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Table 2 Cancer risk genotypes identified in genome-wide association studies of 173 hpEurope isolates

From: A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk

Gene name1 p value (min) Risk genotype Position2 Safe genotype Frequency3 Effect on amino acid sequence4 Function
HP1055 [981621–982,565] (−) 1.4.10−9 A 798 C 0.469/0.125 S, associated with G to A substitution at position 797: non-synonymous with T in safe, A in risk Outer membrane protein
HP0797 [506543–507,325] (+) 2.24.10−8 C + T 325 and 334 T + G 0.592/0.181 NS: L/S in safe, F/A in risk Neuraminyllactose-binding hemagglutinin (HpaA) [29]
HP1243,babA1 [1314192–1,316,405] (−) 3.99.10−8 Presence All genes Absence 0.94/0.51   BabA (outer membrane protein) [16]
HP0747 [317158–317,757] (+) 1.69.10− 7 GGAA 934 to 937 AAAA/GGAG 0.531/0.264 NS: KA in safe, GT in risk tRNA (guanine-N(7)-)-methyltransferase
HP0709 [598549–599,451] (−) 2.13.10− 7 A 145 G 0.327/0.153 NS: D in safe, N in risk Adenosyl-chloride synthase
  A 159 G 0.959/0.792 S
HP0532,cag12 [817677–818,519] (+) 3.62.10− 7 Presence All genes Absence 0.92/0.61   CagT protein (Censini, 1996)
HP0468 [925539–927,026] (+) 4.59.10− 7 CGCC 705 to 708 CACG/TGCG 0.694/0.514 NS: T in safe, A in risk Unknown
  A 729 G 0.796/0.5 S
HP0531,cag11 [816985–817,641] (+) 5.4.10−7 Presence All genes Absence 0.92/0.61   CagU protein (Censini, 1996)
HP0541,cag20 [825334–826,446] (−) 6.6.10−7 Presence All genes Absence 0.92/0.61   CagH protein (Censini, 1996)
  1. Risk and safe genotypes are overrepresented amongst isolates from patients with gastric cancer and non-atrophic gastritis respectively, with p value corresponding to the minimum in each gene (p value ≤ 1 × 10−6)
  2. 1Position in ELS37 genome [ ], + and – strand is denoted in ( )
  3. 2Position in gene
  4. 3Frequency GC strains/NAG strains
  5. 4The effect on the amino acid sequence is indicated as synonymous (S) and non-synonymous (NS)