OncoGenRAG: Evidence-Grounded Retrieval and BioBERT Classification for Precision Oncology Variant Interpretation

Abstract

The increasing use of tumor sequencing has intensified the need for fast, traceable interpretation of genomic variants. General-purpose large language models can produce fluent answers, but unsupported statements, weak provenance, and stale knowledge limit their suitability for clinical genomics. We developed OncoGenRAG, a research framework that combines a parameter-efficiently fine-tuned BioBERT classifier with an entity-aware retrieval system over a curated, multi-source oncology knowledge base. The reported knowledge base contains 933 harmonized records derived from CIViC, ClinVar/dbSNP, Open Targets, UniProtKB/Swiss-Prot, Ensembl Variation, and linked PubMed literature. The classifier assigns one of five labels: Pathogenic, Likely Pathogenic, Variant of Uncertain Significance, Benign, or Oncogenic; the retrieval component ranks evidence records using subword TF-IDF similarity and explicit gene, variant, and cancer-type matches. A rejection rule suppresses answers when retrieval support is below a prespecified threshold. In the authors’ held-out evaluation, the classifier achieved 92.40% accuracy, 93.15% weighted precision, 92.40% weighted recall, and 92.65% weighted F1 score. In a separate benchmark of 100 clinical-style queries, OncoGenRAG achieved reported Precision@1 of 94.5%, Precision@3 of 96.8%, and 100% database grounding. No hallucinated answer was observed under the study’s operational definition, compared with a 41.0% no-hallucination rate for the ungrounded baseline. These results should be interpreted as internal validation rather than proof of universal safety because query construction, annotator agreement, class-specific performance, calibration, and external validation data were not available for independent analysis. OncoGenRAG provides a transparent design for evidence retrieval and abstention, but it is a research prototype and must not be used to select treatment without expert review.