IL4 rs34142320 polymorphism is associated with susceptibility to Helicobacter pylori infection in Chinese Han population in northwestern China

Figures & data

Table 1. The sequences of primers used in this study.

SNP	Forward primer (5'−3’) for PCR	Reverse primer (5'−3’) for PCR	UEP SEQ
IL4 rs2243250	ACGTTGGATGCGACCTGTCCTTCTCAAAAC	ACGTTGGATGGAATAACAGGCAGACTCTCC	AACTTGGGAGAACATTGT
IL4 rs34142320	ACGTTGGATGTTTGCCTCTGTTCCACTTCC	ACGTTGGATGTATGATCACCACTGCACTCC	CTTCCCCGCCCCCCC
TNFA rs1800629	ACGTTGGATGGGTCCCCAAAAGAAATGGAG	ACGTTGGATGGATTTGTGTGTAGGACCCTG	TATAGGTTTTGAGGGGCATG
TNFA rs1800630	ACGTTGGATGCTCTACATGGCCCTGTCTTC	ACGTTGGATGGCAATGGGTAGGAGAATGTC	GGAAATGGCCCTGTCTTCGTTAAG
TNFA rs1799964	ACGTTGGATGTACATGTGGCCATATCTCCC	ACGTTGGATGGGGAAGCAAAGGAGAAGCTG	GACCCTGACTTTTCCTTC
IL10 rs1800871	ACGTTGGATGATGCTAGTCAGGTAGTGCTC	ACGTTGGATGGGTGTACCCTTGTACAGGTG	CAAACTGAGGCACAGAGAT
IL10 rs1800896	ACGTTGGATGATTCCATGGAGGCTGGATAG	ACGTTGGATGGACAACACTACTAAGGCTTC	GGGCCTATCCCTACTTCCCC

UEP SEQ: Unextended mini-sequencing primer.

Table 2. Main characteristics of the participants.

	Numbers	Proportion (%)
Sex
Male	293	41.56
Female	412	58.44
Age, years
≤40	60	8.51
41-50	358	50.78
51-60	205	29.08
>60	82	11.63
Drinking
Yes	96	13.62
No	609	86.38
Smoking
Yes	189	26.81
No	516	73.19
Family history of GC
Yes	89	12.62
No	616	87.38

GC: gastric cancer.

Table 3. Status of Helicobacter pylori infection among participants of different main characteristics.

	H. pylori (+) (%)	H. pylori (–) (%)	Total	Comparison
Sex				χ^2 = 0.257, P = 0.612
Male	183 (62.46)	110 (37.54)	293
Female	265 (64.32)	147 (35.68)	412
Age, years				χ^2 = 1.115, P = 0.774
≤40	40 (66.67)	20 (33.33)	60
41-50	232 (64.80)	126 (35.20)	358
51-60	126 (61.46)	79 (38.54)	205
>60	50 (60.98)	32 (39.02)	82
Drinking				χ^2 = 0.000, P = 0.999
Yes	61 (63.54)	35 (36.46)	96
No	387 (63.55)	222 (36.45)	609
Smoking				χ^2 = 0.025, P = 0.874
Yes	121 (64.02)	68 (35.98)	189
No	327 (63.37)	189 (36.63)	516
Family history of GC				χ^2 = 0.017, P = 0.896
Yes	56 (62.92)	33 (37.08)	89
No	392 (63.64)	224 (36.36)	616

+: positive; –: negative; GC: gastric cancer.

Table 4. Association analysis between IL4, TNFA and IL10 genes polymorphisms and H. pylori infection.

