title: OncoScore: a novel, Internet-based tool to assess the oncogenic potential of genes.
abstract: The complicated, evolving landscape of cancer mutations poses a formidable challenge to identify cancer genes among the large lists of mutations typically generated in NGS experiments. The ability to prioritize these variants is therefore of paramount importance. To address this issue we developed OncoScore, a text-mining tool that ranks genes according to their association with cancer, based on available biomedical literature. Receiver operating characteristic curve and the area under the curve (AUC) metrics on manually curated datasets confirmed the excellent discriminating capability of OncoScore (OncoScore cut-off threshold = 21.09; AUC = 90.3%, 95% CI: 88.1-92.5%), indicating that OncoScore provides useful results in cases where an efficient prioritization of cancer-associated genes is needed.
authors.affiliation: University of Milano-Bicocca, Dept. of Medicine and Surgery, Monza, 20900, Italy.
authors.forename: Rocco
authors.initials: R
authors.lastname: Piazza
authors.affiliation: Stanford University, Dept. of Pathology, California 94305, USA.
authors.forename: Daniele
authors.initials: D
authors.lastname: Ramazzotti
authors.affiliation: University of Milano-Bicocca, Dept. of Medicine and Surgery, Monza, 20900, Italy.
authors.forename: Roberta
authors.initials: R
authors.lastname: Spinelli
authors.affiliation: GalSeq s.r.l., viale Italia 46, Monza, 20900, Italy.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Pirola
authors.affiliation: University of Milano-Bicocca, Dept. of Informatics, 20125, Milano.
authors.forename: Luca
authors.initials: L
authors.lastname: De Sano
authors.affiliation: GalSeq s.r.l., viale Italia 46, Monza, 20900, Italy.
authors.forename: Pierangelo
authors.initials: P
authors.lastname: Ferrari
authors.affiliation: University of Milano-Bicocca, Dept. of Medicine and Surgery, Monza, 20900, Italy.
authors.forename: Vera
authors.initials: V
authors.lastname: Magistroni
authors.affiliation: University of Milano-Bicocca, Dept. of Medicine and Surgery, Monza, 20900, Italy.
authors.forename: Nicoletta
authors.initials: N
authors.lastname: Cordani
authors.affiliation: University of New Mexico, Department of Pediatrics, Albuquerque., USA.
authors.forename: Nitesh
authors.initials: N
authors.lastname: Sharma
authors.affiliation: University of Milano-Bicocca, Dept. of Medicine and Surgery, Monza, 20900, Italy.
authors.forename: Carlo
authors.initials: C
authors.lastname: Gambacorti-Passerini
mesh_terms: D052138:Genes, Neoplasm; D006801:Humans; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D012984:Software