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Murata Y, Nakajima Y, Sato Y, Hizawa N, Yamakawa D, Matsubara D, Noguchi M, Minami Y. High-efficiency EGFR genotyping using cell-free DNA in bronchial washing fluid. Jpn J Clin Oncol 2024; 54:681-688. [PMID: 38476004 PMCID: PMC11144292 DOI: 10.1093/jjco/hyae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/26/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND EGFR mutation testing is required for treatment of lung adenocarcinoma using epidermal growth factor receptor-tyrosine kinase inhibitor. However, the amounts of tumor tissue or tumor cells obtained by bronchoscopy are often insufficient. Bronchial washing fluid, obtained by lavage with saline after tumor biopsy or brushing, and the supernatant of bronchial washing fluid are thought to contain cell-free DNA that would be potentially applicable for EGFR testing. METHODS From among patients with suspected adenocarcinoma or non-small cell lung carcinoma diagnosed from biopsy or surgical specimens at the University of Tsukuba Hospital between 2015 and 2019, cell-free DNAs from 80 specimens of supernatant of bronchial washing fluid (50 with EGFR mutation and 30 with wild type EGFR) and 8 blood serum samples were examined for EGFR mutation using droplet digital PCR. RESULTS Among the 50 patients harboring EGFR mutation, the rate of positivity for cell-free DNA extracted from supernatant of bronchial washing fluid was 80% (40/50). In nine of the EGFR mutation-positive cases, tumor cells were not detected by either biopsy or cytology, but the mutation was detected in four cases (4/9, 44%). Comparison of the cell-free DNA mutation detection rate between supernatant of bronchial washing fluid and blood serum in six cases showed that mutations were detected from the former in all cases (6/6, 100%), but from the latter in only one case (1/6, 17%). CONCLUSIONS Using supernatant of bronchial washing fluid samples, the detection rate of EGFR mutation was high, and EGFR mutations were detectable even when no tumor cells had been detectable by biopsy or cytology. Supernatant of bronchial washing fluid might be an effective sample source for EGFR mutation testing.
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Affiliation(s)
- Yoshihiko Murata
- Department of Pathology, University of Tsukuba Hospital, Tsukuba, Ibaraki, Japan
| | - Yumi Nakajima
- School of Medicine and Health Science, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yukio Sato
- Department of Thoracic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Nobuyuki Hizawa
- Division of Respiratory Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Daichi Yamakawa
- Department of Pathology, Naritatomisato Tokushukai Hospital, Tomisato, Chiba, Japan
| | - Daisuke Matsubara
- Department of Pathology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masayuki Noguchi
- Department of Pathology, Naritatomisato Tokushukai Hospital, Tomisato, Chiba, Japan
- Clinical Cancer Research Division, Shonan Research Institute of Innovative Medicine, Fujisawa, Kanagawa, Japan
| | - Yuko Minami
- Department of Pathology, University of Tsukuba Hospital, Tsukuba, Ibaraki, Japan
- Department of Pathology, National Hospital Organization, Ibarakihigashi National Hospital, The Center of Chest Disease and Severe Motor & Intellectual Disabilities, Naka-gun, Ibaraki, Japan
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2
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Sato Y. Clinical utility of liquid biopsy-based companion diagnostics in the non-small-cell lung cancer treatment. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2022; 3:630-642. [PMID: 36338524 PMCID: PMC9630093 DOI: 10.37349/etat.2022.00104] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/12/2022] [Indexed: 12/04/2022] Open
Abstract
Recently, technological advances in the detection and biological characterization of circulating tumor DNA (ctDNA) have enabled the implementation of liquid biopsy testing into clinical practice. Methods for analysis of liquid biopsies have rapidly evolved over the past few years and have continued to advance, thus providing details about tumor biological characteristics such as tumor progression, metastasis, tumor heterogeneity, genomic mutation profile, clonal evolution, etc. In tandem with technological advances, the implementation of liquid biopsy in routine clinical settings has proceeded. In 2016, the Food and Drug Administration (FDA) approved the first ctDNA liquid biopsy test to detect epidermal growth factor receptor (EGFR) gene mutations in patients with non-small-cell lung cancer (NSCLC) as a companion diagnostic for molecular targeted drug of EGFR-tyrosine kinase inhibitor (TKI, EGFR-TKI). More recently, multigene panel assays of liquid biopsy have been approved as companion diagnostics and have been used in routine clinical settings. The estimation of blood tumor mutation burden (bTMB) to predict the efficacy of immune checkpoint inhibitor (ICI) treatment can be one of the promising approaches to liquid biopsy. The next stage of implementation of liquid biopsy for routine clinical settings is for monitoring of ctDNA after surgical treatment to predict prognosis and to detect disease relapse earlier than conventional imaging diagnosis. Its clinical utility is under assessment in several clinical trials. This review introduces recent advances in liquid biopsy methodology, the development of biomarkers, and its clinical utility in the treatment of NSCLC patients.
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Affiliation(s)
- Yoshiharu Sato
- DNA Chip Research Inc., Tokyo 105-0022, Japan,Correspondence: Yoshiharu Sato, DNA Chip Research Inc., 1-15-1 Kaigan, Minato-ku, Tokyo 105-0022, Japan.
