. 2019 Jun 13;15(6):e1008202. doi: 10.1371/journal.pgen.1008202

Table 2. Associations of constructed PRS with skin cancer traits in MGI.

PRS (Number of SNPs)		Skin cancer n = 4,503 (1,501 / 3,002)^d	Melanoma n = 1,896 (617 / 1,279)^d	Basal cell carcinoma n = 1,303 (419 / 884)^d	Squamous cell carcinoma n = 836 (273 / 563)^d
PRS based on GWAS catalog
Melanoma (29)	PRS OR^a P-value^a AUC^b HL χ², P-value ^c Brier Score	1.3 (1.26,1.34) 2.7x10^-53 0.57 (0.56,0.58) 6.8, 0.56 0.14	1.48 (1.41,1.56) 1.3x10^-56 0.61 (0.59,0.62) 7.6, 0.47 0.093	1.3 (1.23,1.38) 7.3x10^-19 0.58 (0.56,0.6) 12, 0.13 0.093	1.23 (1.14,1.32) 4.3x10^-8 0.55 (0.53,0.58) 2.2, 0.97 0.091
Basal cell carcinoma (32)	PRS OR^a P-value^a AUC^b HL χ², P-value ^c Brier Score	1.32 (1.27,1.36) 8x10^-60 0.58 (0.56,0.59) 9.7, 0.29 0.14	1.31 (1.25,1.37) 7.2x10^-28 0.58 (0.56,0.59) 13, 0.1 0.093	1.65 (1.56,1.75) 3.6x10^-65 0.64 (0.62,0.66) 15, 0.066 0.091	1.32 (1.23,1.42) 1.4x10^-14 0.58 (0.55,0.6) 12, 0.17 0.091
Squamous cell carcinoma (18)	PRS OR^a P-value^a AUC^b HL χ², P-value ^c Brier Score	1.25 (1.21,1.3) 4.8x10^-42 0.56 (0.55,0.57) 8.1, 0.42 0.14	1.32 (1.26,1.39) 5.1x10^-31 0.58 (0.56,0.59) 6.2, 0.63 0.093	1.35 (1.28,1.43) 7.9x10^-26 0.58 (0.56,0.6) 5.9, 0.66 0.093	1.26 (1.17,1.35) 1.8x10^-10 0.55 (0.53,0.58) 18, 0.025 0.091
PRS based on latest GWAS
Melanoma (20)	PRS OR^a P-value^a AUC^b HL χ², P-value ^c Brier Score	1.31 (1.27,1.36) 3.5x10^-55 0.57 (0.56,0.58) 4.9, 0.76 0.14	1.49 (1.42,1.57) 1.2x10^-55 0.6 (0.59,0.62) 13, 0.13 0.093	1.39 (1.3,1.47) 7.9x10^-27 0.59 (0.58,0.61) 16, 0.04 0.092	1.25 (1.16,1.34) 4x10^-9 0.55 (0.53,0.58) 7.6, 0.47 0.091
Basal cell carcinoma (28)	PRS OR^a P-value^a AUC^b HL χ², P-value ^c Brier Score	1.32 (1.28,1.37) 5.8x10^-61 0.58 (0.57,0.59) 5.9, 0.66 0.14	1.33 (1.27,1.4) 5.7x10^-32 0.58 (0.57,0.6) 20, 0.012 0.093	1.62 (1.53,1.71) 2.8x10^-60 0.63 (0.61,0.65) 6.5, 0.59 0.091	1.34 (1.25,1.44) 1.2x10^-15 0.58 (0.55,0.6) 15, 0.052 0.091
Squamous cell carcinoma (10)	PRS OR^a P-value^a AUC^b HL χ², P-value ^c Brier Score	1.34 (1.3,1.38) 1.1x10^-70 0.58 (0.57,0.6) 13, 0.12 0.14	1.42 (1.36,1.49) 6.1x10^-51 0.59 (0.58,0.61) 14, 0.082 0.093	1.47 (1.4,1.56) 1.8x10^-43 0.61 (0.59,0.63) 7.1, 0.53 0.092	1.4 (1.31,1.5) 2.1x10^-21 0.59 (0.56,0.61) 6.4, 0.61 0.091

^a Association of each cancer with continuous PRS that were transformed to standard normal distribution. Point estimates, 95% confidence intervals and P- values are obtained by fitting Firth’s bias-corrected logistic regression adjusted for age, sex, batch and PC1-4 to the full data.

^b Area under the curve of the receiver operating characteristic (ROC) curve with 95% confidence intervals calculated using the test data after fitting a model with the training data.

^c Hosmer-Lemeshow Goodness-of-Fit test for the test data after fitting a model with the training data

^d Number of cases in training / test set