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Han J, Jung JH, Lee SY, Park JH. Nanoplasmonic Detection of EGFR Mutations Based on Extracellular Vesicle-Derived EGFR-Drug Interaction. ACS APPLIED MATERIALS & INTERFACES 2024; 16:8266-8274. [PMID: 38335730 DOI: 10.1021/acsami.3c14907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Analysis of membrane proteins from extracellular vesicles (EVs) has emerged as an important strategy for molecular cancer diagnosis. The epidermal growth factor receptor (EGFR) is one of the most well-known oncogenic membrane proteins, particularly in non-small cell lung cancer (NSCLC), where targeted therapies using tyrosine kinase inhibitors (TKIs) are often addressed based on EGFR mutation status. Consequently, several studies aimed at analyzing oncogenic membrane proteins have been proposed for cancer diagnosis. However, conventional protein analysis still faces limitations due to the requirement for large sample quantities and extensive post-labeling processes. Here, we develop a nanoplasmonic detection method for EGFR mutations in the diagnosis of NSCLC based on interactions between EGFR loaded in EVs and TKI. Gefitinib is selected as a model TKI due to its strong signals in the surface-enhanced Raman spectroscopy (SERS) and mutation-dependent binding affinity to EGFR. We demonstrate an SERS signal attributed to gefitinib at a higher value in the EGFR exon 19 deletion, both in cells and EVs, compared to wild-type and exon 19 deletion/T790M variants. Furthermore, we observe a significantly higher gefitinib SERS signal in EGFR obtained from exon 19 deletion NSCLC patient plasma-derived EVs compared with those from wild-type and exon 19 deletion/T790M EVs. Since our approach utilizes an analysis of the SERS signal generated by the interaction between oncogenic membrane proteins within EVs and targeted drugs, its diagnostic applicability could potentially extend to other liquid biopsy methods based on EVs.
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Affiliation(s)
- Junhee Han
- Department of Bio and Brain Engineering and KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jik-Han Jung
- Department of Bio and Brain Engineering and KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sung Yong Lee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul 08308, Republic of Korea
| | - Ji-Ho Park
- Department of Bio and Brain Engineering and KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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Li C, Shao J, Li P, Feng J, Li J, Wang C. Circulating tumor DNA as liquid biopsy in lung cancer: Biological characteristics and clinical integration. Cancer Lett 2023; 577:216365. [PMID: 37634743 DOI: 10.1016/j.canlet.2023.216365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023]
Abstract
Lung cancer maintains high morbidity and mortality rate globally despite significant advancements in diagnosis and treatment in the era of precision medicine. Pathological analysis of tumor tissue, the current gold standard for lung cancer diagnosis, is intrusive and intrinsically confined to evaluating the limited amount of tissues that could be physically extracted. However, tissue biopsy has several limitations, including the invasiveness of the procedure and difficulty in obtaining samples for patients at advanced stages., there Additionally,has been no major breakthrough in tumor biomarkers with high specificity and sensitivity, particularly for early-stage lung cancer. Liquid biopsy has been considered a feasible auxiliary tool for tearly dianosis, evaluating treatment responses and monitoring prognosis of lung cancer. Circulating tumor DNA (ctDNA), an ideal biomarker of liquid biopsy, has emerged as one of the most reliable tools for monitoring tumor processes at molecular levels. Herein, this review focuses on tumor heterogeneity to elucidate the superiority of liquid biopsy and retrospectively discussdeciphersolution. We systematically elaborate ctDNA biological characteristics, introduce methods for ctDNA detection, and discuss the current role of plasma ctDNA in lung cancer management. Finally, we summarize the drawbacks of ctDNA analysis and highlight its potential clinical application in lung cancer.
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Affiliation(s)
- Changshu Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jun Shao
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Peiyi Li
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiaming Feng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jingwei Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Chengdi Wang
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China.
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3
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Yang F, Gong J, Li M, Jiang X, Zhang J, Liao M, Zhang H, Tremblay PL, Zhang T. Electrochemiluminescent CdS Quantum Dots Biosensor for Cancer Mutation Detection at Different Positions on Linear DNA Analytes. Anal Chem 2023; 95:14016-14024. [PMID: 37683084 DOI: 10.1021/acs.analchem.3c02649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
PCR-based techniques routinely employed for the detection of mutated linear DNA molecules, including circulating tumor DNA (ctDNA), require large nucleotide sections on both sides of the mutation for primer annealing. This means that DNA fragments with a mutation positioned closer to the extremities are unlikely to be detected. Thus, sensors capable of recognizing linear DNA with characteristic mutations closer to the ends would be advantageous over the state-of-the-art approaches. Here, an electrochemiluminescence-resonance energy transfer (ECL-RET) biosensor comprising capped CdS quantum dots and hairpin DNA probes labeled with Au nanoparticles was developed for the detection of epidermal growth factor receptor (EGFR) ctDNA carrying the critical T790M lung cancer mutation. The ECL-RET system detected different DNA molecules including single-stranded 18-nucleotides (nt) and 40-nt as well as double-stranded 100-nt with the single nucleotide polymorphism (SNP) coding for T790M located either in the middle or only 7 nt from one end. For all target DNA, the sensor's limits of detection (LODs) were in the aM range, with excellent selectivity. It was the case of 100-nt target linear ctDNA fragments with LODs of 8.1 and 3.4 aM when the EGFR T790M SNP was either in the middle or at the end, respectively. These results show that ECL-RET systems can sense mutations in DNA fragments that would remain undetected by standard techniques.
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Affiliation(s)
- Fan Yang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, Hubei 430070, China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing, Zhejiang 312300, China
| | - JinBo Gong
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, Hubei 430070, China
| | - Ming Li
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, Hubei 430070, China
| | - Xiangyang Jiang
- School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, Hubei 430070, China
| | - Jiawen Zhang
- Institut WUT-AMU, Wuhan University of Technology, Wuhan, Hubei 430070, China
| | - Meiyan Liao
- Department of Radiology, Zhongnan Hospital of Wuhan Uni-versity, Wuhan, Hubei 430071, China
| | - Hanfei Zhang
- Department of Radiology, Zhongnan Hospital of Wuhan Uni-versity, Wuhan, Hubei 430071, China
| | - Pier-Luc Tremblay
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, Hubei 430070, China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing, Zhejiang 312300, China
- Institut WUT-AMU, Wuhan University of Technology, Wuhan, Hubei 430070, China
| | - Tian Zhang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, Hubei 430070, China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing, Zhejiang 312300, China
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, Hubei 430070, China
- School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, Hubei 430070, China
- Institut WUT-AMU, Wuhan University of Technology, Wuhan, Hubei 430070, China
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Filipits M, Kainz V, Sebek V, Zach H. Epidermal Growth Factor Receptor T790M Mutation Testing in Non-Small Cell Lung Cancer: An International Collaborative Study to Assess Molecular EGFR T790M Testing in Liquid Biopsy. Cancers (Basel) 2023; 15:3528. [PMID: 37444638 DOI: 10.3390/cancers15133528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND The detection of the EGFR T790M (T790M) mutation in non-small cell lung cancer (NSCLC) patients who progressed under treatment with first- or second-generation EGFR-tyrosine kinase inhibitors (TKIs) is important to offer a subsequent therapy with a third-generation EGFR-TKI. Liquid biopsy is a powerful tool to determine the T790M mutation status. Several liquid biopsy platforms with varying degrees of accuracy are available to test for T790M mutations, and sensitivities may differ among these methods. METHODS As no standard exists for the testing of T790M mutation in liquid biopsy, we performed a collaborative study to describe and compare the sensitivity of different in-house liquid biopsy platforms for the detection of the T790M mutation, EGFR exon 19 deletion (del19) and EGFR L858R mutation (L858R) across multiple participating laboratories in seven Central and Eastern European countries. RESULTS Of the 25 invited laboratories across Central and Eastern Europe, 21 centers participated and received 10 plasma samples spiked with cell-line DNA containing the T790M, del19, or L858R mutation in different concentrations. In-house PCR-based and NGS-based methods were used accordingly, and results were reported as in routine clinical practice. Two laboratories, which used the AmoyDx® EGFR 29 Mutations Detection Kit (AmoyDx) with Cobas® cfDNA Sample Preparation Kit and QX200 Droplet Digital PCR (ddPCR) with the QIAamp Circulating Nucleic Acid Kit identified all ten samples correctly. Cobas® EGFR Mutation Test v2 (Cobas), the NGS methods, and the IdyllaTM detection method used in this study performed within the known sensitivity range of each detection method. CONCLUSIONS If a negative result was obtained from methods with lower sensitivity (e.g., Cobas), repeated liquid biopsy testing and/or tissue biopsy analysis should be performed whenever possible, to identify T790M-positive patients to allow them to receive the optimal second-line treatment with a third-generation EGFR TKI.