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Jin Y, Chen Z, Chen Q, Sha L, Shen C. [Role and Significance of Bioactive Substances in Sputum
in the Diagnosis of Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2021; 24:867-873. [PMID: 34923805 PMCID: PMC8695240 DOI: 10.3779/j.issn.1009-3419.2021.102.46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
肺癌是我国目前发病率最高的恶性肿瘤之一,其诊断的金标准需要进行组织活检的病理学检查或脱落细胞学检查,二者的有创性和敏感性限制了他们的使用。痰液中含有大量核酸、蛋白质,是肺功能的良好反映物,肺癌组织也会影响痰液中的生物成分,检测其中的生物活性物质可有助于肺癌的诊断。本文综合目前国内外的研究结果,对痰液中可用于肺癌诊断的生物活性物质做一综述。
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Affiliation(s)
- Yuming Jin
- West China School of Medicine, Sichuan University, Chengdu 610041, China
| | - Zixuan Chen
- West China School of Medicine, Sichuan University, Chengdu 610041, China
| | - Quan Chen
- West China School of Medicine, Sichuan University, Chengdu 610041, China
| | - Leihao Sha
- West China School of Medicine, Sichuan University, Chengdu 610041, China
| | - Cheng Shen
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
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4
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Malapelle U, Pisapia P, Addeo A, Arrieta O, Bellosillo B, Cardona AF, Cristofanilli M, De Miguel-Perez D, Denninghoff V, Durán I, Jantus-Lewintre E, Nuzzo PV, O'Byrne K, Pauwels P, Pickering EM, Raez LE, Russo A, Serrano MJ, Gandara DR, Troncone G, Rolfo C. Liquid biopsy from research to clinical practice: focus on non-small cell lung cancer. Expert Rev Mol Diagn 2021; 21:1165-1178. [PMID: 34570988 DOI: 10.1080/14737159.2021.1985468] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION In the current era of personalized medicine, liquid biopsy has acquired a relevant importance in patient management of advanced stage non-small cell lung cancer (NSCLC). As a matter of fact, liquid biopsy may supplant the problem of inadequate tissue for molecular testing. The term 'liquid biopsy' refers to a number of different biological fluids, but is most clearly associated with plasma-related platforms. It must be taken into account that pre-analytical processing and the selection of the appropriate technology according to the clinical context may condition the results obtained. In addition, novel clinical applications beyond the evaluation of the molecular status of predictive biomarkers are currently under investigation. AREAS COVERED This review summarizes the available evidence on pre-analytical issues and different clinical applications of liquid biopsies in NSCLC patients. EXPERT OPINION Liquid biopsy should be considered not only as a valid alternative but as complementary to tissue-based molecular approaches. Careful attention should be paid to the optimization and standardization of all phases of liquid biopsy samples management in order to determine a significant improvement in either sensitivity or specificity, while significant reducing the number of 'false negative' or 'false positive' molecular results.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico Ii, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico Ii, Naples, Italy
| | - Alfredo Addeo
- Oncology Department, University Hospital Geneva, Geneva, Switzerland
| | - Oscar Arrieta
- Thoracic Oncology Unit, Instituto Nacional de Cancerología (INCan), México City, México
| | - Beatriz Bellosillo
- Department of Pathology, Hospital Del Mar, Barcelona, Spain.,Department of Pathology, Ciberonc, Madrid, Spain
| | - Andres F Cardona
- Department of Oncology, Clinical and Translational Oncology Group, Clínica Del Country, Bogotá, Colombia.,Department of Oncology, Foundation for Clinical and Applied Cancer Research (Ficmac), Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (Fox-g/oncolgroup), Universidad el Bosque, Bogotá, Colombia
| | - Massimo Cristofanilli
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Diego De Miguel-Perez
- GENyO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, Liquid Biopsy and Cancer Interception Group, Granada, Spain.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Valeria Denninghoff
- Department of Pathology, University of Buenos Aires - National Council for Scientific and Technical Research (Conicet), Buenos Aires, Argentina
| | - Ignacio Durán
- Department of Oncology, Hospital Universitario Marques de Valdecilla, IDIVAL, Santander, Spain
| | - Eloísa Jantus-Lewintre
- Department of Pathology, Ciberonc, Madrid, Spain.,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 Biotechnology, Universitat Politècnica De València, Valencia, Spain
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, The Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ken O'Byrne
- Medical Oncology, Princess Alexandra Hospital, Queensland University of Technology, Brisbane City, Australia
| | - Patrick Pauwels
- Center for Oncological Research Antwerp (Core), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp (Uantwerp), Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Edward M Pickering
- Divison of Pulmonary and Critical Care Medicine, Section of Interventional Pulmonology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Luis E Raez
- Thoracic Oncology Program, Memorial Cancer Institute/Memorial Health Care System, Florida International University, Miami, FL, USA
| | - Alessandro Russo
- Department of Oncology, Medical Oncology Unit, A.O. Papardo, Messina, Italy
| | - Maria José Serrano
- GENyO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, Liquid Biopsy and Cancer Interception Group, Granada, Spain
| | - David R Gandara
- Department of Internal Medicine, UC Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico Ii, Naples, Italy
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
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Russo A, Incorvaia L, Del Re M, Malapelle U, Capoluongo E, Gristina V, Castiglia M, Danesi R, Fassan M, Giuffrè G, Gori S, Marchetti A, Normanno N, Pinto C, Rossi G, Santini D, Sartore-Bianchi A, Silvestris N, Tagliaferri P, Troncone G, Cinieri S, Beretta GD. The molecular profiling of solid tumors by liquid biopsy: a position paper of the AIOM-SIAPEC-IAP-SIBioC-SIC-SIF Italian Scientific Societies. ESMO Open 2021; 6:100164. [PMID: 34091263 PMCID: PMC8182269 DOI: 10.1016/j.esmoop.2021.100164] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/02/2021] [Accepted: 05/05/2021] [Indexed: 02/08/2023] Open
Abstract
The term liquid biopsy (LB) refers to the use of various biological fluids as a surrogate for neoplastic tissue to achieve information for diagnostic, prognostic and predictive purposes. In the current clinical practice, LB is used for the identification of driver mutations in circulating tumor DNA derived from both tumor tissue and circulating neoplastic cells. As suggested by a growing body of evidence, however, there are several clinical settings where biological samples other than tissue could be used in the routine practice to identify potentially predictive biomarkers of either response or resistance to targeted treatments. New applications are emerging as useful clinical tools, and other blood derivatives, such as circulating tumor cells, circulating tumor RNA, microRNAs, platelets, extracellular vesicles, as well as other biofluids such as urine and cerebrospinal fluid, may be adopted in the near future. Despite the evident advantages compared with tissue biopsy, LB still presents some limitations due to both biological and technological issues. In this context, the absence of harmonized procedures corresponds to an unmet clinical need, ultimately affecting the rapid implementation of LB in clinical practice. In this position paper, based on experts’ opinions, the AIOM–SIAPEC-IAP–SIBIOC–SIF Italian Scientific Societies critically discuss the most relevant technical issues of LB, the current and emerging evidences, with the aim to optimizing the applications of LB in the clinical setting. In the current clinical practice LB is used for the identification of driver mutations in circulating tumor DNA (ctDNA). New applications in tumors other than non-small-cell lung cancer (NSCLC) are emerging as useful clinical tools. Other blood derivatives, together with other biofluids, are an active field of research and may be adopted in the near future. Despite the evident advantages, liquid biopsy still presents limitations due to both biological and technological issues. Standardization of the procedures needs to be addressed to ensure widespread implementation in clinical practice.
