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Krug AK, Enderle D, Karlovich C, Priewasser T, Bentink S, Spiel A, Brinkmann K, Emenegger J, Grimm DG, Castellanos-Rizaldos E, Goldman JW, Sequist LV, Soria JC, Camidge DR, Gadgeel SM, Wakelee HA, Raponi M, Noerholm M, Skog J. Improved EGFR mutation detection using combined exosomal RNA and circulating tumor DNA in NSCLC patient plasma. Ann Oncol 2018; 29:700-706. [PMID: 29216356 PMCID: PMC5889041 DOI: 10.1093/annonc/mdx765] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background A major limitation of circulating tumor DNA (ctDNA) for somatic mutation detection has been the low level of ctDNA found in a subset of cancer patients. We investigated whether using a combined isolation of exosomal RNA (exoRNA) and cell-free DNA (cfDNA) could improve blood-based liquid biopsy for EGFR mutation detection in non-small-cell lung cancer (NSCLC) patients. Patients and methods Matched pretreatment tumor and plasma were collected from 84 patients enrolled in TIGER-X (NCT01526928), a phase 1/2 study of rociletinib in mutant EGFR NSCLC patients. The combined isolated exoRNA and cfDNA (exoNA) was analyzed blinded for mutations using a targeted next-generation sequencing panel (EXO1000) and compared with existing data from the same samples using analysis of ctDNA by BEAMing. Results For exoNA, the sensitivity was 98% for detection of activating EGFR mutations and 90% for EGFR T790M. The corresponding sensitivities for ctDNA by BEAMing were 82% for activating mutations and 84% for T790M. In a subgroup of patients with intrathoracic metastatic disease (M0/M1a; n = 21), the sensitivity increased from 26% to 74% for activating mutations (P = 0.003) and from 19% to 31% for T790M (P = 0.5) when using exoNA for detection. Conclusions Combining exoRNA and ctDNA increased the sensitivity for EGFR mutation detection in plasma, with the largest improvement seen in the subgroup of M0/M1a disease patients known to have low levels of ctDNA and poses challenges for mutation detection on ctDNA alone. Clinical Trials NCT01526928.
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Affiliation(s)
- A K Krug
- Exosome Diagnostics GmbH, Martinsried, Germany
| | - D Enderle
- Exosome Diagnostics GmbH, Martinsried, Germany
| | | | | | - S Bentink
- Exosome Diagnostics GmbH, Martinsried, Germany
| | - A Spiel
- Exosome Diagnostics GmbH, Martinsried, Germany
| | - K Brinkmann
- Exosome Diagnostics GmbH, Martinsried, Germany
| | - J Emenegger
- Exosome Diagnostics GmbH, Martinsried, Germany
| | - D G Grimm
- Exosome Diagnostics GmbH, Martinsried, Germany
| | | | - J W Goldman
- University of California Los Angeles, Los Angeles
| | | | - J-C Soria
- Institut Gustave Roussy, Villejuif; University Paris-Sud, Paris, France
| | | | - S M Gadgeel
- Karmanos Cancer Institute, Detroit; Wayne State University, Detroit
| | | | - M Raponi
- Clovis Oncology Inc., San Francisco
| | - M Noerholm
- Exosome Diagnostics GmbH, Martinsried, Germany
| | - J Skog
- Exosome Diagnostics Inc, Waltham.
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Lindeman NI, Cagle PT, Aisner DL, Arcila ME, Beasley MB, Bernicker EH, Colasacco C, Dacic S, Hirsch FR, Kerr K, Kwiatkowski DJ, Ladanyi M, Nowak JA, Sholl L, Temple-Smolkin R, Solomon B, Souter LH, Thunnissen E, Tsao MS, Ventura CB, Wynes MW, Yatabe Y. Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology. Arch Pathol Lab Med 2018; 142:321-346. [PMID: 29355391 DOI: 10.5858/arpa.2017-0388-cp] [Citation(s) in RCA: 493] [Impact Index Per Article: 82.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
CONTEXT - In 2013, an evidence-based guideline was published by the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology to set standards for the molecular analysis of lung cancers to guide treatment decisions with targeted inhibitors. New evidence has prompted an evaluation of additional laboratory technologies, targetable genes, patient populations, and tumor types for testing. OBJECTIVE - To systematically review and update the 2013 guideline to affirm its validity; to assess the evidence of new genetic discoveries, technologies, and therapies; and to issue an evidence-based update. DESIGN - The College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology convened an expert panel to develop an evidence-based guideline to help define the key questions and literature search terms, review abstracts and full articles, and draft recommendations. RESULTS - Eighteen new recommendations were drafted. The panel also updated 3 recommendations from the 2013 guideline. CONCLUSIONS - The 2013 guideline was largely reaffirmed with updated recommendations to allow testing of cytology samples, require improved assay sensitivity, and recommend against the use of immunohistochemistry for EGFR testing. Key new recommendations include ROS1 testing for all adenocarcinoma patients; the inclusion of additional genes ( ERBB2, MET, BRAF, KRAS, and RET) for laboratories that perform next-generation sequencing panels; immunohistochemistry as an alternative to fluorescence in situ hybridization for ALK and/or ROS1 testing; use of 5% sensitivity assays for EGFR T790M mutations in patients with secondary resistance to EGFR inhibitors; and the use of cell-free DNA to "rule in" targetable mutations when tissue is limited or hard to obtain.