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Affiliation(s)
- Martin Filipits
- Center for Cancer Research, Medical University of Vienna, 1090 Vienna, Austria
| | - Verena Kainz
- Division of Transplantation, Department of General Surgery, Medical University Vienna, 1090 Vienna, Austria
| | - Viktor Sebek
- Department of Pharmacology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hnevotinska st. 976/3, 779 00 Olomouc, Czech Republic
| | - Herwig Zach
- Boehringer Ingelheim RCV GmbH & Co KG, 1120 Vienna, Austria
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Huang CT, Lin CA, Su TJ, Yang CY, Tsai TH, Hsu CL, Liao WY, Chen KY, Ho CC, Yu CJ. Monitoring of T790M in plasma ctDNA of advanced EGFR-mutant NSCLC patients on first- or second-generation tyrosine kinase inhibitors. BMC Cancer 2023; 23:234. [PMID: 36915101 PMCID: PMC10010021 DOI: 10.1186/s12885-023-10698-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND The T790M mutation is the major resistance mechanism to first- and second-generation TKIs in EGFR-mutant NSCLC. This study aimed to investigate the utility of droplet digital PCR (ddPCR) for detection of T790M in plasma circulating tumor DNA (ctDNA), and explore its impact on prognosis. METHODS This prospective study enrolled 80 advanced lung adenocarcinoma patients treated with gefitinib, erlotinib, or afatinib for TKI-sensitizing mutations between 2015 and 2019. Plasma samples were collected before TKI therapy and at tri-monthly intervals thereafter. Genotyping of ctDNA for T790M was performed using a ddPCR EGFR Mutation Assay. Patients were followed up until the date of death or to the end of 2021. RESULTS Seventy-five of 80 patients experienced progressive disease. Fifty-three (71%) of 75 patients underwent rebiopsy, and T790M mutation was identified in 53% (28/53) of samples. Meanwhile, plasma ddPCR detected T790M mutation in 23 (43%) of 53 patients. The concordance rate of T790M between ddPCR and rebiopsy was 76%, and ddPCR identified 4 additional T790M-positive patients. Ten (45%) of 22 patients who did not receive rebiopsy tested positive for T790M by ddPCR. Serial ddPCR analysis showed the time interval from detection of plasma T790M to objective progression was 1.1 (0-4.1) months. Compared to 28 patients with rebiopsy showing T790M, the overall survival of 14 patients with T790M detected solely by ddPCR was shorter(41.3 [95% CI, 36.6-46.0] vs. 26.6 months [95% CI, 9.9-43.3], respectively). CONCLUSION Plasma ddPCR-based genotyping is a useful technology for detection and monitoring of the key actionable genomic alteration, namely, T790M, in patients treated with gefitinib, erlotinib, or afatinib for activating mutations, to achieve better patient care and outcome.
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Affiliation(s)
- Chun-Ta Huang
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan
| | - Chih-An Lin
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan
| | - Te-Jen Su
- Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
| | - Ching-Yao Yang
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan
| | - Tzu-Hsiu Tsai
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan
| | - Chia-Lin Hsu
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan
| | - Wei-Yu Liao
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan
| | - Kuan-Yu Chen
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan
| | - Chao-Chi Ho
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan.
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Rd, Taipei 100, Taipei, Taiwan
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Incharoen P, Jinawath A, Arsa L, Kamprerasart K, Trachu N, Monnamo N, Khiewngam K, Muntham D, Chansriwong P, Sirachainan E, Reungwetwattana T. Clinical correlations with EGFR circulating tumor DNA testing in all-stage lung adenocarcinoma. Cancer Biomark 2023; 36:71-82. [PMID: 36530081 DOI: 10.3233/cbm-220079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Information on genetic alterations, notably EGFR mutations, is important for guiding non-small-cell lung cancer (NSCLC) treatment. Circulating tumor DNA (ctDNA) analysis represents a less invasive alternative to tissue biopsy for analyzing mutation status, but its clinical value may vary across disease stages. OBJECTIVE To explore clinical correlates of ctDNA and tissue/plasma-based EGFR mutation (EGFRm) status across all NSCLC stages. METHODS Ninety patients were analyzed, representing three cohorts: newly-diagnosed early-stage, advanced-stage, and recurrent NSCLC. Relationships among clinical/surgical parameters, ctDNA, EGFRm status, and survival outcomes were analyzed. RESULTS Plasma/tissue EGFRm concordance was lower in early-stage (58.6%) than in advanced-stage patients (87.5%). In early-stage patients, ctDNA levels were variable and not significantly associated with clinical/surgical parameters. In advanced-stage patients, time to EGFR-TKI treatment failure (TTF), but not overall survival (OS), was significantly longer in EGFRm-positive vs. EGFRm-negative patients. In patients with recurrent disease, 40% of plasma samples were EGFRT790M-positive at recurrence. In T790M-positive patients, we noted slight trends toward longer OS with vs. without osimertinib treatment and longer OS and TTF with second-line vs. later-line osimertinib. CONCLUSIONS Our results affirm the use of ctDNA testing in advanced-stage and recurrent NSCLC. Further studies on osimertinib as early-line therapy, clinical correlates and the utility of plasma-based testing in early-stage NSCLC are warranted.
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Affiliation(s)
- Pimpin Incharoen
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Artit Jinawath
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Lalida Arsa
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Kaettipong Kamprerasart
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Narumol Trachu
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Nanamon Monnamo
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Khantong Khiewngam
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Dittapol Muntham
- Department of Mathematics, Faculty of Science and Technology, Rajamangala University of Technology Suvarnabhumi, Nonthaburi, Thailand
| | - Phichai Chansriwong
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Ekaphop Sirachainan
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Thanyanan Reungwetwattana
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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Lee KS, Seo J, Lee CK, Shin S, Choi Z, Min S, Yang JH, Kwon WS, Yun W, Park MR, Choi JR, Chung HC, Lee ST, Rha SY. Analytical and Clinical Validation of Cell-Free Circulating Tumor DNA Assay for the Estimation of Tumor Mutational Burden. Clin Chem 2022; 68:1519-1528. [DOI: 10.1093/clinchem/hvac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/21/2022] [Indexed: 11/12/2022]
Abstract
Abstract
Background
Ultra-deep sequencing to detect low-frequency mutations in circulating tumor-derived DNA (ctDNA) increases the diagnostic value of liquid biopsy. The demand for large ctDNA panels for comprehensive genomic profiling and tumor mutational burden (TMB) estimation is increasing; however, few ctDNA panels for TMB have been validated. Here, we designed a ctDNA panel with 531 genes, named TMB500, along with a technical and clinical validation.
Methods
Synthetic reference cell-free DNA materials with predefined allele frequencies were sequenced in a total of 92 tests in 6 batches to evaluate the precision, linearity, and limit of detection of the assay. We used clinical samples from 50 patients with various cancers, 11 healthy individuals, and paired tissue samples. Molecular barcoding and data analysis were performed using customized pipelines.
Results
The assay showed high precision and linearity (coefficient of determination, r2 = 0.87) for all single nucleotide variants, with a limit of detection of 0.24%. In clinical samples, the TMB500 ctDNA assay detected most variants present and absent in tissues, showing that ctDNA could assess tumor heterogeneity in different tissues and metastasis sites. The estimated TMBs correlated well between tissue and blood, except in 4 cases with extreme heterogeneity that showed very high blood TMBs compared to tissue TMBs. A pilot evaluation showed that the TMB500 assay could be used for disease monitoring.
Conclusions
The TMB500 assay is an accurate and reliable ctDNA assay for many clinical purposes. It may be useful for guiding the treatment of cancers with diverse genomic profiles, estimating TMB in immune therapy, and disease monitoring.
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Affiliation(s)
- Kwang Seob Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine , Seoul , Republic of Korea
| | - Jieun Seo
- Department of Laboratory Medicine, Yonsei University College of Medicine , Seoul , Republic of Korea
| | - Choong-Kun Lee
- Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine , Seoul , Republic of Korea
- Song-dang Institute for Cancer Research, Yonsei University College of Medicine , Seoul , Republic of Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine , Seoul , Republic of Korea
| | | | | | | | - Woo Sun Kwon
- Song-dang Institute for Cancer Research, Yonsei University College of Medicine , Seoul , Republic of Korea
| | - Woobin Yun
- Department of Laboratory Medicine, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine , Seoul , Republic of Korea
| | - Mi Ri Park
- Department of Laboratory Medicine, Yonsei University College of Medicine , Seoul , Republic of Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine , Seoul , Republic of Korea
- Dxome , Seoul , Republic of Korea
| | - Hyun Cheol Chung
- Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine , Seoul , Republic of Korea
- Song-dang Institute for Cancer Research, Yonsei University College of Medicine , Seoul , Republic of Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine , Seoul , Republic of Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine , Seoul , Republic of Korea
- Dxome , Seoul , Republic of Korea
| | - Sun Young Rha
- Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine , Seoul , Republic of Korea
- Song-dang Institute for Cancer Research, Yonsei University College of Medicine , Seoul , Republic of Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine , Seoul , Republic of Korea
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Liquid biopsy and non-small cell lung cancer: are we looking at the tip of the iceberg? Br J Cancer 2022; 127:383-393. [PMID: 35264788 PMCID: PMC9345955 DOI: 10.1038/s41416-022-01777-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 02/16/2022] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
The possibility to analyse the tumour genetic material shed in the blood is undoubtedly one of the main achievements of translational research in the latest years. In the modern clinical management of advanced non-small cell lung cancer, molecular characterisation plays an essential role. In parallel, immunotherapy is widely employed, but reliable predictive markers are not available yet. Liquid biopsy has the potential to face the two issues and to increase its role in advanced NSCLC in the next future. The aim of this review is to summarise the main clinical applications of liquid biopsy in advanced non-small cell lung cancer, underlining both its potential and limitations from a clinically driven perspective.
