A Bayesian Hierarchical Model for Relating Multiple SNPs within Multiple Genes to Disease Risk

Table 2

Association between selected variants in DNA-damage response genes and CBC risk in the WECARE study.

Gene	rs number	Homozygous; reference allele		Heterozygous		Homozygous; risk allele		lnRR^c		Bayes factors
		Case; (CBC)	Control; (UBC)	Case; (CBC)	Control; (UBC)	Case; (CBC)	Control; (UBC)	(95% CI)	𝑃 value^d	BF SNP	BF gene
ATM	rs1800057^a	680	1322	28	76	0	1	−0.47 (−0.95, −0.01)	0.046	4.58	1.41
	rs4987951^a	674	1278	34	121	0	0	−0.66 (−1.32, −0.25)	0.002	9.04
CHEK2	rs6005861^a,b	680	1311	27	86	1	2	−0.40 (−0.85, 0.06)	0.086	7	0.36
MDC1	rs4713354^a,b	535	1116	157	267	16	16	0.47 (0.26, 0.68)	<0.001	9.72	20.71
	rs2269705^a	589	1220	113	175	6	4	0.50 (0.25, 0.76)	<0.001	15.91
MRE11A	rs13447682^a,b	690	1343	18	54	0	2	−0.56 (−1.12, −0.01)	0.046	5.7	0.52
NBN	rs14448^b	640	1215	60	171	8	13	−0.11 (−0.40, 0.18)	0.447	0.2	2.62
	rs9297757^a,b	651	1233	148	52	5	18	−0.26 (−0.58, 0.05)	0.097	27.33
	rs3736640^a,b	676	1288	32	107	0	4	−0.64 (−1.27, −0.21)	0.003	4.14
RAD51	rs1801320^a	646	1209	58	186	4	4	−0.31 (−0.62, 0.00)	0.048	21.38	3.51

aSNPs identified by Model I based on Bayes factors. Only those SNPs with BF exceeding 3 are listed.
bSNPs identified by Brooks et al. 2012 [25] based on per-allele RR. Only those SNPs with 𝑃 value for trend <0.05 are listed.
^clnRR: regression coefficients of each SNP from simple logistic regression, adjusted for age, menarche, menopause, family history, pregnancy, histology, treatment, the FGFR2 GWAS-identified SNP, and deleterious variants in ATM, BRCA1, BRCA2, CHECK2, and offset term.
^d𝑃 values associated with Wald-𝑧 test for lnRR estimates from simple logistic regression adjusted for fixed covariants listed in d.