ITGA1 polymorphisms and haplotypes are associated with gastric cancer risk in a Korean population

Table 1 Characteristics of the study subjects n (%)

Variables	Controls (n = 477)	Cases (n = 477)	OR (95%CI)
Age (yr) mean ± SD	57.8 ± 10.2	58.7 ± 9.9
Sex
Males	301 (63.1)	301 (63.1)
Females	176 (36.9)	176 (36.9)
Smoking status
Non-smokers	225 (47.6)	194 (41.0)	1.00 (reference)
Smokers	248 (52.4)	279 (59.0)	1.64 (0.95-2.84)
Alcohol intake status
Non-drinkers	194 (40.7)	189 (39.6)	1.00 (reference)
Drinkers	283 (59.3)	288 (60.4)	1.18 (0.71-1.76)

Table 2 Frequency of ITGA1 polymorphisms in cases and controls

SNP	Chromosomal position	Amino acid change	Genotype case/control				Case		Control
							Frequency	HWE1	Frequency	HWE1
rs13188662	2686006	-	AA	AG	GG	N	0.280	0.573	0.276	0.597
			249/253	186/186	40/38	475/477
rs11740785	2707341	-	AA	AC	CC	N	0.241	0.866	0.229	0.259
			279/290	166/156	32/31	477/477
rs1820167	2713715	-	AA	AG	GG	N	0.435	0.806	0.420	0.904
			151/162	237/229	89/83	477/477
rs1862610	2722239	-	CC	AC	AA	N	0.369	0.861	0.387	0.484
			172/205	223/192	82/80	477/477
rs2432143	2725674	-	TT	TC	CC	N	0.104	0.671	0.146	0.658
			382/346	87/121	8/10	477/477
rs2447867	2751733	C/C	CC	TC	TT	N	0.490	0.742	0.430	0.769
			123/155	241/229	113/89	477/473
rs4865745	2770258	-	TT	TC	CC	N	0.270	0.892	0.268	0.124
			253/247	186/198	35/28	474/473
rs13163497	2773367	-	GG	AG	AA	N	0.110	0.409	0.108	0.515
			375/381	97/89	4/7	476/477
rs1904163	2780355	-	CC	TC	TT	N	0.298	0.196	0.272	0.698
			238/245	184/187	48/33	470/465
rs1466445	2789486	-	CC	TC	TT	N	0.460	0.783	0.455	0.696
			139/142	233/229	101/100	473/471
rs16880453	2789866	-	GG	GC	CC	N	0.466	0.914	0.465	0.424
			133/130	235/243	100/98	468/471
rs2452864	2796757	-	TT	TC	CC	N	0.367	0.874	0.369	0.368
			190/183	224/230	63/59	477/472
rs1275659	2828018	-	AA	AG	GG	N	0.257	0.185	0.278	0.864
			256/247	192/189	26/37	474/473
rs1871186	2828974	-	TT	TC	CC	N	0.221	0.723	0.213	0.674
			287/296	166/157	22/23	475/476
rs988574	2835169	E/G	TT	TC	CC	N	0.180	0.723	0.183	0.674
			319/309	141/155	15/9	475/473

¹P value for deviation from Hardy-Weinberg Equilibrium (HWE). SNP: Single nucleotide polymorphism.

Table 3 Association between ITGA1 polymorphisms and gastric cancer in a case-control study of a Korean population

