Sex-specific effects of depression on the incidence and risk factors for coronary heart disease: insights from multi-omics approaches—Supplement dataset

1) The sex-specific GWAS for depression was conducted using data from five international cohorts, including 130,471 female cases and 159,521 controls and 64,805 male cases and 132,185 controls. These cohorts included the Australian Genetics of Depression Study, BIObanks Netherlands Internet Collaboration, Genetic Links to Anxiety and Depression Study, UK Biobank, and All Of Us study (https://doi.org/10.1038/s41467-025-63236-1). 2) The CHD GWAS data were sourced from the Neale Lab and UK Biobank sex-stratified GWAS datasets (http://www.nealelab.is/uk-biobank/) and combined-sex outcome from CARDIoGRAMplusC4D consortium (https://doi.org/10.1038/ng.3396). 3) PRS was calculated using PRSice, an R‐script that calculates PRS across several P-value thresholds using PLINK v2.0 (r2 < 0.1; kb window = 250 kb; PT < 5E-8, 1E-5, 0.001, 0.005, 0.01, 0.05, 0.1, 0.5, 1). Best PT threshold of PRS for prevalent and incident depression events was 0.051) 本研究针对抑郁症的性别特异性全基因组关联研究（Genome-Wide Association Study, GWAS）依托5项国际队列数据开展，共纳入130471名女性病例、159521名女性对照，以及64805名男性病例、132185名男性对照。所使用的队列包括澳大利亚抑郁症遗传学研究（Australian Genetics of Depression Study）、荷兰生物银行互联网合作项目（BIObanks Netherlands Internet Collaboration）、焦虑与抑郁症遗传关联研究（Genetic Links to Anxiety and Depression Study）、英国生物银行（UK Biobank）以及“我们所有人”研究（All Of Us study），相关文献DOI为https://doi.org/10.1038/s41467-025-63236-1。 2) 冠状动脉粥样硬化性心脏病（Coronary Heart Disease, CHD）的全基因组关联研究数据来源于尼尔实验室（Neale Lab）与英国生物银行的按性别分层全基因组关联研究数据集（http://www.nealelab.is/uk-biobank/），其合并性别分析的结局数据则来自CARDIoGRAMplusC4D联盟，相关文献DOI为https://doi.org/10.1038/ng.3396。 3) 多基因风险评分（Polygenic Risk Score, PRS）通过PRSice工具计算得到，该工具为一款R脚本，依托PLINK v2.0软件，在多个P值阈值下计算PRS，具体参数为：连锁不平衡r²<0.1、滑动窗口为250kb、P值阈值（PT）分别为5E-8、1E-5、0.001、0.005、0.01、0.05、0.1、0.5、1。针对抑郁症现患与新发事件的最优PRS P值阈值为0.05。