We then used a checksum based approach (https://personal.broadinstitute.org/sripke/share_links/checksums_download/) to identify and exclude 954 individuals from within the UK Biobank cohort that overlapped with the Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium (PGC) cohorts analysed by Wray, et al. 9. This was possible for a total of 30 out of 33 cohorts that make up the PGC analysis due to the availability of genetic data. We also removed those UK Biobank individuals with a variant call rate < 90% or that were outliers based on heterozygosity, or variants with a call rate < 98%, a minor allele frequency < 0.005, those that deviated from Hardy-Weinberg equilibrium (P < 10-6), or had an imputation accuracy score < 0.1, leaving a total of 10,612,809 variants for 371,437 individuals.
