Journal Article

Clinical and analytical validation of FoundationOne®CDx, a comprehensive genomic profiling assay for solid tumors

Lieber, Daniel, Pattani, Varun, Dewal, Ninad, Creeden, James, Maxwell, Kristi, Tang, Yanhua, Smith, David L., Gjoerup, Ole, Yip, Wai-Ki, Sawchyn, Bethany, Ma, Pei, Meng, Wei, Milbury, Coren A., Bailey, Shannon T., Pavlick, Dean C., Frampton, Garrett M., Vietz, Christine, White, Jared, Burns, Christine, Concepcion, Alvin D., Bai, Xiaobo, Skoletsky, Joel, Thornton, James

2022

Overview

FoundationOne ® CDx (F1CDx) is a United States (US) Food and Drug Administration (FDA)-approved companion diagnostic test to identify patients who may benefit from treatment in accordance with the approved therapeutic product labeling for 28 drug therapies. F1CDx utilizes next-generation sequencing (NGS)-based comprehensive genomic profiling (CGP) technology to examine 324 cancer genes in solid tumors. F1CDx reports known and likely pathogenic short variants (SVs), copy number alterations (CNAs), and select rearrangements, as well as complex biomarkers including tumor mutational burden (TMB) and microsatellite instability (MSI), in addition to genomic loss of heterozygosity (gLOH) in ovarian cancer. CGP services can reduce the complexity of biomarker testing, enabling precision medicine to improve treatment decision-making and outcomes for cancer patients, but only if test results are reliable, accurate, and validated clinically and analytically to the highest standard available. The analyses presented herein demonstrate the extensive analytical and clinical validation supporting the F1CDx initial and subsequent FDA approvals to ensure high sensitivity, specificity, and reliability of the data reported. The analytical validation included several in-depth evaluations of F1CDx assay performance including limit of detection (LoD), limit of blank (LoB), precision, and orthogonal concordance for SVs (including base substitutions [SUBs] and insertions/deletions [INDELs]), CNAs (including amplifications and homozygous deletions), genomic rearrangements, and select complex biomarkers. The assay validation of >30,000 test results comprises a considerable and increasing body of evidence that supports the clinical utility of F1CDx to match patients with solid tumors to targeted therapies or immunotherapies based on their tumor’s genomic alterations and biomarkers. F1CDx meets the clinical needs of providers and patients to receive guideline-based biomarker testing, helping them keep pace with a rapidly evolving field of medicine.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Assaying / Biology / Biology and Life Sciences / Biomarkers / Biomarkers, Tumor - genetics / Breast cancer / Cancer / Clinical trials / Colorectal cancer / Complexity / Copy number / Decision making / FDA approval / Genomics / Genomics - methods / Heterozygosity / High-Throughput Nucleotide Sequencing - methods / Humans / Immunotherapy / Loss of heterozygosity / Mathematical analysis / Medical diagnosis / Medicine / Medicine and Health Sciences / Microsatellite instability / Mutation / Neoplasms - drug therapy / Neoplasms - genetics / Neoplasms - pathology / Next-generation sequencing / Ovarian cancer / Ovarian carcinoma / Patients / Precision medicine / Product development / Prostate cancer / Reliability analysis / Reproducibility of Results / Solid tumors / Tumors