Genome Biology (Apr 2021)
A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
- Wendell Jones,
- Binsheng Gong,
- Natalia Novoradovskaya,
- Dan Li,
- Rebecca Kusko,
- Todd A. Richmond,
- Donald J. Johann,
- Halil Bisgin,
- Sayed Mohammad Ebrahim Sahraeian,
- Pierre R. Bushel,
- Mehdi Pirooznia,
- Katherine Wilkins,
- Marco Chierici,
- Wenjun Bao,
- Lee Scott Basehore,
- Anne Bergstrom Lucas,
- Daniel Burgess,
- Daniel J. Butler,
- Simon Cawley,
- Chia-Jung Chang,
- Guangchun Chen,
- Tao Chen,
- Yun-Ching Chen,
- Daniel J. Craig,
- Angela del Pozo,
- Jonathan Foox,
- Margherita Francescatto,
- Yutao Fu,
- Cesare Furlanello,
- Kristina Giorda,
- Kira P. Grist,
- Meijian Guan,
- Yingyi Hao,
- Scott Happe,
- Gunjan Hariani,
- Nathan Haseley,
- Jeff Jasper,
- Giuseppe Jurman,
- David Philip Kreil,
- Paweł Łabaj,
- Kevin Lai,
- Jianying Li,
- Quan-Zhen Li,
- Yulong Li,
- Zhiguang Li,
- Zhichao Liu,
- Mario Solís López,
- Kelci Miclaus,
- Raymond Miller,
- Vinay K. Mittal,
- Marghoob Mohiyuddin,
- Carlos Pabón-Peña,
- Barbara L. Parsons,
- Fujun Qiu,
- Andreas Scherer,
- Tieliu Shi,
- Suzy Stiegelmeyer,
- Chen Suo,
- Nikola Tom,
- Dong Wang,
- Zhining Wen,
- Leihong Wu,
- Wenzhong Xiao,
- Chang Xu,
- Ying Yu,
- Jiyang Zhang,
- Yifan Zhang,
- Zhihong Zhang,
- Yuanting Zheng,
- Christopher E. Mason,
- James C. Willey,
- Weida Tong,
- Leming Shi,
- Joshua Xu
Affiliations
- Wendell Jones
- Q2 Solutions - EA Genomics
- Binsheng Gong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration
- Natalia Novoradovskaya
- Agilent Technologies
- Dan Li
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration
- Rebecca Kusko
- Immuneering Corporation
- Todd A. Richmond
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc.
- Donald J. Johann
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences
- Halil Bisgin
- Department of Computer Science, Engineering and Physics, University of Michigan-Flint
- Sayed Mohammad Ebrahim Sahraeian
- Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc.
- Pierre R. Bushel
- National Institute of Environmental Health Sciences
- Mehdi Pirooznia
- Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health
- Katherine Wilkins
- Agilent Technologies
- Marco Chierici
- Fondazione Bruno Kessler
- Wenjun Bao
- JMP Life Sciences, SAS Institute Inc.
- Lee Scott Basehore
- Agilent Technologies
- Anne Bergstrom Lucas
- Agilent Technologies
- Daniel Burgess
- (formerly) Research and Development, Roche Sequencing Solutions Inc.
- Daniel J. Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University
- Simon Cawley
- (formerly) Clinical Sequencing Division, Thermo Fisher Scientific
- Chia-Jung Chang
- Stanford Genome Technology Center, Stanford University
- Guangchun Chen
- Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center
- Tao Chen
- University of Texas Southwestern Medical Center
- Yun-Ching Chen
- Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health
- Daniel J. Craig
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo
- Angela del Pozo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, CIBERER Instituto de Salud Carlos III
- Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University
- Margherita Francescatto
- Fondazione Bruno Kessler
- Yutao Fu
- Thermo Fisher Scientific
- Cesare Furlanello
- Fondazione Bruno Kessler
- Kristina Giorda
- Marketing, Integrated DNA Technologies, Inc.
