. 2019 Apr 16;10:1776. doi: 10.1038/s41467-019-09718-5

Table 1.

Information on six common complex diseases and six quantitative traits

Disease/Trait	Abbreviation	GWAS reference	GWAS sample size (case/control)	1 KG ∩ PBK SNPs	1 KG ∩ PBK ∩ HM3 SNPs	PBK sample size (case/control)
Breast cancer	BRCA	Michailidou et al.⁵⁹	228,951 (122,977/105,974)	5,022,127	857,616	10,220 (884/9336)
Coronary artery disease	CAD	Nikpay et al.⁶⁰	184,305 (60,801/123,504)	4,803,592	849,399	16,251 (2759/13,492)
Depression	DEP	Wray et al.⁶¹	173,005 (59,851/113,154)	4,924,025	850,291	15,276 (2361/12,915)
Inflammatory bowel disease	IBD	Liu et al.⁶²	34,652 (12,882/21,770)	4,823,570	849,749	18,998 (750/18,248)
Rheumatoid arthritis	RA	Okada et al.⁶³	58,284 (14,361/43,923)	3,872,637	849,680	18,170 (753/17,417)
Type 2 diabetes mellitus	T2DM	Scott et al.⁶⁴	159,208 (26,676/132,532)	4,901,848	856,912	18,823 (1978/16,845)
Height	HGT	Yengo et al.⁶⁵	693,529	1,578,533	750,888	3957
Body mass index	BMI	Yengo et al.⁶⁵	681,275	1,579,905	751,676	3954
High-density lipoproteins	HDL	Willer et al.⁶⁶	188,578	1,604,577	758,036	2491
Low-density lipoproteins	LDL	Willer et al.⁶⁶	188,578	1,600,625	756,724	1713
Cholesterol	CHOL	Willer et al.⁶⁶	188,578	1,604,391	757,970	2561
Triglycerides	TRIG	Willer et al.⁶⁶	188,578	1,601,270	756,913	2505

The sample size for each external genome-wide association study (GWAS), and the number of genetic markers included in the polygenic prediction are shown, along with the sample size for each disease and quantitative phenotype in the Partners HealthCare Biobank (PBK). For unadjusted PRS and P+T, all common genetic markers (minor allele frequency ≥1%) that passed quality control and are present in the summary statistics and 1000 Genomes Project (1KG) European sample were used in prediction. For LDpred(-inf) and PRS-CS(-auto), genetic markers were further restricted to the HapMap3 (HM3) panel