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Affiliation(s)
- Neal I Lindeman
- From the Departments of Pathology (Drs Lindeman and Sholl) and Medicine (Dr Kwiatkowski), Brigham and Women's Hospital, Boston, Massachusetts; the Cancer Center (Dr Bernicker) and the Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas (Dr Cagle); the Department of Pathology, University of Colorado School of Medicine, Denver (Dr Aisner); the Diagnostic and Molecular Pathology Laboratory (Dr Arcila) and the Molecular Diagnostics Service (Dr Ladanyi), Memorial Sloan Kettering Cancer Center, New York, New York; the Department of Pathology & Medicine, Pulmonary, Critical Care and Sleep Medicine, New York, New York (Dr Beasley); the Pathology and Laboratory Quality Center, College of American Pathologists, Northfield, Illinois (Mss Colasacco and Ventura); the Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania (Dr Dacic); the Department of Medicine and Pathology, University of Colorado, Denver (Dr Hirsch); the Department of Pathology, University of Aberdeen, Aberdeen, Scotland (Dr Kerr); the Department of Molecular Pathology, Roswell Park Cancer Institute, Buffalo, New York (Dr Nowak); the Clinical and Scientific Affairs Division, Association for Molecular Pathology, Bethesda, Maryland (Dr Temple-Smolkin); the Molecular Therapeutics and Biomarkers Laboratory, Peter Maccallum Cancer Center, Melbourne, Australia (Dr Solomon); the Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands (Dr Thunnissen); the Department of Laboratory Medicine and Pathobiology, Princess Margaret Cancer Center, Toronto, Ontario, Canada (Dr Tsao); Scientific Affairs, International Association for the Study of Lung Cancer, Aurora, Colorado (Dr Wynes); and the Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan (Dr Yatabe). Dr Souter is in private practice in Wellanport, Ontario, Canada
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Lindeman NI, Cagle PT, Aisner DL, Arcila ME, Beasley MB, Bernicker EH, Colasacco C, Dacic S, Hirsch FR, Kerr K, Kwiatkowski DJ, Ladanyi M, Nowak JA, Sholl L, Temple-Smolkin R, Solomon B, Souter LH, Thunnissen E, Tsao MS, Ventura CB, Wynes MW, Yatabe Y. Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology. J Thorac Oncol 2018; 13:323-358. [PMID: 29396253 DOI: 10.1016/j.jtho.2017.12.001] [Citation(s) in RCA: 326] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2017] [Indexed: 12/15/2022]
Abstract
CONTEXT In 2013, an evidence-based guideline was published by the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology to set standards for the molecular analysis of lung cancers to guide treatment decisions with targeted inhibitors. New evidence has prompted an evaluation of additional laboratory technologies, targetable genes, patient populations, and tumor types for testing. OBJECTIVE To systematically review and update the 2013 guideline to affirm its validity; to assess the evidence of new genetic discoveries, technologies, and therapies; and to issue an evidence-based update. DESIGN The College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology convened an expert panel to develop an evidence-based guideline to help define the key questions and literature search terms, review abstracts and full articles, and draft recommendations. RESULTS Eighteen new recommendations were drafted. The panel also updated 3 recommendations from the 2013 guideline. CONCLUSIONS The 2013 guideline was largely reaffirmed with updated recommendations to allow testing of cytology samples, require improved assay sensitivity, and recommend against the use of immunohistochemistry for EGFR testing. Key new recommendations include ROS1 testing for all adenocarcinoma patients; the inclusion of additional genes (ERBB2, MET, BRAF, KRAS, and RET) for laboratories that perform next-generation sequencing panels; immunohistochemistry as an alternative to fluorescence in situ hybridization for ALK and/or ROS1 testing; use of 5% sensitivity assays for EGFR T790M mutations in patients with secondary resistance to EGFR inhibitors; and the use of cell-free DNA to "rule in" targetable mutations when tissue is limited or hard to obtain.