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9
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Kim B, Kim Y, Shin S, Lee ST, Cho JY, Lee KA. Application of CRISPR/Cas9-based mutant enrichment technique to improve the clinical sensitivity of plasma EGFR testing in patients with non-small cell lung cancer. Cancer Cell Int 2022; 22:82. [PMID: 35168603 PMCID: PMC8845274 DOI: 10.1186/s12935-022-02504-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Background Approximately 50%–60% of secondary resistance to primary EGFR- tyrosine kinase inhibitors (TKI) therapy is caused by acquired p.Thr790Met (T790M) mutation; however, highly fragmented, low-quantity circulating tumor DNA is an obstacle for detecting mutations. Therefore, more sensitive mutation detection techniques are required. Here, we report a new mutant enrichment technology, the CRISPR system combined with post-polymerase chain reaction (PCR) cell-free DNA (cfDNA) (CRISPR-CPPC) to detect the T790M mutation using droplet digital PCR (ddPCR) from cfDNA. Methods The CRISPR-CPPC process comprises the following three steps: (1) cfDNA PCR, (2) assembly of post-PCR cfDNA and CRISPR/CRISPR associated protein 9 complex, and (3) enrichment of the target DNA template. After CRISPR-CPPC, the target DNA was detected using ddPCR. We optimized and validated CRISPR-CPPC using reference cfDNA standards and cfDNA from patients with non-small cell lung cancer who underwent TKI therapy. We then compared the detection sensitivity of CRISPR-CPPC assay with the results of real-time PCR and those of ddPCR. Results CRISPR-CPPC aided detection of T790M with 93.9% sensitivity and 100% specificity. T790M mutant copies were sensitively detected achieving an approximately 13-fold increase in the detected allele frequency. Furthermore, positive rate of detecting a low T790M copy number (< 10 copies/mL) were 93.8% (15/16) and 43.8% (7/16) for CRISPR-CPPC assay and ddPCR, respectively. Conclusions CRISPR-CPPC is a useful mutant enrichment tool for the sensitive detection of target mutation. When tested in patients with progressive disease, the diagnostic performance of CRISPR-CPPC assay is exceptionally better than that of any other currently available methods. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02504-2.
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Affiliation(s)
- Boyeon Kim
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, 211 Eonju-Ro, Gangnam-Gu, Seoul, 06273, Republic of Korea
| | - Yoonjung Kim
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, 211 Eonju-Ro, Gangnam-Gu, Seoul, 06273, Republic of Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jae Yong Cho
- Division of Medical Oncology, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, 211 Eonju-Ro, Gangnam-Gu, Seoul, 06273, Republic of Korea.
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10
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Kok PS, Lee K, Lord S, John T, Marschner I, Wu YL, Mok TSK, Lee CK. Incorporating circulating tumor DNA detection to radiographic assessment for treatment response in advanced EGFR-mutant lung cancer. Lung Cancer 2021; 163:14-18. [PMID: 34894454 DOI: 10.1016/j.lungcan.2021.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 12/01/2022]
Abstract
PURPOSE Response Evaluation Criteria in Solid Tumors (RECIST) has limitations but remains the conventional approach for tumor assessments. We explored whether circulating tumor DNA (ctDNA) can be incorporated into RECIST to provide a more robust measure of tumor response in advanced EGFR-mutant NSCLC. PATIENTS AND METHODS In FASTACT-2, patients with advanced NSCLC received platinum/gemcitabine intercalated with erlotinib or placebo. EGFR mutation (tumor and plasma ctDNA) was detected using cobas v2. Patients selected for this hypothesis-generating analysis had EGFR mutations (on either tumor or plasma) at baseline and evaluable week 8 plasma EGFR. Week 8 ctDNA and radiologic response status were correlated with survival using landmark cox regression analyses. RESULTS Of the original 451 patients, 86 (19.1%) were eligible for this analysis. 73% (n = 63) had detectable ctDNA at baseline. At week 8, 40% (n = 34) had radiologic partial response (PR), 60% (n = 52) had stable disease (SD); 80% (n = 69) had a ctDNA response (undetectable ctDNA). In patients who had initial PR and undetectable ctDNA, 93% (28/30) had ongoing PR subsequently at week 16. The median duration of response was 14.9 months. In patients with SD and undetectable ctDNA at week 8, 28% had radiological PR at week 16. Amongst those with PR at week 8, survival outcomes for those with undetectable vs detectable ctDNA were not statistically significant (PFS HR 0.49, 95%CI 0.16-1.48, p = 0.21; OS HR 0.39, 95%CI 0.13-1.19, p = 0.10). Amongst those with SD at week 8, there was significantly longer survival for those with undetectable vs detectable ctDNA (PFS HR 0.27, 95% CI 0.13-0.57, p < 0.0001; OS HR 0.40, 95% CI 0.20-0.80, p = 0.009). CONCLUSION In patients with SD, undetectable ctDNA at week 8 correlated with survival improvement. Both radiologic and ctDNA responses are prognostic of PFS. Incorporation of ctDNA with RECIST may improve tumor response assessment in EGFR-mutant NSCLC.
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Affiliation(s)
- Peey-Sei Kok
- National Health and Medical Research Council Clinical Trials Centre, University of Sydney, Sydney, Australia.
| | - Kirsty Lee
- Department of Clinical Oncology, Chinese University of Hong Kong, Hong Kong.
| | - Sally Lord
- National Health and Medical Research Council Clinical Trials Centre, University of Sydney, Sydney, Australia; School of Medicine, University of Notre Dame, Sydney, Australia.
| | - Thomas John
- Peter MacCallum Cancer Centre, Melbourne, Australia.
| | - Ian Marschner
- National Health and Medical Research Council Clinical Trials Centre, University of Sydney, Sydney, Australia.
| | - Yi-Long Wu
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, and Guangdong Academy of Medical Sciences, Guangzhou, China.
| | - Tony S K Mok
- Department of Clinical Oncology, Chinese University of Hong Kong, Hong Kong.
| | - Chee Khoon Lee
- National Health and Medical Research Council Clinical Trials Centre, University of Sydney, Sydney, Australia; Cancer Care Centre, St George Hospital, Sydney, Australia.
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11
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An electrochemiluminescence resonance energy transfer biosensor for the detection of circulating tumor DNA from blood plasma. iScience 2021; 24:103019. [PMID: 34522862 PMCID: PMC8426273 DOI: 10.1016/j.isci.2021.103019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/02/2021] [Accepted: 08/18/2021] [Indexed: 01/14/2023] Open
Abstract
A liquid biopsy is a noninvasive approach for detecting double-stranded circulating tumor DNA (ctDNA) of 90–320 nucleotides in blood plasma from patients with cancer. Most techniques employed for ctDNA detection are time consuming and require expensive DNA purification kits. Electrochemiluminescence resonance energy transfer (ECL-RET) biosensors exhibit high sensitivity, a wide response range, and are promising for straightforward sensing applications. Until now, ECL-RET biosensors have been designed for sensing short single-stranded oligonucleotides of less than 45 nucleotides. In this work, an ECL-RET biosensor comprising graphitic carbon nitride quantum dots was assessed for the amplification-free detection in the blood plasma of DNA molecules coding for the EGFR L858R mutation, which is associated with non-small-cell lung cancer. Following a low-cost pre-treatment, the highly specific ECL-RET biosensor quantified double-stranded EGFR L858R DNA of 159 nucleotides diluted into the blood within a linear range of 0.01 fM to 1 pM, demonstrating its potential for noninvasive biopsies. An ECL-RET biosensor with g-CNQDs was developed for liquid biopsies of ctDNA The biosensor detected DNA molecules coding for the lung cancer EGFR L858R mutation EGFR L858R DNA molecules of 18 and 159 nucleotides activated the biosensor The biosensor detected ctDNA-like EGFR L858R molecules diluted in blood plasma
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12
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Stitz R, Buder A, Silye R, Baumgartner B, Pühringer F, Filipits M, Oberndorfer E, Heitzer E. Validation of a next-generation sequencing assay for the detection of EGFR mutations in cell-free circulating tumor DNA. Exp Mol Pathol 2021; 123:104685. [PMID: 34560086 DOI: 10.1016/j.yexmp.2021.104685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/06/2021] [Accepted: 09/17/2021] [Indexed: 11/27/2022]
Abstract
Detection of EGFR mutations from blood plasma represents a gentle, non-invasive alternative to rebiopsy and can therefore be used for therapy monitoring of non-small-cell lung cancer (NSCLC) patients. The aim of this project was to investigate whether the Reveal ctDNA™ 28 NGS assay (ArcherDX, Boulder, CO), has a comparable sensitivity and specificity to droplet digital PCR (ddPCR, gold-standard) and is therefore suitable for therapy monitoring of progressing lung cancer patients. First, we validated the NGS assay with a commercially available reference material (SeraCare, Massachusetts, US). Using an input of 22 ng, a sensitivity of 96% and a specificity of 100% could be achieved for variant allele frequencies (VAF) of 0.5%. For variants at a VAF of 0.1% the sensitivity was substantially reduced. Next, 28 plasma samples from 16 patients were analyzed and results were compared to existing ddPCR data. This comparative analysis of patient samples revealed a concordance of 91% between NGS and ddPCR. These results confirm that the Reveal ctDNA™ 28 NGS assay can be used for therapy monitoring of patients under TKI therapy. However, due to the slightly superior sensitivity of ddPCR, a combination of NGS (with broad coverage of a large number of genomic loci) and ddPCR (with targeted highly sensitive detection of specific mutations) might be the ideal approach.
