Abstract
Breast cancer (BC) is the most prevalent women cancer and causes an economic healthcare burden worldwide. Early detection of BC can be useful in reducing subsequent exposure to risk factors. Due to the advancement of sequencing technologies in the last two decades, a large number of BC genes have been identified and a significant amount of these genes has been found to be hereditary. Gene panel testing of these hereditary genes assists in early detection of individuals at risk and improves the effectiveness of prevention and pro-active treatment. Many commercial and health companies and research institutes use gene panel testing for the evaluation of hereditary cancers. In this study, we systematically collected 115 publicly available datasets for gene panel testing of BC and identified a total of 214 unique genes from 35 research articles and 80 company lists of gene panel testing. To explore the effectiveness of these genes for testing, we leverage the large-scale cancer genomics dataset to find out their prevalence and penetrance across 3824 patients. In detail, we observed eight highly penetrant (BRCA1, BRCA2, CDH1, PTEN, STK11, TP53, RAD51C, NBN) and six moderately penetrant (ATM, BRIP1, BRIP2, CHEK2, PALB2,RAD50) coding genes across different testing panels. We evaluated the potential effects of microRNAs on the downregulation of target genes. Interestingly, we found that miR-16-5p and hsa-miR-34a-5p down-regulate 137 and 64 genes, respectively, which suggested that these two microRNAs can be used as ideal therapeutic tool to combat metastasis, chemo-resistance and breast cancer recurrence. In summary, our systematic evaluation on the 115 public gene panel dataset and microRNA not only highlighted a number of highly penetrate coding genes but also provide novel angle to include those microRNAs downregulating a large number of genes causing breast cancer.
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