Association Between HTRA1, GAS6 and IFNGR2 Gene Polymorphisms and Stroke Susceptibility in the Chinese Han Population

Figures & data

Table 1 Demographic Characteristic of the Cases with Stroke and Controls

Characteristic		Cases (%)	Controls (%)	p
Total		623	572
Age	Mean ± SD (years)	64.05 ± 10.58	64.12 ± 5.50	0.884
	> 64	299 (48.0%)	222 (38.8%)
	≤ 64	324 (52%)	350 (61.2%)
Gender	Males	394 (63.2%)	336 (58.7%)	0.111
	Females	229 (36.8%)	236 (41.3%)
Drinking	Yes	310 (49.8%)	258 (45.1%)	0.108
	No	313 (52.5%)	314 (54.9%)
Smoking	Yes	331 (53.1%)	272 (47.6%)	0.054
	No	292 (49.5%)	300 (52.4%)
ALT (U/L)	Mean ± SD	26.03 ± 32.49	25.78 ± 18.45	0.880
AST (U/L)	Mean ± SD	25.81 ± 24.38	25.88 ± 9.97	0.954
MONO (%)	Mean ± SD	7.30 ± 1.69	7.06 ± 1.80	0.291
TBA (μmol/L)	Mean ± SD	7.90 ± 8.65	5.78 ± 8.81	< 0.001
Cr (μmol/L)	Mean ± SD	73.10 ± 23.75	67.01 ± 12.96	< 0.001
UA (μmol/L)	Mean ± SD	272.90 ± 92.84	317.28 ± 76.45	< 0.001
TG (mmol/L)	Mean ± SD	1.59 ± 1.27	1.69 ± 1.35	0.196
CHOL (mmol/L)	Mean ± SD	3.91 ± 1.01	4.79 ± 1.02	< 0.001
HDL-C (mmol/L)	Mean ± SD	1.12 ± 0.28	1.15 ± 0.24	0.171
LDL-C (mmol/L)	Mean ± SD	1.94 ± 0.68	2.62 ± 0.77	< 0.001

Note: p < 0.05 in bold type indicates statistical significance.

Abbreviations: SD, standard deviation; ALT, Alanine transaminase; AST, Aspartate aminotransferase; MONO, Monocytes ratio; TBA, Total bile acid; Cr, Creatinine; UA, Uric Acid; TG, Triglyceride; CHOL, Total cholesterol; HDL-C, High density lipid-cholesterol; LDL-C, Low density lipid-cholesterol.

Table 2 Basic Information About SNPs and Association with Risk of Stroke in Allele Model

SNP-ID	Chr: Position	Genes(s)	Alleles A/B	HWE	MAF		OR (95% CI)	p	Function
					Case	Control
rs369149111	10:122461711	HTRA1	T/C	0.431	0.091	0.088	1.03 (0.77–1.36)	0.853	----
rs1803628	13:113827141	GAS6	A/G	0.556	0.185	0.172	1.09 (0.88–1.35)	0.418	SiPhy cons, Enhancer histone marks
rs9808753	21:33415005	IFNGR2	G/A	0.664	0.458	0.404	1.25 (1.06–1.47)	0.007	SiPhy cons, Enhancer histone marks, DNAse, Motifs changed, GRASP QTL hits, Selected eQTL hits

Notes: p values were calculated using Pearson's χ² test. p < 0.05 in bold type indicates statistical significance.

Abbreviations: SNP, single nucleotide polymorphism; Chr, chromosome; A, minor alleles; B, major alleles; HWE, Hardy-Weinberg equilibrium; MAF, minor allele frequency; OR, odds ratio; 95% CI, 95% confidence interval.

