Appendix 3—table 7. Which HLA class I alleles of the AH8.1 haplotype are associate with reduced odds of poor prognosis?

Odds of poor prognosis was determined by logistic regression; we report the Coefficient (Coeff), Odds ratio (OR), P value and number of individuals in the cohort with and without the HLA class I allele of interest. OR = exp(Coeff). An OR <1 (or equivalently a Coeff <0) indicates a protective allele (odds of poor prognosis reduced). To maximise power, only individuals missing information at loci of interest were removed hence there is some variation in cohort size depending on the analysis. ¹ 3 SNPs included: rs5929166, rs147856773 and rs75764599. See Lee et al., 2017 for details. In all cases gender was included as a covariate. Since inclusion of the 3 SNPs had little impact on the OR but reduced power (due to a loss of individuals) we do not include the 3 SNPs as covariates in subsequent analysis but we do check that results are robust to their inclusion.

	Odds of poor prognosis			N
HLA	Coeff	OR	P value	HLA+	HLA-	Total
A*01:01	−0.08	0.92	0.33	859	1643	2502
B*08:01	−0.48	0.62	4.75 × 10−7 ****	620	1837	2457
C*07:01	−0.29	0.75	9.8 × 10−4 ***	784	1866	2650
1 With inclusion of three non-MHC SNPs significant in GWAS as covariates
A*0101	−0.05	0.95	0.55	813	1531	2344
B*08:01	−0.43	0.65	1.57 × 10−5 ****	584	1714	2298
C*07:01	−0.24	0.78	8.3 × 10−3 **	740	1738	2478