Model	Genotype	Case	Control	OR (95% CI)	P-value	P.adj
IL4 rs2243250 HWE: 0.170*
Codominant	T/T	260 (58.56%)	165 (64.96%)	1	0.11
	T/C	164 (36.94%)	75 (29.53%)	0.71 (0.51–1.00)
	C/C	20 (4.50%)	14 (5.51%)	1.10 (0.54–2.25)
Dominant	T/T	260 (58.56%)	165 (64.96%)	1	0.082
	T/C+C/C	184 (41.44%)	89 (35.04%)	0.75 (0.55–1.04)
Recessive	T/T+T/C	424 (95.50%)	240 (94.49%)	1	0.56
	C/C	20 (4.50%)	14 (5.51%)	1.24 (0.61–2.50)
Overdominant	T/T+C/C	280 (63.06%)	179 (70.47%)	1	0.039
	T/C	164 (36.94%)	75 (29.53%)	0.71 (0.51–0.98)
IL4 rs34142320 HWE: 0.062 *
Codominant	G/G	108 (25.00%)	89 (37.24%)	1	0.003
	G/DEL	233 (53.94%)	101 (42.26%)	0.53 (0.37–0.76)
	DEL/DEL	91 (21.06%)	49 (20.50%)	0.65 (0.42–1.02)
Dominant	G/G	108 (25.00%)	89 (37.24%)	1	0.001	0.030
	G/DEL+DEL/DEL	324 (75.00%)	150 (62.76%)	0.57 (0.40–0.80)
Recessive	G/G+G/DEL	341 (78.94%)	190 (79.50%)	1	0.84
	DEL/DEL	91 (21.06%)	49 (20.50%)	0.96 (0.65–1.42)
Overdominant	G/G+DEL/DEL	199 (46.06%)	138 (57.74%)	1	0.005
	G/DEL	233 (53.94%)	101 (42.26%)	0.63 (0.46–0.87)
TNFA rs1800630 HWE: 1.000 *
Codominant	C/C	334 (75.23%)	183 (72.05%)	1	0.48
	C/A	105 (23.65%)	66 (25.98%)	1.15 (0.80–1.64)
	A/A	5 (1.12%)	5 (1.97%)	1.91 (0.54–6.70)
Dominant	C/C	334 (75.23%)	183 (72.05%)	1	0.35
	C/A+A/A	110 (24.77%)	71 (27.95%)	1.18 (0.83–1.68)
Recessive	C/C+C/A	439 (98.88%)	249 (98.03%)	1	0.34
	A/A	5 (1.12%)	5 (1.97%)	1.84 (0.53–6.45)
Overdominant	C/C+A/A	339 (76.35%)	188 (74.02%)	1	0.49
	C/A	105 (23.65%)	66 (25.98%)	1.13 (0.79–1.62)
TNFA rs1800629 HWE: 1.000 *
Codominant	G/G	384 (86.49%)	215 (84.65%)	1	0.78
	A/G	59 (13.29%)	38 (14.96%)	1.14 (0.74–1.78)
	A/A	1 (0.22%)	1 (0.39%)	1.74 (0.11–27.95)
Dominant	G/G	384 (86.49%)	215 (84.65%)	1	0.52
	A/G+A/A	60 (13.51%)	39 (15.35%)	1.15 (0.75–1.79)
Recessive	G/G+A/G	443 (99.78%)	253 (99.61%)	1	0.71
	A/A	1 (0.22%)	1 (0.39%)	1.70 (0.11–27.40)
Overdominant	G/G+A/A	385 (86.71%)	216 (85.04%)	1	0.56
	A/G	59 (13.29%)	38 (14.96%)	1.14 (0.73–1.78)
TNFA rs1799964 HWE: 1.000 *
Codominant	T/T	292 (67.59%)	169 (67.06%)	1	0.95
	T/C	128 (29.63%)	75 (29.76%)	1.01 (0.72–1.42)
	C/C	12 (2.78%)	8 (3.18%)	1.17 (0.47–2.91)
Dominant	T/T	292 (67.59%)	169 (67.06%)	1	0.89
	T/C+C/C	140 (32.41%)	83 (32.94%)	1.02 (0.73–1.43)
Recessive	T/T+T/C	420 (97.22%)	244 (96.82%)	1	0.75
	C/C	12 (2.78%)	8 (3.18%)	1.16 (0.47–2.89)
Overdominant	T/T+C/C	304 (70.37%)	177 (70.24%)	1	0.98
	T/C	128 (29.63%)	75 (29.76%)	1.00 (0.71–1.41)
IL10 rs1800871 HWE: 0.890 *
Codominant	A/A	170 (38.29%)	99 (38.98%)	1	0.80
	A/G	221 (49.77%)	121 (47.64%)	0.93 (0.67–1.30)
	G/G	53(11.94%)	34 (13.38%)	1.09 (0.66–1.79)
Dominant	A/A	170 (38.29%)	99 (38.98%)	1	0.82
	A/G+G/G	274 (61.71%)	155 (61.02%)	0.96 (0.70–1.32)
Recessive	A/A+A/G	391 (88.06%)	220 (86.62%)	1	0.60
	G/G	53 (11.94%)	34 (13.38%)	1.13 (0.71–1.79)
Overdominant	A/A+G/G	223 (50.23%)	133 (52.36%)	1	0.57
	A/G	221 (49.77%)	121 (47.64%)	0.91 (0.67–1.24)
IL10 rs1800896 HWE: 0.380 *
Codominant	T/T	363 (81.76%)	214 (84.25%)	1	0.13
	T/C	77 (17.34%)	40 (15.75%)	0.87 (0.57–1.32)
	C/C	4 (0.90%)	0 (0.00%)	NA
Dominant	T/T	363 (81.76%)	214 (84.25%)	1	0.36
	T/C+C/C	81 (18.24%)	40 (15.78%)	0.82 (0.54–1.25)
Recessive	T/T+T/C	440 (99.10%)	254 (100.0%)	1	NA
	C/C	4 (0.90%)	0 (0.00%)	NA
Overdominant	T/T+C/C	367 (82.66%)	214 (84.25%)	1	0.54
	T/C	77 (17.34%)	40 (15.75%)	0.88 (0.58–1.33)