SNP	Chromosomal position	Codominant			Dominant			Recessive
		OR (95%CI)	P value1	Q2	OR (95%CI)	P value1	Q2	OR (95%CI)	P value1	Q2
rs13188662	2686006	1.040 (0.840-1.281)	0.161	0.483	1.060 (0.811-1.379)	0.689	0.866	1.060 (0.660-1.690)	0.811	0.963
rs11740785	2707341	1.069 (0.869-1.313)	0.528	0.965	1.106 (0.848-1.442)	0.457	0.866	1.032 (0.630-1.692)	0.899	0.963
rs1820167	2713715	1.066 (0.884-1.286)	0.503	0.964	1.115 (0.846-1.468)	0.440	0.866	1.043 (0.751-1.447)	0.801	0.963
rs1862610	2722239	1.151 (0.965-1.372)	0.118	0.483	1.337 (1.029-1.737)	0.029	0.217	1.029 (0.740-1.429)	0.866	0.963
rs2432143	2725674	1.517 (1.144-2.011)	0.003	0.045	1.800 (0.603-5.371)	0.292	0.883	1.559 (1.150-2.114)	0.004	0.060
rs2447867	2751733	1.258 (1.051-1.505)	0.012	0.090	1.412 (1.061-1.881)	0.018	0.217	1.303 (0.966-1.756)	0.083	0.415
rs4865745	2770258	1.016 (0.829-1.246)	0.875	0.965	0.967 (0.750-1.247)	0.795	0.863	1.269 (0.759-2.122)	0.363	0.927
rs13163497	2773367	1.021 (0.768-1.357)	0.884	0.965	1.064 (0.781-1.449)	0.693	0.866	0.571 (0.167-1.952)	0.371	0.927
rs1904163	2780355	1.157 (0.943-1.420)	0.161	0.483	1.104 (0.849-1.436)	0.461	0.866	1.593 (0.984-2.577)	0.058	0.415
rs1466445	2789486	1.013 (0.845-1.213)	0.890	0.965	1.032 (0.778-1.368)	0.829	0.883	1.000 (0.736-1.358)	1.000	1.000
rs16880453	2789866	1.000 (0.832-1.201)	1.000	1.000	0.979 (0.734-1.305)	0.883	0.883	1.025 (0.752-1.398)	0.874	9.632
rs2452864	2796757	0.986 (0.816-1.191)	0.885	0.965	0.947 (0.728-1.233)	0.687	0.883	1.056 (0.728-1.532)	0.775	9.632
rs1275659	2828018	1.136 (0.919-1.404)	0.237	0.592	1.522 (0.899-2.575)	0.117	0.585	1.095 (0.841-1.427)	0.500	9.632
rs1871186	2828974	1.043 (0.841-1.293)	0.701	0.965	1.072 (0.828-1.388)	0.597	0.866	0.957 (0.533-1.716)	0.881	9.632
rs988574	2835169	0.985 (0.772-1.256)	0.901	0.965	0.927 (0.707-1.215)	0.581	0.866	1.667 (0.729-3.808)	0.225	0.843
VEGAS statistics (P)		23.986 (0.105)			16.823 (0.364)			18.732 (0.260)

¹P values for logistic analysis of three alternative models (codominant, dominant and recessive); ²False discovery rate Q value. When the lower P value generated by the dominant and recessive models was applied for every single nucleotide polymorphism (SNP), the value of the versatile gene-based association study (VEGAS) statistic was 29.622 (P = 0.037).

Table 4 Association between ITGA1 haplotypes and gastric cancer

Haplotypes		Codominant			Dominant			Recessive
		OR (95%CI)	P value1	Q2	OR (95%CI)	P value1	Q2	OR (95%CI)	P value1	Q2
ITGA1	AAA	0.771 (0.510-1.165)	0.414	0.973	0.860 (0.666-1.112)	0.250	0.750	0.819 (0.555-1.210)	0.316	0.913
Haplotype	GAG	1.039 (0.643-1.678)	0.973	0.973	1.030 (0.799-1.328)	0.819	0.819	1.026 (0.644-1.636)	0.913	0.913
block 1	ACA	0.992 (0.559-1.760)	0.768	0.973	1.088 (0.839-1.410)	0.525	0.787	0.957 (0.544-1.683)	0.879	0.913
ITGA1	CT	0.982 (0.688-1.407)	0.640	0.640	1.072 (0.800-1.437)	0.641	0.641	0.911 (0.679-1.223)	0.536	0.536
Haplotype	AT	1.316 (0.686-1.407)	0.086	0.129	1.341 (1.034-1.741)	0.027	0.045	1.121 (0.784-1.603)	0.532	0.536
block 2	CC	0.602 (0.212-0.709)	0.021	0.063	0.653 (0.483-0.884)	0.006	0.018	0.661 (0.233-1.872)	0.433	0.536
ITGA1	CCT	1.023 (0.707-1.480)	0.677	0.794	0.934 (0.705-1.236)	0.631	0.916	0.819 (0.555-1.210)	0.316	0.913
Haplotype	TGC	0.973 (0.641-1.475)	0.314	0.794	0.986 (0.761-1.278)	0.916	0.916	1.026 (0.644-1.636)	0.913	0.913
block 3	TGT	1.418 (0.446-4.507)	0.794	0.794	1.084 (0.782-1.505)	0.627	0.916	0.957 (0.544-1.683)	0.879	0.913
ITGA1	TA	0.938 (0.641-1.370)	0.907	0.907	0.928 (0.658-1.310)	0.671	0.671	0.997 (0.765-1.299)	0.981	0.981
Haplotype	CA	0.983 (0.536-1.803)	0.803	0.907	1.079 (0.832-1.400)	0.567	0.671	0.952 (0.523-1.733)	0.873	0.981
block 4	TG	1.619 (0.698-3.756)	0.320	0.907	0.925 (0.708-1.209)	0.569	0.671	1.685 (0.730-3.888)	0.217	0.981

¹P values for logistic analysis of three alternative models (codominant, dominant and recessive). The P value for haplotype associations were calculated using single nucleotide polymorphisms Analyzer™ 2.0 software; ²False discovery rate Q value.