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Affiliation(s)
- Regina Stitz
- Institute of Pathology, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria
| | - Anna Buder
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical Center of Vienna, Vienna, Austria
| | - Rene Silye
- Institute of Pathology, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria
| | - Bernhard Baumgartner
- Department of Pulmonary Medicine, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria
| | - Franz Pühringer
- Institute of Pathology, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria
| | - Martin Filipits
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical Center of Vienna, Vienna, Austria
| | - Eva Oberndorfer
- Institute of Pathology, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.
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13
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Kothari P, Sauerhaft T, Bouvier N, Rodriguez-Sanchez MI, Shia J, Price A, Morjaria S, Gerstle JT, Shukla NN, Ortiz MV. Identification of a TP53 Deletion in an Undifferentiated Embryonal Sarcoma of the Liver Provides Clinically Relevant Longitudinal Detection of Circulating Tumor DNA. JCO Precis Oncol 2021; 5:PO.21.00102. [PMID: 34527851 PMCID: PMC8437221 DOI: 10.1200/po.21.00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/19/2021] [Accepted: 07/30/2021] [Indexed: 11/20/2022] Open
Affiliation(s)
- Prachi Kothari
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Talia Sauerhaft
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nancy Bouvier
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anita Price
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sejal Morjaria
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - J Theodore Gerstle
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neerav N Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael V Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
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14
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Akahori D, Inoue Y, Inui N, Karayama M, Yasui H, Hozumi H, Suzuki Y, Furuhashi K, Fujisawa T, Enomoto N, Nakamura Y, Suda T. Comparative assessment of NOIR-SS and ddPCR for ctDNA detection of EGFR L858R mutations in advanced L858R-positive lung adenocarcinomas. Sci Rep 2021; 11:14999. [PMID: 34294857 PMCID: PMC8298558 DOI: 10.1038/s41598-021-94592-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/07/2021] [Indexed: 12/13/2022] Open
Abstract
Genotyping epidermal growth factor receptor (EGFR) is an essential process to indicate lung adenocarcinoma patients for the most appropriate treatment. Liquid biopsy using circulating tumor DNA (ctDNA) potentially complements the use of tumor tissue biopsy for identifying genotype-specific mutations in cancer cells. We assessed the performance of a high-fidelity sequencing method that uses molecular barcodes called the nonoverlapping integrated read sequencing system (NOIR-SS) for detecting EGFR L858R-mutated alleles in 33 advanced or recurrent patients with L858R mutation-positive lung adenocarcinoma revealed by matched tissue biopsy. We compared NOIR-SS with site-specific droplet digital PCR (ddPCR), which was taken as the reference, in terms of sensitivity and ability to quantify L858R variant allele fractions (VAFs). NOIR-SS and ddPCR had sensitivities of 87.9% (29/33) and 78.8% (26/33) for detecting L858R alleles, respectively. The VAFs measured by each assay were strongly correlated. Notably, one specimen was positive with a VAF of 30.12% for NOIR-SS but marginally positive with that of 0.05% for ddPCR because of a previously poorly recognized mechanism: two-base substitution-induced L858R (c.2573_2574delinsGA). These results indicate that NOIR-SS is a useful method for detecting ctDNA, potentially overcoming a limitation of ddPCR which highly depends on the binding ability of primers to specific targeting sequences.
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Affiliation(s)
- Daisuke Akahori
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Yusuke Inoue
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan.,Department of Clinical Pharmacology and Therapeutics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Naoki Inui
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan. .,Department of Clinical Pharmacology and Therapeutics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan.
| | - Masato Karayama
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan.,Department of Clinical Oncology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hideki Yasui
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Hironao Hozumi
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Yuzo Suzuki
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Kazuki Furuhashi
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Tomoyuki Fujisawa
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Noriyuki Enomoto
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Yutaro Nakamura
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Takafumi Suda
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
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15
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Technical Evaluation of the COBAS EGFR Semiquantitative Index (SQI) for Plasma cfDNA Testing in NSCLC Patients with EGFR Exon 19 Deletions. Diagnostics (Basel) 2021; 11:diagnostics11081319. [PMID: 34441254 PMCID: PMC8392299 DOI: 10.3390/diagnostics11081319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/09/2021] [Accepted: 07/22/2021] [Indexed: 12/25/2022] Open
Abstract
The cobas® EGFR Test provides a semiquantitative index (SQI) that reflects the proportion of mutated versus wild-type copies of the EGFR gene in plasma. The significance of SQI as an indirect measure of the variant allele frequency (VAF) or mutated copies/mL remains unclear. The aim of this study was to evaluate the correlation of SQI with the VAF and the number of mutated copies/mL obtained by a digital droplet PCR (ddPCR) test in NSCLC samples. The study included 118 plasma samples from a retrospective cohort of 25 stage IV adenocarcinoma patients with EGFR exon 19 deletions (Ex19Del), obtained before and during tyrosine kinase inhibitor (TKI) treatment. Both SQI and VAF and SQI and mutated copies/mL showed the same significant correlation (r2 = 0.79, p < 0.00001) across the whole study cohort. We found better correlation in samples collected at the baseline between SQI and VAF (r2 = 0.94, p < 0.00001) and SQI and mutated copies/mL (r2 = 0.97, p < 0.00001) compared to samples collected during TKI treatment: r2 = 0.76; p < 0.00001 for SQI and VAF and r2 = 0.75; p < 0.00001 for SQI and mutated copies/mL. The study indicates that SQI is a robust quantitative indirect measure of VAF and the number of mutated copies/mL in plasma from patients with an EGFR Ex19Del mutation. Further studies are desirable to assess the SQI cut-off values related to the clinical status of the patient.
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16
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Ntzifa A, Kotsakis A, Georgoulias V, Lianidou E. Detection of EGFR Mutations in Plasma cfDNA and Paired CTCs of NSCLC Patients before and after Osimertinib Therapy Using Crystal Digital PCR. Cancers (Basel) 2021; 13:2736. [PMID: 34073111 PMCID: PMC8197887 DOI: 10.3390/cancers13112736] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/13/2021] [Accepted: 05/27/2021] [Indexed: 12/23/2022] Open
Abstract
Circulating tumor DNA (ctDNA) analysis has clinical utility in EGFR mutant NSCLC. Circulating tumor cells (CTCs) consist a unique source of information at the cellular level. Digital PCR (dPCR) is a valuable tool for accurate and valid analysis of gene mutations in liquid biopsy analysis. In the present study we detected EGFR mutations in ctDNA and paired CTCs under osimertinib therapy at two time points using crystal dPCR and the naica® system (Stilla Technologies). We quantified mutation allele frequencies (MAF) of EGFR mutations in 91 plasma cfDNA samples of 48 EGFR mutant NSCLC patients and in 64 matched CTC-derived genomic DNA samples, and the FDA-cleared cobas® EGFR mutation test in 80 identical plasma samples. Direct comparison between crystal dPCR and the cobas EGFR assay revealed a high concordance for all EGFR mutations. Our comparison of crystal dPCR results in ctDNA with the corresponding primary tissue has shown a strong correlation. EGFR mutations analysis in paired CTC-derived gDNA revealed a high heterogeneity. Crystal dPCR offers the unique advantages of high analytical sensitivity, precision, and accuracy for detecting and quantifying multiple EGFR mutations in plasma cfDNA and CTCs of NSCLC patients.
