Table 2.

The top three most significant associations with response to ICI under dominant logistic regression models^a

SNPs	Reported genes	Chromosome position	Major/minor allele	Anti-CTLA-4 (N controls = 78, N cases = 135) (N total = 213)		Anti-PD-1 (N controls = 88, N cases = 81) (N total = 169)		Combined therapy (N controls = 33, N cases = 10) (N total = 43)
				OR (95% CI)	p value	OR (95% CI)	p value	OR (95% CI)	p value
rs10488631	TNPO3, IRF5	chr7:128954129	T/C	1.14 (0.52–2.49)	0.74	1.20 (0.55–2.60)	0.63	31.19 (1.62–597.9)	0.02
rs17388568	IL2, ADAD1, IL21	chr4:122408207	G/A	NA	NA	0.26 (0.12–.53)	0.0002*	0.94 (0.14–6.05)	0.95
rs1893217	PTPN2	chr18:12809341	A/G	2.79 (1.36–5.73)	0.005	1.56 (0.76–3.16)	0.21	6.95 (1.06–45.26)	0.04
rs2111485	FAP, IFIH1	chr2:162254026	G/A	0.62 (0.32–1.19)	0.15	0.96 (0.49–1.87)	0.91	0.21 (0.04–0.98)	0.04
rs2187668	HLA-DQA1	chr6:32638107	C/T	1.36 (0.66–2.78)	0.39	2.14 (1.06–4.31)	0.03	1.15 (0.15–8.48)	0.88
rs2476601	PHTF1, PTPN22	chr1:113834946	G/A	3.17 (1.02–9.85)	0.04	0.36 (0.09–1.48)	0.16	1.52 (0.11–21.01)	0.75
rs6679677	PHTF1, PTPN22	chr1:113761186	C/A	2.95 (1.14–7.60)	0.02	0.59 (0.21–1.61)	0.30	1.52 (0.11–21.01)	0.75

Controls: ICI responders; Cases: ICI non-responders

NA refers to SNPs removed in QC step; the top three SNPs in each treatment cohort are bolded

Asterisk (*) indicates p value surpassing the Bonferroni multiple testing adjustment (p < 0.002)

^aModels adjusted for age, sex and treatment drug (ipilimumab or tremelimumab; nivolumab or pembrolizumab)