Table 2.

Sensitivity analysis results of HNSCC PRS with significant associations in the UK Biobank

Phenotype description	Exclusion analysis1		Exclusion analysis2		Exclusion analysis3
	OR per SD increase (95% CI)	P-value	OR per SD increase (95% CI)	P-value	OR per SD increase (95% CI)	P-value
HNCSS PRS
Tobacco use disorder	1.06 (1.04–1.07)	6.83 × 10−14	1.06 (1.05–1.08)	3.41 × 10−15	1.06 (1.04–1.07)	6.84 × 10−14
Alcoholism	1.06 (1.04–1.08)	5.38 × 10−8	1.06 (1.04–1.09)	6.09 × 10−9	1.06 (1.04–1.08)	5.28 × 10−8
Alcohol-related disorders	1.08 (1.05–1.11)	6.98 × 10−8	1.08 (1.05–1.11)	1.04 × 10−8	1.08 (1.05–1.11)	6.57 × 10−8
Emphysema	1.11 (1.06–1.16)	9.15 × 10−6	1.11 (1.06–1.16)	4.92 × 10−6	1.11 (1.06–1.16)	8.41 × 10−6
Chronic airway obstruction	1.04 (1.02–1.07)	1.20 × 10−4	1.05 (1.02–1.07)	2.70 × 10−5	1.04 (1.02–1.07)	1.12 × 10−4
Cancer of bronchus; lung	1.08 (1.04–1.13)	6.41 × 10−5	1.08 (1.04–1.13)	5.01 × 10−5	1.08 (1.04–1.13)	6.90 × 10−5
OPC PRS
Tobacco use disorder	1.05 (1.04–1.07)	5.51 × 10−12	1.05 (1.04–1.07)	2.72 × 10−12	1.05 (1.04–1.07)	2.44 × 10−11
Cancer of bronchus; lung	1.09 (1.05–1.13)	2.30 × 10−5	1.09 (1.05–1.13)	1.62 × 10−5	1.09 (1.05–1.13)	2.49 × 10−5
Chronic airway obstruction	1.04 (1.02–1.07)	1.62 × 10−4	1.04 (1.02–1.07)	1.06 × 10−4	1.04 (1.02–1.06)	2.99 × 10−4
OC PRS
Tobacco use disorder	1.04 (1.02–1.05)	1.36 × 10−6	1.04 (1.02–1.05)	2.42 × 10−7	1.04 (1.02–1.05)	9.64 × 10−7

Abbreviations: HNSCC, head and neck squamous cell carcinoma; OC, oral cavity cancer; OPC, oropharynx cancer; PRS, polygenic risk score; MHC, major histocompatibility complex; SD, standard deviation; OR, odds ratio; CI, confidence interval; PC, principal component

All analyses were adjusted by age, sex, genotype array, and PC 1 to 10

¹Exclusion analysis in which HNSCC cases were excluded from PheWAS

²Exclusion analysis in which the MHC region was excluded from PRS generation

³Exclusion analysis in which the MHC region was excluded from PRS generation and HNSCC cases were excluded from PheWAS