Responsible Integration of AI in Cancer Genomics: Barriers, Risks, and Pathways to Trustworthy Clinical Translation

Clinical trials are essential for advancing cancer care and drug development, but many fail because of insufficient patient enrollment. While there is growing interest in using AI to support patient recruitment, existing systems largely perform eligibility assessment alone and have rarely been evaluated in real-world oncology workflows. Here we present TrialGPT 2.0, an AI-assisted clinical trial recommendation system designed for real-world deployment. Rather than asking only whether a patient may qualify, the system also assesses which trials warrant further consideration given the patient's current clinical needs and local workflow priorities, and provides structured, inspectable explanations for expert review. Importantly, we evaluated TrialGPT 2.0 retrospectively and prospectively across multiple oncology-focused settings, spanning government, academic cancer-center, patient-advocacy, and NIH referral workflows. In retrospective multicenter cohorts comprising 288 cases, TrialGPT 2.0 retrieved at least one clinician-recommended trial in its top 10 recommendations for approximately 91% of cases while reducing clinician screening time by 55.0%. In a six-month prospective evaluation embedded in an active precision oncology tumor board, TrialGPT 2.0 contributed additional trial opportunities missed by the routine workflow, expanding patient access to clinical trial participation by 90.9%. To support scientific reproducibility, we also introduce NIH-TrialBench, a clinician-authored dataset comprising 126 diverse synthetic patient vignettes and matching scenarios from 11 NIH Institutes and Centers. Together, these results support the value of AI to assist clinical trial matching by improving clinician efficiency and identifying frequently overlooked trial opportunities, ultimately helping to expand and accelerate accrual to cancer trials.

Advances in machine learning and computational power have unlocked the predictive potential of the human genome, yet biologists now demand that these models also elucidate the underlying biological mechanisms. While interpretable machine learning (IML) techniques have been increasingly applied to bridge this gap, there has been a pervasive reliance on anecdotal validation: the vast majority of research relies on a single IML method and reports only isolated successful instances. Through a benchmarking study on transcription factor binding, we demonstrate the risks of current practices. We show that different IML methods can often (1) yield contradictory explanations for the same predictions, (2) fail to localize known regulatory motifs, and (3) fail to faithfully reflect the model's internal decision process. In light of this, we argue for a validation framework analogous to clinical trials: just as trials require rigorous design and adverse-event reporting, genomic interpretability must move beyond cherry-picked plausibility toward systematic assessment of consistency, faithfulness, and biological validity. To facilitate this, we propose a tiered framework to guide rigorous evaluation and reporting of genomic IML methods.

Question: Does atomic fact-checking, which decomposes AI treatment recommendations into individually verifiable claims linked to source guideline documents, increase clinician trust compared to traditional explainability approaches? Findings: In this randomized trial of 356 clinicians generating 7,476 trust ratings, atomic fact-checking produced a large effect on trust (Cohen's d = 0.94), increasing the proportion of clinicians expressing trust from 26.9% to 66.5%. Traditional transparency mechanisms showed a dose-response gradient of improvement over baseline (d = 0.25 to 0.50). Meaning: Decomposing AI recommendations into individually verifiable claims linked to source guidelines produces substantially higher clinician trust than traditional explainability approaches in high-stakes clinical decisions.