On considering the H. pylori infections, the best cutoff values among Hp-negative group for the diagnosis of severe atrophy was determined at PGR ≤6.28 (sensitivity: 85.7%, specificity: 73.9%, positive predictive value: 37.5%, negative predictive value: 99.8%); while for Hp-positive group, the best cutoff value was PGR ≤4.28 (sensitivity: 100%, specificity: 64.3%, positive predictive value: 4.1%, negative predictive value: 100%) (Table 3) (Additional file 1). The gene discussed is HP; the disease is Atrophy.