Table 3 Genetic Model Analyses of the Association Between Three SNPs and the Risk of Stroke (Adjusted by Age and Gender)

SNP-ID	Model	Genotype	Case (%)	Control (%)	OR (95% CI)	p
rs369149111 HTRA1	Genotype	TT	5 (0.8%)	6 (1.1%)	0.77 (0.23–2.55)	0.673
		TC	102 (16.5%)	89 (15.6%)	1.08 (0.79–1.47)	0.650
		CC	511 (82.7%)	476 (83.4%)	1.00	0.819
	Dominant	TT+TC	107 (17.3%)	95 (16.6%)	1.06 (0.78–1.43)	0.728
		CC	511 (82.7%)	476 (83.4%)	1.00
	Recessive	TT	5 (0.8%)	6 (1.1%)	0.76 (0.23–2.52)	0.659
		TC+CC	613 (99.2%)	565 (99%)	1.00
	Additive	/	/	/	1.03 (0.78–1.37)	0.828
rs1803628 GAS6	Genotype	AA	24 (3.9%)	19 (3.3%)	0.77 (0.23–2.55)	0.673
		AG	181 (29.2%)	158 (27.8%)	1.08 (0.79–1.47)	0.650
		GG	414 (66.9%)	392 (68.9%)	1.00	0.819
	Dominant	AA+AG	205 (33.1%)	177 (31.1%)	1.09 (0.85–1.39)	0.508
		GG	414 (66.9%)	392 (68.9%)	1.00
	Recessive	AA	24 (3.9%)	19 (3.3%)	1.19 (0.64–2.19)	0.588
		AG+GG	595 (96.1%)	550 (96.7%)	1.00
	Additive	/	/	/	1.08 (0.88–1.33)	0.455
rs9808753 IFNGR2	Genotype	GG	130 (20.9%)	90 (15.8%)	1.59 (1.14–2.23)	0.007
		GA	311 (49.9%)	280 (49.1%)	1.21 (0.94–1.57)	0.140
		AA	182 (29.2%)	200 (35.1%)	1.00	0.024
	Dominant	GG+GA	441 (70.8%)	370 (64.9%)	1.31 (1.02–1.67)	0.032
		AA	182 (29.2%)	200 (35.1%)	1.00
	Recessive	GG	130 (20.9%)	90 (15.8%)	1.42 (1.05–1.91)	0.022
		GA+AA	493 (79.1%)	480 (84.2%)	1.00
	Additive	/	/	/	1.26 (1.07–1.48)	0.007

Notes: p values were calculated by Wald test under logistic regression. p < 0.05 in bold type indicates statistical significance.

Abbreviations: SNP, single nucleotide polymorphism; OR, odds ratio; 95% CI, 95% confidence interval.

Table 4 Distribution of SNPs in Different Age, Gender, Smoking Status, Drinking Status and Its Association with Risk of Stroke

