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Zhu S, Wu R, Liu X, Xie B, Xie C, Li S, Wu Z, Zhang Z, Tang Z, Gu L. Clinical application of ctDNA in early diagnosis, treatment and prognosis of patients with non-small cell lung cancer. Future Oncol 2024:1-12. [PMID: 39073412 DOI: 10.1080/14796694.2024.2376513] [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: 11/21/2023] [Accepted: 07/02/2024] [Indexed: 07/30/2024] Open
Abstract
Lung cancer is one of the most common malignancies worldwide, with non-small cell lung cancer (NSCLC) being the most common type. As understanding of precise treatment options for NSCLC deepens, circulating tumor DNA (ctDNA) has emerged as a potential biomarker that has become a research hotspot and may represent a new approach for the individualized diagnosis and treatment of NSCLC. This article reviews the applications of ctDNA for the early screening of patients with NSCLC, guiding targeted therapy and immunotherapy, evaluating chemotherapy and postoperative efficacy, assessing prognosis and monitoring recurrence. With the in-depth study of the pathogenesis of NSCLC, plasma ctDNA may become an indispensable part of the precise treatment of NSCLC, which has great clinical application prospects.
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Affiliation(s)
- Shenyu Zhu
- Department of Thoracic Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Key Lab of Brain Injury & Brain Protection, Ganzhou, China
| | - Rongqian Wu
- Department of Endocrinology and Metabolism, Gaoxin Hospital of The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiangjin Liu
- Department of Thoracic Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Bin Xie
- First Clinical Medical College, The Gannan Medical University, Ganzhou, China
| | - Chunfa Xie
- Department of Thoracic Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Key Lab of Brain Injury & Brain Protection, Ganzhou, China
| | - Shulin Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Key Lab of Brain Injury & Brain Protection, Ganzhou, China
| | - Zhicheng Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Key Lab of Brain Injury & Brain Protection, Ganzhou, China
| | - Zuxiong Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Key Lab of Brain Injury & Brain Protection, Ganzhou, China
| | - Zhixian Tang
- Department of Thoracic Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Key Lab of Brain Injury & Brain Protection, Ganzhou, China
| | - Liang Gu
- Department of Thoracic Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Key Lab of Brain Injury & Brain Protection, Ganzhou, China
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Yang M, Mandal E, Liu FX, O’Hara RM, Lesher B, Sanborn RE. Non-small cell lung cancer with MET amplification: review of epidemiology, associated disease characteristics, testing procedures, burden, and treatments. Front Oncol 2024; 13:1241402. [PMID: 38273845 PMCID: PMC10808753 DOI: 10.3389/fonc.2023.1241402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/27/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction Mesenchymal-epidermal transition factor gene amplification (METamp) is being investigated as a therapeutic target in advanced non-small cell lung cancer (NSCLC). We reviewed the epidemiology and disease characteristics associated with primary and secondary METamp, as well as the testing procedures used to identify METamp, in advanced NSCLC. Economic and humanistic burdens, and the practice patterns and treatments under investigation for METamp were also examined. Methods Embase and Medline (via ProQuest), ClinicalTrials.gov, and Cochrane Controlled Register of Trials (2015-2022) were systematically searched. Conference abstracts were searched via Embase and conference proceedings websites (2020-2022). The review focused on evidence from the United States; global evidence was included for identified evidence gaps. Results The median rate of primary METamp in NSCLC across the references was 4.8% (n=4 studies) and of secondary METamp (epidermal growth factor receptor [EGFR]-mutant NSCLC) was 15% (n=10). Next-generation sequencing (NGS; n=12) and/or fluorescence in situ hybridization (FISH; n=11) were most frequently used in real-world studies and FISH testing most frequently used in clinical trials (n=9/10). METamp definitions varied among clinical trials using ISH/FISH testing (MET to chromosome 7 centromere ratio of ≥1.8 to ≥3.0; or gene copy number [GCN] ≥5 to ≥10) and among trials using NGS (tissue testing: GCN ≥6; liquid biopsy: MET copy number ≥2.1 to >5). Limited to no data were identified on the economic and humanistic burdens, and real-world treatment of METamp NSCLC. Promising preliminary results from trials enrolling patients with EGFR-mutated, METamp advanced NSCLC progressing on an EGFR-tyrosine kinase inhibitor (TKI) were observed with MET-TKIs (i.e., tepotinib, savolitinib, and capmatinib) in combination with EGFR-TKIs (i.e., gefitinib and osimertinib). For metastatic NSCLC and high-level METamp, monotherapy with capmatinib, crizotinib, and tepotinib are recommended in the 2022 published NSCLC NCCN Guidelines. Conclusion Primary METamp occurs in approximately 5% of NSCLC cases, and secondary METamp in approximately 15% of cases previously treated with an EGFR inhibitor. Variability in testing methods (including ISH/FISH and NGS) and definitions were observed. Several treatments are promising in treating METamp NSCLC. Additional studies evaluating the clinical, economic, and humanistic burdens are needed.
