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

Autor:	Ryan Woodhouse, Dan Stover, Lucas Dennis, Meijuan Li, Christine Burns, David Delfosse, Jason D. Hughes, Brian M. Alexander, Priti Hegde, Ninad Dewal, Joel Skoletsky, Coren Milbury, Travis A. Clark, Amy Donahue, Mark Kennedy, Wei Meng, Jennifer Dacpano-Komansky, Christine Vietz, Pei Ma
Jazyk:	angličtina
Rok vydání:	2020
Předmět:	0301 basic medicine Genomic profiling Biopsy Lung and Intrathoracic Tumors 0302 clinical medicine Limit of Detection Neoplasms Basic Cancer Research Breast Tumors Medicine and Health Sciences Multidisciplinary medicine.diagnostic_test Genomics Exons Progression-Free Survival ErbB Receptors Oncology 030220 oncology & carcinogenesis Medicine Biological Assay Cell-Free Nucleic Acids Research Article Class I Phosphatidylinositol 3-Kinases Science Surgical and Invasive Medical Procedures Computational biology Biology 03 medical and health sciences Cancer Genomics Malignant Tumors Breast cancer Genomic Medicine Breast Cancer Genetics medicine Humans Progression-free survival Gene Cancers and Neoplasms Biology and Life Sciences Computational Biology Reproducibility of Results Microsatellite instability Cancer Genome Analysis medicine.disease Non-Small Cell Lung Cancer 030104 developmental biology Mutation
Zdroj:	PLoS ONE, Vol 15, Iss 9, p e0237802 (2020) PLoS ONE
ISSN:	1932-6203
Popis:	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®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.
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fb9da6b8079b1bf0a06147432a85460c https://doaj.org/article/c9d36c35db194ad48647b611d39f7516 Zobrazit plný text záznamu Plný text ve formátu PDF Plný text ve formátu HTML
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