- Kira P. Grist
- Q2 Solutions - EA Genomics
- Meijian Guan
- JMP Life Sciences, SAS Institute Inc.
- Yingyi Hao
- College of Chemistry, Sichuan University
- Scott Happe
- Agilent Technologies
- Gunjan Hariani
- Q2 Solutions - EA Genomics
- Nathan Haseley
- Illumina Inc.
- Jeff Jasper
- Q2 Solutions - EA Genomics
- Giuseppe Jurman
- Fondazione Bruno Kessler
- David Philip Kreil
- Bioinformatics Research, Institute of Molecular Biotechnology, Boku University Vienna
- Paweł Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University
- Kevin Lai
- Bioinformatics, Integrated DNA Technologies, Inc.
- Jianying Li
- Kelly Government Solutions, Inc.
- Quan-Zhen Li
- Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center
- Yulong Li
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University
- Zhiguang Li
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University
- Zhichao Liu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration
- Mario Solís López
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, CIBERER Instituto de Salud Carlos III
- Kelci Miclaus
- JMP Life Sciences, SAS Institute Inc.
- Raymond Miller
- Agilent Technologies
- Vinay K. Mittal
- Thermo Fisher Scientific
- Marghoob Mohiyuddin
- Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc.
- Carlos Pabón-Peña
- Agilent Technologies
- Barbara L. Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration
- Fujun Qiu
- Research and Development, Burning Rock Biotech
- Andreas Scherer
- EATRIS ERIC- European Infrastructure for Translational Medicine
- Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University
- Suzy Stiegelmeyer
- University of North Carolina Health
- Chen Suo
- Department of Epidemiology, School of Public Health, Fudan University
- Nikola Tom
- EATRIS ERIC- European Infrastructure for Translational Medicine
- Dong Wang
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration
- Zhining Wen
- College of Chemistry, Sichuan University
- Leihong Wu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration
- Wenzhong Xiao
- Stanford Genome Technology Center, Stanford University
- Chang Xu
- Research and Development, QIAGEN Sciences Inc.
- Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University
- Jiyang Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University
- Yifan Zhang
- University of Arkansas at Little Rock
- Zhihong Zhang
- Research and Development, Burning Rock Biotech
- Yuanting Zheng
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration
- Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University
- James C. Willey
- Departments of Medicine, Pathology, and Cancer Biology, College of Medicine and Life Sciences, University of Toledo Health Sciences Campus
- Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration
- Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University
- Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration
- DOI
- https://doi.org/10.1186/s13059-021-02316-z
- Journal volume & issue
-
Vol. 22,
no. 1
pp. 1 – 38
Abstract
Abstract Background Oncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference samples having a suitably large number of pre-identified variants for properly assessing oncopanel assay analytical quality and performance. The FDA-led Sequencing and Quality Control Phase 2 (SEQC2) consortium analyze ten diverse cancer cell lines individually and their pool, termed Sample A, to develop a reference sample with suitably large numbers of coding positions with known (variant) positives and negatives for properly evaluating oncopanel analytical performance. Results In reference Sample A, we identify more than 40,000 variants down to 1% allele frequency with more than 25,000 variants having less than 20% allele frequency with 1653 variants in COSMIC-related genes. This is 5–100× more than existing commercially available samples. We also identify an unprecedented number of negative positions in coding regions, allowing statistical rigor in assessing limit-of-detection, sensitivity, and precision. Over 300 loci are randomly selected and independently verified via droplet digital PCR with 100% concordance. Agilent normal reference Sample B can be admixed with Sample A to create new samples with a similar number of known variants at much lower allele frequency than what exists in Sample A natively, including known variants having allele frequency of 0.02%, a range suitable for assessing liquid biopsy panels. Conclusion These new reference samples and their admixtures provide superior capability for performing oncopanel quality control, analytical accuracy, and validation for small to large oncopanels and liquid biopsy assays.