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Affiliation(s)
- Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.
| | - Philip T Cagle
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Dara L Aisner
- Department of Pathology, University of Colorado School of Medicine, Denver, New York
| | - Maria E Arcila
- Diagnostic and Molecular Pathology Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mary Beth Beasley
- Department of Pathology & Medicine, Pulmonary, Critical Care and Sleep Medicine, New York, New York
| | | | - Carol Colasacco
- Pathology and Laboratory Quality Center, College of American Pathologists, Northfield, Illinois
| | - Sanja Dacic
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Fred R Hirsch
- Department of Medicine and Pathology, University of Colorado, Denver, New York
| | - Keith Kerr
- Department of Pathology, University of Aberdeen, Aberdeen, Scotland
| | | | - Marc Ladanyi
- Molecular Diagnostics Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jan A Nowak
- Department of Molecular Pathology, Roswell Park Cancer Institute, Buffalo, New York
| | - Lynette Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Robyn Temple-Smolkin
- Clinical and Scientific Affairs Division, Association for Molecular Pathology, Bethesda, Maryland
| | - Benjamin Solomon
- Molecular Therapeutics and Biomarkers Laboratory, Peter Maccallum Cancer Center, Melbourne, Australia
| | | | - Erik Thunnissen
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Ming S Tsao
- Department of Laboratory Medicine and Pathobiology, Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Christina B Ventura
- Pathology and Laboratory Quality Center, College of American Pathologists, Northfield, Illinois
| | - Murry W Wynes
- Scientific Affairs, International Association for the Study of Lung Cancer, Aurora, Colorado
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
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204
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Nishikawa S, Kimura H, Koba H, Yoneda T, Watanabe S, Sakai T, Hara J, Sone T, Kasahara K, Nakao S. Selective gene amplification to detect the T790M mutation in plasma from patients with advanced non-small cell lung cancer (NSCLC) who have developed epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) resistance. J Thorac Dis 2018; 10:1431-1439. [PMID: 29707292 DOI: 10.21037/jtd.2018.01.144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background The epidermal growth factor receptor (EGFR) T790M mutation is associated with resistance to EGFR tyrosine kinase inhibitors (EGFR-TKIs) in non-small cell lung cancer (NSCLC). However, tissues for the genotyping of the EGFR T790M mutation can be difficult to obtain in a clinical setting. The aims of this study were to evaluate a blood-based, non-invasive approach to detecting the EGFR T790M mutation in advanced NSCLC patients using the PointMan™ EGFR DNA enrichment kit, which is a novel method for the selective amplification of specific genotype sequences. Methods Blood samples were collected from NSCLC patients who had activating EGFR mutations and who were resistant to EGFR-TKI treatment. Using cell-free DNA (cfDNA) from plasma, EGFR T790M mutations were amplified using the PointMan™ enrichment kit, and all the reaction products were confirmed using direct sequencing. The concentrations of plasma DNA were then determined using quantitative real-time PCR. Results Nineteen patients were enrolled, and 12 patients (63.2%) were found to contain EGFR T790M mutations in their cfDNA, as detected by the kit. T790M mutations were detected in tumor tissues in 12 cases, and 11 of these cases (91.7%) also exhibited the T790M mutation in cfDNA samples. The concentrations of cfDNA were similar between patients with the T790M mutation and those without the mutation. Conclusions The PointMan™ kit provides a useful method for determining the EGFR T790M mutation status in cfDNA.
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Affiliation(s)
- Shingo Nishikawa
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Hideharu Kimura
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Hayato Koba
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Taro Yoneda
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Satoshi Watanabe
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Tamami Sakai
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Johsuke Hara
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Takashi Sone
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Kazuo Kasahara
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Shinji Nakao
- Department of Cellular Transplantation Biology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
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205
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Lindeman NI, Cagle PT, Aisner DL, Arcila ME, Beasley MB, Bernicker EH, Colasacco C, Dacic S, Hirsch FR, Kerr K, Kwiatkowski DJ, Ladanyi M, Nowak JA, Sholl L, Temple-Smolkin R, Solomon B, Souter LH, Thunnissen E, Tsao MS, Ventura CB, Wynes MW, Yatabe Y. Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology. J Mol Diagn 2018; 20:129-159. [PMID: 29398453 DOI: 10.1016/j.jmoldx.2017.11.004] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2017] [Indexed: 02/07/2023] Open
Abstract
CONTEXT In 2013, an evidence-based guideline was published by the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology to set standards for the molecular analysis of lung cancers to guide treatment decisions with targeted inhibitors. New evidence has prompted an evaluation of additional laboratory technologies, targetable genes, patient populations, and tumor types for testing. OBJECTIVE To systematically review and update the 2013 guideline to affirm its validity; to assess the evidence of new genetic discoveries, technologies, and therapies; and to issue an evidence-based update. DESIGN The College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology convened an expert panel to develop an evidence-based guideline to help define the key questions and literature search terms, review abstracts and full articles, and draft recommendations. RESULTS Eighteen new recommendations were drafted. The panel also updated 3 recommendations from the 2013 guideline. CONCLUSIONS The 2013 guideline was largely reaffirmed with updated recommendations to allow testing of cytology samples, require improved assay sensitivity, and recommend against the use of immunohistochemistry for EGFR testing. Key new recommendations include ROS1 testing for all adenocarcinoma patients; the inclusion of additional genes (ERBB2, MET, BRAF, KRAS, and RET) for laboratories that perform next-generation sequencing panels; immunohistochemistry as an alternative to fluorescence in situ hybridization for ALK and/or ROS1 testing; use of 5% sensitivity assays for EGFR T790M mutations in patients with secondary resistance to EGFR inhibitors; and the use of cell-free DNA to "rule in" targetable mutations when tissue is limited or hard to obtain.