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Affiliation(s)
- Aliki Ntzifa
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece;
| | - Athanasios Kotsakis
- Department of Medical Oncology, General University Hospital of Larissa, 41110 Larissa, Greece;
| | | | - Evi Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece;
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17
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18
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Buder A, Heitzer E, Waldispühl-Geigl J, Weber S, Moser T, Hochmair MJ, Hackner K, Errhalt P, Setinek U, Filipits M. Somatic Copy-Number Alterations in Plasma Circulating Tumor DNA from Advanced EGFR-Mutated Lung Adenocarcinoma Patients. Biomolecules 2021; 11:biom11050618. [PMID: 33919291 PMCID: PMC8143372 DOI: 10.3390/biom11050618] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/08/2021] [Accepted: 04/16/2021] [Indexed: 11/29/2022] Open
Abstract
Background: To assess the clinical relevance of genome-wide somatic copy-number alterations (SCNAs) in plasma circulating tumor DNA (ctDNA) from advanced epidermal growth factor receptor (EGFR)-mutated lung adenocarcinoma patients. Methods: We included 43 patients with advanced EGFR T790M-positive lung adenocarcinoma who were treated with osimertinib after progression under previous EGFR-TKI therapy. We performed genomic profiling of ctDNA in plasma samples from each patient obtained pre-osimertinib and after patients developed resistance to osimertinib. SCNAs were detected by shallow whole-genome plasma sequencing and EGFR mutations were assessed by droplet digital PCR. Results: SCNAs in resistance-related genes (rrSCNAs) were detected in 10 out of 31 (32%) evaluable patients before start of osimertinib. The presence of rrSCNAs in plasma before the initiation of osimertinib therapy was associated with a lower response rate to osimertinib (50% versus 81%, p = 0.08) and was an independent predictor for shorter progression-free survival (adjusted HR 3.33, 95% CI 1.37–8.10, p = 0.008) and overall survival (adjusted HR 2.54, 95% CI 1.09–5.92, p = 0.03). Conclusions: Genomic profiling of plasma ctDNA is clinically relevant and affects the efficacy and clinical outcome of osimertinib. Our approach enables the comprehensive assessment of SCNAs in plasma samples of lung adenocarcinoma patients and may help to guide genotype-specific therapeutic strategies in the future.
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Affiliation(s)
- Anna Buder
- Comprehensive Cancer Center, Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria;
| | - Ellen Heitzer
- Diagnostic and Research Center for Molecular BioMedicine, Institute of Human Genetics, Medical University of Graz, 8036 Graz, Austria; (E.H.); (J.W.-G.); (S.W.); (T.M.)
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, 8036 Graz, Austria
| | - Julie Waldispühl-Geigl
- Diagnostic and Research Center for Molecular BioMedicine, Institute of Human Genetics, Medical University of Graz, 8036 Graz, Austria; (E.H.); (J.W.-G.); (S.W.); (T.M.)
| | - Sabrina Weber
- Diagnostic and Research Center for Molecular BioMedicine, Institute of Human Genetics, Medical University of Graz, 8036 Graz, Austria; (E.H.); (J.W.-G.); (S.W.); (T.M.)
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, 8036 Graz, Austria
| | - Tina Moser
- Diagnostic and Research Center for Molecular BioMedicine, Institute of Human Genetics, Medical University of Graz, 8036 Graz, Austria; (E.H.); (J.W.-G.); (S.W.); (T.M.)
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, 8036 Graz, Austria
| | - Maximilian J. Hochmair
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Department of Respiratory and Critical Care Medicine, Hospital North, 1210 Vienna, Austria;
| | - Klaus Hackner
- Department of Pneumology, University Hospital Krems, Karl Landsteiner University of Health Sciences, 3500 Krems, Austria; (K.H.); (P.E.)
| | - Peter Errhalt
- Department of Pneumology, University Hospital Krems, Karl Landsteiner University of Health Sciences, 3500 Krems, Austria; (K.H.); (P.E.)
| | - Ulrike Setinek
- Department of Pathology and Bacteriology, Otto Wagner Hospital, 1140 Vienna, Austria;
| | - Martin Filipits
- Comprehensive Cancer Center, Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria;
- Correspondence: ; Tel.: +43-1-40160-57528
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19
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Hackner K, Buder A, Hochmair MJ, Strieder M, Grech C, Fabikan H, Burghuber OC, Errhalt P, Filipits M. Detection of EGFR Activating and Resistance Mutations by Droplet Digital PCR in Sputum of EGFR-Mutated NSCLC Patients. CLINICAL MEDICINE INSIGHTS-ONCOLOGY 2021; 15:1179554921993072. [PMID: 33642890 PMCID: PMC7894584 DOI: 10.1177/1179554921993072] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 01/15/2021] [Indexed: 11/16/2022]
Abstract
Background Proof of the T790M resistance mutation is mandatory if patients with EGFR-mutated non-small cell lung cancer (NSCLC) progress under first- or second-generation tyrosine kinase inhibitor therapy. In addition to rebiopsy, analysis of plasma circulating tumor DNA is used to detect T790M resistance mutation. We studied whether sputum is another feasible specimen for detection of EGFR mutations. Methods Twenty-eight patients with advanced EGFR-mutated NSCLC were included during stable and/or progressive disease. The initial activating EGFR mutations (exon 19 deletions or L858R mutations) at stable disease and at progressive disease (together with T790M) were assessed in simultaneously collected plasma and sputum samples and detected by droplet digital polymerase chain reaction (ddPCR). Results Activating EGFR mutations were detected in 47% of the plasma samples and 41% of sputum samples during stable disease, and in 57% of plasma samples and 64% of sputum samples during progressive disease. T790M was detected in 44% of the plasma samples and 66% of the sputum samples at progressive disease. In ddPCR T790M-negative results for both specimens (plasma and sputum), negativity was confirmed by rebiopsy in 5 samples. Concordance rate of plasma and sputum for T790M was 0.86, with a positive percent agreement of 1.0 and a negative percent agreement of 0.80. Conclusions We demonstrated that EGFR mutation analysis with ddPCR is feasible in sputum samples. Combination of plasma and sputum analyses for detection of T790M in NSCLC patients with progressive disease increases the diagnostic yield compared with molecular plasma analysis alone.
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Affiliation(s)
- Klaus Hackner
- Department of Pneumology, University Hospital Krems, Karl Landsteiner University of Health Sciences, Krems, Austria.,Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, Vienna, Austria
| | - Anna Buder
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Maximilian J Hochmair
- Department of Respiratory and Critical Care Medicine, Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
| | - Matthaeus Strieder
- Department of Pneumology, University Hospital Krems, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Christina Grech
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Hannah Fabikan
- Department of Respiratory and Critical Care Medicine, Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
| | - Otto C Burghuber
- Department of Respiratory and Critical Care Medicine, and Ludwig Boltzmann Institute of COPD and Respiratory Epidemiology, Otto Wagner Hospital and Sigmund Freud University Medical School, Vienna, Austria
| | - Peter Errhalt
- Department of Pneumology, University Hospital Krems, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Martin Filipits
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
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20
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Kim Y, Shin S, Lee KA. Exosome-based detection of EGFR T790M in plasma and pleural fluid of prospectively enrolled non-small cell lung cancer patients after first-line tyrosine kinase inhibitor therapy. Cancer Cell Int 2021; 21:50. [PMID: 33435996 PMCID: PMC7802208 DOI: 10.1186/s12935-021-01761-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/06/2021] [Indexed: 12/17/2022] Open
Abstract
Background The exosomal nucleic acid (exoNA) from the plasma and pleural fluid can potentially provide means to identify genomic changes in non-small cell lung cancer (NSCLC) patients who develop resistance to targeted epidermal growth factor receptor (EGFR) inhibitor therapy. Methods We compared the performance of the following tools to detect EGFR mutations in 54 plasma samples and 13 pleural fluid using cfDNA, combined TNA (exoTNA + cfTNA), or total cellular DNA: droplet digital PCR (ddPCR), the Cobas® EGFR Mutation Test v2 (Cobas) and NGS with Oncomine Pan-Cancer Cell-Free Assay. Results All three of these platforms demonstrated 100% specificity in the detection of EGFR mutations in the plasma. In the detection of an activating mutation (exon 19 deletion and L858R), Cobas using cfDNA, ddPCR using combined TNA, and NGS using combined TNA showed a sensitivity of 93, 95.3, and 93.8%, respectively. For T790M mutation detection, the Cobas, ddPCR, and NGS showed a sensitivity of 64.7, 88.2, and 93.3%, respectively. Pleural fluid analysis revealed enrichment of the T790M mutant copies in the exosomes. ddPCR using exoTNA showed higher sensitivity than did total cellular DNA from the pleural fluid. Conclusion These results demonstrated that combined TNA in the plasma and exoTNA in the pleural fluid can be used to evaluate low-abundant EGFR mutant copies in NSCLC.
