Detecting disease rare alleles using single SNPs in families and haplotyping in unrelated subjects from the Genetic Analysis Workshop 17 data.

ABSTRACT: We present an evaluation of discovery power for two association tests that work well with common alleles but are applied to the Genetic Analysis Workshop 17 simulations with rare causative single-nucleotide polymorphisms (SNPs) (minor allele frequency [MAF] < 1%). The methods used were genome-wide single-SNP association tests based on a linear mixed-effects model for discovery and applied to the familial sample and sliding windows haplotype association tests for replication, implemented within causative genes in the unrelated individuals sample. Both methods are evaluated with respect to the simulated trait Q2. The linear mixed-effects model and haplotype association tests failed to detect the rare alleles of the simulated associations. In contrast, the linear mixed-effects model and haplo

SUBMITTER: Kraja AT 

PROVIDER: S-EPMC3287938 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature