OncoScore: a novel, Internet-based tool to assess the oncogenic potential of genes

TL;DR

OncoScore is an innovative internet-based text-mining tool that effectively ranks genes by their cancer association, aiding in the prioritization of mutations from large genomic datasets.

Contribution

The paper introduces OncoScore, a novel tool leveraging biomedical literature to assess the oncogenic potential of genes, with validated high discriminative accuracy.

Findings

OncoScore achieved an AUC of 90.3% in distinguishing cancer genes.

The tool provides reliable prioritization of cancer-related genes.

Validated on curated datasets, demonstrating high accuracy.

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.