Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

Genome Biology - Tập 22 - Trang 1-23 - 2021
Binsheng Gong1, Dan Li1, Rebecca Kusko2, Natalia Novoradovskaya3, Yifan Zhang1,4, Shangzi Wang5, Carlos Pabón-Peña6, Zhihong Zhang7, Kevin Lai8, Wanshi Cai9, Jennifer S. LoCoco10, Eric Lader11, Todd A. Richmond12, Vinay K. Mittal13, Liang-Chun Liu14, Donald J. Johann15, James C. Willey16, Pierre R. Bushel17, Ying Yu5, Chang Xu11, Guangchun Chen18, Daniel Burgess19, Simon Cawley20, Kristina Giorda21, Nathan Haseley10, Fujun Qiu7, Katherine Wilkins6, Hanane Arib22, Claire Attwooll10, Kevin Babson23, Longlong Bao24,25,26, Wenjun Bao27, Anne Bergstrom Lucas6, Hunter Best28,29, Ambica Bhandari30, Halil Bisgin31, James Blackburn32,33, Thomas M. Blomquist34,35, Lisa Boardman36, Blake Burgher37, Daniel J. Butler38, Chia-Jung Chang39, Alka Chaubey23, Tao Chen40, Marco Chierici41, Christopher R. Chin38, Devin Close29, Jeffrey Conroy37, Jessica Cooley Coleman23, Daniel J. Craig42, Erin Crawford42, Angela del Pozo43,44, Ira W. Deveson45,46, Daniel Duncan47, Agda Karina Eterovic48, Xiaohui Fan49, Jonathan Foox38, Cesare Furlanello41,50, Abhisek Ghosal30, Sean Glenn37, Meijian Guan27, Christine Haag51, Xinyi Hang9, Scott Happe52, Brittany Hennigan23, Jennifer Hipp53, Huixiao Hong1, Kyle Horvath30, Jianhong Hu54, Li-Yuan Hung55, Mirna Jarosz56, Jennifer Kerkhof57, Benjamin Kipp58, David Philip Kreil59, Paweł Łabaj60,61, Pablo Lapunzina62,63,44, Peng Li55, Quan-Zhen Li18, Weihua Li64, Zhiguang Li65, Yu Liang66, Shaoqing Liu67, Zhichao Liu1, Charles Ma47, Narasimha Marella47, Rubén Martín-Arenas68, Dalila B. Megherbi69, Qingchang Meng54, Piotr A. Mieczkowski70, Tom Morrison71, Donna Muzny54, Baitang Ning1, Barbara L. Parsons40, Cloud P. Paweletz72, Mehdi Pirooznia73, Wubin Qu9, Amelia Raymond74, Paul Rindler29, Rebecca Ringler30, Bekim Sadikovic57,75, Andreas Scherer76,44, Egbert Schulze77, Robert Sebra22, Rita Shaknovich47, Qiang Shi78, Tieliu Shi79, Juan Carlos Silla-Castro80, Melissa Smith22, Mario Solís López43,44, Ping Song48, Daniel Stetson74, Maya Strahl22, Alan Stuart57, Julianna Supplee72, Philippe Szankasi29, Haowen Tan81, Lin-ya Tang48, Yonghui Tao24,25,26, Shraddha Thakkar1, Danielle Thierry-Mieg82, Jean Thierry-Mieg82, Venkat J. Thodima47, David Thomas45,33, Boris Tichý83,44, Nikola Tom83,44, Elena Vallespin Garcia43,44, Suman Verma30, Kimbley Walker54, Charles Wang84,85, Junwen Wang86,87,88, Yexun Wang11, Zhining Wen89, Valtteri Wirta90, Leihong Wu1, Chunlin Xiao82, Wenzhong Xiao55,39, Shibei Xu91, Mary Yang4, Jianming Ying64, Shun H. Yip86,92, Guangliang Zhang93, Sa Zhang93, Meiru Zhao94, Yuanting Zheng5, Xiaoyan Zhou24,25,26, Christopher E. Mason38, Timothy Mercer95,96, Weida Tong1, Leming Shi5,97,98, Wendell Jones99, Joshua Xu1
1Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, USA
2Immuneering Corporation, Cambridge, USA
3Agilent Technologies, La Jolla, USA
4Department of Information Science, University of Arkansas at Little Rock, Little Rock, USA
5State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, China
6Agilent Technologies, Santa Clara, USA
7Research and Development, Burning Rock Biotech, Shanghai, China
8Bioinformatics, Integrated DNA Technologies, Inc., Coralville, USA
9iGeneTech, Beijing, China
10Illumina Inc., San Diego, USA
11Research and Development, QIAGEN Sciences Inc., Frederick, USA
12Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, USA
13Thermo Fisher Scientific, Ann Arbor, USA
14Clinical Diagnostic Division, Thermo Fisher Scientific, Fremont, USA
15Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, USA
16Departments of Medicine, Pathology, and Cancer Biology, College of Medicine and Life Sciences, University of Toledo Health Sciences Campus, Toledo, USA
17National Institute of Environmental Health Sciences, Research Triangle Park, USA
18Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, Dallas, USA
19Research and Development, Roche Sequencing Solutions Inc., Madison, USA
20Clinical Sequencing Division, Thermo Fisher Scientific, South San Francisco, USA
21Marketing, Integrated DNA Technologies, Inc., Coralville, USA
22Icahn Institute and Dept. of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, New York, USA
23Greenwood Genetic Center, Greenwood, USA
24Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
25Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
26Institute of Pathology, Fudan University, Shanghai, China
27JMP Life Sciences, SAS Institute Inc., Cary, USA
28Departments of Pathology and Pediatrics, University of Utah School of Medicine, Salt Lake City, USA
29R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, USA
30ResearchDx, Inc., Irvine, USA
31Department of Computer Science, Engineering and Physics, University of Michigan-Flint, Flint, USA
32Garvan Institute of Medical Research, Sydney, Australia