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Affiliation(s)
- A Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy.
| | - L Incorvaia
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - M Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - U Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - E Capoluongo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; CEINGE, Biotecnologie Avanzate, Naples, Italy
| | - V Gristina
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - M Castiglia
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - R Danesi
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - M Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, Italy; Veneto Institute of Oncology (IOV-IRCCS), Padua, Italy
| | - G Giuffrè
- Department of Human Pathology in Adult and Developmental Age 'Gaetano Barresi', Section of Pathology, University of Messina, Messina, Italy
| | - S Gori
- Department of Oncology, IRCCS Ospedale Sacro Cuore Don Calabria, Negrar di Valpolicella, Italy
| | - A Marchetti
- Center of Predictive Molecular Medicine, University-Foundation, CeSI Biotech Chieti, Chieti, Italy
| | - N Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy
| | - C Pinto
- Medical Oncology Unit, Clinical Cancer Centre, IRCCS-AUSL di Reggio Emilia, Reggio Emilia, Italy
| | - G Rossi
- Pathology Unit, Ospedale Santa Maria Delle Croci, Ravenna, Italy
| | - D Santini
- Department of Medical Oncology, University Campus Biomedico, Rome, Italy
| | - A Sartore-Bianchi
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - N Silvestris
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori 'Giovanni Paolo II' of Bari, Bari, Italy; Department of Biomedical Sciences and Human Oncology, Aldo Moro University of Bari, Bari, Italy
| | - P Tagliaferri
- Medical and Translational Oncology Unit, Department of Experimental and Clinical Medicine, Magna Graecia University, Catanzaro, Italy
| | - G Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - S Cinieri
- Medical Oncology Division and Breast Unit, Senatore Antonio Perrino Hospital, ASL Brindisi, Brindisi, Italy
| | - G D Beretta
- Department of Oncology, Humanitas Gavazzeni, Bergamo, Italy
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6
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Li N, Dhilipkannah P, Jiang F. High-Throughput Detection of Multiple miRNAs and Methylated DNA by Droplet Digital PCR. J Pers Med 2021; 11:jpm11050359. [PMID: 33946992 PMCID: PMC8146424 DOI: 10.3390/jpm11050359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 01/04/2023] Open
Abstract
Altered miRNA expression and DNA methylation have highly active and diverse roles in carcinogenesis. Simultaneous detection of the molecular aberrations may have a synergistic effect on the diagnosis of malignancies. Herein, we develop a high-throughput assay for detecting multiple miRNAs and DNA methylation using droplet digital PCR (ddPCR) coupled with a 96-microwell plate. The microplate-based ddPCR could absolutely and reproducibly quantify 15 miRNAs and 14 DNA methylation sites with a high sensitivity (one copy/µL and 0.1%, respectively). Analyzing sputum and plasma of 40 lung cancer patients and 36 cancer-free smokers by this approach identified an integrated biomarker panel consisting of two sputum miRNAs (miRs-31-5p and 210-3p), one sputum DNA methylation (RASSF1A), and two plasma miRNAs (miR-21-5p and 126) for the diagnosis of lung cancer with higher sensitivity and specificity compared with a single type of biomarker. The diagnostic value of the integrated biomarker panel for the early detection of lung cancer was confirmed in a different cohort of 36 lung cancer patients and 39 cancer-free smokers. The high-throughput assay for quantification of multiple molecular aberrations across sputum and plasma could improve the early detection of lung cancer.
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7
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Isaka T, Yokose T, Ito H, Nakayama H, Miyagi Y, Saito H, Masuda M. Detection of EGFR mutation of pulmonary adenocarcinoma in sputum using droplet digital PCR. BMC Pulm Med 2021; 21:100. [PMID: 33757469 PMCID: PMC7988937 DOI: 10.1186/s12890-021-01468-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/15/2021] [Indexed: 12/28/2022] Open
Abstract
Background It is still unclear whether epidermal growth factor receptor (EGFR) mutation of primary lung adenocarcinoma can be detected on sputum samples. This study aimed to examine EGFR mutations of primary lung adenocarcinoma in sputum samples using droplet digital polymerase chain reaction (ddPCR) and compare it with an EGFR mutation in surgically resected lung cancer. Methods Sputum was prospectively collected from the patients before complete resection of the primary lung cancer at Kanagawa Cancer Center from September 2014 to May 2016. ddPCR was performed to detect EGFR exon 21 L858R point mutation (Ex21) and EGFR exon 19 deletion mutation (Ex19) in sputum samples from patients with lung adenocarcinoma. The concordance of EGFR mutation status in sputum samples and tumors in surgically resected specimen was evaluated for each positive and negative cytology group. Results One hundred and eighteen patients with primary lung adenocarcinoma provided sputum samples. Sputum cytology was positive in 13 patients (11.0%). ddPCR detected two cases of Ex21 and two cases of Ex19 in sputum cytology positive cases. Compared to surgically resected specimens, the sensitivity, specificity, and positive predictive value of EGFR mutation (Ex19 and Ex21) detection were 80.0%, 100%, and 100%, respectively, in sputum cytology positive cases. In contrast, the sensitivity, specificity, and positive predictive value of EGFR mutation (Ex19 and Ex21) detection were 3.1%, 100%, and 100%, respectively, in sputum cytology negative cases. Conclusions EGFR mutations in primary lung adenocarcinoma can be detected with high sensitivity in sputum samples if sputum cytology is positive.