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Affiliation(s)
- Mo Yang
- North America Evidence and Value Development, North America Medical Affairs, EMD Serono, Inc., Rockland, MA, United States, an affiliate of Merck KGaA
| | - Erin Mandal
- Evidence and Access, OPEN Health, Parsippany, NJ, United States
| | - Frank X. Liu
- North America Evidence and Value Development, North America Medical Affairs, EMD Serono, Inc., Rockland, MA, United States, an affiliate of Merck KGaA
| | - Richard M. O’Hara
- North America Evidence and Value Development, North America Medical Affairs, EMD Serono, Inc., Rockland, MA, United States, an affiliate of Merck KGaA
| | - Beth Lesher
- Evidence and Access, OPEN Health, Parsippany, NJ, United States
| | - Rachel E. Sanborn
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, United States
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Di Sario G, Rossella V, Famulari ES, Maurizio A, Lazarevic D, Giannese F, Felici C. Enhancing clinical potential of liquid biopsy through a multi-omic approach: A systematic review. Front Genet 2023; 14:1152470. [PMID: 37077538 PMCID: PMC10109350 DOI: 10.3389/fgene.2023.1152470] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
In the last years, liquid biopsy gained increasing clinical relevance for detecting and monitoring several cancer types, being minimally invasive, highly informative and replicable over time. This revolutionary approach can be complementary and may, in the future, replace tissue biopsy, which is still considered the gold standard for cancer diagnosis. "Classical" tissue biopsy is invasive, often cannot provide sufficient bioptic material for advanced screening, and can provide isolated information about disease evolution and heterogeneity. Recent literature highlighted how liquid biopsy is informative of proteomic, genomic, epigenetic, and metabolic alterations. These biomarkers can be detected and investigated using single-omic and, recently, in combination through multi-omic approaches. This review will provide an overview of the most suitable techniques to thoroughly characterize tumor biomarkers and their potential clinical applications, highlighting the importance of an integrated multi-omic, multi-analyte approach. Personalized medical investigations will soon allow patients to receive predictable prognostic evaluations, early disease diagnosis, and subsequent ad hoc treatments.
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Huang S, Yang J, Shen N, Xu Q, Zhao Q. Artificial intelligence in lung cancer diagnosis and prognosis: Current application and future perspective. Semin Cancer Biol 2023; 89:30-37. [PMID: 36682439 DOI: 10.1016/j.semcancer.2023.01.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Lung cancer is one of the malignant tumors with the highest incidence and mortality in the world. The overall five-year survival rate of lung cancer is relatively lower than many leading cancers. Early diagnosis and prognosis of lung cancer are essential to improve the patient's survival rate. With artificial intelligence (AI) approaches widely applied in lung cancer, early diagnosis and prediction have achieved excellent performance in recent years. This review summarizes various types of AI algorithm applications in lung cancer, including natural language processing (NLP), machine learning and deep learning, and reinforcement learning. In addition, we provides evidence regarding the application of AI in lung cancer diagnostic and clinical prognosis. This review aims to elucidate the value of AI in lung cancer diagnosis and prognosis as the novel screening decision-making for the precise treatment of lung cancer patients.
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Affiliation(s)
- Shigao Huang
- Department of Radiation Oncology, The First Affiliated Hospital, Air Force Medical University, Xi'an, Shanxi, China
| | - Jie Yang
- Chongqing Industry&Trade Polytechnic, Chongqing, China
| | - Na Shen
- Hong Kong Shue Yan University, Hong Kong, China
| | - Qingsong Xu
- Faculty of Science and Technology, University of Macau, Taipa, Macau SAR, China
| | - Qi Zhao
- Cancer Center, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China; MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau SAR, China.
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Katakami N, Yokoyama T, Morita S, Okamoto T, Urata Y, Hattori Y, Iwamoto Y, Sato Y, Ikeda N, Takahashi T, Daga H, Oguri T, Fujisaka Y, Nishino K, Sugawara S, Kozuki T, Oki M, Yamamoto N, Nakagawa K. Overall survival analysis of patients enrolled in a randomized phase III trial comparing gefitinib and erlotinib for previously treated advanced lung adenocarcinoma (WJOG5108LFS). Int J Clin Oncol 2023; 28:79-88. [PMID: 36414827 DOI: 10.1007/s10147-022-02266-x] [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: 08/03/2022] [Accepted: 11/02/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Since the overall survival (OS) of patients enrolled in the first clinical phase III trial (WJOG5108L) was not recorded owing to time constraints, the present study (WJOG5108LFS) with a longer follow-up (66.6 months) aimed to compare OS of those treated with erlotinib (ER) and gefitinib (GE) for lung adenocarcinoma with epidermal growth factor receptor (EGFR) mutation. METHODS Among 536 enrolled patients, 362 (67.5%) were EGFR mutation-positive, including 182 in the ER arm and 180 in the GE arm. Median survival time (MST) and progression-free survival (PFS) were calculated using Kaplan-Meier survival curves. OS and PFS were determined for patients with EGFR mutation. RESULTS MSTs of ER (n = 182) and GE arms (n = 180) were 31.97 and 27.98 months, respectively (P = 0.3573, hazard ratio = 1.116). MSTs of exon 19 mutation patients in ER (n = 99) and GE arms (n = 89) were 37.49 and 28.91 months, respectively (P = 0.3791). MSTs of L858 mutation patients in ER (n = 82) and GE arms (n = 89) were 22.98 and 27.79 months, respectively (P = 0.7836). In patients with brain metastasis harboring mutation, response rates were 32.8% and 22.2% (P = 0.160), MSTs were 23.46 and 23.89 months (P = 0.7410), and PFS were 9.49 and 6.98 months (P = 0.1481) in the ER (n = 67) and GE arms (n = 72), respectively. CONCLUSIONS No significant differences in OS were observed between the ER and GE arms in all patients with EGFR mutation and those with brain metastasis harboring EGFR mutation.
