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. 2019 May 30;104(6):1169–1181. doi: 10.1016/j.ajhg.2019.05.001

Table 1.

Summary of the Background GWAS and Our Polygenic Scores

Trait Study Method GWAS Ancestry GWAS N Finnish Samples Filtering in PS SNPs in PS
CAD CARDIoGRAMplusC4D (Nikpay et al., 201523) Logistic European + South Asian + East Asian 60,801/123,504 5,825/5,639 P value, MAF, MHC, INFO, #Cohorts 19,597
RA Okada et al., 201424 Logistic European 18,136/49,724 – P value, MAF, MHC 32,736
CD IIBDGC (Liu et al., 201525) Logistic European 5,956/14,927 – P value, MAF, MHC, INFO, #Cohorts 21,771
UC IIBDGC (Liu et al., 201525) Logistic European 6,968/20,464 – P value, MAF, MHC, INFO, #Cohorts 23,513
SCZa PGC (Ripke et al., 201426) Logistic European + East Asian 36,989/113,075 –a P value, MAF, MHC, INFO, #Cohorts 30,311
WHR GIANT (Locke et al., 201527) Linear European 224,459 ∼16,000 P value, MAF, MHC, #Samples 13,727
FINRISK20 Linear Finnish 24,919 24,919 P value, MAF, MHC 43,252
BMI GIANT (Shungin et al., 201528) Linear European 322,154 ∼23,000 P value, MAF, MHC, #Samples 12,742
UKBB (Neale lab29) Linear White British 337,199 – P value, MAF, MHC 75,979
FINRISK20 Linear Finnish 24,919 24,919 P value, MAF, MHC 44,920
HG GIANT (Wood et al., 201430) Linear European 253,288 ∼23,000 P value, MAF, MHC, #Samples 27,066
UKBB (Neale lab29) Linear White British 337,199 – P value, MAF, MHC 113,079
FINRISK20 Linear Finnish 24,919 24,919 P value, MAF, MHC 50,536

For diseases, GWAS N = affected individuals/controls. The filtering column describes the thresholds used as follows: p value = p value < 0.05; MAF = Minor allele frequency > 0.01; MHC = major histocompatibility complex removed; INFO = imputation quality > 0.9; #Cohorts = exists in over 90% of GWAS cohorts; #Samples = exists in over 90% of GWAS samples. Other abbreviations are as follows: CAD = coronary artery disease; RA = rheumatoid arthritis; CD = Crohn disease; UC = ulcerative colitis; SCZ = schizophrenia; WHR = waist-hip ratio; BMI = body-mass index; and HG = height.

a

Our SCZ-PS excludes Finnish samples (546/2,011) from Ripke et al. In Figures S6 and S7 we show SCZ-PS, including these Finnish samples.