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Affiliation(s)
- Tetsuya Isaka
- Department of Thoracic Surgery, Kanagawa Cancer Center, 2-3-2 Nakao, Asahi, Yokohama, Kanagawa, 241-8515, Japan. .,Department of Surgery, Yokohama City University, 3-9 Fukuura, Kanazawa, Yokohama, Kanagawa, 236-0004, Japan.
| | - Tomoyuki Yokose
- Department of Pathology, Kanagawa Cancer Center, 2-3-2 Nakao, Asahi, Yokohama, Kanagawa, 241-8515, Japan
| | - Hiroyuki Ito
- Department of Thoracic Surgery, Kanagawa Cancer Center, 2-3-2 Nakao, Asahi, Yokohama, Kanagawa, 241-8515, Japan
| | - Haruhiko Nakayama
- Department of Thoracic Surgery, Kanagawa Cancer Center, 2-3-2 Nakao, Asahi, Yokohama, Kanagawa, 241-8515, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, 2-3-2 Nakao, Asahi, Yokohama, Kanagawa, 241-8515, Japan
| | - Haruhiro Saito
- Department of Thoracic Oncology, Kanagawa Cancer Center, 2-3-2 Nakao, Asahi, Yokohama, Kanagawa, 241-8515, Japan
| | - Munetaka Masuda
- Department of Surgery, Yokohama City University, 3-9 Fukuura, Kanazawa, Yokohama, Kanagawa, 236-0004, Japan
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8
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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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Nishikawa T, Fujii T, Tatsumi S, Sugimoto A, Sekita-Hatakeyama Y, Shimada K, Yamazaki M, Hatakeyama K, Ohbayashi C. Molecular Analysis of Liquid-Based Cytological Specimen Using Virtually Positive Sputum with Adenocarcinoma Cells. Diagnostics (Basel) 2020; 10:diagnostics10020084. [PMID: 32033355 PMCID: PMC7168204 DOI: 10.3390/diagnostics10020084] [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: 01/09/2020] [Revised: 01/29/2020] [Accepted: 02/03/2020] [Indexed: 12/12/2022] Open
Abstract
Liquid-based cytology (LBC) analysis of sputum is a useful diagnostic and prognostic tool for detecting lung cancer. DNA and RNA derived from lung cancer cells can be used for this diagnosis. However, the quality of cytological material is not always adequate for molecular analysis due to the effect of formalin in the commercially available fixation kits. In this study, we examined DNA and RNA extraction methods for LBC analysis with formalin fixation, using lung carcinoma cell lines and sputum. The human non-small cell lung cancer cell lines were fixed with LBC fixation reagents, such as CytoRich red preservative. Quantification of thyroid transcription factor-1 (TTF-1) and actin mRNA, epidermal growth factor receptor (EGFR) DNA in HCC827, H1975, and H1299 cells, and mutation analysis of EGFR in HCC827 and H1975 cells were performed by quantitative PCR (qPCR) and fluorescence resonance energy transfer (FRET)-based preferential homoduplex formation assay (F-PHFA) method, respectively. mRNA and DNA extracted from cell lines using RNA and/or DNA extraction kits for formalin-fixed paraffin-embedded (FFPE) fixed with various LBC solutions were efficiently detected by qPCR. The detection limit of EGFR mutations was at a rate of 5% mutated positive cells in LBC. The detection limit of the EGFR exon 19 deletion in HCC827 was detected in more than 1.5% of the positive cells in sputum. In contrast, the detection limit of the T790M/L858R mutation in H1975 was detected in more than 13% of the positive cells. We also detected EGFR mutations using next generation sequencing (NGS). The detection limit of NGS for EGFR mutation was lower than that of the F-PHFA method. Furthermore, more than 0.1% of positive cells could be cytomorphologically detected. Our results demonstrate that LBC systems are powerful tools for cytopathological and genetic analyses. However, careful attention should be paid to the incidence of false negative results in the genetic analysis of EGFR mutations detected by LBC.
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Affiliation(s)
- Takeshi Nishikawa
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan; (T.N.); (S.T.); (A.S.); (Y.S.-H.); (K.H.); (C.O.)
| | - Tomomi Fujii
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan; (T.N.); (S.T.); (A.S.); (Y.S.-H.); (K.H.); (C.O.)
- Correspondence: ; Tel.: +81-744-22-3051 (ext. 4307); Fax: +81-744-23-5687
| | - Shigenobu Tatsumi
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan; (T.N.); (S.T.); (A.S.); (Y.S.-H.); (K.H.); (C.O.)
| | - Aya Sugimoto
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan; (T.N.); (S.T.); (A.S.); (Y.S.-H.); (K.H.); (C.O.)
| | - Yoko Sekita-Hatakeyama
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan; (T.N.); (S.T.); (A.S.); (Y.S.-H.); (K.H.); (C.O.)
| | - Keiji Shimada
- Department of Diagnostic Pathology, Nara City Hospital, Nara 630-8305, Japan;
| | - Masaharu Yamazaki
- Department of Central Clinical Laboratory, Nara Medical University Hospital, Nara 634-8521, Japan;
| | - Kinta Hatakeyama
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan; (T.N.); (S.T.); (A.S.); (Y.S.-H.); (K.H.); (C.O.)
| | - Chiho Ohbayashi
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan; (T.N.); (S.T.); (A.S.); (Y.S.-H.); (K.H.); (C.O.)
