title: Identifying cancer type specific oncogenes and tumor suppressors using limited size data.
abstract: Cancer is a complex and heterogeneous genetic disease. Different mutations and dysregulated molecular mechanisms alter the pathways that lead to cell proliferation. In this paper, we explore a method which classifies genes into oncogenes (ONGs) and tumor suppressors. We optimize this method to identify specific (ONGs) and tumor suppressors for breast cancer, lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC) and colon adenocarcinoma (COAD), using data from the cancer genome atlas (TCGA). A set of genes were previously classified as ONGs and tumor suppressors across multiple cancer types (Science 2013). Each gene was assigned an ONG score and a tumor suppressor score based on the frequency of its driver mutations across all variants from the catalogue of somatic mutations in cancer (COSMIC). We evaluate and optimize this approach within different cancer types from TCGA. We are able to determine known driver genes for each of the four cancer types. After establishing the baseline parameters for each cancer type, we identify new driver genes for each cancer type, and the molecular pathways that are highly affected by them. Our methodology is general and can be applied to different cancer subtypes to identify specific driver genes and improve personalized therapy.
authors.affiliation: 1 Graduate Program in Bioinformatics, Boston University, 24 Cummington Mall, MA 02215, Boston, USA.
authors.forename: Ana B
authors.initials: AB
authors.lastname: Pavel
authors.affiliation: 2 Laboratory for Information and Decision Systems, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
authors.forename: Cristian I
authors.initials: CI
authors.lastname: Vasile
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics; D000077192:Adenocarcinoma of Lung; D001943:Breast Neoplasms / Q000235:genetics; D002294:Carcinoma, Squamous Cell / Q000235:genetics; D003110:Colonic Neoplasms / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D005260:Female; D016147:Genes, Tumor Suppressor; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics; D009857:Oncogenes
keywords: Oncogene; cancer; driver gene; driver mutation; tumor suppressor