For the mtCOJO analysis (see Online Methods), all eight conditioned versions of the depression GWAS demonstrated substantial similarity to the unconditioned depression GWAS. We observed no changes in h2. All conditioned GWAS had correlation coefficient = 1.00 with the unconditioned GWAS, and genomic control factor and intercepts consistently indicated a lack of population substructure (Figure S2). Though the genome-wide architecture of depression was robust to shared etiology with all other listed comorbid conditions, shared etiology with schizophrenia and anxiety symptoms resulted in substantial loss of GWS SNPs associated with depression when conditioned upon those traits (Figure S2).
