OncoDigger Prioritizes Mutation-Associated Genes in Cancer-Specific PubMed Abstracts

Abstract OncoDigger is a biomedical text-mining tool designed to identify and rank genes associated with user-defined queries across cancer-specific PubMed literature. This study systematically evaluates OncoDigger's performance in prioritizing genes associated with mutation-focused literature and examines the factors underlying its results. Ranking involves no gene-specific mutation extraction, so concordance with IntOGen measures agreement with a driver catalogue, not mutation-reporting accuracy. Using the query "mutation mutations", we analyzed PubMed abstract collections representing 19 cancer types and evaluated the top 10 ranked genes per cancer against the IntOGen cancer-driver catalogue. Across 190 gene–cancer pairs, 93.7% (178/190) involved genes recognized as drivers in at least one cancer, while 78.9% (150/190) matched drivers of the corresponding cancer type. Exact cancer-type concordance exceeded that of a pooled, cancer-blind control (53.2%), which by construction returns one list for all cancers, by 25.8 percentage points and CancerMine (60.0%) by 18.9 percentage points. Controlled comparisons identified cancer-specific document retrieval and gene-name quality control as principal contributors to performance, whereas the full scoring formula provided only a small, statistically nonsignificant improvement over matched gene counting. Sensitivity analyses supported the stability of the principal findings. These results provide evidence of OncoDigger's effectiveness for cancer-specific, mutation-focused gene prioritization from published literature. By providing traceable gene rankings and distinguishing literature associations from driver genes called in tumour-sequencing cohorts, OncoDigger offers an accessible and reproducible resource for exploring cancer-associated genes. Availability: The web application is available at https://oncodigger.com. Code, data, and reproducibility materials are available at https://github.com/jfataphd/OncoDigger-gene-prioritization (release v1.3, archived at Zenodo, https://doi.org/10.5281/zenodo.23774746).