A new design without control population for identification of gastric cancer-related allele combinations based on interaction of genes

Objective: The purpose of this study was to develop a novel approach without control population to examine the relationship between the presence of specific allele combinations at different loci with the onset of gastric cancer. Methods: DNA samples were collected from patients with gastric cancer. Alleles from short tandem repeat loci were determined using the STR Profiler Plus PCR amplification kit (15 SIR loci). The observed and expected frequencies of specific allele combinations were calculated; statistically significant allele combinations were identified by comparing the observed frequency with the expected frequency. The age at disease onset of patients carrying a specific allele combination was further analysed; allele combinations related to the gastric cancer were effectively identified from the large number of possible allele combinations by cross-validation of the 2 sets of analytical results. Results: A total of 2209 pairwise combinations were obtained by computer counting, of which 11 pairs of genes showed significant differences between the observed and expected frequencies (p < 0.05). The p value for the cross-validation was also less than 0.05 for 2 pair of alleles (D8S1179-16 and D5S818-13; D2S1338-23 and D6S1043-11). Conclusion: Gastric cancer onset may be associated with these allele combinations. The new methodology without control group will enable additional discoveries pertaining to the relationship between specific allele combinations at different loci and the onset of complex diseases. (c) 2014 Elsevier B.V. All rights reserved.