A summary of the data available for analysis is listed in Table 1 and comprise data used in the PGC–Cross-Disorder Group analysis25 together with newly available ADHD samples27–30. Data upload to the PGC central server follows strict guidelines to ensure local ethics committee approval for all contributed data (PGC; see URLs). Data from all study cohorts were processed through the stringent PGC pipeline25. Imputation of autosomal SNPs used CEU (Utah residents of Northern and Western European ancestry) and TSI (Toscani in Italia) HapMap Phase 3 data as the reference panel21. For each analysis (univariate or bivariate), we retained only SNPs that had MAF of >0.01 and imputation R2 of >0.6 in all contributing cohort subsamples (imputation cohorts). Different quality control strategies were investigated in detail for the raw and PGC imputed genotyped data of the International Schizophrenia Consortium, a subset of the PGC schizophrenia sample35. The Crohn’s disease samples from IIBDGC42 were processed through the same quality control and imputation pipeline as the PGC data, generating a data set of 5,054 cases and 11,496 controls from 6 imputation cohorts.
