if the alleles were flipped were excluded from imputation, but not from the association analyses.5 AT/GC SNPs were not present in previously genotyped lower density arrays. Because all imputation was performed to the same standard all SNPs had the same orientation at the time of imputation. The OncoArray whole genome data were imputed in a two-stage procedure using SHAPEIT to derive phased genotypes, and IMPUTEv229 to perform imputation of the phased data. We included for imputation only the more common variant if more than one variant yielded a match at the same position. The detailed parameter settings are in the Supplementary Note.
