Comprehensive analysis of HFE gene in hereditary hemochromatosis and in diseases associated with acquired iron overload

Table 1 The single nucleotide polymorphism reference number (rs), the usual single nucleotide polymorphism names (H63DC>G, C282YG>A, IVS2(+4)T>C and IVS4(-44)T>C) and new variation sites

SNPs	Allele/genotype	HH	HCV-IO+	HCV-IO-	HCC HCV-IO+	HCC-IO?	CTL
H63DC>G (rs1799945) [+3511]	C	0.893	0.859	0.864	0.805	0.921	0.825
	G	0.107	0.141	0.136	0.195	0.079	0.175
	GG	0.000	0.042	0.000	0.024	0.000	0.030
	CG	0.214	0.197	0.271	0.341	0.158	0.290
	CC	0.786	0.761	0.729	0.634	0.842	0.680
	HW P value	1.000	1.000	0.580	1.000	1.000	1.000
IVS2(+4)T>C (rs2071303) [+3668]	T	0.857	0.641	0.669	0.585	0.684	0.610
	C	0.143	0.359	0.331	0.415	0.316	0.390
	TT	0.7141	0.408	0.424	0.390	0.526	0.390
	TC	0.286	0.465	0.492	0.390	0.316	0.440
	CC	0.000	0.127	0.085	0.220	0.158	0.170
	HW P value	0.528	1.000	0.556	0.212	0.295	0.528
G>C (rs807209) [+5197]	G	0.000	0.007	0.017	0.000	0.053	0.035
	C	1.000	0.993	0.983	1.000	0.947	0.965
	GG	0.000	0.000	0.000	0.000	0.000	0.010
	GC	0.000	0.014	0.034	0.000	0.105	0.050
	CC	1.000	0.986	0.966	1.000	0.895	0.940
	HW P value	-	-	1.000	-	1.000	0.103
C282YG>A (rs1800562) [+5473]	G	0.2862	0.979	0.983	0.902	1.000	0.955
	A	0.7142	0.021	0.017	0.098	0.000	0.045
	GG	0.0712	0.958	0.966	0.854	1.000	0.910
	GA	0.429	0.042	0.034	0.098	0.000	0.090
	AA	0.5002	0.000	0.000	0.049	0.000	0.000
	HW P value	1.000	1.000	1.000	0.031	-	1.000
IVS4(–44)T>C (rs1800708) [+5635]	T	1.000	0.880	0.907	0.817	0.842	0.925
	C	0.000	0.120	0.093	0.183	0.158	0.075
	CC	0.000	0.014	0.000	0.024	0.000	0.000
	TC	0.000	0.211	0.186	0.317	0.316	0.150
	TT	1.000	0.775	0.814	0.659	0.684	0.850
	HW P value	1.000	1.000	1.000	1.000	1.000	1.000
New mutation (G>Del) at intron 5 [+5811]	G	1.000	1.000	1.000	1.000	1.000	0.995
	Del	0.000	0.000	0.000	0.000	0.000	0.005
	GG	1.000	1.000	1.000	1.000	1.000	0.990
	G Del	0.000	0.000	0.000	0.000	0.000	0.010
	Del Del	0.000	0.000	0.000	0.000	0.000	0.000
	HW P value	-	-	-	-	-	-

Frequency of single nucleotide polymorphism (SNP) alleles and genotypes observed at the HFE coding region (ordered from 5’ to 3’) in patients with hereditary hemochromatosis (HH), hepatitis C exhibiting (HCV-IO⁺) or not (HCV-IO^-) iron overload, hepatocellular carcinoma and hepatitis C plus iron overload (HCC HCV-IO⁺), hepatocellular carcinoma caused by diverse etiologies other than HCV and without information regarding iron overload (HCC-IO^?), and in healthy control individuals (CTL). The reference SNP numbers (rs) and the position SNP base [ ] are also shown for the previously described HFE variation sites and were assigned according to NCBI (http://www.ncbi.nlm.nih.gov) and Ensembl (http://www.ensembl.org) databases. Significant Fisher’s exact test P values (≤ 0.05) and Hardy-Weinberg equilibrium adherence are shown in table.

¹HH x CTL: TT (P = 0.04; OR = 3.91; 95%CI: 1.14-13.34);

²HH x CTL: G (P < 0.001; OR = 0.01; 95%CI: 0.006-0.05), A (P < 0.001; OR = 53.06; 95%CI: 18.41-152.90), GG (P < 0.001; OR = 0.007; 95%CI: 0.0008-0.065) and AA (P < 0.001; OR = 201.00; 95%CI: 10.44-3.871). The most frequent allele/genotype different of healthy controls. In italics: alleles and genotypes that presented statistically significant values.