Validation of a Next Generation Sequencing Assay for NCI-MATCH: Implications for Precision Medicine Clinical Trials

The NCI-MATCH (NCI-Molecular Analysis for Therapy CHoice) clinical trial is designed to screen tumors from patients refractory to previous therapy to identify cancer-related mutations matched to specific targeted treatments. The trial is led by ECOG-ACRIN and NCI and is available for enrollment at NCI-sponsored cooperative groups (National Clinical Trials Network) and associated clinics (more than 1,000 sites) through the Cancer Trials Support Unit (CTSU). The study is novel because it can enroll patients with any solid tumor or lymphoma and contains 24 treatment arms in one overarching protocol. A major component of patient enrollment is tumor profiling with a targeted Next Generation Sequencing (NGS) assay. NGS is a relatively new molecular diagnostic tool that identifies mutations in crucial genes that may serve as targets for therapy. While NGS is a promising tool for clinical research, it is a complex assay that has not been tested for yielding reproducible results across multiple laboratories.

In preparation for the analytical validation of the 143 gene panel used to identify mutations of interest (MOI) for potential targeted therapies in NCI-MATCH, the four collaborating Clinical Laboratory Improvement Amendments- (CLIA) approved/accredited laboratories (Molecular Characterization Laboratory at the Frederick National Laboratory for Cancer Research, Massachusetts General Hospital Center for Integrated Diagnostics, Yale Clinical Molecular Pathology Laboratory, and MD Anderson Molecular Diagnostics Laboratory) worked together to harmonize laboratory protocols and analytically validated the proposed NCI-MATCH NGS assay. The analytical validation was required to ensure that assay performance was acceptable for the intended use for screening patients and that assay standardization and reproducibility could be achieved across the four participating molecular diagnostic sites, as these laboratories would be processing and analyzing all of the patient biopsy specimens in NCI-MATCH.

A description of the assay that detects 4,066 pre-defined genomic variations (a subset of which are “actionable” MOIs and are used for treatment selection in NCI-MATCH) and the results of the studies demonstrating assay validation for sensitivity, specificity, reproducibility, and limit-of-detection were recently published in the Journal of Molecular Diagnostics (Lih, 2017). The four collaborating laboratories used clinical specimens and cell lines of multiple cancer types and followed harmonized assay standard operating procedures for the assay, data analysis, and reporting. The results indicate that the data analysis from the NGS assay was accurate and highly reproducible across the four laboratories (mean overall concordances over all MOI loci were ≥ 99.99 % among all intra- and inter-operator pairwise comparisons) and that the assay performance met all criteria as outlined for the assay’s intended use. This analytical validation provided confidence that the NCI-MATCH NGS assay could be used in a multi-site approach to screen biopsies from cancer patients across the U.S. for MOIs in multiple tumor types. It also provides a framework for validation of any NGS assay intended to select patients for clinical trials or for treatment.

View the Journal of Molecular Diagnostics commentary on the publication.

Analytical Validation of the Next Generation Sequencing Assay for a Nationwide Signal-Finding Clinical Trial: Molecular Analysis for Therapy CHoice Clinical Trial (NCI-MATCH, EAY131). Lih C-J, Harrington RD, Sims DJ, Harper KN, Bouk CH, Datta V, Yau J, Singh RR, Routbort MJ, Luthra R, Patel KP, Mantha GS, Krishnamurthy S, Ronski K, Walther Z, Finberg KE, Canosa S, Robinson H, Raymond A, Le LP, McShane LM, Polley EC, Conley BA, Doroshow JH, Iafrate AJ, Sklar JL, Hamilton SR, Williams PM. J Mol Diagn. 2017;19:313-327.