After all 24 plates were processed and scanned, the overall marker call-rates for each sample were ranked. [Call-rate is the proportion of genotypes for a given SNP that can be confidently interrogated, or ‘called’ (e.g. AA, AB, BB) based on a plot of the raw output from the genotyping assays in which genotypic classes are represented by a cluster of distinct data points.] The 23 poorest performing samples [determined by quality control (QC) call rate %] were removed, stock DNAs thawed and distributed onto a final plate, and then processed. A total of 598 experiments were performed on all samples, sample duplicates and controls over the entire genotyping effort. Scanned chip feature intensities were analyzed using the Affymetrix GeneChip Targeted Genotyping Analysis Software (TGAS) package, which normalized the data and made the individual marker genotype calls for all samples.
