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Peng R, Lin G, Li L, Li J. Development of a Novel Reference Material for Tumor Mutational Burden Measurement Based on CRISPR/Cas9 Technology. Front Oncol 2022; 12:845636. [PMID: 35574377 PMCID: PMC9098197 DOI: 10.3389/fonc.2022.845636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 04/08/2022] [Indexed: 12/03/2022] Open
Abstract
As a biomarker that affects treatment decisions of immune checkpoint inhibitors, the accuracy, reliability, and comparability of tumor mutational burden (TMB) estimation is of paramount importance. To improve the consistency and reliability of these tests, qualified reference materials providing ground-truth data are crucial. In this study, we developed a set of formalin-fixed and paraffin-embedded (FFPE) samples with different TMB values as the novel reference materials for TMB estimation. By introducing several clinically relevant variants in MutS Homolog 2 (MSH2) gene and DNA polymerase epsilon (POLE) gene into human cell lines using CRISPR/Cas9 technology, we first constructed four typical cell lines which verified with hypermutator or ultramutator phenotype. Followed by cell mixing and paraffin embedding, the novel FFPE samples were prepared. It was confirmed that our novel FFPE samples have sufficient quantity of cells, high reproducibility, and they can provide matched wild type sample as the genetic background. The double-platform whole exome sequencing validation showed that our FFPE samples were also highly flexible as they containing different TMB values spanning a clinically relevant range (2.0–106.1 mut/Mb). Without limitations on production and TMB values, our novel FFPE samples based on CRISPR/Cas9 editing are suitable as candidate reference materials. From a practical point of view, these samples can be used for the validation, verification, internal quality control, and proficiency testing of TMB assessment.
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Affiliation(s)
- Rongxue Peng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| | - Lin Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, 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
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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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Li R, Zhang R, Tan P, Wang M, Chen Y, Zhang J, Han D, Han Y, Li J, Zhang R. Development of novel quality control material based on CRISPR/Cas9 editing and xenografts for MLH1 protein deficiency testing. J Clin Lab Anal 2021; 35:e23746. [PMID: 33826163 PMCID: PMC8128289 DOI: 10.1002/jcla.23746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Mismatch repair deficiency (dMMR) status induced by MLH1 protein deficiency plays a pivotal role in therapeutic decision-making for cancer patients. Appropriate quality control (QC) materials are necessary for monitoring the accuracy of MLH1 protein deficiency assays used in clinical laboratories. METHODS CRISPR/Cas9 technology was used to edit the MLH1 gene of GM12878Cas9 cells to establish MLH1 protein-deficient cell lines. The positive cell lines were screened and validated by Sanger sequencing, Western blot (WB), and next-generation sequencing (NGS) and were then used to prepare formalin-fixed, paraffin-embedded (FFPE) samples through xenografting. These FFPE samples were tested by hematoxylin and eosin (H&E) staining and immunohistochemistry (IHC) for suitability as novel QC materials for MLH1 protein deficiency testing. RESULTS We successfully cultured 358 monoclonal cells, with a survival rate of 37.3% (358/960) of the sorted monoclonal cells. Through Sanger sequencing, cell lines with MLH1 gene mutation were identified. Subsequently, two cell lines with MLH1 protein deficiency were identified by WB and named as GM12878Cas9_6 and GM12878Cas9_10. The NGS results further confirmed that the MLH1 gene mutation in these two cell lines would cause the formation of stop codons and terminate the expression of the MLH1 protein. The H&E staining and IHC results also verified the deficiency of the MLH1 protein, and FFPE samples from xenografts proved their similarity and consistency with clinical samples. CONCLUSIONS We successfully established MLH1 protein-deficient cell lines. Followed by xenografting, we developed novel FFPE QC materials with homogenous, sustainable, and typical histological structures advantages that are suitable for the standardization of clinical IHC methods.
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Affiliation(s)
- Rui Li
- National Center for Clinical LaboratoriesBeijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Graduate School of Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Runling Zhang
- National Center for Clinical LaboratoriesBeijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Graduate School of Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Ping Tan
- National Center for Clinical LaboratoriesBeijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Graduate School of Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Meng Wang
- National Center for Clinical LaboratoriesBeijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Graduate School of Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Yuqing Chen
- National Center for Clinical LaboratoriesBeijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Graduate School of Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Jiawei Zhang
- National Center for Clinical LaboratoriesBeijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Graduate School of Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Dongsheng Han
- National Center for Clinical LaboratoriesBeijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Graduate School of Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Yanxi Han
- National Center for Clinical LaboratoriesBeijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Jinming Li
- National Center for Clinical LaboratoriesBeijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Graduate School of Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Rui Zhang
- National Center for Clinical LaboratoriesBeijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Graduate School of Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
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Zhou L, Li R, Zhang R, Peng R, Chen K, Gao P, Zhang J, Zhang R, Li J. Utilizing CRISPR/Cas9 technology to prepare lymphoblastoid cell lines harboring genetic mutations for generating quality control materials in genetic testing. J Clin Lab Anal 2020; 34:e23256. [PMID: 32118319 PMCID: PMC7370731 DOI: 10.1002/jcla.23256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/01/2020] [Accepted: 02/04/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND To meet the requirements of the rapidly progressing genetic testing technologies in clinical laboratories, assuring the quality of genetic tests by utilizing appropriate quality control materials is of paramount importance. The CRISPR/Cas9 technology was used to prepare quality control materials because genome-edited human cell lines are one of the major resources for quality control materials. METHODS In this study, in vitro transcribed sgRNA were transfected into a Cas9-expressing lymphoblastoid cell line (LCL)-by electroporation-to simulate the SEA-type deletion observed in α-thalassemia. The edited positive cell line was screened and identified by polymerase chain reaction (PCR) followed by Sanger sequencing. The whole-genome sequencing was also performed to show evidence of predicted mutation. RESULTS The results showed that electroporation of the in vitro transcribed gRNAs into stable Cas9-expressing LCL was a more efficient gene-editing technique as compared to plasmid-mediated transfection, and that the positive rates could reach up to 35.9%. The predominance of indel sizes relative to the predicted deletion length was clustered between 10 and 0 bp. The results of whole-genome sequencing also demonstrated the existence of SEA-type deletion of α-thalassemia. CONCLUSIONS Gene-editing based on Cas9-expressing LCL by electroporation of sgRNA was a more efficient approach to introduce mutations for generating quality control materials for genetic testing. The edited lymphoblastoid cell lines were feasible to serve as quality control materials in genetic testing.