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Affiliation(s)
- Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
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21
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Moreno-Manuel A, Calabuig-Fariñas S, Obrador-Hevia A, Blasco A, Fernández-Díaz A, Sirera R, Camps C, Jantus-Lewintre E. dPCR application in liquid biopsies: divide and conquer. Expert Rev Mol Diagn 2020; 21:3-15. [PMID: 33305634 DOI: 10.1080/14737159.2021.1860759] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: Precision medicine is already a reality in oncology, since biomarker-driven therapies have clearly improved patient survival. Furthermore, a new, minimally invasive strategy termed 'liquid biopsy' (LB) has revolutionized the field by allowing comprehensive cancer genomic profiling through the analysis of circulating tumor DNA (ctDNA). However, its detection requires extremely sensitive and efficient technologies. A powerful molecular tool based on the principle of 'divide and conquer' has emerged to solve this problem. Thus, digital PCR (dPCR) allows absolute and accurate quantification of target molecules.Areas covered: In this review we will discuss the fundamentals of dPCR and the most common approaches used for partition of samples and quantification. The advantages and limitations of dPCR will be mentioned in the context of LB in oncology.Expert opinion: In our opinion, dPCR has proven to be one of the most sensitive methods available for LB analysis, albeit some aspects such as its capacity of multiplexing and protocol standardization still require further improvements. Furthermore, the increasing sensitivities and lower costs of next generation sequencing (NGS) methods position dPCR as a confirmatory and complementary technique for NGS results which will likely prove to be very useful for treatment monitoring and assessing minimal residual disease.
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Affiliation(s)
- Andrea Moreno-Manuel
- Molecular Oncology Laboratory, Fundación Para La Investigación del Hospital General Universitario De Valencia, Valencia, Spain.,Mixed Unit TRIAL, (Príncipe Felipe Research Centre & Fundación Para La Investigación Del Hospital General Universitario De Valencia), Valencia, Spain
| | - Silvia Calabuig-Fariñas
- Molecular Oncology Laboratory, Fundación Para La Investigación del Hospital General Universitario De Valencia, Valencia, Spain.,Mixed Unit TRIAL, (Príncipe Felipe Research Centre & Fundación Para La Investigación Del Hospital General Universitario De Valencia), Valencia, Spain.,Department of Pathology, Universitat de València, València, Spain.,CIBERONC, Madrid, Spain
| | - Antonia Obrador-Hevia
- Group of Advanced Therapies and Biomarkers in Clinical Oncology, Health Research Institute of the Balearic Islands (Idisba), Son Espases University Hospital, Palma, Spain.,Molecular Diagnosis Unit, Son Espases University Hospital, Palma, Spain
| | - Ana Blasco
- CIBERONC, Madrid, Spain.,Medical Oncology Department, General University Hospital of Valencia, Valencia, Spain
| | - Amaya Fernández-Díaz
- Medical Oncology Department, General University Hospital of Valencia, Valencia, Spain
| | - Rafael Sirera
- Mixed Unit TRIAL, (Príncipe Felipe Research Centre & Fundación Para La Investigación Del Hospital General Universitario De Valencia), Valencia, Spain.,CIBERONC, Madrid, Spain.,Department of Biotechnology, Universitat Politècnica De València, Valencia, Spain
| | - Carlos Camps
- Molecular Oncology Laboratory, Fundación Para La Investigación del Hospital General Universitario De Valencia, Valencia, Spain.,Mixed Unit TRIAL, (Príncipe Felipe Research Centre & Fundación Para La Investigación Del Hospital General Universitario De Valencia), Valencia, Spain.,CIBERONC, Madrid, Spain.,Medical Oncology Department, General University Hospital of Valencia, Valencia, Spain.,Department of Medicine, Universitat De València, Valencia, Spain
| | - Eloisa Jantus-Lewintre
- Molecular Oncology Laboratory, Fundación Para La Investigación del Hospital General Universitario De Valencia, Valencia, Spain.,Mixed Unit TRIAL, (Príncipe Felipe Research Centre & Fundación Para La Investigación Del Hospital General Universitario De Valencia), Valencia, Spain.,CIBERONC, Madrid, Spain.,Department of Biotechnology, Universitat Politècnica De València, Valencia, Spain
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The Allele Frequency of EGFR Mutations Predicts Survival in Advanced EGFR T790M-Positive Non-small Cell Lung Cancer Patients Treated with Osimertinib. Target Oncol 2020; 16:77-84. [PMID: 33270169 PMCID: PMC7810636 DOI: 10.1007/s11523-020-00781-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2020] [Indexed: 01/08/2023]
Abstract
Background The allele frequency of epidermal growth factor receptor (EGFR) mutations could be a potential molecular biomarker for the outcome of osimertinib therapy. Objective The purpose of our study was to assess the clinical relevance of the allele frequency of EGFR mutations in plasma-based circulating tumor DNA (ctDNA) before starting osimertinib therapy in patients with advanced EGFR-mutated non-small cell lung cancer (NSCLC) who had progressed under treatment with EGFR tyrosine kinase inhibitors (TKIs). Patients and Methods We enrolled 141 patients with advanced EGFR T790M-positive NSCLC who underwent second-line osimertinib treatment. Plasma ctDNA was tested for EGFR-activating mutations (EGFR deletions in exon 19, L858R, L861Q, S768I) and T790M by means of droplet digital polymerase chain reaction (ddPCR). Results The allele frequency of EGFR-activating mutations in plasma ctDNA before osimertinib initiation ranged from 0 to 81,543 copies/ml and was independently associated with progression-free survival (PFS) and overall survival (OS) after adjusting for known clinicopathological risk factors (PFS: adjusted hazard ratio [HR] 1.26, 95% confidence interval [CI] 1.15–1.39, P < 0.0001; OS: adjusted HR 1.32, 95% CI 1.18–1.47, P < 0.0001). The allele frequency of T790M in plasma ctDNA before starting osimertinib therapy ranged from 0 to 38,092 copies/ml. Multivariate analyses showed that a higher T790M allele frequency was associated with a trend towards a shorter PFS (adjusted HR 1.19, 95% CI 0.99–1.42, P = 0.05) and a significantly shorter OS (adjusted HR 1.25, 95% CI 1.02–1.53, P = 0.03) of the patients. Conclusion A higher allele frequency of EGFR mutations, particularly EGFR-activating mutations, in plasma ctDNA is a poor prognostic marker. Further studies on the clinical utility of liquid biopsy are needed.
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23
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Takeda Y, Naka G, Yamaguchi Y, Hashimoto M, Suzuki M, Izumi S, Sugiyama H. Genetic diagnostic features after failure of initial treatment with epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors among non-small-cell lung cancer patients harboring EGFR mutations. BMC Cancer 2020; 20:951. [PMID: 33008313 PMCID: PMC7531095 DOI: 10.1186/s12885-020-07424-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 09/16/2020] [Indexed: 12/25/2022] Open
Abstract
Background Osimertinib, a third-generation epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitor (TKI), can be used as second-line treatment for lung cancer patients harboring the T790M substitution. Although osimertinib is more effective than the first-generation EGFR-TKIs used for first-line treatment, its efficacy with respect to long-term patient survival remains unclear even upon the administration of a complete sequence of EGFR-TKI therapy. Moreover, limited information is available regarding genetic diagnostic approaches after the treatment of EGFR-TKI–naïve patients. This study investigated the clinical characteristics of EGFR-mutated lung cancer patients harboring the T790M substitution resistant to EGFR-TKIs, as well as the advantages of rebiopsy and liquid biopsy for these patients. Methods The medical records of patients screened for EGFR mutations were reviewed. Upon failure of naïve treatment with EGFR-TKIs, except for osimertinib, single-plexus cobas version 2 was repeatedly used to detect the T790M substitution in EGFR via tissue or liquid biopsy. Results From April 2016 through May 2019, 113 patients were found to harbor EGFR mutations. Sixty patients were treated with EGFR-TKIs, among whom 46 underwent tissue or liquid biopsy. Twenty-nine of these 46 (63%) patients harbored the T790M substitution. In total, 141 rebiopsies were performed. The T790M substitution was detected in 24 of 43 tissue biopsies and 11 of 98 liquid biopsies. If patients displayed an EGFR exon 19 deletion, had a new lesion, and were administered gefitinib as first-line therapy, they were suspected to harbor the T790M substitution. Furthermore, the T790M substitution was detected through rebiopsy in patients with coexisting original mutations, brain metastases, tumor enlargement by ≥12 mm, or metastases at minor sites. Conclusion Among patients with positive factors associated with the T790M mutation, repeated tissue or liquid biopsies are useful to maximize the detection rate of the T790M substitution. Furthermore, these biopsies need to be repeated numerous times in order to reduce “detection overlook” among such patients.
