Fan et al. [16] and Gunderson et al. [17] provide a detailed description of the Illumina genotyping platform. All samples were genotyped using the Linkage III Panel containing 4,763 SNP markers. All genotypes were evaluated using a quantitative quality score called GenCall score. A GenCall score ranges from 0 to 1 and reflects the proximity within a cluster plot of the intensities of that genotype to the centroid of the nearest cluster. In addition, we compared the 25 original and replacement paired DNA samples using the GenCall score metric and selected a single sample in each pair of first and second aliquots. Using the GenCall score, we also identified 20 samples with very poor genotyping quality in relation to controls and all other samples. Poorly performing samples were removed from the genotyping report files, and individual genotypes with GenCall scores below 0.25 were assigned a no-call.
