GWAS meta-analyses were conducted for BD I (25,060 cases, 449,978 controls from 55 cohorts, effective n = 64,802) and BD II (6,781 cases, 364,075 controls from 31 cohorts, effective n = 22,560) (Supplementary Table 1) using the same procedures described for the main GWAS. BD subtypes were defined based on international consensus criteria (DSM-IV, ICD-9, or ICD-10), established using structured diagnostic instruments from assessments by trained interviewers, clinician-administered checklists or medical record review. In the external biobank cohorts, BD subtypes were defined using ICD codes (Supplementary Note). LDSC35 was used to estimate the hSNP2 of each subtype, and the genetic correlation between the subtypes. The difference between the LDSC hSNP2 estimates for BD I and BD II was tested for deviation from 0 using the block jackknife122. The LDSC genetic correlation (rg) was tested for difference from 1 by calculating a chi-square statistic corresponding to the estimated rg as ((rg − 1)/ SE)2.
