Due to the compelling predictive value of companion diagnostic (CDx) biomarkers tied to targeted and immune-based therapies, well-characterized robust analytic and clinical validation of genomic assays has become mandatory. An NGS-based CGP (comprehensive genomic profiling) platform was developed in compliance with FDA guidelines for CDx indications.
DNA extracted from FFPE tumor tissue underwent whole-genome shotgun library construction and hybridization-based capture, followed by sequencing using Illumina HiSeq 4000. Sequence data were processed using a proprietary analysis pipeline designed to identify sub substitutions, indels, copy number alterations, genomic rearrangements, microsatellite instability (MSI), and tumor mutational burden (TMB) in 324 genes.
Clinical validity was demonstrated by establishing statistical non-inferiority between CGP and the respective approved CDx, e.g. cobas EGFR and BRAF mutational testing, ALK rearrangements with FISH and IHC, ERBB2 amplification with FISH, and others. For analytical validity, concordance with an orthogonal NGS platform was 94.6% for substitutions and indels, and within-assay reproducibility had positive percent agreement (PPA) of 99.4%. TMB was analytically validated via concordance with whole-exome sequencing. For the first 616 patients (25% non-small cell lung cancer) assayed in clinical care, 6.8% of cases had TMB exceeding 20 mut/Mb, with 25% of these also harboring microsatellite instability. For 143 NSCLC cases, >50% harbored 10 mut/Mb. Of 354 cases with CDx findings possible, 25.6% had such findings, which were split nearly evenly between indications to benefit from and contraindications to targeted therapies.
We developed a CGP assay and demonstrated clinical and analytical validity for CDx biomarkers for targeted therapy, with clinical validation for TMB in progress via correlation with prospective immunotherapy trials. Initial oncologist feedback indicates impact of assay results on course of treatment decisions in patient care.
Clinical trial identification
Legal entity responsible for the study
Foundation Medicine, Inc.
Foundation Medicine, Inc.
Y. Li: Employee of and stockholder: Foundation Medicine Inc. J.X. Sun: Stockholder: Foundation Medicine Inc. J. Skoletsky, C. Milbury, C. Burns, W-K. Yip, N. Dewal, J. He, J. Tuesdell, J.A. Elvin, G. Otto, D. Lipson, J.S. Ross, V.A. Miller, M. Doherty, C. Vietz: Employee and stockholder: Foundation Medicine Inc. E. Peters, E. Schleifman, J. Noe: Employee and stockholder: Genentech Inc. S. Jenkins: Employee and stockholder: AstraZeneca.