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Affiliation(s)
- Yuichiro Takeda
- Department of Respiratory Medicine, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan.
| | - Go Naka
- Department of Respiratory Medicine, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Yoh Yamaguchi
- Department of Respiratory Medicine, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Masao Hashimoto
- Department of Respiratory Medicine, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Manabu Suzuki
- Department of Respiratory Medicine, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Shinyu Izumi
- Department of Respiratory Medicine, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Haruhito Sugiyama
- Department of Respiratory Medicine, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
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Cortiula F, Pasello G, Follador A, Nardo G, Polo V, Scquizzato E, Conte AD, Miorin M, Giovanis P, D’Urso A, Girlando S, Settanni G, Picece V, Veccia A, Corvaja C, Indraccolo S, De Maglio G. A Multi-Center, Real-Life Experience on Liquid Biopsy Practice for EGFR Testing in Non-Small Cell Lung Cancer (NSCLC) Patients. Diagnostics (Basel) 2020; 10:diagnostics10100765. [PMID: 32998450 PMCID: PMC7601690 DOI: 10.3390/diagnostics10100765] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 02/07/2023] Open
Abstract
Background: circulating tumor DNA (ctDNA) is a source of tumor genetic material for EGFR testing in NSCLC. Real-word data about liquid biopsy (LB) clinical practice are lacking. The aim of the study was to describe the LB practice for EGFR detection in North Eastern Italy. Methods: we conducted a multi-regional survey on ctDNA testing practices in lung cancer patients. Results: Median time from blood collection to plasma separation was 50 min (20–120 min), median time from plasma extraction to ctDNA analysis was 24 h (30 min–5 days) and median turnaround time was 24 h (6 h–5 days). Four hundred and seventy five patients and 654 samples were tested. One hundred and ninety-two patients were tested at diagnosis, with 16% EGFR mutation rate. Among the 283 patients tested at disease progression, 35% were T790M+. Main differences in LB results between 2017 and 2018 were the number of LBs performed for each patient at disease progression (2.88 vs. 1.2, respectively) and the percentage of T790M+ patients (61% vs. 26%).
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Affiliation(s)
- Francesco Cortiula
- Dipartimento di Oncologia, Azienda Sanitaria Universitaria Friuli Centrale, 33100 Udine, Italy; (A.F.); (C.C.)
- Dipartimento di Medicina (DAME), Università degli Studi di Udine, 33100 Udine, Italy
- Correspondence: (F.C.); (S.I.)
| | - Giulia Pasello
- Oncologia Medica 2, Istituto Oncologico Veneto IOV IRCCS, 35128 Padova, Italy;
| | - Alessandro Follador
- Dipartimento di Oncologia, Azienda Sanitaria Universitaria Friuli Centrale, 33100 Udine, Italy; (A.F.); (C.C.)
| | - Giorgia Nardo
- U.O.C. Immunologia e Diagnostica Molecolare Oncologica, Istituto Oncologico Veneto IOV IRCCS, 35128 Padova, Italy;
| | - Valentina Polo
- Dipartimento di Oncologia, AULSS 2 Marca Trevigiana, Ospedale Ca’ Foncello, 31100 Treviso, Italy;
| | - Elisa Scquizzato
- Dipartimento interaziendale di Anatomia Patologica, ULSS 2 Marca Trevigiana, 31100 Treviso, Italy;
| | - Alessandro Del Conte
- S.O.C. Oncologia Medica e dei Tumori Immunocorrelati, Centro di Riferimento Oncologico (CRO) IRCCS, 33081 Aviano, Italy;
| | - Marta Miorin
- SSD Genetica medica, Azienda Sanitaria Friuli Occidentale, Presidio Ospedaliero di Pordenone, 33170 Pordenone, Italy;
| | - Petros Giovanis
- U.O.C. Oncologia, ULSS1 Dolomiti, Presidio Ospedaliero di Feltre, 32032 Feltre, Italy;
| | - Alessandra D’Urso
- U.O.C. Anatomia Patologica, ULSS1 Dolomiti, Presidio Ospedaliero di Feltre, 32032 Feltre, Italy;
| | - Salvator Girlando
- U.O. Anatomia Patologica, Ospedale Santa Chiara, 38122 Trento, Italy;
| | - Giulio Settanni
- Servizio di Anatomia-Istologia Patologica, IRCCS Ospedale Sacro Cuore Don Calabria, 37024 Negrar, Italy;
| | - Vincenzo Picece
- Dipartimento di Oncologia Medica, IRCCS Ospedale Sacro Cuore Don Calabria, 37024 Negrar, Italy;
| | - Antonello Veccia
- U.O. Oncologia Medica, Ospedale Santa Chiara, 38122 Trento, Italy;
| | - Carla Corvaja
- Dipartimento di Oncologia, Azienda Sanitaria Universitaria Friuli Centrale, 33100 Udine, Italy; (A.F.); (C.C.)
- Dipartimento di Medicina (DAME), Università degli Studi di Udine, 33100 Udine, Italy
| | - Stefano Indraccolo
- U.O.C. Immunologia e Diagnostica Molecolare Oncologica, Istituto Oncologico Veneto IOV IRCCS, 35128 Padova, Italy;
- Correspondence: (F.C.); (S.I.)
| | - Giovanna De Maglio
- SOC Anatomia Patologica, Azienda Sanitaria UniversitariaFriuli Centrale, 33100 Udine, Italy;
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Chan DLH, Toh GLX, Goh LL. Clinical implementation of plasma EGFR T790M testing using droplet digital PCR in TKI-resistant NSCLC patients. Exp Mol Pathol 2020; 116:104515. [PMID: 32738312 DOI: 10.1016/j.yexmp.2020.104515] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/23/2020] [Accepted: 07/25/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Majority of non-small cell lung cancer (NSCLC) patients progressed on epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) due to acquired T790M mutation. Blood sample is increasingly used in clinical setting for EGFR T790M detection and our laboratory employed the droplet digital PCR (ddPCR) methodology for testing. This study investigated the positive rate, specimen type for rebiopsy and clinical impact of blood-based EGFR T790M testing. METHODS We retrospectively evaluated clinical samples that underwent plasma EGFR T790M testing in TTSH Molecular Diagnostic Laboratory from August 2017 to September 2019. Data on diagnosis, EGFR activating and T790M mutations, and treatment strategies were recorded. RESULTS A total of 104 progressive NSCLC cases were included in this study. Overall, 46 patients (44.2%) were tested T790M positive, and 47.8% of these tested positive had low levels (defined as ≤3% fractional abundance and <50 copies/mL plasma), which may be missed by the conventional methods with lower sensitivity. Of these tested with low T790M abundance, 77.3% subsequently received osimertinib. Activating mutations were not detected in 42 (40.4%) cases, indicating that the tumors were not actively shedding ctDNA. Among these, 24 patients underwent repeat testing with tissue or blood specimens. Thirteen patients were subsequently tested T790M positive and 12 of them switched treatment to osimertinib. The recommendation to repeat testing with a different biopsy or after a suitable interval increased the overall positive rate to 56.7% (59/104). CONCLUSION The use of a highly sensitive platform such as ddPCR for the detection of low abundance T790M, and the approach of repeat testing in cases with insufficient ctDNA increased the positive rate. This in turn identified more patients who are eligible for targeted therapy.
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Affiliation(s)
| | | | - Liuh Ling Goh
- Molecular Diagnostic Laboratory, Tan Tock Seng Hospital, Singapore.
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26
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Buder A, Hochmair MJ, Setinek U, Pirker R, Filipits M. EGFR mutation tracking predicts survival in advanced EGFR-mutated non-small cell lung cancer patients treated with osimertinib. Transl Lung Cancer Res 2020; 9:239-245. [PMID: 32420063 PMCID: PMC7225165 DOI: 10.21037/tlcr.2020.03.02] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background Osimertinib has become standard therapy of advanced epidermal growth factor receptor (EGFR)-mutated non-small cell lung cancer (NSCLC) patients and T790M-mediated resistance. We investigated the clinical utility of EGFR mutation tracking in plasma-based circulating tumor DNA (ctDNA) after start of osimertinib therapy in metastatic, EGFR-mutant NSCLC patients who had progressed on prior therapy with EGFR tyrosine kinase inhibitors (TKIs). Methods We enrolled 141 patients with advanced EGFR-mutated NSCLC who underwent second-line osimertinib treatment for T790M-positive disease. After initiation of osimertinib, we obtained plasma samples from 108 patients. Plasma ctDNA was tested for EGFR mutations by means of droplet digital PCR and was termed positive if any EGFR mutation was detected. Results Plasma ctDNA was detected in 58 of 108 (54%) patients after osimertinib initiation and was associated with poor progression-free survival (PFS) [hazard ratio (HR) 4.26, 95% confidence interval (CI): 2.55–7.10, P<0.0001] and overall survival (OS) (HR 3.23, 95% CI: 1.80–5.78, P<0.0001). In multivariable analysis, ctDNA status remained significantly associated with PFS and OS (HR 4.87, 95% CI: 2.81–8.44, P<0.0001; HR 3.49, 95% CI: 1.88–6.50, P<0.0001). Patients with persistence of activating EGFR mutations within eight weeks had shorter durations of PFS (HR 6.17, 95% CI: 3.03–12.56, P<0.0001) and OS (HR 4.83, 95% CI: 2.25–10.36, P<0.0001) than patients with total clearance of the activating EGFR mutation. Persistence of activating EGFR mutations in plasma ctDNA remained an independent predictor of poor PFS and OS in multivariable analyses. Conclusions Patients with persistence of activating EGFR mutations in plasma ctDNA within eight weeks after osimertinib initiation have worse prognosis and may require the addition of chemotherapy or other treatments in order to achieve better outcome.
