Case and control cohorts used in the study.

‘N’, number of individuals in the cohort after excluding ethnic outliers and samples with poor data quality. ‘Analyses’, describes whether the cohort was included in primary CNV analyses (‘C’), replication CNV analyses (‘R’), and autozygosity analyses (‘A’). Note that due to small sample sizes, the 17 Weill Cornell samples with SNP array data were merged with Porto samples and the combined set treated as a single cohort for the primary CNV analyses. Thus the total number of cases with whole-genome array data are 83+17+162+61 = 323. Many more samples were sourced from Cornell for replication analysis. Full details of each cohort are available in Text S1.