least 7 days in a row? [Yes/No]”; SP “Did you have a plan? [Yes/No]”; and SA “Have you ever tried to kill yourself? [Yes/No]”. Individuals not reporting SI were not asked about persistent SI and SP. Accordingly, individuals who did not endorse SI were also coded as not having persistent SI and SP. However, regardless of reporting SI, persistent SI, and SP, all participants were asked if they had ever attempted suicide. This is because SA can be an impulsive behavior with no previous ideation and planning. Suicidality and polysubstance dependence phenotypic information was available for 15,557 Yale-Penn participants. Full genome-wide data were available for a subset (~10,000) of these individuals via genotyping done with the Illumina HumanOmni1-Quad microarray, the Illumina HumanCoreExome array, or the Illumina Multi-Ethnic Global Array. Principal component (PC) analysis was conducted based on each genotyping array and for each ancestry group (African and European ancestries) separately. Detailed information about the quality control pipeline is available in our previous studies14–16. Briefly, Individuals and SNPs with genotype call rates <98%, and SNPs with minor allele frequency <1% and Hardy–Weinberg equilibrium P < 1 × 10−6 were removed from downstream analyses. After the pre-imputation quality control, genotype data were
