Samples were processed at the Broad Institute (Boston, MA, USA) using the Infinium PsychChip v1.0 array (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s instructions.42 Genotyping was conducted in 25 waves. Variant calls were trained using GenTrain2 (Illumina) on the first wave (4146 samples) using the PsychChip 15048346 B manifest and GenomeStudio version v2011.1. Following autoclustering, loci were manually curated if they had a call frequency below 90%, GenTrain scores below 0.5 or cluster separation below 0.2. During this processing, 3890 loci were excluded and 928 were manually modified. The resulting GenTrain was used to produce GenCall variant calls used for sample level quality control of the entire cohort.43 Samples with call rates below 95% (N=2270) were designated to fail sample quality control (QC). Sex was inferred using heterozygosity on chromosome X; below 20% in males; above 20% in females. Sex obtained from genotyping was compared to the sex recorded in the Danish Civil Registration System and mismatches were excluded. It is extremely unlikely to observe errors in recorded sex in the Danish Civil Registration System.26 About 0.25%