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Affiliation(s)
- Anna Buder
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Maximilian J Hochmair
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Department of Respiratory and Critical Care Medicine, Hospital North, Vienna, Austria
| | - Ulrike Setinek
- Institute for Pathology and Bacteriology, Otto Wagner Hospital, Vienna, Austria
| | - Robert Pirker
- Division of Oncology, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Martin Filipits
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
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27
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The 2020 update of the recommendations of the Austrian working group on lung pathology and oncology for the diagnostic workup of non-small cell lung cancer with focus on predictive biomarkers. MEMO-MAGAZINE OF EUROPEAN MEDICAL ONCOLOGY 2020. [DOI: 10.1007/s12254-019-00565-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Wang X, Wu J, Mao W, He X, Ruan L, Zhu J, Shu P, Zhang Z, Jiang B, Zhang X. A tetrahedral DNA nanostructure-decorated electrochemical platform for simple and ultrasensitive EGFR genotyping of plasma ctDNA. Analyst 2020; 145:4671-4679. [PMID: 32458862 DOI: 10.1039/d0an00591f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In this study, we propose an on-site electrochemical platform for sensitive simultaneous genotyping of the two major EGFR mutations (19del and L858R) through plasma ctDNA based on tetrahedral DNA nanostructure decorated screen-printed electrodes.
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Del Re M, Petrini I, Mazzoni F, Valleggi S, Gianfilippo G, Pozzessere D, Chella A, Crucitta S, Rofi E, Restante G, Miccoli M, Garassino MC, Danesi R. Incidence of T790M in Patients With NSCLC Progressed to Gefitinib, Erlotinib, and Afatinib: A Study on Circulating Cell-free DNA. Clin Lung Cancer 2019; 21:232-237. [PMID: 31735523 DOI: 10.1016/j.cllc.2019.10.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/02/2019] [Accepted: 10/02/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND Insights into the mechanism of resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) could provide important information for further patient management, including the choice of second-line treatment. The EGFR T790M mutation is the most common mechanism of resistance to first- and second-generation EGFR TKIs. Owing to its biologic relevance in the response of non-small-cell lung cancer (NSCLC) to the selective pressure of treatment, the present study investigated whether the occurrence of T790M at progression differed among patients receiving gefitinib, erlotinib, or afatinib. PATIENTS AND METHODS The present retrospective study included patients with NSCLC with an EGFR activating mutation, who had received gefitinib, erlotinib, or afatinib as first-line treatment. Plasma samples for the analysis of cell-free DNA were taken at disease progression and analyzed using a digital droplet polymerase chain reaction EGFR mutation assay. RESULTS A total of 83 patients were enrolled; 42 had received gefitinib or erlotinib and 41afatinib. The patient characteristics were comparable across the 2 groups. The median time to progression (TTP) was 14.4 months for the gefitinib and erlotinib group and 10.2 months for the afatinib group (P = .09). Of the 83 patients, 47 (56.6%) were positive for the T790M in plasma. A greater incidence of T790M was observed in patients with progression during gefitinib or erlotinib therapy compared with patients treated with afatinib (33 [79%] vs. 14 [34%], respectively; odds ratio, 7.1; 95% confidence interval, 2.7-18.5; P = .0001). CONCLUSIONS Although gefitinib, erlotinib, and afatinib showed a comparable TTP in patients receiving first-line therapy, the incidence of T790M differed among them, as demonstrated by the present study, which could have implications for the choice of second-line treatment.
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Affiliation(s)
- Marzia Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Iacopo Petrini
- Unit of Pneumology, Azienda Ospedaliero-Universitaria Pisana and Department of Translational Research and New Technologies in Medicine, University of Pisa, Pisa, Italy
| | - Francesca Mazzoni
- Unit of Medical Oncology, Department of Oncology, University Hospital of Firenze, Firenze, Italy
| | - Simona Valleggi
- Unit of Pneumology, Azienda Ospedaliero-Universitaria Pisana and Department of Translational Research and New Technologies in Medicine, University of Pisa, Pisa, Italy
| | - Giulia Gianfilippo
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Daniele Pozzessere
- Unit of Medical Oncology, Department of Oncology, Hospital of Prato, Prato, Italy
| | - Antonio Chella
- Unit of Pneumology, Azienda Ospedaliero-Universitaria Pisana and Department of Translational Research and New Technologies in Medicine, University of Pisa, Pisa, Italy
| | - Stefania Crucitta
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Eleonora Rofi
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Giuliana Restante
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Mario Miccoli
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Marina Chiara Garassino
- Thoraco-pulmonary Medical Oncology Unit, Medical Oncology and Hematology Department, National Tumor Institute, IRCCS, Milan, Italy
| | - Romano Danesi
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.
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Kim Y, Shin S, Kim B, Lee KA. Selecting short length nucleic acids localized in exosomes improves plasma EGFR mutation detection in NSCLC patients. Cancer Cell Int 2019; 19:251. [PMID: 31582907 PMCID: PMC6771088 DOI: 10.1186/s12935-019-0978-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 09/24/2019] [Indexed: 02/08/2023] Open
Abstract
Background Exosomal nucleic acid (exoNA) is a feasible target to improve the sensitivity of EGFR mutation testing in non-small cell lung cancer patients with limited cell-free DNA (cfDNA) mutant copies. However, the type and size of target exoNA related to the sensitivity of EGFR mutation testing has not been explored extensively. Methods The type and size of target exoNA related to the sensitivity of EGFR mutation testing was evaluated using ddPCR. A total of 47 plasma samples was tested using short-length exoTNA (exosomal DNA and RNA) and cfDNA. Results The sensitivity of short-length exoTNA (76.5%) was higher than that of cfDNA (64.7%) for detecting EGFR mutations in NSCLC patients. In EGFR-mutant NSCLC patients with intrathoracic disease (M0/M1a) or cases with low-copy T790M, the positive rate was 63.6% (N = 7/11) and 45.5% (N = 5/11) for short-length exoTNA and cfDNA, respectively. On average, the number absolute mutant copies of short-length exoTNA were 1.5 times higher than that of cfDNA. The mutant allele copies (Ex19del and T790M) in short-length exoTNA were relatively well preserved at 4 weeks after storage. The difference (%) in absolute mutant allele copies (Ex19del) between 0 days and 4 weeks after storage was − 61.0% for cfDNA. Conclusion Target nucleic acids and their size distribution may be critical considerations for selecting an extraction method and a detection assay. A short-length exoTNA (200 bp) contained more detectable tumor-derived nucleic acids than exoDNA (~ 200 bp length or a full-length) or cfDNA. Therefore, a short-length exoTNA as a sensitive biomarker might be useful to detect EGFR mutants for NSCLC patients with low copy number of the mutation target.
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Affiliation(s)
- Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Boyeon Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
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Recent Advances in Droplet-based Microfluidic Technologies for Biochemistry and Molecular Biology. MICROMACHINES 2019; 10:mi10060412. [PMID: 31226819 PMCID: PMC6631694 DOI: 10.3390/mi10060412] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/16/2019] [Accepted: 06/18/2019] [Indexed: 12/16/2022]
Abstract
Recently, droplet-based microfluidic systems have been widely used in various biochemical and molecular biological assays. Since this platform technique allows manipulation of large amounts of data and also provides absolute accuracy in comparison to conventional bioanalytical approaches, over the last decade a range of basic biochemical and molecular biological operations have been transferred to drop-based microfluidic formats. In this review, we introduce recent advances and examples of droplet-based microfluidic techniques that have been applied in biochemistry and molecular biology research including genomics, proteomics and cellomics. Their advantages and weaknesses in various applications are also comprehensively discussed here. The purpose of this review is to provide a new point of view and current status in droplet-based microfluidics to biochemists and molecular biologists. We hope that this review will accelerate communications between researchers who are working in droplet-based microfluidics, biochemistry and molecular biology.
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Hochmair MJ. How can better identification of T790M help to inform treatment sequencing decisions in EGFR mutation-positive non-small-cell lung cancer? Future Oncol 2019; 15:2895-2898. [PMID: 31030557 DOI: 10.2217/fon-2019-0142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Maximilian J Hochmair
- Department of Respiratory & Critical Care Medicine & Ludwig Boltzmann Institute for COPD & Respiratory Epidemiology, Otto Wagner Hospital, 1140 Vienna, Austria
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