Cases were initially evaluated with PLINK24 using a subset of approximately 85,000 SNPs. Pairwise estimates of identity-by-descent detected 3 unexpected duplicates and 21 cryptic relatives (estimated kinship ≥ 0.1); for each pair the sample with the lower call rate was excluded. Four additional cases were removed for unusual degrees of SNP heterozygosity. To evaluate ancestry differences, Multidimensional Scaling (MDS) vectors were computed and plotted, and 230 outliers to the main European-ancestry cluster were removed -- most self-identified Hispanics were excluded, but 24 had scores within the main European cluster and were retained. We also removed cases with ambiguous gender (N=20), or call rate < 97% (N=1 for autosomal and 11 for chromosome X analyses), leaving 1,221 cases for autosomal analyses and 1,211 for chromosome X. QC procedures for the 1,636 controls have been described in the companion paper4 and in Supplementary Methods; briefly, samples were excluded for genotyping call rate <97%; inconsistency between reported and genotypic gender; outlier values for mean heterozygosity across genotypes; outliers in the distributions of principle component scores for ancestry; outliers in the number of other subjects with which kinship was estimated at > 10%; and cryptic relatives (retaining the sample with the best call rate).
