DGAT-onco: A powerful method to detect oncogenes by integrating differential mutational analysis and functional impacts of somatic mutations

Motivation: Oncogenes are genes whose malfunctions play critical roles in cancer development, and their discovery is a major aim of cancer mechanisms study. By counting the mutation frequency, oncogenes have been identified with frequent mutations, while it is believed that many more oncogenes could be discovered by differential mutational profile analysis. However, it is common that current methods only utilize mutations in the cancer population, which have an obvious bias in background mutation modelling. Methods: To predict oncogenes efficiently, we developed a method, DGAT-onco that analyzed the frequency distribution and functional impacts of mutations in both cancer and natural population. Our method can capture the mutational difference of two population, and provide a comprehensive view of genomics basis underlying cancer development. DGAT-onco was constructed by germline mutations from the 1000 Genomes project and somatic mutations of 33 cancer types from the Cancer Genome Atlas (TCGA) dataset. Its reliability was verified on an independent test set including 19 cancers from other sources. Results: We demonstrated that our method is more effective than alternative methods in onco-genes discovering. Using this approach achieves higher classification performance in oncogene discovery than 6 alternative methods, and 22.8% significant genes identified by our method were verified as oncogenes by the Cancer Gene Census (CGC). Availability: DGAT-onco is available at https://github.com/zhanghaoyang0/DGAT-onco.