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Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology

IW. Deveson, B. Gong, K. Lai, JS. LoCoco, TA. Richmond, J. Schageman, Z. Zhang, N. Novoradovskaya, JC. Willey, W. Jones, R. Kusko, G. Chen, BS. Madala, J. Blackburn, I. Stevanovski, A. Bhandari, D. Close, J. Conroy, M. Hubank, N. Marella, PA....

. 2021 ; 39 (9) : 1115-1128. [pub] 20210412

Jazyk angličtina Země Spojené státy americké

Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, Research Support, N.I.H., Intramural, práce podpořená grantem, validační studie

Perzistentní odkaz   https://www.medvik.cz/link/bmc21025052

Grantová podpora
E0765001 U.S. Department of Health & Human Services | U.S. Food and Drug Administration (U.S. Food & Drug Administration)
BAA grant HHSF223201510172C U.S. Department of Health & Human Services | U.S. Food and Drug Administration (U.S. Food & Drug Administration)
2017SHZDZX01 Science and Technology Commission of Shanghai Municipality (Shanghai Municipal Science and Technology Commission)
R15 GM137288 NIGMS NIH HHS - United States
FD999999 Intramural FDA HHS - United States
APP1108254 Department of Health | National Health and Medical Research Council (NHMRC)
Early Career Fellowship 2018/ECF013 Cancer Institute NSW (Cancer Institute New South Wales)
P50 GM021700 NIGMS NIH HHS - United States
E0767001 U.S. Department of Health & Human Services | U.S. Food and Drug Administration (U.S. Food & Drug Administration)

E-zdroje Online Plný text

NLK ProQuest Central od 2000-01-01 do Před 1 rokem
Health & Medicine (ProQuest) od 2000-01-01 do Před 1 rokem

Odkazy

PubMed 33846644
DOI 10.1038/s41587-021-00857-z
Knihovny.cz E-zdroje

Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation of the analytical performance of five industry-leading ctDNA assays. We evaluated each stage of the ctDNA sequencing workflow with simulations, synthetic DNA spike-in experiments and proficiency testing on standardized, cell-line-derived reference samples. Above 0.5% variant allele frequency, ctDNA mutations were detected with high sensitivity, precision and reproducibility by all five assays, whereas, below this limit, detection became unreliable and varied widely between assays, especially when input material was limited. Missed mutations (false negatives) were more common than erroneous candidates (false positives), indicating that the reliable sampling of rare ctDNA fragments is the key challenge for ctDNA assays. This comprehensive evaluation of the analytical performance of ctDNA assays serves to inform best practice guidelines and provides a resource for precision oncology.

Accugenomics Inc Wilmington NC USA

Agilent Technologies Cedar Creek TX USA

Agilent Technologies La Jolla CA USA

Agilent Technologies Santa Clara CA USA

Astrazeneca Pharmaceuticals Waltham MA USA

Australian Institute of Bioengineering and Nanotechnology University of Queensland Queensland QLD Australia

Bioinformatics and Computational Biology Laboratory National Heart Lung and Blood Institute National Institutes of Health Bethesda MD USA

Bioinformatics Integrated DNA Technologies Inc Coralville IA USA

Cancer Genetics Inc Rutherford NJ USA

Cancer Theme Garvan Institute of Medical Research Sydney NSW Australia

Center for Bioinformatics and Computational Biology and the Institute of Biomedical Sciences School of Life Sciences East China Normal University Shanghai China

Center of Molecular Medicine Central European Institute of Technology Masaryk University Brno Czech Republic

Clinical Diagnostic Division Thermo Fisher Scientific Fremont CA USA

Clinical Laboratory Burning Rock Biotech Guangzhou China

Clinical Sequencing Division Thermo Fisher Scientific Austin TX USA

Clinical Sequencing Division Thermo Fisher Scientific South San Francisco CA USA

CMINDS Research Center Department of Electrical and Computer Engineering College of Engineering University of Massachusetts Lowell Lowell MA USA

Department of Genetics University of North Carolina Chapel Hill NC USA

Department of Immunology Genomics and Microarray Core Facility University of Texas Southwestern Medical Center Dallas TX USA

Department of Information Science University of Arkansas at Little Rock Little Rock AR USA

Department of Physiology and Biophysics Weill Cornell Medicine Cornell University New York NY USA

Departments of Medicine Pathology and Cancer Biology College of Medicine and Life Sciences University of Toledo Health Sciences Campus Toledo OH USA

Departments of Pathology and Pediatrics University of Utah School of Medicine Salt Lake City UT USA

Division of Bioinformatics and Biostatistics National Center for Toxicological Research US Food and Drug Administration Jefferson AR USA

EATRIS ERIC European Infrastructure for Translational Medicine Amsterdam The Netherlands

Elim Biopharmaceuticals Inc Hayward CA USA

Fudan Gospel Joint Research Center for Precision Medicine Fudan University Shanghai China

Genomics and Epigenetics Theme Garvan Institute of Medical Research Sydney NSW Australia

Human Phenome Institute Fudan University Shanghai China

Icahn Institute and Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New York NY USA

Illumina Inc San Diego CA USA

Immuneering Corporation Cambridge MA USA

Institute for Molecular Medicine Finland University of Helsinki Helsinki Finland

Institute for Personalized Cancer Therapy MD Anderson Cancer Center Houston TX USA

Intramural Research Program Laboratory of Epidemiology and Population Sciences National Institute on Aging National Institutes of Health Baltimore MD USA

Kinghorn Centre for Clinical Genomics Garvan Institute of Medical Research Sydney NSW Australia

Market and Application Development Bioinformatics Roche Sequencing Solutions Inc Pleasanton CA USA

Marketing Integrated DNA Technologies Inc Coralville IA USA

Massachusetts General Hospital Harvard Medical School Boston MA USA

National Institute of Environmental Health Sciences Research Triangle Park Morrisville NC USA

NGS Products and Services Integrated DNA Technologies Inc Coralville IA USA

NIHR Biomedical Research Centre Royal Marsden Hospital Sutton Surrey UK

OmniSeq Inc Buffalo NY USA

Primbio Genes Biotechnology East Lake High tech Development Zone Wuhan Hubei China

Q2 Solutions EA Genomics Morrisville NC USA

R and D Genomics MPS Institute for Clinical and Experimental Pathology ARUP Laboratories Salt Lake City UT USA

Research and Development Burning Rock Biotech Shanghai China

Research and Development Integrated DNA Technologies Inc Coralville IA USA

Research and Development QIAGEN Sciences Inc Frederick MD USA

ResearchDx Inc Irvine CA USA

Roche Sequencing Solutions Inc Pleasanton CA USA

St Vincent's Clinical School Faculty of Medicine University of New South Wales Sydney NSW Australia

St Vincent's Clinical School University of New South Wales Sydney NSW Australia

Stanford Genome Technology Center Stanford University Palo Alto CA USA

State Key Laboratory of Genetic Engineering School of Life Sciences and Shanghai Cancer Hospital Cancer Institute Fudan University Shanghai China

Winthrop P Rockefeller Cancer Institute University of Arkansas for Medical Sciences Little Rock AR USA

Citace poskytuje Crossref.org

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