We employed a method used by the International Schizophrenia Consortium (12) and developed by Visscher, Wray and Purcell to calculate both BP polygenic scores in SCZ cases and SCZ polygenic scores in BP cases. Briefly, we defined the SCZ case-control GWAS as our discovery sample and the BP case-control GWAS as our target sample. Based on the discovery sample association statistics, large sets of nominally-associated alleles were selected as “score alleles”, for different significance thresholds. In the target sample, we calculated the total score for each individual as the number of score alleles weighted by the log of the odds ratio from the discovery sample. We repeated this exercise with the BP case-control GWAS as discovery and the SCZ case-control GWAS as the target. We created scores using ten different p-value thresholds (P < 0.0001, P < 0.001, P < 0.01, P < 0.05, P < 0.1, P < 0.2, P < 0.3, P < 0.4, P < 0.5, P < 1). For each threshold, we performed a logistic regression of disease status on the polygenic score covarying for MDS components and sample.
