Show simple item record

dc.contributor.authorChatterjee, Nilanjan
dc.contributor.authorChen, Yi-Hau
dc.contributor.authorLuo, Sheng
dc.contributor.authorCarroll, Raymond J.
dc.date.accessioned2016-02-25T12:41:56Z
dc.date.available2016-02-25T12:41:56Z
dc.date.issued2009-11
dc.identifier.citationChatterjee N, Chen Y-H, Luo S, Carroll RJ (2009) Analysis of Case-Control Association Studies: SNPs, Imputation and Haplotypes. Statist Sci 24: 489–502. Available: http://dx.doi.org/10.1214/09-STS297.
dc.identifier.issn0883-4237
dc.identifier.doi10.1214/09-STS297
dc.identifier.urihttp://hdl.handle.net/10754/597553
dc.description.abstractAlthough prospective logistic regression is the standard method of analysis for case-control data, it has been recently noted that in genetic epidemiologic studies one can use the "retrospective" likelihood to gain major power by incorporating various population genetics model assumptions such as Hardy-Weinberg-Equilibrium (HWE), gene-gene and gene-environment independence. In this article we review these modern methods and contrast them with the more classical approaches through two types of applications (i) association tests for typed and untyped single nucleotide polymorphisms (SNPs) and (ii) estimation of haplotype effects and haplotype-environment interactions in the presence of haplotype-phase ambiguity. We provide novel insights to existing methods by construction of various score-tests and pseudo-likelihoods. In addition, we describe a novel two-stage method for analysis of untyped SNPs that can use any flexible external algorithm for genotype imputation followed by a powerful association test based on the retrospective likelihood. We illustrate applications of the methods using simulated and real data. © Institute of Mathematical Statistics, 2009.
dc.description.sponsorshipChatterjee's research was supported by a gene environment initiative grant from the National Heart Lung and Blood Institute (RO1HL091172-01) and by the Intramural Research Program of the National Cancer Institute. Chen's research was supported by the National Science Council of ROC (NSC 95-2118-M-001-022-MY3). Carroll's research was supported by a grant from the National Cancer Institute (CA57030) and by Award Number KUS-CI-016-04, made by King Abdullah University of Science and Technology (KAUST).
dc.publisherInstitute of Mathematical Statistics
dc.subjectCase-control studies
dc.subjectEmpirical-Bayes
dc.subjectGenetic epidemiology
dc.subjectHaplotypes
dc.subjectModel averaging
dc.subjectModel robustness
dc.subjectModel selection
dc.subjectRetrospective studies
dc.subjectShrinkage
dc.titleAnalysis of Case-Control Association Studies: SNPs, Imputation and Haplotypes
dc.typeArticle
dc.identifier.journalStatistical Science
dc.contributor.institutionNational Cancer Institute, Bethesda, United States
dc.contributor.institutionInstitute of Statistical Science, Academia Sinica, Nankang, Taiwan
dc.contributor.institutionUniversity of Texas School of Public Health, Houston, United States
dc.contributor.institutionTexas A and M University, College Station, United States
kaust.grant.numberKUS-CI-016-04


This item appears in the following Collection(s)

Show simple item record