Conditional Likelihood Methods for Haplotype-Based Association Analysis Using Matched Case-Control Data

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Conditional likelihood methods for haplotype-based association analysis using matched case-control data.

Genetic epidemiologists routinely assess disease susceptibility in relation to haplotypes, that is, combinations of alleles on a single chromosome. We study statistical methods for inferring haplotype-related disease risk using single nucleotide polymorphism (SNP) genotype data from matched case-control studies, where controls are individually matched to cases on some selected factors. Assuming...

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Association studies, both family-based and population-based, can be powerful means of detecting disease-liability alleles. To increase the information of the test, various researchers have proposed targeting haplotypes. The larger number of haplotypes, however, relative to alleles at individual loci, could decrease power because of the additional degrees of freedom required for the test. An opt...

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Multi-locus association analyses, including haplotype-based analyses, can sometimes provide greater power than single-locus analyses for detecting disease susceptibility loci. This potential gain, however, can be compromised by the large number of degrees of freedom caused by irrelevant markers. Exhaustive search for the optimal set of markers might be possible for a small number of markers, ye...

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Inference of the haplotype effect in a matched case-control study using unphased genotype data.

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 sev...

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Haplotype association analysis based on arbitrarily chosen markers might lower statistical power because of the larger number of degrees of freedom caused by irrelevant makers.On the other hand, an exhaustive search for all possible combinations of markers for haplotype analysis is computationally expensive for genome-wide association analysis.To improve power, we applied our recently developed...

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ژورنال

عنوان ژورنال: Biometrics

سال: 2007

ISSN: 0006-341X

DOI: 10.1111/j.1541-0420.2007.00797.x