Evaluating the concordance between sequencing, imputation and microarray genotype calls in the GAW18 data.

ABSTRACT: Genotype errors are well known to increase type I errors and/or decrease power in related tests of genotype-phenotype association, depending on whether the genotype error mechanism is associated with the phenotype. These relationships hold for both single and multimarker tests of genotype-phenotype association. To assess the potential for genotype errors in Genetic Analysis Workshop 18 (GAW18) data, where no gold standard genotype calls are available, we explored concordance rates between sequencing, imputation, and microarray genotype calls. Our analysis shows that missing data rates for sequenced individuals are high and that there is a modest amount of called genotype discordance between the 2 platforms, with discordance most common for lower minor allele frequency (MAF) single-nucleoti

SUBMITTER: Rogers A 

PROVIDER: S-EPMC4143748 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature