In the validation stage, 980 SCOOP cases and 2,000 EPIC-Norfolk controls were genotyped at the WTSIby Sequenom® or Taqman® (Applied Biosystems). Sequenom genotyping was performed using the iPLEX™ Gold Assay (Sequenom® Inc.) according to manufacturer's instructions. Variants that failed or could not be designed on the Sequenom® platform were genotyped individually as TaqMan® assays (Applied Biosystems, California USA) on 8ng DNA per sample following the standard protocol. Replication samples were excluded on the basis of (i) call-rate<80% or mismatch between inferred and supplied gender. SNPs all had call-rate>90%, Hardy-Weinberg equilibrium P>10−4 and MAF≥0.01 in cases and controls apart from rs17025867 and rs7255638 indicated in Supplementary Table 1.