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Wu Z, Yang Z, Li CS, Zhao W, Liang ZX, Dai Y, Zhu Q, Miao KL, Cui DH, Chen LA. Differences in the genomic profiles of cell-free DNA between plasma, sputum, urine, and tumor tissue in advanced NSCLC. Cancer Med 2019; 8:910-919. [PMID: 30767431 PMCID: PMC6434190 DOI: 10.1002/cam4.1935] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/28/2018] [Accepted: 11/27/2018] [Indexed: 12/13/2022] Open
Abstract
Liquid biopsy has provided an efficient way for detection of gene alterations in advanced non-small-cell lung cancer (NSCLC). However, the correlation between systematic determination of somatic genomic alterations in liquid biopsy and tumor biopsy still remained unclear, and the concordance rate between cell-free DNA (cfDNA) and matched tumor tissue DNA needs to be increased. A prospective study was performed to detect differences in genetic profiles of cfDNA in sputum, plasma, urine, and tumor tissue from 50 advanced NSCLC patients in parallel by the same next-generation sequencing (NGS) platform. Driver genes alterations were identified in cfDNA sample and matched tumor sample, with an overall concordance rate of 86% in plasma cfDNA, 74% in sputum cfDNA, 70% in urine cfDNA, and 90% in cfDNA of combination of plasma, sputum, and urine. And the concordant rate of cfDNA in sputum in patients with smoking history was higher than that in patients without history of smoking (89% vs. 66%, P = 0.033) and equal to that in plasma cfDNA of the smoking patients (89% vs. 89%). In conclusion, sputum cfDNA can be considered as an alternative medium to liquid biopsy, while the complementarity of genomic profiles in cfDNA among plasma, sputum, and urine was beneficial to detect more diver genes alterations and improve the utility of liquid biopsy in advanced NSCLC (Liquid Biopsy for Detection of Driver Mutation in NSCLC; NCT02778854).
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Affiliation(s)
- Zhen Wu
- Respiratory Department of Chinese PLA General Hospital, Beijing, China
| | - Zhen Yang
- Respiratory Department of Chinese PLA General Hospital, Beijing, China
| | - Chun Sun Li
- Respiratory Department of Chinese PLA General Hospital, Beijing, China
| | - Wei Zhao
- Respiratory Department of Chinese PLA General Hospital, Beijing, China
| | - Zhi Xin Liang
- Respiratory Department of Chinese PLA General Hospital, Beijing, China
| | - Yu Dai
- Respiratory Department of Chinese PLA General Hospital, Beijing, China
| | - Qiang Zhu
- Respiratory Department of Chinese PLA General Hospital, Beijing, China
| | - Kai Ling Miao
- Respiratory Department of Chinese PLA General Hospital, Beijing, China
| | - Dong Hua Cui
- Respiratory Department of Chinese PLA General Hospital, Beijing, China
| | - Liang An Chen
- Respiratory Department of Chinese PLA General Hospital, Beijing, China
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11
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Fucosylation genes as circulating biomarkers for lung cancer. J Cancer Res Clin Oncol 2018; 144:2109-2115. [PMID: 30101373 DOI: 10.1007/s00432-018-2735-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 08/09/2018] [Indexed: 12/21/2022]
Abstract
PURPOSE Fucosyltransferases (FUTs) catalyze fucosylation, which plays a central role in biological processes. Aberrant fucosylation is associated with malignant transformation. Here we investigated whether transcriptional levels of genes coding the FUTs in plasma could provide cell-free circulating biomarkers for lung cancer. METHODS mRNA expression of all 13 Futs (Fut1-11, Pofut1, and Pofut2) was evaluated by PCR assay in 48 lung tumor tissues and the 48 matched noncancerous lung tissues, and plasma of 64 lung cancer patients and 32 cancer-free individuals to develop plasma Fut biomarkers. The developed plasma Fut biomarkers were validated in an independent cohort of 40 lung cancer patients and 20 controls for their diagnostic performance. RESULTS Four of the 13 Futs showed a different transcriptional level in 48 lung tumor tissues compared with the 48 matched nonconscious tissues (all < 0.05). Two (Fut8, and Pofut1) of the four Futs had a higher plasma level in 64 lung cancer patients compared with 32 control subjects, and consistent with that in lung tissue specimens. Combined analysis of the two Futs produced 81% sensitivity and 86% specificity for diagnosis of lung cancer, and was independent of stage and histology of lung tumors. The diagnostic performance of the two plasma biomarkers was successfully validated in the different cohort of 40 lung cancer patients and 20 control individuals. CONCLUSION The fucosylation genes may provide new circulating biomarkers for the early detection of lung cancer.
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12
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Su Y, Fang HB, Jiang F. An epigenetic classifier for early stage lung cancer. Clin Epigenetics 2018; 10:68. [PMID: 29796119 PMCID: PMC5964676 DOI: 10.1186/s13148-018-0502-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 05/14/2018] [Indexed: 12/19/2022] Open
Abstract
Background Methylated genes detected in sputum are promise biomarkers for lung cancer. Yet the current PCR technologies for quantification of DNA methylation and diagnostic value of the sputum biomarkers are not sufficient to be used for lung cancer early detection. The emerging droplet digital PCR (ddPCR) is a straightforward means for precise, direct, and absolute quantification of nucleic acids. Here, we investigate whether ddPCR can sensitively and robustly quantify DNA methylation in sputum for more precise diagnosis of lung cancer. Results First, the analytic performance of methylation-specific ddPCR (ddMSP) and quantitative methylation-specific PCR (qMSP) is determined in methylated and unmethylated DNA samples. Second, 29 genes, previously proposed as potential sputum biomarkers for lung cancer, are analyzed by using ddMSP in a training set of 127 lung cancer patients and 159 controls. ddMSP has higher sensitivity, precision, and reproducibility for quantification of methylation compared with qMSP (all p < 0.05). A classifier comprising four sputum methylation biomarkers for lung cancer is developed by using ddMSP, producing 86.6% sensitivity and 90.6% specificity, independent of stage and histology of lung cancer (all p > 0.05). The classifier has higher accuracy compared with sputum cytology (88.8 vs. 70.6%, p < 0.01). The diagnostic performance is confirmed in a testing set of 89 cases and 107 controls. Conclusions ddMSP is a robust tool for reliable quantification of DNA methylation in sputum, and the epigenetic classifier could help diagnose lung cancer at the early stage.
