2
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Lin G, Zhang K, Han Y, Peng R, Li J. Preparation of multiplexed control materials for cancer mutation analysis by genome editing in GM12878 cells. J Clin Lab Anal 2021; 36:e24139. [PMID: 34811797 PMCID: PMC8761438 DOI: 10.1002/jcla.24139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 11/06/2022] Open
Abstract
Background Quality control materials are necessary for assay development, test validation, and proficiency testing in cancer mutation analysis. Most of the existing controls for somatic mutations only harbor a single variant and are derived from unstable cell lines. This study aimed to establish a method to create stable multianalyte controls in a defined background by genome editing in GM12878 cells, which also can be applied for the reference of next‐generation sequencing. Methods GM12878 cells were electroporated with a donor plasmid containing a mutant DNA sequence and a Cas9/sgRNA expressing vector. The genome‐edited GM12878 cell was validated with Sanger sequencing, amplification refractory mutation system (ARMS), and next‐generation sequencing (NGS). Results We have successfully generated a mutant GM12878 cell line harboring the defined variants including single‐nucleotide variants (SNVs), small insertions and deletions (indels), and structural variants (SVs). The introduction of intended mutations in GM12878 cell line was confirmed by both ARMS and sequencing methods. Conclusions We developed a method for the preparation of the multiplexed controls for reference mutations in cancer gene by genome editing in GM12878 cells. This methodology can be used to generate other stable cancer reference materials with an unlimited supply.
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Affiliation(s)
- Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rongxue Peng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
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3
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Fang LT, Zhu B, Zhao Y, Chen W, Yang Z, Kerrigan L, Langenbach K, de Mars M, Lu C, Idler K, Jacob H, Zheng Y, Ren L, Yu Y, Jaeger E, Schroth GP, Abaan OD, Talsania K, Lack J, Shen TW, Chen Z, Stanbouly S, Tran B, Shetty J, Kriga Y, Meerzaman D, Nguyen C, Petitjean V, Sultan M, Cam M, Mehta M, Hung T, Peters E, Kalamegham R, Sahraeian SME, Mohiyuddin M, Guo Y, Yao L, Song L, Lam HYK, Drabek J, Vojta P, Maestro R, Gasparotto D, Kõks S, Reimann E, Scherer A, Nordlund J, Liljedahl U, Jensen RV, Pirooznia M, Li Z, Xiao C, Sherry ST, Kusko R, Moos M, Donaldson E, Tezak Z, Ning B, Tong W, Li J, Duerken-Hughes P, Catalanotti C, Maheshwari S, Shuga J, Liang WS, Keats J, Adkins J, Tassone E, Zismann V, McDaniel T, Trent J, Foox J, Butler D, Mason CE, Hong H, Shi L, Wang C, Xiao W. Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing. Nat Biotechnol 2021; 39:1151-1160. [PMID: 34504347 PMCID: PMC8532138 DOI: 10.1038/s41587-021-00993-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 06/18/2021] [Indexed: 02/08/2023]
Abstract
The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.