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Affiliation(s)
- Nobuyuki Katakami
- Division of Medical Oncology, Takarazuka City Hospital, 4-5-1 Kohama, Takarazuka, 665-0827, Japan.
| | | | - Satoshi Morita
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tatsuro Okamoto
- National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | | | | | | | - Yuki Sato
- Kobe City Medical Center General Hospital, Kobe, Japan
| | | | | | | | - Tetsuya Oguri
- Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | | | | | | | - Toshiyuki Kozuki
- National Hospital Organization Shikoku Cancer Center, Matsuyama, Japan
| | - Masahide Oki
- National Hospital Organization Nagoya Medical Center, Nagoya, Japan
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Montella M, Ciani G, Granata V, Fusco R, Grassi F, Ronchi A, Cozzolino I, Franco R, Zito Marino F, Urraro F, Monti R, Sirica R, Savarese G, Chianese U, Nebbioso A, Altucci L, Vietri MT, Nardone V, Reginelli A, Grassi R. Preliminary Experience of Liquid Biopsy in Lung Cancer Compared to Conventional Assessment: Light and Shadows. J Pers Med 2022; 12:jpm12111896. [PMID: 36422072 PMCID: PMC9698369 DOI: 10.3390/jpm12111896] [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: 08/31/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Purpose: To assess the qualitative relationship between liquid biopsy and conventional tissue biopsy. As a secondary target, we evaluated the relationship between the liquid biopsy results and the T stage, N stage, M stage, and compared to grading. Methods: The Local Ethics Committee of the “Università degli Studi della Campania Luigi Vanvitelli”, with the internal resolution number 24997/2020 of 12.11.2020, approved this spontaneous prospective study. According to the approved protocol, patients with lung cancer who underwent Fine-Needle Aspiration Cytology (FNAC), CT-guided biopsy, and liquid biopsy were enrolled. A Yates chi-square test was employed to analyze differences in percentage values of categorical variables. A p-value < 0.05 was considered statistically significant. Data analysis was performed using the Matlab Statistic Toolbox (The MathWorks, Inc., Natick, MA, USA). Results: When a genetic mutation is present on the pathological examination, this was also detected on the liquid biopsy. ROS1 and PDL1 mutations were found in 2/29 patients, while EGFR Exon 21 was identified in a single patient. At liquid biopsy, 26 mutations were identified in the analyzed samples. The mutations with the highest prevalence rate in the study populations were: ALK (Ile1461Val), found in 28/29 patients (96.6%), EML4 (Lys398Arg), identified in 16/29 (55.2%) patients, ALK (Asp1529Glu), found in 14/29 (48.3%) patients, EGFR (Arg521Lys), found in 12/29 (41.4%) patients, ROS (Lys2228Gln), identified in 11/29 (37.9%) patients, ROS (Arg167Gln) and ROS (Ser2229Cys), identified in 10/29 (34.5%) patients, ALK (Lys1491Arg) and PIK3CA (Ile391Met), identified in 8/29 (27.6%) patients, ROS (Thr145Pro), identified in 6/29 (20.7%) patients, and ROS (Ser1109Leu), identified in 4/29 (13.8%) patients. No statistically significant differences can be observed in the mutation rate between the adenocarcinoma population and the squamous carcinoma population (p > 0.05, Yates chi-square test). Conclusions: We showed that, when a genetic mutation was detected in pathological examination, this was always detected by liquid biopsy, demonstrating a very high concordance rate of genomic testing between tissues and their corresponding mutations obtained by liquid biopsy, without cases of false-negative results. In addition, in our study, liquid biopsy highlighted 26 mutations, with the prevalence of ALK mutation in 96.6% of patients, supporting the idea that this approach could be an effective tool in cases with insufficient tumor tissue specimens or in cases where tissue specimens are not obtainable.
