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Article: Bayes Factor Based on the Trend Test Incorporating Hardy–Weinberg Disequilibrium: More Power to Detect Genetic Association

TitleBayes Factor Based on the Trend Test Incorporating Hardy–Weinberg Disequilibrium: More Power to Detect Genetic Association
Authors
KeywordsBayes Factor
Comparing Association Studies
Genome‐wide Association Studies
Hardy–weinberg Disequilibrium
Pearson’s Test
Trend Test
Issue Date2012
PublisherBlackwell Publishing Ltd. The Journal's web site is located at http://www.blackwellpublishing.com/journals/AHG
Citation
Annals of Human Genetics, 2012, v. 76, p. 301-311 How to Cite?
AbstractIn the analysis of case‐control genetic association, the trend test and Pearson’s test are the two most commonly used tests. In genome‐wide association studies (GWAS), Bayes factor (BF) is a useful tool to support significant ‐values, and a better measure than ‐value when results are compared across studies with different sample sizes. When reporting the ‐value of the trend test, we propose a BF directly based on the trend test. To improve the power to detect association under recessive or dominant genetic models, we propose a BF based on the trend test and incorporating Hardy–Weinberg disequilibrium in cases. When the true model is unknown, or both the trend test and Pearson’s test or other robust tests are applied in genome‐wide scans, we propose a joint BF, combining the previous two BFs. All three BFs studied in this paper have closed forms and are easy to compute without integrations, so they can be reported along with ‐values, especially in GWAS. We discuss how to use each of them and how to specify priors. Simulation studies and applications to three GWAS are provided to illustrate their usefulness to detect nonadditive gene susceptibility in practice.
Persistent Identifierhttp://hdl.handle.net/10722/221679
ISSN
2015 Impact Factor: 1.889
2015 SCImago Journal Rankings: 1.191
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorXu, J-
dc.contributor.authorYuan, A-
dc.contributor.authorZheng, G-
dc.date.accessioned2015-12-04T15:29:02Z-
dc.date.available2015-12-04T15:29:02Z-
dc.date.issued2012-
dc.identifier.citationAnnals of Human Genetics, 2012, v. 76, p. 301-311-
dc.identifier.issn0003-4800-
dc.identifier.urihttp://hdl.handle.net/10722/221679-
dc.description.abstractIn the analysis of case‐control genetic association, the trend test and Pearson’s test are the two most commonly used tests. In genome‐wide association studies (GWAS), Bayes factor (BF) is a useful tool to support significant ‐values, and a better measure than ‐value when results are compared across studies with different sample sizes. When reporting the ‐value of the trend test, we propose a BF directly based on the trend test. To improve the power to detect association under recessive or dominant genetic models, we propose a BF based on the trend test and incorporating Hardy–Weinberg disequilibrium in cases. When the true model is unknown, or both the trend test and Pearson’s test or other robust tests are applied in genome‐wide scans, we propose a joint BF, combining the previous two BFs. All three BFs studied in this paper have closed forms and are easy to compute without integrations, so they can be reported along with ‐values, especially in GWAS. We discuss how to use each of them and how to specify priors. Simulation studies and applications to three GWAS are provided to illustrate their usefulness to detect nonadditive gene susceptibility in practice.-
dc.languageeng-
dc.publisherBlackwell Publishing Ltd. The Journal's web site is located at http://www.blackwellpublishing.com/journals/AHG-
dc.relation.ispartofAnnals of Human Genetics-
dc.subjectBayes Factor-
dc.subjectComparing Association Studies-
dc.subjectGenome‐wide Association Studies-
dc.subjectHardy–weinberg Disequilibrium-
dc.subjectPearson’s Test-
dc.subjectTrend Test-
dc.titleBayes Factor Based on the Trend Test Incorporating Hardy–Weinberg Disequilibrium: More Power to Detect Genetic Association-
dc.typeArticle-
dc.identifier.emailXu, J: xujf@hku.hk-
dc.identifier.authorityXu, J=rp02086-
dc.identifier.doi10.1111/j.1469-1809.2012.00714.x-
dc.identifier.pmid22607017-
dc.identifier.pmcidPMC3372619-
dc.identifier.scopuseid_2-s2.0-84862135099-
dc.identifier.volume76-
dc.identifier.spage301-
dc.identifier.epage311-
dc.identifier.isiWOS:000305072200005-

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