SNP-ID	Model	Genotype	Case	Control	OR (95% CI)	p	Case	Control	OR (95% CI)	p
Smoking status			Smoking				Non-smoking
rs1803628	Genotype	AA	10 (3%)	10 (3.7%)	0.79 (0.32–1.94)	0.606	14 (4.8%)	9 (3%)	1.83 (0.77–4.34)	0.168
GAS6		AG	82 (24.9%)	78 (28.8%)	0.80 (0.56–1.16)	0.239	99 (34.1%)	80 (26.9%)	1.45 (1.01–2.07)	0.042
		GG	237 (72%)	183 (67.5%)	1.00	0.463	177 (61%)	209 (70.1%)	1.00	0.068
	Dominant	AA+AG	92 (28%)	88 (32.5%)	0.80 (0.56–1.14)	0.215	113 (39%)	89 (29.9%)	1.49 (1.06–2.09)	0.023
		GG	237 (72%)	183 (67.5%)	1.00		177 (61%)	209 (70.1%)	1.00
	Recessive	AA	10 (3%)	10 (3.7%)	0.84 (0.34–2.05)	0.695	14 (4.8%)	9 (3%)	1.63 (0.69–3.83)	0.263
		AG+GG	319 (97%)	261 (96.3%)	1.00		276 (95.2%)	289 (97%)	1.00
	Additive	/	/	/	0.83 (0.62–1.13)	0.236	/	/	1.41 (1.05–1.89)	0.021
Age			Age ≤ 64				Age > 64
rs9808753 IFNGR2	Genotype	GG	70 (21.6%)	58 (16.7%)	1.65 (1.01–2.71)	0.046	60 (20.1%)	32 (14.4%)	1.50 (0.86–2.6)	0.152
		GA	164 (50.6%)	167 (48%)	1.31 (0.88–1.93)	0.181	147 (49.2%)	113 (50.9%)	1.04 (0.69–1.57)	0.849
		AA	90 (27.8%)	123 (35.3%)	1.00	0.125	92 (30.8%)	77 (34.7%)	1.00	0.316
	Dominant	GG+GA	234 (72.2%)	225 (64.7%)	1.40 (0.97–2.03)	0.076	207 (69.2%)	145 (65.3%)	1.14 (0.77–1.68)	0.504
		AA	90 (27.8%)	123 (35.3%)	1.00		92 (30.8%)	77 (34.7%)	1.00
	Recessive	GG	70 (21.6%)	58 (16.7%)	1.41 (0.91–2.17)	0.122	60 (20.1%)	32 (14.4%)	1.46 (0.89–2.39)	0.132
		GA+AA	254 (78.4%)	290 (83.3%)	1.00		239 (79.9%)	190 (85.6%)	1.00
	Additive	/	/	/	1.29 (1.01–1.65)	0.042	/	/	1.19 (0.91–1.55)	0.201
Gender			Females				Males
rs9808753 IFNGR2	Genotype	GG	48 (21%)	43 (18.3%)	1.33 (0.79–2.24)	0.285	82 (20.8%)	47 (14%)	1.82 (1.17–2.84)	0.008
		GA	111 (48.5%)	109 (46.4%)	1.21 (0.80–1.83)	0.366	200 (50.8%)	171 (51%)	1.22 (0.88–1.70)	0.232
		AA	70 (30.6%)	83 (35.3%)	1.00	0.509	112 (28.4%)	117 (34.9%)	1.00	0.029
	Dominant	GG+GA	159 (69.4%)	152 (64.7%)	1.24 (0.84–1.83)	0.271	282 (71.6%)	218 (65.1%)	1.35 (0.99–1.85)	0.059
		AA	70 (30.6%)	83 (35.3%)	1.00		112 (28.4%)	117 (34.9%)	1.00
	Recessive	GG	48 (21%)	43 (18.3%)	1.19 (0.75–1.88)	0.465	82 (20.8%)	47 (14%)	1.61 (1.09–2.39)	0.017
		GA+AA	181 (79%)	192 (81.7%)	1.00		312 (79.2%)	288 (86%)	1.00
	Additive	/	/	/	1.16 (0.89–1.49)	0.257	/	/	1.33 (1.07–1.65)	0.009
Drinking status			Drinking				Non-drinking
rs9808753 IFNGR2	Genotype	GG	58 (18.7%)	29 (11.3%)	2.21 (1.30–3.74)	0.003	72 (23%)	61 (19.5%)	1.30 (0.83–2.03)	0.249
		GA	161 (51.9%)	128 (49.8%)	1.38 (0.95–1.98)	0.089	150 (47.9%)	152 (48.6%)	1.08 (0.75–1.56)	0.667
		AA	91 (29.4%)	100 (38.9%)	1.00	0.012	91 (29.1%)	100 (31.9%)	1.00	0.507
	Dominant	GG+GA	219 (70.7%)	157 (61.1%)	1.53 (1.08–2.17)	0.018	222 (70.9%)	213 (68%)	1.15 (0.81–1.61)	0.437
		AA	91 (29.4%)	100 (38.9%)	1.00		91 (29.1%)	100 (31.9%)	1.00
	Recessive	GG	58 (18.7%)	29 (11.3%)	1.83 (1.13–2.95)	0.014	72 (23%)	61 (19.5%)	1.24 (0.84–1.82)	0.278
		GA+AA	252 (81.3%)	228 (88.7%)	1.00		241 (77%)	252 (80.5%)	1.00
	Additive	/	/	/	1.46 (1.14–1.87)	0.003	/	/	1.14 (0.91–1.41)	0.261

Notes: p values were calculated by Wald test under logistic regression with adjustment for gender and age. p < 0.05 in bold type indicates statistical significance.