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Affiliation(s)
- Marco Montella
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Giovanni Ciani
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Vincenza Granata
- Division of Radiology, Istituto Nazionale Tumori IRCCS Fondazione Pascale-IRCCS di Napoli, 80131 Naples, Italy
| | - Roberta Fusco
- Medical Oncology Division, Igea SpA, 80013 Napoli, Italy
| | - Francesca Grassi
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
- Correspondence:
| | - Andrea Ronchi
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Immacolata Cozzolino
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Renato Franco
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Federica Zito Marino
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Fabrizio Urraro
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Riccardo Monti
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Roberto Sirica
- AMES-Centro Polidiagnostico Strumentale, SRL, 80013 Naples, Italy
| | | | - Ugo Chianese
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Angela Nebbioso
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Lucia Altucci
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Maria Teresa Vietri
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Valerio Nardone
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Alfonso Reginelli
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Roberta Grassi
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
- Italian Society of Medical and Interventional Radiology (SIRM), SIRM Foundation, 20122 Milan, Italy
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Liu S, Wang J. Current and Future Perspectives of Cell-Free DNA in Liquid Biopsy. Curr Issues Mol Biol 2022; 44:2695-2709. [PMID: 35735625 PMCID: PMC9222159 DOI: 10.3390/cimb44060184] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022] Open
Abstract
A liquid biopsy is a minimally invasive or non-invasive method to analyze a range of tumor material in blood or other body fluids, including circulating tumor cells (CTCs), cell-free DNA (cfDNA), messenger RNA (mRNA), microRNA (miRNA), and exosomes, which is a very promising technology. Among these cancer biomarkers, plasma cfDNA is the most widely used in clinical practice. Compared with a tissue biopsy of traditional cancer diagnosis, in assessing tumor heterogeneity, a liquid biopsy is more reliable because all tumor sites release cfDNA into the blood. Therefore, a cfDNA liquid biopsy is less invasive and comprehensive. Moreover, the development of next-generation sequencing technology makes cfDNA sequencing more sensitive than a tissue biopsy, with higher clinical applicability and wider application. In this publication, we aim to review the latest perspectives of cfDNA liquid biopsy clinical significance and application in cancer diagnosis, treatment, and prognosis. We introduce the sequencing techniques and challenges of cfDNA detection, analysis, and clinical applications, and discuss future research directions.
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Peng Y, Mei W, Ma K, Zeng C. Circulating Tumor DNA and Minimal Residual Disease (MRD) in Solid Tumors: Current Horizons and Future Perspectives. Front Oncol 2021; 11:763790. [PMID: 34868984 PMCID: PMC8637327 DOI: 10.3389/fonc.2021.763790] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022] Open
Abstract
Circulating tumor DNA (ctDNA) is cell-free DNA (cfDNA) fragment in the bloodstream that originates from malignant tumors or circulating tumor cells. Recently, ctDNA has emerged as a promising non-invasive biomarker in clinical oncology. Analysis of ctDNA opens up new avenues for individualized cancer diagnosis and therapy in various types of tumors. Evidence suggests that minimum residual disease (MRD) is closely associated with disease recurrence, thus identifying specific genetic and molecular alterations as novel MRD detection targets using ctDNA has been a research focus. MRD is considered a promising prognostic marker to identify individuals at increased risk of recurrence and who may benefit from treatment. This review summarizes the current knowledge of ctDNA and MRD in solid tumors, focusing on the potential clinical applications and challenges. We describe the current state of ctDNA detection methods and the milestones of ctDNA development and discuss how ctDNA analysis may be an alternative for tissue biopsy. Additionally, we evaluate the clinical utility of ctDNA analysis in solid tumors, such as recurrence risk assessment, monitoring response, and resistance mechanism analysis. MRD detection aids in assessing treatment response, patient prognosis, and risk of recurrence. Moreover, this review highlights current advancements in utilizing ctDNA to monitor the MRD of solid tumors such as lung cancer, breast cancer, and colon cancer. Overall, the clinical application of ctDNA-based MRD detection can assist clinical decision-making and improve patient outcomes in malignant tumors.
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Affiliation(s)
- Yan Peng
- Department of Obstetrics, Longhua District Central Hospital, Shenzhen, China
| | - Wuxuan Mei
- Clinical Medical College, Hubei University of Science and Technology, Xianning, China
| | - Kaidong Ma
- Department of Obstetrics, Longhua District Central Hospital, Shenzhen, China
| | - Changchun Zeng
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen, China
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Lin J, Li M, Chen S, Weng L, He Z. Efficacy and Safety of First-Generation EGFR-TKIs Combined with Chemotherapy for Treatment-Naïve Advanced Non-Small-Cell Lung Cancer Patients Harboring Sensitive EGFR Mutations: A Single-Center, Open-Label, Single-Arm, Phase II Clinical Trial. J Inflamm Res 2021; 14:2557-2567. [PMID: 34168480 PMCID: PMC8216733 DOI: 10.2147/jir.s313056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/02/2021] [Indexed: 12/26/2022] Open
Abstract
Purpose This single-center, open-label, single-arm, phase II clinical trial aimed to examine the efficacy and safety of the first-generation EGFR-TKIs combined with chemotherapy among treatment-naïve advanced non-small-cell lung cancer (NSCLC) patients harboring sensitive EGFR mutations. Materials and Methods Patients with advanced EGFR-mutant NSCLC were given concurrent gefitinib (250 mg orally daily) and 3-week cycle of carboplatin plus pemetrexed for 4 to 6 cycles, followed by gefitinib maintenance until disease progression or unacceptable toxicity. The primary endpoint was progression-free survival (PFS), and the secondary endpoints were overall survival (OS), objective response rate (ORR), disease control rate (DCR) and safety. This trial was registered at ClinicalTrials.gov (NCT02886195). Results Of the 21 patients enrolled in this study, a 76.2% ORR and 100% DCR were observed and a higher ORR was seen in patients with EGFR 21L858R mutations than in those with 19del mutations (P = 0.012). The subjects had a median PFS of 15.0 months and a median OS of 26.0 months, and numerically longer PFS was seen in patients with EGFR 21L858R mutations than in those with 19del mutations (P = 0.281). There were 15 NSCLC patients without cerebral metastases at baseline, with 4 cases developing cerebral metastases during the treatment, and the 6-, 12- and 24-month cumulative incidence rates of the central nervous system metastasis were 6.67%, 13.3% and 26.7%, respectively. There were 17 subjects with progressive diseases tested for EGFR T790M mutations, and 11 cases were positive for T790M mutations. Grade 3 toxicity included neutropenia (9.5%), leukopenia (4.8%), liver dysfunction (9.5%) and diarrhea (4.8%), and no grade 4 adverse events or treatment-related death occurred. Conclusion The combination of first-generation EGFR-TKIs and chemotherapy achieves a satisfactory PFS, ORR and DCR and well-tolerated toxicity in advanced NSCLC patients with EGFR mutations, notably in patients with EGFR L858R mutations.