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Affiliation(s)
- Yun Su
- 1Department of Surgery, Jiangsu Province Hospital of Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023 China
| | - Hong Bin Fang
- 2Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University Medical Center, 4000 Reservoir Road, N.W, Washington D.C., 20057 USA
| | - Feng Jiang
- 3Department of Pathology, University of Maryland School of Medicine, Baltimore, MD USA
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Yang X, Zhuo M, Ye X, Bai H, Wang Z, Sun Y, Zhao J, An T, Duan J, Wu M, Wang J. Quantification of mutant alleles in circulating tumor DNA can predict survival in lung cancer. Oncotarget 2018; 7:20810-24. [PMID: 26989078 PMCID: PMC4991494 DOI: 10.18632/oncotarget.8021] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 02/15/2016] [Indexed: 01/05/2023] Open
Abstract
Purpose We aimed to investigate the feasibility of droplet digital PCR (ddPCR) for the quantitative and dynamic detection of EGFR mutations and next generation sequencing (NGS) for screening EGFR-tyrosine kinase inhibitors (EGFR-TKIs) resistance-relevant mutations in circulating tumor DNA (ctDNA) from advanced lung adenocarcinoma (ADC) patients. Results Detection limit of EGFR mutation in ctDNA by ddPCR was 0.04%. Taking the EGFR mutation in tumor tissue as the golden standard, the concordance of EGFR mutations detected in ctDNA was 74% (54/73). Patients with EGFR mutation in ctDNA (n = 54) superior progression-free survival (PFS, median, 12.6 vs. 6.7 months, P < 0.001) and overall survival (OS, median, 35.6 vs. 23.8 months, P = 0.028) compared to those with EGFR wild type in ctDNA (n = 19). Patients with high EGFR-mutated abundance in ctDNA (> 5.15%) showed better PFS compared to those with low EGFR mutated abundance (≤ 5.15%) (PFS, median, 15.4 vs. 11.1 months, P = 0.021). NGS results showed that 66.6% (8/12) total mutational copy number were elevated and 76.5% (26/34) mutual mutation frequency increased after disease progression. Methods Seventy-three advanced ADC patients with tumor tissues carrying EGFR mutations and their matched pre- and post-EGFR-TKIs plasma samples were enrolled in this study. Absolute quantities of plasma EGFR mutant and wild-type alleles were measured by ddPCR. Multi-genes testing was performed using NGS in 12 patients. Conclusions Dynamic and quantitative analysis of EGFR mutation in ctDNA could guide personalized therapy for advanced ADC. NGS shows good performance in multiple genes testing especially novel and uncommon genes.
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Affiliation(s)
- Xue Yang
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Minglei Zhuo
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Xin Ye
- Asia and Emerging Markets Innovative Medicine of AstraZeneca R & D, Shanghai, China
| | - Hua Bai
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Zhijie Wang
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Yun Sun
- Asia and Emerging Markets Innovative Medicine of AstraZeneca R & D, Shanghai, China
| | - Jun Zhao
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Tongtong An
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Jianchun Duan
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Meina Wu
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Jie Wang
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
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Xu T, Kang X, You X, Dai L, Tian D, Yan W, Yang Y, Xiong H, Liang Z, Zhao GQ, Lin S, Chen KN, Xu G. Cross-Platform Comparison of Four Leading Technologies for Detecting EGFR Mutations in Circulating Tumor DNA from Non-Small Cell Lung Carcinoma Patient Plasma. Am J Cancer Res 2017; 7:1437-1446. [PMID: 28529628 PMCID: PMC5436504 DOI: 10.7150/thno.16558] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 01/22/2017] [Indexed: 01/13/2023] Open
Abstract
Analysis of circulating tumor DNA (ctDNA) is emerging as a powerful tool for guiding targeted therapy and monitoring tumor evolution in patients with non-small cell lung cancer (NSCLC), especially when representative tissue biopsies are not available. Here, we have compared the ability of four leading technology platforms to detect epidermal growth factor receptor (EGFR) mutations (L858R, exon 19 deletion, T790M and G719X) in ctDNA from NSCLC patients. Two amplification refractory mutation systems (cobas-ARMS and ADx-ARMS), a droplet digital polymerase chain reaction (ddPCR) and a next-generation sequencing (Firefly NGS) platform were included in the comparison. Fifteen EGFR mutations across twenty NSCLC patients were identified. Firefly NGS, cobas-ARMS and ddPCR all displayed superior sensitivity while ADx-ARMS was better suited for the qualitative detection of EGFR mutations with allele frequency higher than 1% in plasma and tissue samples. We observed high coincidence between the plasma and tissue EGFR mutational profiles for three driver mutations (L858R, exon 19 deletion and G719X) that are known targets of first generation EGFR-TKI therapies among patients who relapsed. Discrepancies between tissue and plasma EGFR mutational profiles were mainly attributable to spatial and temporal tumor heterogeneity, mutation inhibition due to therapy response and drug resistance (T790M). This study illustrates the challenges associated with selection of a technology platform for EGFR ctDNA analysis in the context of treatment evaluation and drug resistance detection.
