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Inference of the Haplotype Effect in a Matched Case-Control Study Using Unphased Genotype Data*

Content Provider	PubMed Central
Author	Sinha, Samiran Gruber, Stephen B. Mukherjee, Bhramar Rennert, Gad
Copyright Year	2008
Abstract	Typically locus specific genotype data do not contain information regarding the gametic phase of haplotypes, especially when an individual is heterozygous at more than one locus among a large number of linked polymorphic loci. Thus, studying disease-haplotype association using unphased genotype data is essentially a problem of handling a missing covariate in a case-control design. There are several methods for estimating a disease-haplotype association parameter in a matched case-control study. Here we propose a conditional likelihood approach for inference regarding the disease-haplotype association using unphased genotype data arising from a matched case-control study design. The proposed method relies on a logistic disease risk model and a Hardy-Weinberg equilibrium (HWE) among the control population only. We develop an expectation and conditional maximization (ECM) algorithm for jointly estimating the haplotype frequency and the disease-haplotype association parameter(s). We apply the proposed method to analyze the data from the Alpha-Tocopherol, Beta-Carotene Cancer prevention study, and a matched case-control study of breast cancer patients conducted in Israel. The performance of the proposed method is evaluated via simulation studies.
Related Links	http://dx.doi.org/10.2202/1557-4679.1079
Starting Page	6
File Format	PDF
ISSN	15574679
e-ISSN	15574679
Journal	The International Journal of Biostatistics
Issue Number	1
Volume Number	4
Language	English
Publisher	Berkeley Electronic Press
Publisher Date	2008-01-08
Access Restriction	Open
Rights Holder	Berkeley Electronic Press
Subject Keyword	Statistics, Probability and Uncertainty Statistics and Probability Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Statistics and Probability Medicine Statistics, Probability and Uncertainty

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