P.adj: significant P-value after multiple-comparison correction; HWE: Hardy–Weinberg equilibrium; *: HWE of control groups; NA: not applicable.

Figure 1. LD analysis of the candidate gene SNPs. The results of LD analysis for IL4 (A), TNFA (B) and IL10 (C) genes were described. The color shift from white to red represented that the results of D’ and r² changed from 0 to 1. A deep red block means the result is 1. The closer the value is to 1, the higher degree of LD is. Kb represented the distance between two SNPs in the genome. LD was observed from the three SNPs of TNFA gene and the two SNPs of IL10 gene, respectively.

Table 5. Results of haplotype analysis.

Combinations of SNPs	Haplotype	Case (%)	Control (%)	OR (95% CI)	P-value
IL4
rs34142320-rs2243250	G-T	43.79	52.92	1
	DEL-T	33.15	26.85	0.64 (0.48-0.86)	0.003
	DEL-C	14.86	14.81	0.84 (0.61-1.17)	0.31
	G-C	8.20	5.42	0.52 (0.30-0.90)	0.021
TNFA
rs1800629 – rs1800630 – rs1799964	G-C-T	75.52	73.86	1
	G-A-C	12.95	14.92	1.19 (0.86-1.65)	0.28
	A-C-T	6.88	7.78	1.16 (0.76-1.78)	0.49
	G-C-C	4.65	3.44	0.72 (0.40-1.29)	0.27
IL10
rs1800871 – rs1800896	A-T	63.15	63.05	1
	G-T	27.27	29.15	1.08 (0.84-1.38)	0.57
	G-C	9.58	7.80	0.81 (0.54-1.22)	0.32

Data availability statement

The data that support the findings of this study are openly available in figshare at https://doi.org/10.6084/m9.figshare.21563523.