Before detailing the principal results for each disease, we first summarize our main observations. Table 2 details the findings from the WTCCC scan for the 15 variants for which there was strong prior evidence of association with one or more of the diseases studied, based on extensive replication studies. All but two of these show associations in our study, with the magnitude of the evidence generally consistent with their effect sizes as estimated from prior studies. One of the signals for which we failed to obtain evidence of replication (APOE in CAD) is poorly tagged by the Affymetrix 500K chip. The other (INS in T1D) is represented by a single SNP that marginally failed our study-wide quality control filters (overall missingness 5.2%) but which was nonetheless strongly associated with T1D when examined. Quantile-quantile plots for the trend test for each of the seven disease show only very minor deviations from the null distribution, except in the extreme tails which correspond to associations reported below (Fig. 3). The quantile-quantile plots and the results at positive controls (Table 2) give confidence in the quality of our data and the robustness of our analyses.
