A comprehensive candidate gene approach identifies genetic variation associated with osteosarcoma

BMC Cancer

Table 2 Significant SNPs after Bonferroni correction by gene (P _adj)

Pathway	Gene	SNP	Genomic position		Minor Allele	MAF (%) Controls	MAF (%) Cases	OR^†	95% CI	P	P _adj	Model or Test^§	Gene P
DNA repair	FANCM	rs1367580	Chr14: 44714339	Ex14+316 (V878L)	T	10.4	16.7	1.97	(1.26-3.08)	0.0031	0.034	Dominant	0.019
		rs11845507	Chr14: 44721715	IVS16-1012	A	10.5	16.7	1.96	(1.25-3.06)	0.0033	0.037	Dominant
		rs4900664	Chr14: 44732264	IVS20-2861	T	9.3	15.3	2.00	(1.25-3.17)	0.0035	0.038	Dominant
		rs7141145	Chr14: 44733578	IVS20-1547	A	10.3	16.5	1.95	(1.24-3.07)	0.0039	0.043	Dominant
	MDM2	rs1690916	Chr12: 67521673	downstream, no gene	A	42.5	31.3	0.62	(0.45-0.85)	0.0029	0.026	Additive	0.016
	MPG	rs216614	Chr16: 60334	upstream, in RHBDF1	A	0.7	3.1	4.80	--	0.0036	0.047	Fisher's	0.027
Growth and hormone	FGF2	rs11737764	Chr4: 124046230	downstream, in NUDT6	T	8.1	14.1	2.12	(1.33-3.39)	0.0016	0.036	Dominant	0.020
	FGFR3	rs6599400	Chr4: 1754823	upstream, no gene	A	33.0	42.6	1.51	(1.12-2.03)	0.0069	0.021	Additive	0.017
	GH1	rs11079515	Chr17: 59359377	downstream, no gene	G	37.9	49.5	1.61	(1.20-2.16)	0.0016	0.005	Additive	0.002
		rs7921	Chr17: 59359991	downstream, in CD79B	A	27.2	16.1	0.52	(0.35-0.76)	0.0009	0.003	Additive
	GNRH2	rs3761243	Chr20: 2971022	upstream, no gene	C	29.7	40.5	1.60	(1.19-2.16)	0.0020	0.031	Additive	0.021
	IGF1	rs7956547	Chr12: 101382946	IVS2+10605	C	26.3	15.8	0.53	(0.36-0.79)	0.0019	0.040	Additive	0.021

MAF = minor allele frequency;
^† Odds ratios were estimated using logistic regression models with the most common allele or genotype as the referent, adjusted for gender;
^§ Results are shown for the model or test chosen to deal with rare variants in the sequence of logistic regression on the additive trend model, logistic regression on the dominant model, or the Fisher's Exact Test.

ISSN: 1471-2407