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

被引:0
|
作者
Ira W. Deveson
Binsheng Gong
Kevin Lai
Jennifer S. LoCoco
Todd A. Richmond
Jeoffrey Schageman
Zhihong Zhang
Natalia Novoradovskaya
James C. Willey
Wendell Jones
Rebecca Kusko
Guangchun Chen
Bindu Swapna Madala
James Blackburn
Igor Stevanovski
Ambica Bhandari
Devin Close
Jeffrey Conroy
Michael Hubank
Narasimha Marella
Piotr A. Mieczkowski
Fujun Qiu
Robert Sebra
Daniel Stetson
Lihyun Sun
Philippe Szankasi
Haowen Tan
Lin-ya Tang
Hanane Arib
Hunter Best
Blake Burgher
Pierre R. Bushel
Fergal Casey
Simon Cawley
Chia-Jung Chang
Jonathan Choi
Jorge Dinis
Daniel Duncan
Agda Karina Eterovic
Liang Feng
Abhisek Ghosal
Kristina Giorda
Sean Glenn
Scott Happe
Nathan Haseley
Kyle Horvath
Li-Yuan Hung
Mirna Jarosz
Garima Kushwaha
Dan Li
机构
[1] Kinghorn Centre for Clinical Genomics,Departments of Medicine, Pathology, and Cancer Biology, College of Medicine and Life Sciences
[2] Garvan Institute of Medical Research,Department of Immunology, Genomics and Microarray Core Facility
[3] St. Vincent’s Clinical School,Department of Genetics
[4] Faculty of Medicine,Departments of Pathology and Pediatrics
[5] University of New South Wales,Department of Physiology and Biophysics, Weill Cornell Medicine
[6] Division of Bioinformatics and Biostatistics,CMINDS Research Center, Department of Electrical and Computer Engineering, College of Engineering
[7] National Center for Toxicological Research,Department of Information Science
[8] US Food and Drug Administration,Human Phenome Institute
[9] Bioinformatics,Australian Institute of Bioengineering and Nanotechnology
[10] Integrated DNA Technologies,undefined
[11] Inc.,undefined
[12] Illumina,undefined
[13] Inc.,undefined
[14] Market & Application Development Bioinformatics,undefined
[15] Roche Sequencing Solutions Inc.,undefined
[16] Clinical Sequencing Division,undefined
[17] Thermo Fisher Scientific,undefined
[18] Research and Development,undefined
[19] Burning Rock Biotech,undefined
[20] Agilent Technologies,undefined
[21] University of Toledo Health Sciences Campus,undefined
[22] Q2 Solutions - EA Genomics,undefined
[23] Immuneering Corporation,undefined
[24] University of Texas Southwestern Medical Center,undefined
[25] Genomics and Epigenetics Theme,undefined
[26] Garvan Institute of Medical Research,undefined
[27] Cancer Theme,undefined
[28] Garvan Institute of Medical Research,undefined
[29] St. Vincent’s Clinical School,undefined
[30] University of New South Wales,undefined
[31] ResearchDx,undefined
[32] Inc.,undefined
[33] R&D Genomics MPS,undefined
[34] Institute for Clinical and Experimental Pathology ARUP Laboratories,undefined
[35] OmniSeq,undefined
[36] Inc.,undefined
[37] NIHR Biomedical Research Centre,undefined
[38] Royal Marsden Hospital,undefined
[39] Cancer Genetics,undefined
[40] Inc.,undefined
[41] University of North Carolina,undefined
[42] Icahn Institute and Department of Genetics and Genomic Sciences,undefined
[43] Icahn School of Medicine at Mount Sinai,undefined
[44] Astrazeneca Pharmaceuticals,undefined
[45] Elim Biopharmaceuticals,undefined
[46] Inc.,undefined
[47] Primbio Genes Biotechnology,undefined
[48] East Lake High-tech Development Zone,undefined
[49] Institute for Personalized Cancer Therapy,undefined
[50] MD Anderson Cancer Center,undefined
来源
Nature Biotechnology | 2021年 / 39卷
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摘要
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.
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页码:1115 / 1128
页数:13
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