Clinical and analytical validation of FoundationOne Liquid CDx, a novel 324-Gene cfDNA-based comprehensive genomic profiling assay for cancers of solid tumor origin

• Published in: PloS one 2020-09, Vol.15 (9), p.e0237802-e0237802
• Main Authors: Woodhouse, Ryan, Li, Meijuan, Hughes, Jason, Delfosse, David, Skoletsky, Joel, Ma, Pei, Meng, Wei, Dewal, Ninad, Milbury, Coren, Clark, Travis, Donahue, Amy, Stover, Dan, Kennedy, Mark, Dacpano-Komansky, Jennifer, Burns, Christine, Vietz, Christine, Alexander, Brian, Hegde, Priti, Dennis, Lucas
• Format: Article
• Language: English
• Subjects: Alleles; Assaying; Biology and Life Sciences; Biomarkers; Biometrics; Biopsy; Blood; Breast cancer; Cancer; Cancer diagnosis; Cancer genetics; Cancer therapies; Copy number; Deoxyribonucleic acid; DNA; Evaluation; FDA approval; Genes; Genetic aspects; Genetic testing; Laboratories; Medical equipment; Medicine; Medicine and Health Sciences; Methods; Microsatellite instability; Product development; Solid tumors; Supervision; Tumors; Validity
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0237802

As availability of precision therapies expands, a well-validated circulating cell-free DNA (cfDNA)-based comprehensive genomic profiling assay has the potential to provide considerable value as a complement to tissue-based testing to ensure potentially life-extending therapies are administered to patients most likely to benefit. Additional data supporting the clinical validity of cfDNA-based testing is necessary to inform optimal use of these assays in the clinic. The FoundationOne.sup.® Liquid CDx assay is a pan-cancer cfDNA-based comprehensive genomic profiling assay that was recently approved by FDA. Validation studies included >7,500 tests and >30,000 unique variants across >300 genes and >30 cancer types. Clinical validity results across multiple tumor types are presented. Additionally, results demonstrated a 95% limit of detection of 0.40% variant allele fraction for select substitutions and insertions/deletions, 0.37% variant allele fraction for select rearrangements, 21.7% tumor fraction for copy number amplifications, and 30.4% TF for copy number losses. The limit of detection for microsatellite instability and blood tumor mutational burden were also determined. The false positive variant rate was 0.013% (approximately 1 in 8,000). Reproducibility of variant calling was 99.59%. In comparison with an orthogonal method, an overall positive percent agreement of 96.3% and negative percent agreement of >99.9% was observed. These study results demonstrate that FoundationOne Liquid CDx accurately and reproducibly detects the major types of genomic alterations in addition to complex biomarkers such as microsatellite instability, blood tumor mutational burden, and tumor fraction. Critically, clinical validity data is presented across multiple cancer types.