Abstract

Introduction: Antibody-drug conjugates (ADC) have recently emerged as a leading class of targeted oncology therapies. Their usage remains complex, with approvals ranging from broad, tumor-agnostic immunohistochemistry (IHC) companion diagnostic approvals to narrower indication-specific labels. The ongoing ADC MATCH clinical trial (NCT06311214) examines whether a treatment algorithm defined by reflex RNA/IHC testing of the HER2, TROP2, and NECTIN4 gene/proteins can lead to successful biomarker-directed treatment of advanced solid tumors. This study describes the validation of an RNA-seq algorithm for identifying likely IHC-positive patients as required by the ADC MATCH study.

Methods: Three retrospective, de-identified RNA+IHC datasets were collected to enable accuracy studies of CAP/CLIA lab-developed tests for HER2 IHC prediction, TROP2 IHC prediction, and NECTIN4 IHC prediction. RNA-seq was performed by Tempus AI, Inc (Tempus xR), while IHC was performed by Neogenomics, Inc (HER2; clone 4B5), Tempus AI, Inc. (TROP2; clone SP294), or Histologix (NECTIN4; AB192033). IHC positivity was defined as 2+/3+ score groups (i.e., approximately an H-score > 100). High expressors were defined as binary thresholds using log2 gene tpm values of 7.9 (HER2), 4.9 (TROP2), and 6.8 (NECTIN4).

Results: The sample sizes for the three accuracy studies were 2,018 (HER2), 184 (TROP2), and 478 (NECTIN4), respectively. The performance of IHC prediction was assessed for these three targets using positive percent agreement (PPA) and negative percent agreement (NPA). The PPA of each target was found to be 47% (HER2; n=545), 93% (TROP2; n=146), and 35% (NECTIN4; n=71). The corresponding NPA of each target was found to be 89% (HER2; n=1473), 55% (TROP2; n = 38), 92% (NECTIN4; n=407). PPA and NPA varied among cancer types; for example, the TROP2 PPA in colorectal cancer was substantially lower than other cancers (62% vs 95%; p < .05).

Conclusion: IHC prediction using RNA-seq data is a promising approach to identify patients who are likely to test positive for specific protein biomarkers, potentially aiding in clinical trial screening and treatment decisions. Future studies, such as the ADC MATCH clinical trial, will assess the clinical value and outcomes of this approach.

VIEW THE PUBLICATION