Genome-wide association of breast cancer: composite likelihood with imputed genotypes.

ABSTRACT: We describe composite likelihood-based analysis of a genome-wide breast cancer case-control sample from the Cancer Genetic Markers of Susceptibility project. We determine 14 380 genome regions of fixed size on a linkage disequilibrium (LD) map, which delimit comparable levels of LD. Although the numbers of single-nucleotide polymorphisms (SNPs) are highly variable, each region contains an average of ∼35 SNPs and an average of ∼69 after imputation of missing genotypes. Composite likelihood association mapping yields a single P-value for each region, established by a permutation test, along with a maximum likelihood disease location, SE and information weight. For single SNP analysis, the nominal P-value for the most significant SNP (msSNP) requires substantial correction given the number of

SUBMITTER: Politopoulos I 

PROVIDER: S-EPMC3025787 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature