The MHC risk score was derived by an adaption of the lasso approach27 to logistic regression of case/control status versus all SNPs in the MHC region (defined as spanning from 24.7 Mb to 34.0 Mb on chromosome 6). This was applied to the combined Affymetrix data, with a dummy variable in the regression to differentiate WTCCC and GoKinD/NIMH studies and, separately to the T1DGC Illumina data. The coefficients for the selected regression equations are shown in Supplementary Table 3. The degree of risk prediction, as demonstrated by the receiver operating curves (Supplementary Figure 4) was very similar in the three study groups.
