Each sample in the COGA dataset was analyzed with the standard Mapping 10k assay. Of the 1,396 samples supplied, 1,381 yielded enough DNA to analyze [The following 15 samples did not yield enough DNA to genotype: CR1371, CR1315, CR1259, CR1169, CR0959, CR0967, CR0859, CR0789, CR0563, CR0370, CR0269, CR0227, CR0150, CR0047, CR0062]. The median call rate over all 1,381 samples was over 95% with an estimated accuracy of greater than 99%. Two forms of quality control were performed on the samples before the final submission of the dataset to GAW14: calls on the X chromosome were checked against the labeled sex of each sample and families within the study were checked for Mendelian inheritance errors. These quality controls revealed 10 problematic samples (sex or pedigree inconsistencies) [The following 10 samples exhibited gender and/or Mendelian inconsistencies: sex errors: CR1234, CR1112, CR1125, CR1037, CR0728, CR0542; Mendelian inconsistencies: CR1224, CR0221; sex and Mendelian inconsistencies: CR1337, CR0538] in the samples supplied by COGA.
