Tumor mutational burden (TMB) has demonstrated clinical validation as a predictive biomarker for combination immunotherapy in first line (1L) non-small cell lung cancer (NSCLC) (Hellman, et al, PMID 29731394) . As TMB evolves from an exploratory biomarker towards an FDA approved companion diagnostic, more robust and stringent validation requirements must be utilized and broadly shared in order to align on best practices. Herein, we describe in detail the results of the analytic validation used to support TMB from the FDA approved FoundationOne CDx™ (F1CDx) platform as a companion diagnostic for the combination immunotherapy of nivolumab plus ipilimumab (nivo/ipi) in 1L NSCLC.
TMB is calculated by counting all synonymous and non-synonymous base substitutions and short insertions and deletions across 0.8Mb of coding region from the F1CDx next generation sequencing assay, and filtering both germline and oncogenic driver mutations. Analytic validation for TMB classification based on the clinical cutoff of 10 mut/Mb was performed by assessing intermediate precision, limit of detection (LoD), and accuracy on approximately 1,300 clinical specimens. Precision evaluated both reproducibility and repeatability of TMB and LoD evaluated the minimum tumor purity of a sample required to maintain consistent TMB calling around the cutoff. Accuracy evaluated the agreement in TMB calling around the cutoff of 10 mut/Mb between F1CDx and whole exome sequencing (WES).
Reproducibility for TMB was 97.3% (95% CI; 95.7%-98.5%), and repeatability was 95.3% (95% CI; 92.2%-97.4%). An LoD of 21.9% tumor purity was determined with 100% probability of detection, and 18.0% tumor purity for 95% probability of detection. Accuracy according to WES exceeded 84%.
Highly reproducible, sensitive and accurate calling of TMB on F1CDx is analytically validated and requires only 20% tumor content in a sample, supporting the clinical cutoff of 10 mut/Mb for combination immunotherapy in 1L NSCLC. Taken together, this represents the first prospective clinical validation of TMB as a predictive biomarker for immunotherapy that is supported by a rigorous analytic validation standard.
Clinical trial identification
Legal entity responsible for the study
Foundation Medicine, Inc.
Has not received any funding.
D.A. Fabrizio, C. Milbury, W-K. Yip, L. Ramamurthy, X. Bai, V. Pattani, P. Maness, A. Cowen, K. Fedorchak, P. Ma, G.M. Frampton, C. Connelly, Y. Li: Employee and stockholder: Foundation Medicine.