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

Abstract

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.

Fig 1. FoundationOne^®CDx workflow.

CAP = College of American Pathologists; CDx = companion diagnostic; CLIA = Clinical Laboratory Improvement Amendments; DNA = deoxyribonucleic acid; FDA = United States Food and Drug Administration; FFPE = formalin-fixed, paraffin-embedded.

Fig 2

LoD ranges for (A) SVs and (B) amplifications and rearrangements ^a LoD calculations for the platform variants were based on the hit rate approach for variants with less than three levels with hit rate between 10% and 90% and probit approach for variants with at least three levels with hit rate between 10% and 90%. LoD from the hit rate approach is defined as the lowest level with 95% hit rate (worst-case scenario). ^b Data includes an alteration in the TERT promoter, 124C>T (LoD of 7.9%). TERT is the only promoter region interrogated and is highly enriched for repetitive context of poly-Gs, not present in coding regions. ^c Alterations classified as “known” are defined as those that are listed in COSMIC. ^d Alterations classified as “other” include truncating events in tumor suppressor genes (splice, frameshift, and nonsense) as well as variants that appear in hot-spot locations but do not have a specific COSMIC association or are considered VUS due to lack of reported evidence and conclusive change in function. ^e Sensitivity calculations for the platform variants were based on the hit rate approach for variants with less than three levels with hit rate between 10% and 90% and probit approach for variants with at least three levels with hit rate between 10% and 90%. LoD from the hit rate approach is defined as the lowest level with 95% hit rate (worst-case scenario). ^f Max represents VUS alteration at calling threshold. bp = base pair; CN = copy number; Mb = megabase; MSI = microsatellite instability; mut = mutation; TMB = tumor mutation burden; VUS = variants of unknown significance.

Fig 3. LoDs per driver status (known, likely and unknown) for SUBs using the hit rate approach.

LoD = limit of detection.

Fig 4. Frequencies of targetable known/likely rearrangements in common tumor types detected by F1CDx between 2018 and 2020.

Source: from over 504,000 Foundation Medicine profiles consented for secondary research, 191,575 unique US patients tested with F1CDx from Jan. 14, 2018 through Mar. 31, 2021. CRC = colorectal cancer; NSCLC = non-small cell lung cancer.

Fig 5. Growth and evolution of precision medicine therapies and companion diagnostic biomarkers over time, as demonstrated by increasing number of approved therapies included on Foundation Medicine test results and increasing number of companion diagnostic indications and biomarkers.

¹ FoundationOne^®CDx. Technical Information. Foundation Medicine, Inc; 2020. www.F1CDxLabel.com. ² Data on File, Foundation Medicine, Inc., 2021. ³ FoundationOne^®Liquid CDx. Technical Information. Foundation Medicine, Inc; 2020. www.F1LCDxLabel.com. Updated July 26, 2021. CDx = companion diagnostic.

Fig 6

Frequency of F1CDx reports with potential therapeutic implications by disease group and definition of actionability: (A) therapy options available within the tumor type indicated; (B) therapy options available in tumor types other than the assigned indication; (C) disease groups with clinical trial options; and (D) disease groups with FDA approved companion/complementary diagnostics within the tumor type indicated. Source: 191,575 unique US patients tested with F1CDx and consented for secondary research from January 14, 2018 through March 31, 2021. All disease groups contain ≥100 specimens. Values indicate counts per disease group. CRC = colorectal cancer; CUP = cancer of unknown primary; GIST = gastrointestinal stromal tumor; NSCLC = non-small cell lung cancer; PNS = peripheral nervous system.