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

doi:10.3748/wjg.v19.i35.5870

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World Journal of Gastroenterology

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1007-9327

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World J Gastroenterol. Sep 21, 2013; 19(35): 5870-5876
Published online Sep 21, 2013. doi: 10.3748/wjg.v19.i35.5870

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

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
SNP	Chromosomal position	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
Haplotypes		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.

Citation: Yim DH, Zhang YW, Eom SY, Moon SI, Yun HY, Song YJ, Youn SJ, Hyun T, Park JS, Kim BS, Lee JY, Kim YD, Kim H. ITGA1 polymorphisms and haplotypes are associated with gastric cancer risk in a Korean population. World J Gastroenterol 2013; 19(35): 5870-5876
URL: https://www.wjgnet.com/1007-9327/full/v19/i35/5870.htm
DOI: https://dx.doi.org/10.3748/wjg.v19.i35.5870