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Kumar V, Becker K, Zheng HX, Huang Y, Xu Y. The performance of NLST screening criteria in Asian lung cancer patients. BMC Cancer 2015; 15:916. [PMID: 26582178 PMCID: PMC4652411 DOI: 10.1186/s12885-015-1922-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 11/10/2015] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Screening high-risk individuals with low dose CT decreased lung cancer mortality in the National Lung Screening Trial (NLST), but the validity of directly extrapolating these results to an Asian population is unclear. Using statistical models on Surveillance, Epidemiology and End Result (SEER) data, 27% of lung cancer patients in the United States were estimated to meet the screening criteria. This study aims to evaluate the performance of the NLST criteria in Asian lung cancer patients and to examine the characteristics of those who did not meet the criteria. METHODS We conducted a retrospective study of Asian lung cancer patients treated at Maimonides Cancer Center between 1/2008 and 6/2013. Data on demographics, smoking history, cancer stage, histology, and EGFR/ALK mutation status were collected and analyzed. RESULTS Of 116 eligible patients, 75 patients (65%) were smokers which included 26 light smokers (22%). Thirty-two patients (27.8%) met the NLST criteria. Extending the age limit to 79 would cover 8% more patients while removing the lower age limit would only cover 2% more. None of the female patients met the criteria as they were all never or light smokers. Two-thirds of male patients younger than age 55 were never or light smokers. The EGFR mutation rate was 67% in female and 28% in male patients. CONCLUSION The percentage of Asian patients meeting the NLST criteria is similar to that estimated for the United States population, suggesting that extension of the criteria to an Asian population is valid. One-third of the patients were non-smokers and an additional one-fourth were light smokers, comprised mostly of female and young male patients. Further strategies for screening these individuals based on non-tobacco factors are urgently needed.
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Affiliation(s)
- Vivek Kumar
- Department of Internal Medicine Maimonides Medical Center, 4802 10th Avenue, Brooklyn New York, 11219, USA.
| | - Kevin Becker
- Department of Hematology and Oncology Maimonides Cancer Center, 6300 Brooklyn, New York, 11220, USA.
| | - Huo Xiang Zheng
- Department of Hematology and Oncology Maimonides Cancer Center, 6300 Brooklyn, New York, 11220, USA.
| | - Yiwu Huang
- Department of Hematology and Oncology Maimonides Cancer Center, 6300 Brooklyn, New York, 11220, USA.
| | - Yiqing Xu
- Department of Hematology and Oncology Maimonides Cancer Center, 6300 Brooklyn, New York, 11220, USA.
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Sun Y, Song Z. [Progress in Tissue Specimens Alternative for the Driver Genes Testing of Non-small Cell Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2015; 18:387-90. [PMID: 26104897 PMCID: PMC5999900 DOI: 10.3779/j.issn.1009-3419.2015.06.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Target treatment based on driver genes in advanced non-small cell lung cancer is very important currently. Tumor tissues is the gold standard for driver genes testing. However, most of patients could not get the gene information for lack of enough tissues. To explore the tissue specimens alternatives is a hot spot in clinical work. This report reviews the tissue specimen alternatives of driver gene testing in non-small cell lung cancer.
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Affiliation(s)
- Yan Sun
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Zhengbo Song
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China
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17
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Techniques et stratégie de prise en charge des prélèvements anatomopathologiques dans le cadre de l’approche diagnostique et thérapeutique du cancer bronchique. Rev Mal Respir 2015; 32:381-93. [DOI: 10.1016/j.rmr.2014.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 12/12/2014] [Indexed: 12/25/2022]
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18
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Chao A, Lai CH, Lee YS, Ueng SH, Lin CY, Wang TH. Molecular characteristics of endometrial cancer coexisting with peritoneal malignant mesothelioma in Li-Fraumeni-like syndrome. BMC Cancer 2015; 15:8. [PMID: 25588929 PMCID: PMC4312462 DOI: 10.1186/s12885-015-1010-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 01/06/2015] [Indexed: 11/22/2022] Open
Abstract
Background Endometrial cancer that occurs concurrently with peritoneal malignant mesothelioma (PMM) is difficult to diagnose preoperatively. Case presentation A postmenopausal woman had endometrial cancer extending to the cervix, vagina and pelvic lymph nodes, and PMM in bilateral ovaries, cul-de-sac, and multiple peritoneal sites. Adjuvant therapies included chemotherapy and radiotherapy. Targeted, massively parallel DNA sequencing and molecular inversion probe microarray analysis revealed a germline TP53 mutation compatible with Li-Fraumeni-like syndrome, somatic mutations of PIK3CA in the endometrial cancer, and a somatic mutation of GNA11 and JAK3 in the PMM. Large-scale genomic amplifications and some deletions were found in the endometrial cancer. The patient has been stable for 24 months after therapy. One of her four children was also found to carry the germline TP53 mutation. Conclusions Molecular characterization of the coexistent tumors not only helps us make the definite diagnosis, but also provides information to select targeted therapies if needed in the future. Identification of germline TP53 mutation further urged us to monitor future development of malignancies in this patient and encourage cancer screening in her family. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1010-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Angel Chao
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan.
| | - Chyong-Huey Lai
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan.
| | - Yun-Shien Lee
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan. .,Department of Biotechnology, Ming-Chuan University, Taoyuan, Taiwan.
| | - Shir-Hwa Ueng
- Department of Pathology, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan.
| | - Chiao-Yun Lin
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan.
| | - Tzu-Hao Wang
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan. .,Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan.
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Fleischhacker M, Schmidt B. Extracellular Nucleic Acids and Cancer. ADVANCES IN PREDICTIVE, PREVENTIVE AND PERSONALISED MEDICINE 2015. [DOI: 10.1007/978-94-017-9168-7_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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20
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Walsh K, Wallace WA. Molecular pathology in lung cancer: a guide to the techniques used in clinical practice. Histopathology 2014; 65:731-41. [PMID: 25130601 DOI: 10.1111/his.12505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Five year survival rates for lung cancer patients are poor; however the development of new therapeutic options, which benefit subsets of the population, offer hope of improvement. These novel therapies frequently rely upon the analysis of biomarkers in pathology samples; in lung cancer patients, testing is now routinely carried out to identify small mutations and chromosomal rearrangements in order to predict response to treatment. The recent increase in biomarker analyses in pathology samples has lead to the development of a new specialty, molecular pathology. The use of molecular pathology assays in clinical samples is largely under the control of the histopathologist; who is likely to be asked, as a minimum, to select tissue sections for molecular analysis and mark areas of H&E stained slides for macro or microdissection. Many histopathologists will also be involved in the sourcing and implementation of new assays. This review aims to provide a guide to some of the most commonly used molecular pathology methods - their advantages and their limitations.