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Affiliation(s)
- Li Zhou
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Graduate SchoolPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Rui Li
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Graduate SchoolPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Runling Zhang
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Graduate SchoolPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Rongxue Peng
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Graduate SchoolPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Kun Chen
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Graduate SchoolPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Peng Gao
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Graduate SchoolPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Jiawei Zhang
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Graduate SchoolPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Rui Zhang
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Jinming Li
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Graduate SchoolPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
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Peng R, Zhang R, Zhang J, Tan P, Han Y, Zhang K, Lin G, Xie J, Li J. Continual Improvement of the Reliability of EML4-ALK Rearrangement Detection in Non-Small-Cell Lung Cancer: A Long-Term Comparison of ALK Detection in China. J Mol Diagn 2020; 22:876-884. [PMID: 32302779 DOI: 10.1016/j.jmoldx.2020.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/24/2019] [Accepted: 03/30/2020] [Indexed: 12/01/2022] Open
Abstract
The results of EML4-ALK testing are critical to manage ALK tyrosine kinase receptor inhibitor treatment. Thus, the accurate detection of ALK rearrangement is increasingly becoming a matter of serious concern. To address this issue, a long-term EML4-ALK proficiency testing (PT) scheme was launched in China in 2015, serving as an educational tool for assessing and improving the testing quality of EML4-ALK fusion detection. Responses across 20 different PT samples interrogating three different variants and wild-type samples were collected between 2015 and 2019. Performance was analyzed by evaluating the detection methods, kits, and pre-analytic practices used to further display the landscape of changing conditions of the reliability of EML4-ALK testing. During the 5 years, 3224 results reported from 988 laboratories were evaluated, with an overall error rate of 5.36%. Along with an increasing number of participating laboratories, the error rate within each of the different methods showed a significantly downward trend over the years. No obvious differences in the error rates were found regarding the testing methods or kit manufacturers. Moreover, the individual performance of the laboratories improved when they participated in more PT scheme rounds. The data demonstrated that the performance of individual Chinese laboratories for EML4-ALK testing continuously improved over time by participating PT schemes, regardless of their method. However, care must be taken in standardized operations and validations.
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Affiliation(s)
- Rongxue Peng
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiawei Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ping Tan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiehong Xie
- National Center for Clinical Laboratories, 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, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
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Fluorometric Detection of Oncogenic EML4-ALK Fusion Gene based on a Graphene Oxide System. BIOCHIP JOURNAL 2019. [DOI: 10.1007/s13206-019-3408-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Lin G, Zhang K, Peng R, Han Y, Xie J, Li J. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR-Associated Endonuclease Cas9-Mediated Homology-Independent Integration for Generating Quality Control Materials for Clinical Molecular Genetic Testing. J Mol Diagn 2019; 20:373-380. [PMID: 29680088 DOI: 10.1016/j.jmoldx.2018.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/15/2017] [Accepted: 02/02/2018] [Indexed: 11/29/2022] Open
Abstract
Genome-edited human cell lines are important resources for producing quality control materials for clinical molecular genetic testing. Generating cell lines with defined mutations through homology-directed repair-based methods are inefficient and can lead to unwanted insertions and deletions in the target loci. Nonhomologous end joining in the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated endonuclease Cas9 (Cas9) system was harnessed to generate genome-engineered cell lines harboring target mutations. Donor plasmids containing target sites for the single guide RNA (sgRNA) and homologous DNA fragments harboring important cancer gene mutations were cotransfected with the Cas9/sgRNA vector into wild-type human cells. The introduced mutations were validated in-house and in 44 laboratories using various techniques, including next-generation sequencing. Exogenous sequences containing the target mutations were efficiently integrated into the ALK receptor tyrosine kinase (ALK) locus in HEK293T and A549 cells. Successful introduction of artificial mutations was confirmed via both Sanger sequencing and the amplification refractory mutation system. Results of external pilot testing revealed that the DNA samples derived from genome-edited cell lines were widely applicable across multiple platforms and laboratories. This study demonstrates that CRISPR/Cas9-induced nonhomologous end joining is a valuable and novel method for generating artificial mutants for use in quality control applications in clinical molecular genetics.
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Affiliation(s)
- Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rongxue Peng
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Yanxi Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jiehong Xie
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
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8
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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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