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Affiliation(s)
- Li Tai Fang
- Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yongmei Zhao
- Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Wanqiu Chen
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Zhaowei Yang
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Liz Kerrigan
- ATCC (American Type Culture Collection), Manassas, VA, USA
| | | | | | - Charles Lu
- Computational Genomics, Genomics Research Center (GRC), AbbVie, North Chicago, IL, USA
| | - Kenneth Idler
- Computational Genomics, Genomics Research Center (GRC), AbbVie, North Chicago, IL, USA
| | - Howard Jacob
- Computational Genomics, Genomics Research Center (GRC), AbbVie, North Chicago, IL, USA
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | | | | | | | - Keyur Talsania
- Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Justin Lack
- Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tsai-Wei Shen
- Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Zhong Chen
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Seta Stanbouly
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Bao Tran
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jyoti Shetty
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yuliya Kriga
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Daoud Meerzaman
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD, USA
| | - Cu Nguyen
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD, USA
| | - Virginie Petitjean
- Biomarker Development, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Marc Sultan
- Biomarker Development, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Margaret Cam
- CCR Collaborative Bioinformatics Resource (CCBR), Office of Science and Technology Resources, Center for Cancer Research, Bethesda, MD, USA
| | - Monika Mehta
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tiffany Hung
- Genentech, a member of the Roche group, South San Francisco, CA, USA
| | - Eric Peters
- Genentech, a member of the Roche group, South San Francisco, CA, USA
| | - Rasika Kalamegham
- Genentech, a member of the Roche group, South San Francisco, CA, USA
| | | | - Marghoob Mohiyuddin
- Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
| | - Yunfei Guo
- Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
| | - Lijing Yao
- Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hugo Y K Lam
- Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
| | - Jiri Drabek
- IMTM, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
| | - Petr Vojta
- IMTM, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
| | - Roberta Maestro
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, Unit of Oncogenetics and Functional Oncogenomics, Aviano, Italy
| | - Daniela Gasparotto
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, Unit of Oncogenetics and Functional Oncogenomics, Aviano, Italy
| | - Sulev Kõks
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Perron Institute for Neurological and Translational Science, Nedlands, Western Australia, Australia
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Ene Reimann
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andreas Scherer
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Jessica Nordlund
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ulrika Liljedahl
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Roderick V Jensen
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Mehdi Pirooznia
- Bioinformatics and Computational Biology Core, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhipan Li
- Sentieon Inc., Mountain View, CA, USA
| | - Chunlin Xiao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Stephen T Sherry
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Malcolm Moos
- Center for Biologics Evaluation and Research, FDA, Silver Spring, MD, USA
| | - Eric Donaldson
- Center for Drug Evaluation and Research, FDA, Silver Spring, MD, USA
| | - Zivana Tezak
- Center for Devices and Radiological Health, FDA, Silver Spring, MD, USA
| | - Baitang Ning
- National Center for Toxicological Research, FDA, Jefferson, AR, USA
| | - Weida Tong
- National Center for Toxicological Research, FDA, Jefferson, AR, USA
| | - Jing Li
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | | | | | | | | | - Winnie S Liang
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jonathan Keats
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Erica Tassone
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | | | - Jeffrey Trent
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Huixiao Hong
- National Center for Toxicological Research, FDA, Jefferson, AR, USA.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China.
| | - Charles Wang
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA.
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, CA, USA.
| | - Wenming Xiao
- Center for Devices and Radiological Health, FDA, Silver Spring, MD, USA.
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7
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Jia S, Zhang R, Lin G, Peng R, Gao P, Han Y, Fu Y, Ding J, Wu Q, Zhang K, Xie J, Li J. A novel cell line generated using the CRISPR/Cas9 technology as universal quality control material for KRAS G12V mutation testing. J Clin Lab Anal 2018; 32:e22391. [PMID: 29380513 DOI: 10.1002/jcla.22391] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 12/30/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND KRAS mutations are the key indicator for EGFR monoclonal antibody-targeted therapy and acquired drug resistance, and their accurate detection is critical to the clinical decision-making of colorectal cancer. However, no proper quality control material is available for the current detection methods, particularly next-generation sequencing (NGS). The ideal quality control material for NGS needs to provide both the tumor mutation gene and the matched background genomic DNA, which is uncataloged in public databases, to accurately distinguish germline polymorphisms and somatic mutations. METHODS We developed a novel KRAS G12V mutant cell line using the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) technique to make up for the deficiencies in existing quality control material and further validated the feasibility of the cell line as quality control material by amplification refractory mutation system (ARMS), Sanger sequencing, digital PCR (dPCR), and NGS. RESULTS We verified that the edited cell line specifically had the G12V mutation, and the validation results presented a high consistency among the four methods of detection. The three cell lines screened contained the G12V mutation and the mutation allele fractions of G12V-1, G12V-2, and G12V-3 were 52.01%, 82.06%, and 17.29%, respectively. CONCLUSION The novel KRAS G12V cell line generated using the CRISPR/Cas9 gene editing system is suitable as a quality control material for all current detection methods and provides a new direction in the development of quality control material.
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Affiliation(s)
- Shiyu Jia
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Guigao Lin
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rongxue Peng
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Peng Gao
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Yu Fu
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jiansheng Ding
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Qisheng Wu
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Kuo Zhang
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiehong Xie
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jinming Li
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
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