The benefits of attention to QC/QA of genotypic data are difficult to quantify, but some examples have been reported. Pluzhnikov et al. [2008] describe a genotyping plate effect (due to a small number of low quality samples) that resulted in spurious associations. The Wellcome Trust Case Control Consortium [2007] (supplement) reported a decrease in the genomic inflation factor with the application of a series of quality filters and we observed a similar effect in the GENEVA Addiction study, where the genomic inflation factor changes from 1.08 to 1.04 after filtering.
