At both genotyping centers, DNA samples provided by study investigators are fingerprinted with a 24- or 79-SNP panel. The fingerprints are used to assess genotyping performance and to track sample identity. If gender discrepancies or unexpected duplicates are detected, study investigators may correct sample annotation or replace DNA samples prior to high density genotyping. Laboratory Information Management Systems (LIMS) are used to track and monitor samples, reagents and equipment at all stages of the genotyping process. Daily and monthly reports are reviewed to identify quality issues. Metrics based on raw intensities are used to eliminate low quality samples prior to genotype calling. Genotype calling was done using normalized intensities with the Birdseed algorithm [Korn, et al. 2008] for Affymetrix and with BeadStudio (see Web Resources) for Illumina projects. Genotypes were called by plate for Affymetrix and by project for Illumina. The software calculates a confidence score for each sample-SNP data point and those beyond a fixed threshold have their genotype set to missing. Samples with low quality scans are repeated. Post-production metrics are used to eliminate low quality samples and
