Physical Sciences and Mathematics Commons^™

On Quality Control Measures In Genome-Wide Association Studies: A Test To Assess The Genotyping Quality Of Individual Probands In Family-Based Association Studies And An Application To The Hapmap Data, David W. Fardo, Iuliana Ionita-Laza, Christoph Lange

Biostatistics Faculty Publications

Allele transmissions in pedigrees provide a natural way of evaluating the genotyping quality of a particular proband in a family-based, genome-wide association study. We propose a transmission test that is based on this feature and that can be used for quality control filtering of genome-wide genotype data for individual probands. The test has one degree of freedom and assesses the average genotyping error rate of the genotyped SNPs for a particular proband. As we show in simulation studies, the test is sufficiently powerful to identify probands with an unreliable genotyping quality that cannot be detected with standard quality control filters. …