SGENE was initially made up of 1,321 cases and 12,277 controls typed at deCODE Genetics using the Illumina HumanHap300 BeadChip. For SGENE-plus, an additional 859 cases and 854 controls typed at Duke University using either the Illumina HumanHap300 BeadChip or the Illumina HumanHap550 BeadChip as well as 483 cases and 367 controls typed at the University of Bonn using the HumanHap550 BeadChip were also included. Samples were excluded if they were low yield (low yield was defined as below 98% except for the samples typed at Duke, in which case low yield was below 96%), if they were duplicates of other samples included in the study, if they had a sex determined by X chromosome marker homozygosity different from their reported sex or if they were estimated to have less than 90% European ancestry by running STRUCTURE29 using the HapMap CEU, YRI and CHB/JPT individuals as reference samples. Of the 317,503 markers on the HumanHap300 BeadChip, 2,635 were deemed unusable due to lack of polymorphism, severe deviation from Hardy–Weinberg equilibrium (P < 1 × 10−10), low yield (<95% in either
