Prediction of gastric cancer risk by a polygenic risk score of Helicobacter pylori

doi:10.4251/wjgo.v14.i9.1844

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World Journal of Gastrointestinal Oncology

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1948-5204

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Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA

Evidence-Based Medicine

World J Gastrointest Oncol. Sep 15, 2022; 14(9): 1844-1855
Published online Sep 15, 2022. doi: 10.4251/wjgo.v14.i9.1844

Table 1 Selected and validated single nucleotide polymorphisms associated with gastric cancer in the global dataset

SNP	Corresponding locus in the strain 26695	Gene name	Description	Position in gene	Position in chromosome	Risk allele	Amino acid change	Prevalence of risk allele	P value	LogOR-value
1¹	HP0082¹	tlpC¹	Chemotaxis sensor¹	163¹	88029¹	A¹	K217E,Q¹	16.2%¹	2.88E-15¹	1.29¹
2¹	HP0130¹	triH¹	BIR, Dps/NapA, RAD21 similarity¹	345¹	140797¹	C¹	Synonymous¹	16.2%¹	2.88E-15¹	2.26¹
3¹	HP0231¹	dsbG/K¹	Thiol:disulfide interchange protein¹	433¹	241625¹	A¹	T145A¹	23.2%¹	5.34E-15¹	1.24¹
4	HP0468		Unknown	729	489762	A	Synonymous	34.6%	0.110
5	HP0468		Unknown	705-708	489783-489786	CGCC	A236T	1.2%	0.313
6	HP0709		Adenosyl-chloride synthase	145	762953	A	N49D	14.6%	0.08
7	HP0709		Adenosyl-chloride synthase	159	762967	A	Synonymous	90.0%	0.274
8¹	HP0747¹	trmB¹	tRNA ([guanine-N(7)-]-methyltransferase¹	(934-937)¹	(803467-803470)¹	GGAA¹	G312K,G,R+T313A,T,S¹	38.7%¹	1.17E-14¹	1.20¹
9	HP0797	hpaA	Neuraminyllactose-binding hemagglutinin	334	854406	T	S112A	26.8%	0.567
10¹	HP0797¹	hpaA¹	Neuraminyllactose-binding hemagglutinin¹	325¹	854415¹	C¹	L109F¹	40.1%¹	1.12E-14¹	2.16¹
11	HP0807	fecA-2	Iron importer in outer membrane	2010	861345	C	Synonymous	96.7%	0.158
12¹	HP1055¹		Outer membrane protein¹	798¹	1117402¹	A¹	Synonymous¹	34.6%¹	2.93E-14¹	2.58¹
13	HP1250	csd5	Cell shape determinant	370	1325727	A	N116H,D	65.8%	1
14	HP1440	isp	Inactive Ser protease	533	1513405	G	G173E	92.0%	0.505
15	HP1467	ompA101	Outer membrane protein of OmpA family	53	1538114	T	I18T	98.4%	0.246

¹The single nucleotide polymorphisms validated in this work.

Risk allele: Allele associated with gastric cancer. SNP: Single nucleotide polymorphism; OR: Odds ratio.

Table 2 Associations between polygenic risk score and gastric cancer risk

Quintile	Non-GC	GC	OR (95%CI)	P value
1	315 (41.0%)	44 (17.3%)	0.79 (0.46-1.34)	0.405
2	98 (12.7%)	7 (2.8%)	0.40 (0.17-0.97)	0.052
3	141 (18.3%)	25 (9.9%)	1	-
4	141 (18.3%)	49 (19.4%)	1.96 (1.15-3.35)	0.013
5	74 (9.6%)	128 (50.6%)	9.76 (5.84-16.29)	1.25E-14

CI: Confidence interval; OR: Odds ratio; GC: Gastric cancer

Citation: Wang XY, Wang LL, Liang SZ, Yang C, Xu L, Yu MC, Wang YX, Dong QJ. Prediction of gastric cancer risk by a polygenic risk score of Helicobacter pylori. World J Gastrointest Oncol 2022; 14(9): 1844-1855
URL: https://www.wjgnet.com/1948-5204/full/v14/i9/1844.htm
DOI: https://dx.doi.org/10.4251/wjgo.v14.i9.1844