Evolving Landscape of Molecular Prescreening Strategies for Oncology Early Clinical Trials

Abstract

Most academic precision oncology programs have been designed to facilitate enrollment of patients in early clinical trials with matched targeted agents. Over the last decade, major changes were seen both in the targetable molecular alteration landscape and in drug development trends. In this article, we describe how the Vall d'Hebron Institute of Oncology molecular prescreening program adapted to a dynamic model of biomarker-drug codevelopment. We started with a tumor-agnostic hotspot mutation panel plus in situ hybridization and immunohistochemistry of selected markers and subsequently transitioned to tumor-specific amplicon-based next-generation sequencing (NGS) tests together with custom copy number, fusion, and outlier gene expression panels. All assays are optimized for archived formalin-fixed paraffin-embedded tumor tissues without matched germline sequencing. In parallel, biomarker-matched trials evolved from a scenario of few targets and large populations (such as PI3K inhibitors in PIK3CA mutants) to a complex situation with many targets and small populations (such as multiple targetable fusion events). Recruitment rates in clinical trials with mandatory biomarkers decreased over the last 3 years. Molecular tumor board meetings proved critical to guide oncologists on emerging biomarkers for clinical testing and interpretation of NGS results. The substantial increase of immunotherapy trials had a major impact in target prioritization and guided clinical implementation of new markers, such as tumor mutational burden, with larger exon-based NGS assays and gene expression signatures to capture microenvironment infiltration patterns. This new multiomics era of precision oncology is expected to increase the opportunities for early clinical trial matching.

FIG 1.

Vall d’Hebron Institute of Oncology molecular prescreening program. (A) Timeline detailing most important changes in prescreening tests in the last years. (B) Number of tests performed each year by category. CNA nCounter, Copy Number Alteration NanoString Panel; FISH, fluorescent in situ hybridization; Fusion and GEX nCounter, Fusion and gene expression NanoString Panel; IHC, immunohistochemistry; MSI, microsatellite instability; NGS, next-generation sequencing.

FIG 2.

Vall d’Hebron Institute of Oncology phase I clinical trial unit. (A) Evolution of phase I clinical trials with targeted agents over time. (B) Phase I clinical trials investigating drugs with other mechanisms of action. (C) Inclusions in biomarker-based phase I trials of targeted agents. (D) Inclusions in biomarker-based phase I trials investigating drugs with other mechanisms of action. Other biomarkers: HDM2, KIT, PDGFR, IDH1-2, RET, NTRK1-3, CDK, and Wnt pathway alterations. Chemo, chemotherapy; Immuno, immunotherapy; MSI, microsatellite instability.

FIG 3.

Vall d’Hebron Institute of Oncology molecular prescreening impact on clinical trial recruitment during the last 3 years. (A) Distribution of tumor types over the years. (B) Recruitment in biomarker-guided (mandatory or enrichment) and other alternative trials (immunotherapy or nonimmunotherapy).