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Affiliation(s)
- Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.
| | - Philip T Cagle
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Dara L Aisner
- Department of Pathology, University of Colorado School of Medicine, Denver, Colorado
| | - Maria E Arcila
- Diagnostic and Molecular Pathology Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mary Beth Beasley
- Department of Pathology & Medicine, Pulmonary, Critical Care and Sleep Medicine, New York, New York
| | - Eric H Bernicker
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas
| | - Carol Colasacco
- Pathology and Laboratory Quality Center, College of American Pathologists, Northfield, Illinois
| | - Sanja Dacic
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Fred R Hirsch
- Department of Medicine and Pathology, University of Colorado, Denver, Colorado
| | - Keith Kerr
- Department of Pathology, University of Aberdeen, Aberdeen, Scotland
| | | | - Marc Ladanyi
- Molecular Diagnostics Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jan A Nowak
- Department of Molecular Pathology, Roswell Park Cancer Institute, Buffalo, New York
| | - Lynette Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Robyn Temple-Smolkin
- Clinical and Scientific Affairs Division, Association for Molecular Pathology, Bethesda, Maryland
| | - Benjamin Solomon
- Molecular Therapeutics and Biomarkers Laboratory, Peter Maccallum Cancer Center, Melbourne, Australia
| | | | - Erik Thunnissen
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Ming S Tsao
- Department of Laboratory Medicine and Pathobiology, Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Christina B Ventura
- Pathology and Laboratory Quality Center, College of American Pathologists, Northfield, Illinois
| | - Murry W Wynes
- Scientific Affairs, International Association for the Study of Lung Cancer, Aurora, Colorado
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
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Zhang Y, Xu Y, Zhong W, Zhao J, Chen M, Zhang L, Li L, Wang M. Total DNA input is a crucial determinant of the sensitivity of plasma cell-free DNA EGFR mutation detection using droplet digital PCR. Oncotarget 2018; 8:5861-5873. [PMID: 28052016 PMCID: PMC5351596 DOI: 10.18632/oncotarget.14390] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 12/16/2016] [Indexed: 01/22/2023] Open
Abstract
We evaluated the use of droplet digital PCR (ddPCR) to detect plasma cell-free DNA (cfDNA) epidermal growth factor receptor (EGFR) mutations in advanced non-small cell lung cancer (NSCLC) patients. Compared with tumor-tissue-based detection, the sensitivity of ddPCR for detecting plasma cfDNA tyrosine kinase inhibitor (TKI)-sensitizing EGFR mutations was 61.3%, the specificity was 96.7%, and the consistency rate was 81.4% (?=0.605, 95% confidence interval: 0.501-0.706, p <0.0001). The sensitivity declined from 82.6% to 46.7% with decreasing cfDNA inputs (p=0.028). The plasma cfDNA concentration correlated with gender (males vs.females =11.69 ng/mL vs. 9.508 ng/mL; p=0.044), EGFR mutation status (tumor-tissue EGFR mutation-positive (EGFR M+) vs. EGFR mutation-negative (EGFR M-) = 9.61 ng/mL vs. 12.82 ng/mL; p =0.049) and specimen collection time (=2 years vs. >2 years=13.83 ng/mL vs. 6.575 ng/mL; p <0.001), and was greater in tumor-tissue EGFR M+ / plasma EGFR M+ patients than in tumor-tissue EGFR M+/plasma EGFR M- patients (11.61 vs. 7.73 ng/mL, respectively; p=0.003). Thus total cfDNA input crucially influences the sensitivity of plasma cfDNA EGFR mutation testing with ddPCR. Such analysis could be an effective supplemental test for advanced NSCLC patients.