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Affiliation(s)
- Kathy Walsh
- Pathology, Division of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK
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21
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Mukaide M, Sugiyama M, Korenaga M, Murata K, Kanto T, Masaki N, Mizokami M. High-throughput and sensitive next-generation droplet digital PCR assay for the quantitation of the hepatitis C virus mutation at core amino acid 70. J Virol Methods 2014; 207:169-77. [PMID: 25019167 DOI: 10.1016/j.jviromet.2014.07.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 07/02/2014] [Accepted: 07/04/2014] [Indexed: 01/08/2023]
Abstract
The next-generation droplet digital polymerase chain reaction (ddPCR) assay employs an emulsion-based endpoint to quantitate the amount of target DNA and is more robust than real-time PCR when analyzing sequence variations. However, no studies have applied this technique to quantitate mutations in polymorphic viral genomes. To develop this approach, a ddPCR-based assay was designed to quantitate with high-throughput and sensitivity mutations and their frequencies in codon 70 of the hepatitis C virus (HCV) gene that encodes the Core protein. The assay was linear from 2.5 to 10(5) copies per assay, and the limit of detection of mutants in the presence of a 20,000-fold excess of wild type was 0.005%. The results correlated well with those obtained using the COBAS(®) TaqMan(®) HCV Test, which is a real-time PCR assay for the quantitative detection of HCV RNA in human serum (n=87; range, 2.3-7.7log10IU/mL; Pearson's R(2)=0.9120; p<0.0001). The median frequencies of mutations by ddPCR were 0.262% (n=55; range, 0-37.951%) and 99.687% (n=32; range, 52.191-100%) for the wild-type and mutant sequences, respectively, by direct sequencing. The ddPCR assay should be useful for quantitating mutations in other polymorphic viral genomes.
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Affiliation(s)
- Motokazu Mukaide
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohonodi, Ichikawa, Chiba 272-8516 Japan; Research and development department, SRL, Inc., 5-6-50 Shin, Hino, Tokyo 191-0002, Japan
| | - Masaya Sugiyama
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohonodi, Ichikawa, Chiba 272-8516 Japan
| | - Masaaki Korenaga
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohonodi, Ichikawa, Chiba 272-8516 Japan.
| | - Kazumoto Murata
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohonodi, Ichikawa, Chiba 272-8516 Japan
| | - Tatsuya Kanto
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohonodi, Ichikawa, Chiba 272-8516 Japan
| | - Naohiko Masaki
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohonodi, Ichikawa, Chiba 272-8516 Japan
| | - Masashi Mizokami
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohonodi, Ichikawa, Chiba 272-8516 Japan
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Wong SQ, Li J, Tan AYC, Vedururu R, Pang JMB, Do H, Ellul J, Doig K, Bell A, MacArthur GA, Fox SB, Thomas DM, Fellowes A, Parisot JP, Dobrovic A. Sequence artefacts in a prospective series of formalin-fixed tumours tested for mutations in hotspot regions by massively parallel sequencing. BMC Med Genomics 2014; 7:23. [PMID: 24885028 PMCID: PMC4032349 DOI: 10.1186/1755-8794-7-23] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 04/30/2014] [Indexed: 12/16/2022] Open
Abstract
Background Clinical specimens undergoing diagnostic molecular pathology testing are fixed in formalin due to the necessity for detailed morphological assessment. However, formalin fixation can cause major issues with molecular testing, as it causes DNA damage such as fragmentation and non-reproducible sequencing artefacts after PCR amplification. In the context of massively parallel sequencing (MPS), distinguishing true low frequency variants from sequencing artefacts remains challenging. The prevalence of formalin-induced DNA damage and its impact on molecular testing and clinical genomics remains poorly understood. Methods The Cancer 2015 study is a population-based cancer cohort used to assess the feasibility of mutational screening using MPS in cancer patients from Victoria, Australia. While blocks were formalin-fixed and paraffin-embedded in different anatomical pathology laboratories, they were centrally extracted for DNA utilising the same protocol, and run through the same MPS platform (Illumina TruSeq Amplicon Cancer Panel). The sequencing artefacts in the 1-10% and the 10-25% allele frequency ranges were assessed in 488 formalin-fixed tumours from the pilot phase of the Cancer 2015 cohort. All blocks were less than 2.5 years of age (mean 93 days). Results Consistent with the signature of DNA damage due to formalin fixation, many formalin-fixed samples displayed disproportionate levels of C>T/G>A changes in the 1-10% allele frequency range. Artefacts were less apparent in the 10-25% allele frequency range. Significantly, changes were inversely correlated with coverage indicating high levels of sequencing artefacts were associated with samples with low amounts of available amplifiable template due to fragmentation. The degree of fragmentation and sequencing artefacts differed between blocks sourced from different anatomical pathology laboratories. In a limited validation of potentially actionable low frequency mutations, a NRAS G12D mutation in a melanoma was shown to be a false positive. Conclusions These findings indicate that DNA damage following formalin fixation remains a major challenge in laboratories working with MPS. Methodologies that assess, minimise or remove formalin-induced DNA damaged templates as part of MPS protocols will aid in the interpretation of genomic results leading to better patient outcomes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Alexander Dobrovic
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia.
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Altmüller J, Budde BS, Nürnberg P. Enrichment of target sequences for next-generation sequencing applications in research and diagnostics. Biol Chem 2014; 395:231-7. [DOI: 10.1515/hsz-2013-0199] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/30/2013] [Indexed: 12/21/2022]
Abstract
Abstract
Targeted re-sequencing such as gene panel sequencing (GPS) has become very popular in medical genetics, both for research projects and in diagnostic settings. The technical principles of the different enrichment methods have been reviewed several times before; however, new enrichment products are constantly entering the market, and researchers are often puzzled about the requirement to take decisions about long-term commitments, both for the enrichment product and the sequencing technology. This review summarizes important considerations for the experimental design and provides helpful recommendations in choosing the best sequencing strategy for various research projects and diagnostic applications.
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