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Affiliation(s)
- Jinghui Lin
- Department of Thoracic Medical Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou City, Fujian Province, 350014, People's Republic of China
| | - Meifang Li
- Department of Thoracic Medical Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou City, Fujian Province, 350014, People's Republic of China
| | - Shijie Chen
- Department of Thoracic Medical Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou City, Fujian Province, 350014, People's Republic of China
| | - Lihong Weng
- Department of Thoracic Medical Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou City, Fujian Province, 350014, People's Republic of China
| | - Zhiyong He
- Department of Thoracic Medical Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou City, Fujian Province, 350014, People's Republic of China
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Kato R, Hayashi H, Sakai K, Suzuki S, Haratani K, Takahama T, Tanizaki J, Nonagase Y, Tanaka K, Yoshida T, Takeda M, Yonesaka K, Kaneda H, Nishio K, Nakagawa K. CAPP-seq analysis of circulating tumor DNA from patients with EGFR T790M-positive lung cancer after osimertinib. Int J Clin Oncol 2021; 26:1628-1639. [PMID: 34117553 DOI: 10.1007/s10147-021-01947-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/25/2021] [Indexed: 01/16/2023]
Abstract
BACKGROUND We here applied cancer personalized profiling by deep sequencing (CAPP-seq) to analysis of circulating tumor DNA (ctDNA) to identify resistance mechanisms in osimertinib-treated patients with EGFR T790M-positive non-small cell lung cancer (NSCLC). METHODS The study included patients with EGFR activating mutation-positive advanced NSCLC who were positive for T790M in tumor tissue or plasma after previous treatment with an EGFR tyrosine kinase inhibitor, who received osimertinib at Kindai University Hospital between August 2014 and September 2017, and for whom plasma collected after progression on osimertinib was available. Clinical data were extracted from medical records. Patients with innate resistance to osimertinib were defined as those whose best response was progressive disease or stable disease for < 6 months, whereas patients with a complete or partial response or stable disease for > 6 months were considered as having acquired resistance. RESULTS We performed CAPP-seq for 20 patients at progression on osimertinib. Distinct patterns of genomic alterations were apparent in patients with innate versus acquired resistance. Mutations in PIK3CA, KRAS, or BRAF and copy number gain for EGFR, ERBB2, or MET were more common in patients with innate resistance than in those with acquired resistance. In addition, one patient who underwent a repeat biopsy was found to harbor the C797S mutation of EGFR after disease progression during osimertinib rechallenge, with this mutation not having been detected at the time of initial progression on osimertinib. CONCLUSIONS CAPP-seq analysis of ctDNA was able to identify potentially targetable genetic alterations in patients with osimertinib resistance.
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Affiliation(s)
- Ryoji Kato
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Hidetoshi Hayashi
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan.