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Affiliation(s)
- Yu Zhang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yan Xu
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Zhong
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jing Zhao
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Minjiang Chen
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Li Zhang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Longyun Li
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Mengzhao Wang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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207
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Wu SG, Shih JY. Management of acquired resistance to EGFR TKI-targeted therapy in advanced non-small cell lung cancer. Mol Cancer 2018; 17:38. [PMID: 29455650 PMCID: PMC5817870 DOI: 10.1186/s12943-018-0777-1] [Citation(s) in RCA: 443] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/01/2018] [Indexed: 12/12/2022] Open
Abstract
Recent advances in diagnosis and treatment are enabling a more targeted approach to treating lung cancers. Therapy targeting the specific oncogenic driver mutation could inhibit tumor progression and provide a favorable prognosis in clinical practice. Activating mutations of epidermal growth factor receptor (EGFR) in non-small cell lung cancer (NSCLC) are a favorable predictive factor for EGFR tyrosine kinase inhibitors (TKIs) treatment. For lung cancer patients with EGFR-exon 19 deletions or an exon 21 Leu858Arg mutation, the standard first-line treatment is first-generation (gefitinib, erlotinib), or second-generation (afatinib) TKIs. EGFR TKIs improve response rates, time to progression, and overall survival. Unfortunately, patients with EGFR mutant lung cancer develop disease progression after a median of 10 to 14 months on EGFR TKI. Different mechanisms of acquired resistance to first-generation and second-generation EGFR TKIs have been reported. Optimal treatment for the various mechanisms of acquired resistance is not yet clearly defined, except for the T790M mutation. Repeated tissue biopsy is important to explore resistance mechanisms, but it has limitations and risks. Liquid biopsy is a valid alternative to tissue re-biopsy. Osimertinib has been approved for patients with T790M-positive NSCLC with acquired resistance to EGFR TKI. For other TKI-resistant mechanisms, combination therapy may be considered. In addition, the use of immunotherapy in lung cancer treatment has evolved rapidly. Understanding and clarifying the biology of the resistance mechanisms of EGFR-mutant NSCLC could guide future drug development, leading to more precise therapy and advances in treatment.
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Affiliation(s)
- Shang-Gin Wu
- Department of Internal Medicine, National Taiwan University Hospital, No. 7, Chung-Shan South Road, Taipei, 100, Taiwan
| | - Jin-Yuan Shih
- Department of Internal Medicine, National Taiwan University Hospital, No. 7, Chung-Shan South Road, Taipei, 100, Taiwan.
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208
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Villaflor V, Won B, Nagy R, Banks K, Lanman RB, Talasaz A, Salgia R. Biopsy-free circulating tumor DNA assay identifies actionable mutations in lung cancer. Oncotarget 2018; 7:66880-66891. [PMID: 27602770 PMCID: PMC5341844 DOI: 10.18632/oncotarget.11801] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 08/13/2016] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION The potential of oncogene-driven targeted therapy is perhaps most fully realized in non-small cell lung cancer (NSCLC), given the number of genomic targets and approved matched therapies. However, invasive tissue biopsy at the time of each disease progression may not be possible and is associated with high morbidity and cost. Use of newly available "liquid biopsies" can circumvent these issues. RESULTS 83% of subjects had at least one genomic alteration identified in plasma. Most commonly mutated genes were TP53, KRAS and EGFR. Subjects with no detectable ctDNA were more likely to have small volume disease, lepidic growth pattern, mucinous tumors or isolated leptomeningeal disease. METHODS Subjects were individuals with NSCLC undergoing analysis of cell-free circulating tumor DNA using a validated, commercially-available next-generation sequencing assay at a single institution. Demographic, clinicopathologic information and results from tissue and plasma-based genomic testing were reviewed for each subject. CONCLUSIONS This is the first clinic-based series of NSCLC patients assessing outcomes of targeted therapies using a commercially available ctDNA assay. Over 80% of patients had detectable ctDNA, concordance between paired tissue and blood for truncal oncogenic drivers was high and patients with biomarkers identified in plasma had PFS in the expected range. These data suggest that biopsy-free ctDNA analysis is a viable first choice when the diagnostic tissue biopsy is insufficient for genotyping or at the time of progression when a repeated invasive tissue biopsy is not possible/preferred.
