Table 1.

Meta-analysis of five validated SNPs in the folate metabolic pathway genes using two independently published melanoma GWAS datasets

SNP	Allele1	Gene	Discovery-MDACC (n=858)				Validation-NHS/HPFS (n=409)				Combined-Meta-analysis (n=1267)
			EAF	HR (95% CI)2	P2	BFDP3	EAF	HR (95% CI)4	P4	BFDP3	Phet	I2	HR (95% CI)5	P5
rs19509026	G>A	MTHFD1	0.19	1.68 (1.17–2.41)	0.005	0.462	0.18	1.87 (1.18–2.94)	0.007	0.555	0.718	0	1.75 (1.32–2.32)	9.96×10−5
rs120863867	C>T	ALPL	0.05	2.07 (1.19–3.59)	0.010	0.649	0.06	2.17 (1.19–3.95)	0.012	0.686	0.910	0	2.12 (1.41–3.18)	3.04×10−4
rs562225347	T>C	ALPL	0.06	1.94 (1.16–3.25)	0.011	0.662	0.07	2.34 (1.32–4.16)	0.004	0.541	0.634	0	2.12 (1.44–3.09)	1.32×10−4
rs109170066	C>T	ALPL	0.06	1.83 (1.09–3.09)	0.023	0.746	0.07	2.34 (1.32–4.16)	0.004	0.541	0.534	0	2.05 (1.39–3.01)	2.84×10−4
rs115869777	C>A	ALPL	0.06	1.83 (1.09–3.09)	0.023	0.746	0.07	2.34 (1.32–4.16)	0.004	0.541	0.534	0	2.05 (1.39–3.01)	2.84×10−4

¹Reference allele/effect allele

²Adjusted for age, sex, Breslow thickness, distant/regional metastasis, ulceration and mitotic rate in an additive genetic model

³BFDP was used for multiple test correction with detected a highest HR of 2.0 and a prior probability of 0.1

⁴Adjusted for age and sex in an additive genetic model

⁵Meta-analysis in a fix-effects model

⁶Genotyped SNPs in the MDACC dataset

⁷Imputed SNPs in the MDACC dataset.

Abbreviations: SNP, single-nucleotide polymorphism; GWAS, genome-wide association study; MDACC, The University of Texas MD Anderson Cancer Center; NHS/HPFS, the Nurses’ Health Study/Health Professionals Follow-up Study; EAF, effect allele frequency; HR, hazards ratio; CI, confidence interval; BFDP, Bayesian false-discovery probability; P_het, P value for heterogeneity by Cochrane’s Q test; I², heterogeneity statistic; MTHFD1, methylenetetrahydrofolate dehydrogenase 1; ALPL, alkaline phosphatase