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Shinichiro Suzuki
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Koji Haratani
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Takayuki Takahama
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
- Department of Medical Oncology, Kindai University Nara Hospital, 1248-1 Otoda-cho, Ikoma, Nara, 630-0293, Japan
| | - Junko Tanizaki
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
- Department of Medical Oncology, Kishiwada City Hospital, 1001 Gakuhara-cho, Kishiwada-shi, Osaka, 596-8501, Japan
| | - Yoshikane Nonagase
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
- Department of Medical Oncology, Kishiwada City Hospital, 1001 Gakuhara-cho, Kishiwada-shi, Osaka, 596-8501, Japan
| | - Kaoru Tanaka
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Takeshi Yoshida
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Masayuki Takeda
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Kimio Yonesaka
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Hiroyasu Kaneda
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
- Department of Clinical Oncology, Graduate School of Medicine, Osaka City University, 1-4-3 Asahi-machi, Abeno-ku, Osaka City, Osaka, 545-8585, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
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11
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Obradovic J, Todosijevic J, Jurisic V. Application of the conventional and novel methods in testing EGFR variants for NSCLC patients in the last 10 years through different regions: a systematic review. Mol Biol Rep 2021; 48:3593-3604. [PMID: 33973139 DOI: 10.1007/s11033-021-06379-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/24/2021] [Indexed: 12/12/2022]
Abstract
Variants in the epidermal growth factor receptor (EGFR) gene are recognized as predictors of therapy response and are correlated with progression-free and overall survival in non-small cell lung cancer (NSCLC) patients. Molecularly guided therapy needs precise and cost-effective molecular tests. This review focused primarily on screening or target methods for the EGFR variants detection with diagnostic and prognostic potential in the clinical research published papers. Concerning the inclusion and exclusion criteria, the search interval comprised available articles published from 2010 until 2020 in three electronic databases, ISI Web of Science, Pub Med, and Scopus. The analysis of eligible studies started with 5647 and obtained the final 987 full-text articles analyzed as clinical research. The regions comprised were Africa, America, Australia, Asia, Euro-Asia, Europe, or a consortium of different countries. All of the tested methods were applied prevalently in Asia. In clinical research, the polymerase chain reaction (PCR), followed by sequencing methods have been involved mostly over the years. The identified high-through output approaches evolved to improve the survival and quality of the NSCLC patient's life becoming more sensitive, specific, and cost-effective.
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Affiliation(s)
- Jasmina Obradovic
- Department of Sciences, Institute for Information Technologies Kragujevac, University of Kragujevac, Kragujevac, Serbia
| | - Jovana Todosijevic
- Faculty of Science, Institute of Biology and Ecology, University of Kragujevac, Kragujevac, Serbia
| | - Vladimir Jurisic
- Faculty of Medical Sciences, University of Kragujevac, 34000, Kragujevac, Serbia.
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12
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Vaclova T, Grazini U, Ward L, O'Neill D, Markovets A, Huang X, Chmielecki J, Hartmaier R, Thress KS, Smith PD, Barrett JC, Downward J, de Bruin EC. Clinical impact of subclonal EGFR T790M mutations in advanced-stage EGFR-mutant non-small-cell lung cancers. Nat Commun 2021; 12:1780. [PMID: 33741979 PMCID: PMC7979775 DOI: 10.1038/s41467-021-22057-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
Advanced non-small-cell lung cancer (NSCLC) patients with EGFR T790M-positive tumours benefit from osimertinib, an epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI). Here we show that the size of the EGFR T790M-positive clone impacts response to osimertinib. T790M subclonality, as assessed by a retrospective NGS analysis of 289 baseline plasma ctDNA samples from T790M-positive advanced NSCLC patients from the AURA3 phase III trial, is associated with shorter progression-free survival (PFS), both in the osimertinib and the chemotherapy-treated patients. Both baseline and longitudinal ctDNA profiling indicate that the T790M subclonal tumours are enriched for PIK3CA alterations, which we demonstrate to confer resistance to osimertinib in vitro that can be partially reversed by PI3K pathway inhibitors. Overall, our results elucidate the impact of tumour heterogeneity on response to osimertinib in advanced stage NSCLC patients and could help define appropriate combination therapies in these patients.
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Affiliation(s)
- Tereza Vaclova
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | | | - Lewis Ward
- Discovery Science, BioPharmaceutical R&D, AstraZeneca, Cambridge, UK
| | - Daniel O'Neill
- Discovery Science, BioPharmaceutical R&D, AstraZeneca, Cambridge, UK
| | | | - Xiangning Huang
- Biometrics Oncology, Oncology R&D, AstraZeneca, Cambridge, UK
| | | | - Ryan Hartmaier
- Translational Medicine, Oncology R&D, AstraZeneca, Boston, MA, USA
| | - Kenneth S Thress
- Translational Medicine, Oncology R&D, AstraZeneca, Boston, MA, USA
- Global Marketing Diagnostics, Oncology Business, AstraZeneca, Gaithersburg, MD, USA
| | - Paul D Smith
- Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
| | - J Carl Barrett
- Translational Medicine, Oncology R&D, AstraZeneca, Boston, MA, USA
| | | | - Elza C de Bruin
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK.