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Affiliation(s)
- Victoria Villaflor
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Brian Won
- University of Chicago School of Medicine, MC 2115, Chicago, IL 60637, USA
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Mellert H, Foreman T, Jackson L, Maar D, Thurston S, Koch K, Weaver A, Cooper S, Dupuis N, Sathyanarayana UG, Greer J, Hahn W, Shelton D, Stonemetz P, Pestano GA. Development and Clinical Utility of a Blood-Based Test Service for the Rapid Identification of Actionable Mutations in Non-Small Cell Lung Carcinoma. J Mol Diagn 2018; 19:404-416. [PMID: 28433077 DOI: 10.1016/j.jmoldx.2016.11.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 11/15/2016] [Accepted: 11/28/2016] [Indexed: 10/19/2022] Open
Abstract
Nearly 80% of cancer patients do not have genetic mutation results available at initial oncology consultation; up to 25% of patients begin treatment before receiving their results. These factors hinder the ability to pursue optimal treatment strategies. This study validates a blood-based genome-testing service that provides accurate results within 72 hours. We focused on targetable variants in advanced non-small cell lung carcinoma-epidermal growth factor receptor gene (EGFR) variant L858R, exon 19 deletion (ΔE746-A750), and T790M; GTPase Kirsten ras gene (KRAS) variants G12C/D/V; and echinoderm microtubule associated protein like and 4 anaplastic lymphoma receptor tyrosine kinase fusion (EML4-ALK) transcripts 1/2/3. Test development included method and clinical validation using samples from donors with (n = 219) or without (n = 30) cancer. Clinical sensitivity and specificity for each variant ranged from 78.6% to 100% and 94.2% to 100%, respectively. We also report on 1643 non-small cell lung carcinoma samples processed in our CLIA-certified laboratory. Mutation results were available within 72 hours for 94% of the tests evaluated. We detected 10.5% mutations for EGFR sensitizing (n = 2801 samples tested), 13.8% mutations for EGFR resistance (n = 1055), 13.2% mutations in KRAS (n = 3477), and 2% mutations for EML4-ALK fusion (n = 304). This rapid, highly sensitive, and actionable blood-based assay service expands testing options and supports faster treatment decisions.
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Affiliation(s)
| | | | | | - Dianna Maar
- Bio-Rad Digital Biology Center, Pleasanton, California
| | | | | | | | | | | | | | | | | | - Dawne Shelton
- Bio-Rad Digital Biology Center, Pleasanton, California
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210
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Rachiglio AM, Esposito Abate R, Sacco A, Pasquale R, Fenizia F, Lambiase M, Morabito A, Montanino A, Rocco G, Romano C, Nappi A, Iaffaioli RV, Tatangelo F, Botti G, Ciardiello F, Maiello MR, De Luca A, Normanno N. Limits and potential of targeted sequencing analysis of liquid biopsy in patients with lung and colon carcinoma. Oncotarget 2018; 7:66595-66605. [PMID: 27448974 PMCID: PMC5341823 DOI: 10.18632/oncotarget.10704] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 05/29/2016] [Indexed: 12/12/2022] Open
Abstract
The circulating free tumor DNA (ctDNA) represents an alternative, minimally invasive source of tumor DNA for molecular profiling. Targeted sequencing with next generation sequencing (NGS) can assess hundred mutations starting from a low DNA input. We performed NGS analysis of ctDNA from 44 patients with metastatic non-small-cell lung carcinoma (NSCLC) and 35 patients with metastatic colorectal carcinoma (CRC). NGS detected EGFR mutations in 17/22 plasma samples from EGFR-mutant NSCLC patients (sensitivity 77.3%). The concordance rate between tissue and plasma in NSCLC was much lower for other mutations such as KRAS that, based on the allelic frequency and the fraction of neoplastic cells, were likely to be sub-clonal. NGS also identified EGFR mutations in plasma samples from two patients with EGFR wild type tumor tissue. Both mutations were confirmed by droplet digital PCR (ddPCR) in both plasma and tissue samples. In CRC, the sensitivity of the NGS plasma analysis for RAS mutations was 100% (6/6) in patients that had not resection of the primary tumor before blood drawing, and 46.2% (6/13) in patients with primary tumor resected before enrollment. Our study showed that NGS is a suitable method for plasma testing. However, its clinical sensitivity is significantly affected by the presence of the primary tumor and by the heterogeneity of driver mutations.
