We analyzed the overlap of common variants with rPTVs in a subset of iPSYCH samples that have also been whole exome sequenced. A major part of the data (Pilot 1, Wave 1, Wave 2) was also included in the recent study by Satterstrom et al.17, and the same quality control procedure was applied in this study. Description of whole-exome sequencing procedure, QC and annotation can be found in the Supplementary Note. Variants were defined as PTVs if they were annotated as having large effects on gene function (nonsense variant, frameshift, splice site). We defined a variant as being rare if it had an allele count of five or less across the combination of the full iPSYCH exome-sequencing dataset (n = 28,448) and non-Finnish Europeans in the nonpsychiatric gnomAD exome database (n = 44,779).
