Table 2

The association of each wGRS model with RA

													Sample size
wGRS	45 Susceptibility SNPs	HLA-DRB1 tag SNP	5 Amino acids	Smoking	Gender	OR	95% CI		AUC	Threshold	Sensitivity (%)	Specificity (%)	Cases	Controls
Discovery dataset
wGRSfull_G	+	−	+	−	+	2.01	1.96	2.05	0.7375	>9.85	35	91	11 366	15 489
Anti-CCP-positive cases and healthy controls
wGRS45_G	+	−	−	−	+	2.41	2.30	2.52	0.6667	>7.79	33	85	6370	15 489
wGRStag_G	+	+	−	−	+	2.52	2.42	2.62	0.7039	>8.49	37	87	6370	15 489
wGRSfull_G	+	−	+	−	+	2.42	2.35	2.49	0.7875	>9.51	44	90	6370	15 489
wGRSHLA_G		−	+	−	+	2.40	2.33	2.48	0.7563	>1.54	40	88	6370	15 489
wGRSfull_SG	+	−	+	+	+	2.64	2.45	2.85	0.8013	>10.81	28	95	1978 (1269 smoke)	1224 (851 smoke)
Anti-CCP-negative cases and healthy controls
wGRSfull_G	+	−	+	−	+	1.43	1.38	1.48	0.6205	>9.27	32	82	2868	15 489
Validation
All cases and controls
wGRS_full_G	+	−	+	−	+	1.98	1.87	2.11	0.7175	>8.70	30	92	2200	1856
Anti-CCP-positive cases and healthy controls
wGRStag_G	+	+	−	−	+	2.50	2.26	2.76	0.6937	>7.39	32	89	1406	1856
wGRSfull_G	+	−	+	−	+	2.50	2.31	2.69	0.7774	>8.73	36	92	1406	1856
wGRSHLA_G	−	−	+	−	+	2.61	2.41	2.83	0.7632	>3.53	36	92	1406	1856

The OR shown are from the logistic regression testing the association of each weighted genetic risk score (wGRS) with rheumatoid arthritis (RA). Sensitivity and specificity values were based on the high-risk threshold being set at the 5th quintile and are shown in the threshold column.
AUC, area under ROC curve; CCP, cyclic citrullinated peptide; ROC, receiver operator characteristic; SNP, single-nucleotide polymorphism; wGRSfull_G, wGRS including all 45 susceptibility SNPs, five HLA amino acids and gender; wGRStag_G, wGRS including all 45 susceptibility SNPs, HLA tag SNP and gender; wGRSHLA_G, wGRS containing five HLA amino acids and gender; wGRSfull_SG, wGRS containing 45 susceptibility SNPs, five HLA amino acids, smoking and gender.