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Affiliation(s)
- Anna Maria Rachiglio
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Riziero Esposito Abate
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Alessandra Sacco
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Raffaella Pasquale
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Francesca Fenizia
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Matilde Lambiase
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Alessandro Morabito
- Thoraco-Pulmonary, Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Agnese Montanino
- Thoraco-Pulmonary, Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Gaetano Rocco
- Thoracic Surgery, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Carmen Romano
- Gastro-Intestinal Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Anna Nappi
- Gastro-Intestinal Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Rosario Vincenzo Iaffaioli
- Gastro-Intestinal Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Fabiana Tatangelo
- Surgical Pathology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Gerardo Botti
- Surgical Pathology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Fortunato Ciardiello
- Department of Clinical and Experimental Medicine 'F. Magrassi' - Medical Oncology, Seconda Università degli Studi di Napoli, Napoli, Italy
| | - Monica R Maiello
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Nicola Normanno
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy.,Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
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211
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Decraene C, Silveira AB, Bidard FC, Vallée A, Michel M, Melaabi S, Vincent-Salomon A, Saliou A, Houy A, Milder M, Lantz O, Ychou M, Denis MG, Pierga JY, Stern MH, Proudhon C. Multiple Hotspot Mutations Scanning by Single Droplet Digital PCR. Clin Chem 2018; 64:317-328. [DOI: 10.1373/clinchem.2017.272518] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 10/10/2017] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Progress in the liquid biopsy field, combined with the development of droplet digital PCR (ddPCR), has enabled noninvasive monitoring of mutations with high detection accuracy. However, current assays detect a restricted number of mutations per reaction. ddPCR is a recognized method for detecting alterations previously characterized in tumor tissues, but its use as a discovery tool when the mutation is unknown a priori remains limited.
METHODS
We established 2 ddPCR assays detecting all genomic alterations within KRAS exon 2 and EGFR exon 19 mutation hotspots, which are of clinical importance in colorectal and lung cancer, with use of a unique pair of TaqMan® oligoprobes. The KRAS assay scanned for the 7 most common mutations in codons 12/13 but also all other mutations found in that region. The EGFR assay screened for all in-frame deletions of exon 19, which are frequent EGFR-activating events.
RESULTS
The KRAS and EGFR assays were highly specific and both reached a limit of detection of <0.1% in mutant allele frequency. We further validated their performance on multiple plasma and formalin-fixed and paraffin-embedded tumor samples harboring a panel of different KRAS or EGFR mutations.
CONCLUSIONS
This method presents the advantage of detecting a higher number of mutations with single-reaction ddPCRs while consuming a minimum of patient sample. This is particularly useful in the context of liquid biopsy because the amount of circulating tumor DNA is often low. This method should be useful as a discovery tool when the tumor tissue is unavailable or to monitor disease during therapy.
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Affiliation(s)
- Charles Decraene
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- CNRS UMR144, Institut Curie, PSL Research University, Paris, France
| | - Amanda B Silveira
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
| | - François-Clément Bidard
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - Audrey Vallée
- Department of Biochemistry and INSERM U1232, Nantes University Hospital, Nantes, France
| | - Marc Michel
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
| | - Samia Melaabi
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Anne Vincent-Salomon
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
- Inserm U934, Institut Curie, PSL Research University, Paris, France
| | - Adrien Saliou
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
| | - Alexandre Houy
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Inserm U830, Institut Curie, PSL Research University, Paris, France
| | - Maud Milder
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Inserm CIC BT 1418, Institut Curie, PSL Research University, Paris, France
| | - Olivier Lantz
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Inserm CIC BT 1418, Institut Curie, PSL Research University, Paris, France
- Inserm U932, Institut Curie, PSL Research University, Paris, France
| | - Marc Ychou
- Department of Medical Oncology, Montpellier Cancer Institute, Montpellier, France
| | - Marc G Denis
- Department of Biochemistry and INSERM U1232, Nantes University Hospital, Nantes, France
| | - Jean-Yves Pierga
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
- University Paris Descartes, Paris, France
| | - Marc-Henri Stern
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Inserm U830, Institut Curie, PSL Research University, Paris, France
| | - Charlotte Proudhon
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
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212
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Yang M, Forbes ME, Bitting RL, O'Neill SS, Chou PC, Topaloglu U, Miller LD, Hawkins GA, Grant SC, DeYoung BR, Petty WJ, Chen K, Pasche BC, Zhang W. Incorporating blood-based liquid biopsy information into cancer staging: time for a TNMB system? Ann Oncol 2018; 29:311-323. [PMID: 29216340 PMCID: PMC5834142 DOI: 10.1093/annonc/mdx766] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Tissue biopsy is the standard diagnostic procedure for cancer. Biopsy may also provide material for genotyping, which can assist in the diagnosis and selection of targeted therapies but may fall short in cases of inadequate sampling, particularly from highly heterogeneous tumors. Traditional tissue biopsy suffers greater limitations in its prognostic capability over the course of disease, most obviously as an invasive procedure with potential complications, but also with respect to probable tumor clonal evolution and metastasis over time from initial biopsy evaluation. Recent work highlights circulating tumor DNA (ctDNA) present in the blood as a supplemental, or perhaps an alternative, source of DNA to identify the clinically relevant cancer mutational landscape. Indeed, this noninvasive approach may facilitate repeated monitoring of disease progression and treatment response, serving as a means to guide targeted therapies based on detected actionable mutations in patients with advanced or metastatic solid tumors. Notably, ctDNA is heralding a revolution in the range of genomic profiling and molecular mechanisms to be utilized in the battle against cancer. This review will discuss the biology of ctDNA, current methods of detection and potential applications of this information in tumor diagnosis, treatment, and disease prognosis. Conventional classification of tumors to describe cancer stage follow the TNM notation system, heavily weighting local tumor extent (T), lymph node invasion (N), and detectable metastasis (M). With recent advancements in genomics and bioinformatics, it is conceivable that routine analysis of ctDNA from liquid biopsy (B) may make cancer diagnosis, treatment, and prognosis more accurate for individual patients. We put forward the futuristic concept of TNMB tumor classification, opening a new horizon for precision medicine with the hope of creating better outcomes for cancer patients.
