Genotyping was conducted using a custom Illumina Infinium array (iCOGS) in seven centers, of which four were used for BCAC. Genotypes were called using Illumina’s proprietary GenCall algorithm. Initial calling used a cluster file generated from 270 samples from HapMap 2. To generate the final calls, we first selected a subset of 3,018 individuals, including samples from each of the genotyping centers, each of the participating consortia and each major ancestry group. Only plates with a consistently high call rate in the initial calling were used. We also included 380 samples of European, Asian or African ancestry genotyped as part of the HapMap Project and 1000 Genomes Project and 160 samples that were known positive controls for rare variants on the array. This subset was used to generate a cluster file that was then applied to call the genotypes for the remaining samples. We also investigated two other calling algorithms: Illumnus65 and GenoSNP66. All three algorithms were >99% concordant in their calling for 91% of the SNPs on the array. However, manual inspection of a sample of the SNPs with
