Relationships between SNPs and prognosis of breast cancer and pathogenic mechanism

Background Association between several single‐nucleotide polymorphisms (SNPs) and breast cancer risk has been identified through genome‐wide association studies (GWAS), but little is known about their significance in patients’ prognosis. We screened SNPs which were related to the prognosis of breast cancer in Henan Han population, analyzed relevant genes by bioinformatics in database, and further constructed the genetic regulatory network involved in the pathogenesis of breast cancer. Methods We evaluated five SNPs in 232 cases of breast cancer at the Affiliated Tumor Hospital of Zhengzhou University. Relationships between five SNPs, clinical prognostic indicators, and disease‐free survival (DFS) were evaluated by Kaplan–Meier analysis and Cox proportional hazards model. Gene ontology (GO) functional annotation and Kyoto Encyclopedia of genes and Genome (KEGG) analysis were carried out to preliminarily establish genetic regulation network model of breast cancer. Bayesian algorithm was used to optimize the model. Results The multivariate Cox proportional hazards model confirmed that SNP rs3803662 (TOX3/TNRC9) had correlation with DFS independently. In the multivariate Cox proportional hazards model, compared with GA/AA, GG increased the recurrent risk of breast cancer (p = .021, hazard ratio [HR] = 2.914). GO analysis showed that the function of TOX3/TNRC9 included biological_process, molecular_function, and cellular_component. According to KEGG signaling pathway database, the map of breast cancer‐related gene regulatory network was obtained. IGF‐IGF1R‐PI3K‐Akt‐mTOR‐S6K was the best possible pathway for the differentiation of breast cancer cells in this network and ER‐TOX3/TNRC9 was the best possible pathway for the survival of tumor cells in this network by Bayesian theorem optimization. Conclusions SNP rs3803662 (TOX3/TNRC9) is an independent prognostic factor for breast cancer in Henan Han Population. ER‐TOX3/TNRC9 is the best possible pathway involved in the pathogenesis of breast cancer.