The Munich cohort was genotyped using the Illumina HumanHap300 chip with a total of 317,503 SNPs and the Aberdeen cohort was genotyped using the Illumina HumanHap550 chip with a total of 555,352 SNPs. We carried out a series of quality control (QC) checks and tests of cryptic relatedness, ultimately excluding a total of 15 and 28 participants in Munich and Aberdeen respectively (Text S1). We also employed a “one percent rule” that discarded from analysis any SNP that had more than 1% of samples that could not be reliably scored, to reduce the scope for spurious association. After employing this rule the average success rate of genotyping was 98.4% and the concordance rate for duplicate genotyping was 99.997%. The US cohort was genotyped using the Human-610 Quad Beadchip at the Institute for Genome Sciences and Policy Genotyping Core, and the same quality control procedures were applied as those used for the discovery cohorts.