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13
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Peng W, Pu X, Jiang M, Wang J, Li J, Li K, Xu Y, Xu F, Chen B, Wang Q, Cao J, Chen Y, Wu L. Dacomitinib induces objective responses in metastatic brain lesions of patients with EGFR-mutant non-small-cell lung cancer: A brief report. Lung Cancer 2020; 152:66-70. [PMID: 33352385 DOI: 10.1016/j.lungcan.2020.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/27/2020] [Accepted: 12/07/2020] [Indexed: 11/18/2022]
Abstract
OBJECTIVE Dacomitinib is a potent, irreversible and pan-HER tyrosine kinase inhibitor (TKI) of epidermal growth factor receptor (EGFR) mutant non-small cell lung cancer (NSCLC). Currently, evidence of its activity on brain metastasis is lacking. MATERIALS AND METHODS NSCLC patients diagnosed at Hunan Cancer Hospital between July, 2019 and July, 2020 with enhanced MRI-detected brain metastasis prior to treatment and laboratory-confirmed EGFR mutations were reviewed. In total, 14 EGFR-mutant NSCLC patients with brain metastasis were treated with first-line dacomitinib. The first radiographic review of chest CT and brain MRI was after one month and thereafter every 2 months. The objective response rate (ORR) and the depth of the brain metastasis response were determined via RECIST 1.1 and RANO-LM criteria. RESULTS In total, 14 of 59 EGFR-mutant advanced NSCLC patients who received first-line dacomitinib therapy had brain metastasis before treatment. Among these patients, 5 were given a dacomitinib starting dose of 45 mg once daily, while 9 received 30 mg daily until disease progression or unbearable toxicity. Eight patients harbored EGFR 19del, 5 had EGFR L858R, and one patient had EGFR G719A and I706 T co-mutations. The median duration of follow-up was 4.5 months. All patients received at least one review. The ORR was 92.9 % (13/14) and the disease control rate (DCR) was 100 %. A measurable response of the intracranial metastases was observed in 12 of 14 patients (85.7 %), including 12 of 13 (92.3 %) with brain parenchymal metastasis, but the one patient with meningeal metastasis did not respond well. All patients (100 %) had grade 1-2 adverse effects, but none discontinued treatment or required a dosage adjustment. CONCLUSIONS This case series study of 14 patients has shown that dacomitinib has potent efficacy for central nervous system (CNS) metastasis in EGFR-positive NSCLC. More data are required to confirm its advantages and optimize its clinical application.
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Affiliation(s)
- Wenying Peng
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital / The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000, PR China
| | - Xingxiang Pu
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital / The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000, PR China
| | - Meilin Jiang
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital / The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000, PR China
| | - Jingyi Wang
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital / The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000, PR China
| | - Jia Li
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital / The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000, PR China
| | - Kang Li
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital / The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000, PR China
| | - Yan Xu
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital / The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000, PR China
| | - Fang Xu
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital / The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000, PR China
| | - Bolin Chen
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital / The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000, PR China
| | - Qianzhi Wang
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital / The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000, PR China
| | - Jun Cao
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital / The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000, PR China
| | - Yong Chen
- Department of Oncology, The Central Hospital of Shaoyang City, No. 36, Qianyuan Alley, Shaoyang, 422000, PR China
| | - Lin Wu
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital / The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410000, PR China.
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14
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Sakai K, Takahama T, Shimokawa M, Azuma K, Takeda M, Kato T, Daga H, Okamoto I, Akamatsu H, Teraoka S, Ono A, Ohira T, Yokoyama T, Yamamoto N, Nakagawa K, Nishio K. Predicting osimertinib-treatment outcomes through EGFR mutant-fraction monitoring in the circulating tumor DNA of EGFR T790M-positive patients with non-small cell lung cancer (WJOG8815L). Mol Oncol 2020; 15:126-137. [PMID: 33131198 PMCID: PMC7782093 DOI: 10.1002/1878-0261.12841] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 02/01/2023] Open
Abstract
The WJOG8815L phase II clinical study involves patients with non‐small cell lung cancer (NSCLC) that harbored the EGFR T790M mutation, which confers resistance to EGFR tyrosine kinase inhibitors (TKIs). The purpose of this study was to assess the predictive value of monitoring EGFR genomic alterations in circulating tumor DNA (ctDNA) from patients with NSCLC that undergo treatment with the third‐generation EGFR‐TKI osimertinib. Plasma samples of 52 patients harboring the EGFR T790M mutation were obtained pretreatment (Pre), on day 1 of treatment cycle 4 (C4) or cycle 9 (C9), and at diagnosis of disease progression or treatment discontinuation (PD/stop). CtDNA was screened for EGFR‐TKI‐sensitizing mutations, the EGFR T790M mutation, and other genomic alterations using the cobas EGFR Mutation Test v2 (cobas), droplet digital PCR (ddPCR), and targeted deep sequencing. Analysis of the sensitizing—and T790M—EGFR mutant fractions (MFs) was used to determine tumor mutational burden. Both MFs were found to decrease during treatment, whereas rebound of the sensitizing EGFR MF was observed at PD/stop, suggesting that osimertinib targeted both T790M mutation‐positive tumors and tumors with sensitizing EGFR mutations. Significant differences in the response rates and progression‐free survival were observed between the sensitizing EGFR MF‐high and sensitizing EGFR MF‐low groups (cutoff: median) at C4. In conclusion, ctDNA monitoring for sensitizing EGFR mutations at C4 is suitable for predicting the treatment outcomes in NSCLC patients receiving osimertinib (Clinical Trial Registration No.: UMIN000022076).
