Of the 3,820 Dutch samples sent to Perlegen (excluding the 20 HapMap internal control samples), genotypes were delivered for 3,761 samples. Fifty-nine samples did not have GWAS data: 39 samples with uncertain linkage between genotype and phenotype records, 7 samples with evidence of contamination, 6 samples that failed genotyping, and 7 miscellaneous failures (2 of these were excluded as chrX and chrY genotyping data were consistent with the presence of XO and XXY sex chromosome status). After further analysis, 8 subjects were removed for excessive missing genotype data (>25%), 1 case for high genomewide homozygosity (∼75%), 38 subjects whose genomewide IBS estimates were consistent with first- or second-degree relationships, and 57 additional subjects whose ancestry diverged from the remainder of the sample (see Supplemental Methods for details). After these exclusions (N=104) and removing duplicated and trio quality control sample, there were 3,540 subjects in the final analysis dataset including 1,738 cases and 1,802 controls. The principal reason for fewer cases than controls was the higher prevalence of substantial non-European ancestry. The list of subjects in the final analyses dataset is included as a Supplemental File (“mddC.fam”).
