Samples: For fatSNP phase 2, we genotyped the UK National Blood Service (NBS) controls (N=1428) used by the Welcome Trust Case Control Consortium(15) that we had also used in our GWAS study, and additional UK schizophrenia samples (N=163) for whom GWAS array data were not available, that we had used as part of the follow up sample in the previous publication(4). The combined set of UK cases (N=642) and blood donor/1958 birth cohort controls (N = 2873 available for in house genotyping, N = 2937 with Affymetrix 500K data) are subsequently referred to for brevity as the Cardiff Full sample. fatSNP2 also included 3 additional case control series from Bulgaria, Ireland (referred to as the Dublin sample) and Germany (referred to as the Munich sample), the combination of which is referred to for brevity (and consistency with the previous paper) as REP1 and comprises an additional 1664 cases and 3541 controls. All cases met DSMIV criteria for schizophrenia; full details of these samples are given in our previous study(4). The results of the REP1 sample were combined with those of the Cardiff Full sample to derive an overall fatSNP2 P-value as described below.
