Cancer‐related genetic variants of Helicobacter pylori strains determined using gastric wash‐based whole‐genome analysis with single‐molecule real‐time technology

Abstract Helicobacter pylori ( H . pylori ) are a primary factor in the pathogenesis of gastric cancer (GC); GC ranks third among cancer‐related mortality. A clear understanding of the H . pylori genome factors underlying GC is necessary to develop more effective methods to prevent GC. A single‐molecule real‐time DNA sequencing‐based H . pylori genome‐wide association study analysis was performed using the H . pylori genome present in five early‐stage GC (EGC) and five non‐GC clinical DNA samples recovered from gastric washes. A total of 275 genes with 702 nucleotide variants (NVs) were found to be common to three or more patients with EGC but no non‐GC patients (single‐NV: 654/702, 93.2%; multi‐NV: 40/702, 5.7%; deletion: 3/702, 0.4%; insertion: 3/702, 0.7%). Gene ontology analysis of H . pylori revealed that genes involved in the mitochondrial electron transport system, glycolytic processes and the TCA cycle were highly enriched. Cancer‐related NVs were most frequently found in a member of the Helicobacter outer membrane protein family, hopL . In particular, one of the NVs in hopL was a novel six‐nucleotide insertion (1159095̂1159096, TACTTC); this mutant was detected more frequently in a validation set of 50 additional EGC samples (22/50, 44.0%) than in 18 non‐GC samples (3/18, 16.7%, P = .04). These results suggest that the hopL variant is associated with the development of GC and may serve as a genetic biomarker of H . pylori virulence and GC risk. Our assay can serve as a potent tool to expand our understanding of bacteria‐associated tumorigenesis.