For the T1DGC study, genotyping was performed on the Illumina 550K Infinium platform and, for comparability, all genotypes were re-scored using the ILLUMINUS algorithm23. The WTCCC study used the Affymetrix GeneChip Human Mapping 500K Array set, while the GoKinD/NIMH study used genotype data generated with the Affymetrix Genome-wide Human SNP Array 5.0. The 5.0 array incorporates all of the SNPs on the earlier 500K array but on a single chip along with an additional 420K non-polymorphic probes. Details of the scoring of genotypes may be found in the original publications7, 12. The criteria for discarding some SNPs from the analysis are discussed in Supplementary Methods.