Abbreviations: SNP, single nucleotide polymorphism; OR, odds ratio; 95% CI, 95% confidence interval.

Table 5 Summary of SNP-SNP Interactions on the Risk of Stroke Analyzed by MDR Method

Model	Training Bal. Acc	Testing Bal. Acc	CVC	OR (95% CI)	p
rs9808753*	0.529	0.529	10/10	1.31 (1.02–1.68)	0.036
rs369149111, rs9808753	0.534	0.504	10/10	1.39 (1.07–1.82)	0.015
rs369149111, rs1803628, rs9808753	0.540	0.490	10/10	1.38 (1.09–1.76)	0.008

Notes: p values were calculated using χ² test. p < 0.05 in bold type indicates statistical significance. *The best model in MDR analysis.

Abbreviations: MDR, multifactor dimensionality reduction; Bal. Acc, balanced accuracy; CVC, cross-validation consistency; OR, odds ratio; 95% CI, 95% confidence interval.

Figure 1 Dendrogram about the analysis of SNP-SNP interactions. Colors in the dendrogram indicate synergies or redundancies. Red indicates a high degree of synergistic interaction; Orange indicates a lesser degree, whereas brown represents the midpoint; blue represents the highest level of redundancy, followed by green. The shorter the distance between nodes, the stronger the interaction between them.

Table 6 Clinical Characteristics of Stroke Patients Based on the Genotypes of Selected SNPs

Characteristics	GAS6 rs1803628				IFNGR2 rs9808753
	AA	AG	GG	p	AA	AG	GG	p
ALT (U/L)	64.47 ± 112.44	21.88 ± 11.81	25.69 ± 27.73	< 0.001	27.81 ± 33.81	26.76 ± 37.25	21.66 ± 11.93	0.328
AST (U/L)	58.29 ± 95.53	22.02 ± 10.05	25.65 ± 17.49	< 0.001	26.50 ± 23.67	26.16 ± 27.17	23.97 ± 17.50	0.706
MONO (%)	5.12 ± 0.31	6.79 ± 1.63	7.71 ± 1.62	0.018	0.42 ± 0.17	0.41 ± 0.21	0.44 ± 0.20	0.636
TBA (μmol/L)	10.54± 9.62	8.16 ± 6.52	7.64 ± 9.42	0.376	8.08 ± 11.70	8.06 ± 7.17	7.21 ± 6.20	0.701
Cr (μmol/L)	77.75 ± 24.83	72.46 ± 28.81	73.16 ± 21.23	0.678	72.72 ± 21.71	72.79 ± 20.43	74.48 ± 33.08	0.832
UA (μmol/L)	245.23 ± 85.00	278.45 ± 95.22	272.15 ± 91.83	0.279	277.04 ± 97.29	271.04 ± 92.25	271.59 ± 88.34	0.800
TG (mmol/L)	1.51 ± 1.18	1.58 ± 1.56	1.59 ± 1.11	0.961	1.53 ± 0.79	1.70 ± 1.58	1.38 ± 0.88	0.113
CHOL (mmol/L)	3.97 ± 1.08	3.93 ± 1.05	3.89 ± 0.99	0.890	3.87 ± 0.98	4.03 ± 1.02	3.67 ± 0.98	0.014
HDL-C (mmol/L)	1.25 ± 0.33	1.13 ± 0.26	1.11 ± 0.28	0.083	1.08 ± 0.22	1.15 ± 0.30	1.13 ± 0.29	0.065
LDL-C (mmol/L)	1.92 ± 0.76	2.01 ± 0.71	1.91 ± 0.67	0.399	1.92 ± 0.65	2.00 ± 0.70	1.82 ± 0.67	0.096

Note: p < 0.05 in bold type indicates statistical significance.

Abbreviations: ALT, Alanine transaminase; AST, Aspartate aminotransferase; MONO, Monocytes ratio; TBA, Total bile acid; Cr, Creatinine; UA, Uric Acid; TG, Triglyceride; CHOL, Cholesterol; HDL-C, High density lipid-cholesterol; LDL-C, Low density lipid-cholesterol.