene with parent-of-origin effects. Based on case-parents trios, the parental-asymmetry test (PAT) is simple and powerful in detecting parent-of-origin effects. However, it is common in practice to collect nuclear families with both parents as well as nuclear families with only one parent. In this paper, when only one parent is available for each family with an arbitrary number of affected children, we firstly develop a new test statistic 1-PAT to test for parent-of-origin effects in the presence of association between an allele at the marker locus under study and a disease gene. Then we extend the PAT to accommodate complete nuclear families each with one or more affected children. Combining families with both parents and families with only one parent, the C-PAT is proposed to detect parent-of-origin effects. The validity of the test statistics is verified by simulation in various scenarios of parameter values. A power study shows that using the additional information from incomplete nuclear families in the analysis greatly improves the power of the tests, compared to that based on only complete nuclear families. Also, utilizing all affected children in each family, the proposed tests have a higher power than when only one affected child from each family is selected. Additional power comparison also demonstrates that the C-PAT is more powerful than a number of other tests for detecting parent-of-origin effects. Copyright © 2008 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.subjectAssortative mating demographic modelen_HK
dc.subjectComplete nuclear familyen_HK
dc.subjectGenomic imprintingen_HK
dc.subjectGenotypic relative risken_HK
dc.subjectIncomplete nuclear familyen_HK
dc.subjectMissing parenten_HK
dc.subjectParent-of-origin effectsen_HK
dc.subjectPopulation stratification demographic modelen_HK
dc.titleDetection of parent-of-origin effects based on complete and incomplete nuclear families with multiple affected childrenen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0001-5652&volume=67&spage=1&epage=12&date=2009&atitle=Detection+of+parent-of-origin+effects+based+on+complete+and+incomplete+nuclear+families+with+multiple+affected+childrenen_HK
dc.identifier.emailHu, YQ: yqhu@hku.hken_HK
dc.identifier.emailFung, WK: wingfung@hku.hken_HK
dc.identifier.authorityHu, YQ=rp00708en_HK
dc.identifier.authorityFung, WK=rp00696en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1159/000164394en_HK
dc.identifier.pmid18931505-
dc.identifier.scopuseid_2-s2.0-53849132413en_HK
dc.identifier.hkuros158072en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-53849132413&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume67en_HK
dc.identifier.issue1en_HK
dc.identifier.spage1en_HK
dc.identifier.epage12en_HK
dc.identifier.isiWOS:000260892000001-
dc.publisher.placeSwitzerlanden_HK
dc.relation.projectTransmission disequilibrium test under imprinting for quantitative traits based on case-parents trios and for qualitative traits when only one parent is available-
dc.identifier.scopusauthoridZhou, JY=16240300900en_HK
dc.identifier.scopusauthoridHu, YQ=13410089000en_HK
dc.identifier.scopusauthoridLin, S=7407613676en_HK
dc.identifier.scopusauthoridFung, WK=13310399400en_HK

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