33St Vincent's Clinical School, University of New South Wales, Sydney, Australia
34Department of Pathology, College of Medicine and Life Sciences, the University of Toledo, Toledo, USA
35Lucas County Coroner’s Office, Toledo, USA
36Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, USA
37OmniSeq, Buffalo, USA
38Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, USA
39Stanford Genome Technology Center, Stanford University, Palo Alto, USA
40Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, USA
41Fondazione Bruno Kessler, Trento, Italy
42Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, USA
43Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, CIBERER Instituto de Salud Carlos III, Madrid, Spain
44EATRIS ERIC- European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
45Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
46St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
47Cancer Genetics Inc, Rutherford, USA
48Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, USA
49Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
50HK3 Lab, Milan, Italy
51Molecular Laboratory, Prof. F. Raue, Heidelberg, Germany
52Agilent Technologies, Cedar Creek, USA
53Department of Pathology, Strata Oncology, Inc., Ann Arbor, USA
54Human Genome Sequencing Center, Baylor College of Medicine, Houston, USA
55Massachusetts General Hospital, Harvard Medical School, Boston, USA
56NGS Products and Services, Integrated DNA Technologies, Inc., Coralville, USA
57Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Canada
58Division of Anatomic Pathology, Mayo Clinic, Rochester, USA
59Bioinformatics Research, Institute of Molecular Biotechnology, Boku University Vienna, Vienna, Austria
60Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
61Department of Biotechnology, BOKU University Vienna, Austria
62Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPaz, CIBERER Instituto de Salud Carlos III, Madrid, Spain
63ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, European Commission, Lille, France
64Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
65Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
66Geneis, Beijing, China
67GeneSmile Ltd Co., Jiangsu Cancer Hospital, Nanjing, China
68Genycell Biotech España, Calle Garrido Atienza, Granada, Spain
69CMINDS Research Center, Department of Electrical and Computer Engineering, College of Engineering, University of Massachusetts Lowell, Lowell, USA
70Department of Genetics, University of North Carolina, Chapel Hill, USA
71Accugenomics, Inc, Wilmington, USA
72Translational Research Laboratory, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, USA
73Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, USA
74AstraZeneca Pharmaceuticals, Waltham, USA
75Department of Pathology and Laboratory Medicine, Western University, London, Canada
76Institute for Molecular Medicine Finland (FIMM), Nordic EMBL Partnership for Molecular Medicine, HiLIFE Unit, Biomedicum Helsinki 2U (D302b), Helsinki, Finland
77Laboratory for Molecular Genetics, Endocrine Practice, Heidelberg, Germany
78Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, USA
79Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
80National Centre for Cardiovascular Research (CNIC), Madrid, Spain
81Primbio Genes Biotechnology, Wuhan, China
82National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA.
83Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
84Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, USA
85Division of Microbiology & Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, USA
86Center for Individualized Medicine, Mayo Clinic, Scottsdale, USA
87Department of Health Sciences, Mayo Clinic, Scottsdale, USA
88Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, USA
89College of Chemistry, Sichuan University, Chengdu, China
90Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
91Department of Biostatistics, Columbia Mailman School of Public Health, New York, USA
92Center for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
93Clinical Laboratory, Burning Rock Biotech, Guangzhou, China
94Geneplus, PKUCare Industrial Park, Beijing, China
95Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, Australia
96Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, Australia
97Human Phenome Institute, Fudan University, Shanghai, China
98Fudan-Gospel Joint Research Center for Precision Medicine, Fudan University, Shanghai, China
99Q2 Solutions - EA Genomics, Morrisville, USA

Tóm tắt

Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing. All panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5–20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden. This comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.

Tài liệu tham khảo

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