title: Proteogenomics for understanding oncology: recent advances and future prospects.
abstract: The concept of proteogenomics has emerged rapidly as a valuable approach to integrate mass spectrometry-derived proteomic data with genomic and transcriptomic data. It is used to harness the full potential of the former dataset in the discovery of potential biomarkers, therapeutic targets and novel proteins associated with various biological processes including diseases. Proteogenomic strategies have been successfully utilized to identify novel genes and redefine annotation of existing gene models in various genomes. In recent years, this approach has been extended to the field of cancer biology to unravel complexities in the tumor genomes and proteomes. Standard proteomics workflows employing translated cancer genomes and transcriptomes can potentially identify peptides from mutant proteins, splice variants and fusion proteins in the tumor proteome, which in addition to the currently available biomarker panels can serve as potential diagnostic and prognostic biomarkers, besides having therapeutic utility. This review focuses on the role of proteogenomics to understand cancer biology.
authors.affiliation: a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.|b Institute of Bioinformatics , Bangalore , India.
authors.forename: Yashwanth
authors.initials: Y
authors.lastname: Subbannayya
authors.affiliation: a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.|b Institute of Bioinformatics , Bangalore , India.
authors.forename: Sneha M
authors.initials: SM
authors.lastname: Pinto
authors.affiliation: a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.|b Institute of Bioinformatics , Bangalore , India.
authors.forename: Harsha
authors.initials: H
authors.lastname: Gowda
authors.affiliation: a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.|b Institute of Bioinformatics , Bangalore , India.|c NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre , National Institute of Mental Health and Neurosciences , Bangalore , India.
authors.forename: T S Keshava
authors.initials: TS
authors.lastname: Prasad
mesh_terms: D000818:Animals; D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism*; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D009369:Neoplasms / Q000175:diagnosis / Q000188:drug therapy / Q000235:genetics / Q000378:metabolism*; D000071696:Proteogenomics / Q000379:methods* / Q000639:trends
chemical_list: D014408:Biomarkers, Tumor
keywords: Carcinogenesis; NextGen sequencing; Oncoproteogenomics; Proteomics; Systems biology