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Affiliation(s)
- Kazuko Sakai
- Department of Genome Biology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Takayuki Takahama
- Department of Medical Oncology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Mototsugu Shimokawa
- Department of Biostatistics, Yamaguchi University Graduate School of Medicine, Yamaguchi, Japan
| | - Koichi Azuma
- Division of Respirology, Neurology, and Rheumatology, Department of Internal Medicine, Kurume University School of Medicine, Fukuoka, Japan
| | - Masayuki Takeda
- Department of Medical Oncology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Terufumi Kato
- Department of Thoracic Oncology, Kanagawa Cancer Center, Yokohama, Japan
| | - Haruko Daga
- Department of Medical Oncology, Osaka City General Hospital, Osaka, Japan
| | - Isamu Okamoto
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroaki Akamatsu
- Internal Medicine III, Wakayama Medical University, Wakayama, Japan
| | - Shunsuke Teraoka
- Internal Medicine III, Wakayama Medical University, Wakayama, Japan
| | - Akira Ono
- Division of Thoracic Oncology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Tatsuo Ohira
- Department of Surgery, Tokyo Medical University, Tokyo, Japan
| | - Toshihide Yokoyama
- Department of Respiratory Medicine, Kurashiki Central Hospital, Okayama, Japan
| | | | - Kazuhiko Nakagawa
- Department of Medical Oncology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Faculty of Medicine, Kindai University, Osaka, Japan
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15
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Comparison of Target Enrichment Platforms for Circulating Tumor DNA Detection. Sci Rep 2020; 10:4124. [PMID: 32139724 PMCID: PMC7057974 DOI: 10.1038/s41598-020-60375-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/04/2020] [Indexed: 12/20/2022] Open
Abstract
Cancer-related mortality of solid tumors remains the major cause of death worldwide. Circulating tumor DNA (ctDNA) released from cancer cells harbors specific somatic mutations. Sequencing ctDNA opens opportunities to non-invasive population screening and lays foundations for personalized therapy. In this study, two commercially available platforms, Roche’s Avenio ctDNA Expanded panel and QIAgen’s QIAseq Human Comprehensive Cancer panel were compared for (1) panel coverage of clinically relevant variants; (2) target enrichment specificity and sequencing performance; (3) the sensitivity; (4) concordance and (5) sequencing coverage using the same human blood sample with ultra-deep next-generation sequencing. Our finding suggests that Avenio detected somatic mutations in common cancers in over 70% of patients while QIAseq covered nearly 90% with a higher average number of variants per patient (Avenio: 3; QIAseq: 8 variants per patient). Both panels demonstrated similar on-target rate and percentage of reads mapped. However, Avenio had more uniform sequencing coverage across regions with different GC content. Avenio had a higher sensitivity and concordance compared with QIAseq at the same sequencing depth. This study identifies a unique niche for the application of each of the panel and allows the scientific community to make an informed decision on the technologies to meet research or application needs.
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16
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Noguchi T, Sakai K, Iwahashi N, Matsuda K, Matsukawa H, Yahata T, Toujima S, Nishio K, Ino K. Changes in the gene mutation profiles of circulating tumor DNA detected using CAPP-Seq in neoadjuvant chemotherapy-treated advanced ovarian cancer. Oncol Lett 2020; 19:2713-2720. [PMID: 32218822 PMCID: PMC7068231 DOI: 10.3892/ol.2020.11356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/03/2019] [Indexed: 01/09/2023] Open
Abstract
Cancer Personalized Profiling by deep Sequencing (CAPP-Seq) is a novel ultrasensitive next-generation sequencing-based approach that is used to detect circulating tumor DNA (ctDNA). The aim of the present study was to compare the gene mutation profiles and blood tumor mutation burden (bTMB) measured between pre- and post-neoadjuvant chemotherapy (NAC), utilizing CAPP-seq for plasma ctDNA in patients with advanced ovarian cancer. The current study included 10 patients (6 NAC-sensitive and 4 NAC-resistant) clinically diagnosed as having stage III or IV ovarian cancer and were administered NAC between May 2017 and February 2019. The plasma ctDNA samples were collected at pre- and post-NAC, and comprehensive gene mutation analysis was performed using CAPP-seq. In 5 out of 6 NAC-sensitive cases, the variant allele frequency (VAF) of non-synonymous somatic mutations decreased following NAC. In 2 out of the 4 NAC-resistant cases, the VAF of non-synonymous somatic mutations increased, and new somatic mutations emerged following NAC. In regard to TP53 mutation, the rate of TP53 mutation in the NAC-resistant cases was significantly higher compared with NAC-sensitive cases. Finally, the bTMB decreased significantly after NAC treatment in the NAC-sensitive cases, even though there were no significant differences in the pretreatment bTMB levels between the NAC-sensitive and NAC-resistant cases. These results indicated that gene mutation can be profiled and monitored using liquid biopsy-based CAPP-Seq in patients with advanced ovarian cancer with NAC treatment, and TP53 mutation in the ctDNA and bTMB may be novel biomarkers that can be used for patient monitoring during NAC treatment.
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Affiliation(s)
- Tomoko Noguchi
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka 589-8511, Japan
| | - Naoyuki Iwahashi
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Kaho Matsuda
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Hitomi Matsukawa
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Tamaki Yahata
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Saori Toujima
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka 589-8511, Japan
| | - Kazuhiko Ino
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
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