We applied PRS-CS, PRS-CS-auto, and alternative methods to predict six curated common complex diseases (breast cancer, coronary artery disease, depression, inflammatory bowel disease, rheumatoid arthritis, and type 2 diabetes mellitus), and six quantitative traits (height, body mass index, high-density lipoproteins, low-density lipoproteins, cholesterol, and triglycerides) in the Partners HealthCare Biobank. Large-scale GWAS summary statistics for each disease and trait were downloaded from public domains (Table 1 and Supplementary Data 1). SNP heritability for each disease (both on the observed scale and the liability scale) and trait estimated using GWAS summary statistics and LD score regression23 are presented in Supplementary Table 13.Table 1Information on six common complex diseases and six quantitative traitsDisease/TraitAbbreviationGWAS referenceGWAS sample size (case/control)1 KG ∩ PBK SNPs1 KG ∩ PBK ∩ HM3 SNPsPBK sample size (case/control)Breast cancerBRCAMichailidou et al.59228,951 (122,977/105,974)5,022,127857,61610,220 (884/9336)Coronary artery diseaseCADNikpay et al.60184,305 (60,801/123,504)4,803,592849,39916,251 (2759/13,492)DepressionDEPWray et al.61173,005 (59,851/113,154)4,924,025850,29115,276 (2361/12,915)Inflammatory bowel diseaseIBDLiu et al.6234,652 (12,882/21,770)4,823,570849,74918,998 (750/18,248)Rheumatoid arthritisRAOkada et al.6358,284 (14,361/43,923)3,872,637849,68018,170 (753/17,417)Type 2 diabetes mellitusT2DMScott et al.64159,208 (26,676/132,532)4,901,848856,91218,823 (1978/16,845)HeightHGTYengo et al.65693,5291,578,533750,8883957Body mass indexBMIYengo et al.65681,2751,579,905751,6763954High-density lipoproteinsHDLWiller et al.66188,5781,604,577758,0362491Low-density lipoproteinsLDLWiller et al.66188,5781,600,625756,7241713CholesterolCHOLWiller et al.66188,5781,604,391757,9702561TriglyceridesTRIGWiller et al.66188,5781,601,270756,9132505The sample size for
