We performed all genotyping of the SNPs using the GoldenGate™ assay, which uses the Illumina platform (Illumina, San Diego, CA, USA) at the Genomics Core Facility at USC/Norris Comprehensive Cancer Center. We had various levels of quality control. This included automated protocols for the entire genotyping process utilizing robotics and barcoding, and the inclusion of replicates and CEPH trios to aid in genotyping and identification of errors. After initial auto-clustering, each SNP is edited to define three genotypes with the intent of maximizing call rate and minimizing possible error rate. Genotype calls are then evaluated for five criteria: (1) HapMap is queried for the results of the CEPH trios for each SNP and compared with our genotype calls; (2) replicate and trio errors are calculated for all plates/samples in a project; (3) non-informative frequency is calculated for each SNP; (4) deviation from the expected heterozygosity is determined; and (5) MAF is calculated. These criteria are used to identify any SNPs with genotyping errors that may require additional visual inspection, re-calling, or determination that a ‘no call’ be made.