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Affiliation(s)
- M Yang
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA; Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - M E Forbes
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - R L Bitting
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Section of Hematology and Oncology, Department of Internal Medicine, Winston-Salem, USA
| | - S S O'Neill
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Pathology, Wake Forest School of Medicine, Winston-Salem, USA
| | - P-C Chou
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - U Topaloglu
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - L D Miller
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - G A Hawkins
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, USA
| | - S C Grant
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Section of Hematology and Oncology, Department of Internal Medicine, Winston-Salem, USA
| | - B R DeYoung
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Pathology, Wake Forest School of Medicine, Winston-Salem, USA
| | - W J Petty
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Section of Hematology and Oncology, Department of Internal Medicine, Winston-Salem, USA
| | - K Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.
| | - B C Pasche
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA; Section of Hematology and Oncology, Department of Internal Medicine, Winston-Salem, USA
| | - W Zhang
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA.
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213
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Liu L, Liu H, Shao D, Liu Z, Wang J, Deng Q, Tang H, Yang H, Zhang Y, Qiu Y, Cui F, Tan M, Zhang P, Li Z, Liu J, Liang W, Wang Y, Peng Z, Wang J, Yang H, Mao M, Kristiansen K, Ye M, He J. Development and clinical validation of a circulating tumor DNA test for the identification of clinically actionable mutations in nonsmall cell lung cancer. Genes Chromosomes Cancer 2018; 57:211-220. [PMID: 29277949 DOI: 10.1002/gcc.22522] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/20/2017] [Accepted: 12/21/2017] [Indexed: 12/31/2022] Open
Abstract
Molecular analysis of potentially actionable mutations has become routine practice in oncological pathology. However, testing a wide range of oncogenes and mutations can be technically challenging because of limitations associated with tumor biopsy. Circulating tumor DNA (ctDNA) is a potential tool for the noninvasive profiling of tumors. In this study, we developed a next-generation sequencing (NGS)-based test for the detection of clinically relevant mutations in ctDNA and evaluated the feasibility of using this ctDNA NGS-based assay as an alternative to tissue genotyping. Tissue and matched blood samples were obtained from 72 patients with advanced nonsmall cell lung cancer (NSCLC). NGS-based testing was performed using plasma cell-free DNA (cfDNA) samples of all 72 patients as well as tumor DNA samples of 46 patients. Of the remaining 26 patients, tDNA was tested by amplification refractory mutation system PCR (ARMS-PCR) because of insufficient tissue sample or quality for NGS. Of the 46 patients who had tDNA and cfDNA NGS performed, we found 20 patients were concordant between tDNA and ctDNA alterations and 21 sample pairs were discordant because of additional alterations found in tDNA. Considering all clinically relevant alterations, the concordance rate between tDNA and ctDNA alterations was 54.9% with a sensitivity of 53.2% and a specificity of 75.0%. Our findings demonstrate that targeted NGS using cfDNA is a feasible approach for rapid and accurate identification of actionable mutations in patients with advanced NSCLC, and may provide a safe and robust alternative approach to tissue biopsy.
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Affiliation(s)
- Liping Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Disease, Guangzhou, 510120, China.,The Translational Medicine Laboratory, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Han Liu
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Di Shao
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China.,BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, DK 2200, Denmark
| | - Zu Liu
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Jingjing Wang
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Qiuhua Deng
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Disease, Guangzhou, 510120, China.,The Translational Medicine Laboratory, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Hailing Tang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Disease, Guangzhou, 510120, China.,The Translational Medicine Laboratory, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Haihong Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Yalei Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Yuan Qiu
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Fei Cui
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Meihua Tan
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China.,BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Pan Zhang
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Zhilong Li
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Jilong Liu
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Wenhua Liang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Disease, Guangzhou, 510120, China.,Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Yuying Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Mao Mao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, DK 2200, Denmark.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Mingzhi Ye
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China.,BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, DK 2200, Denmark
| | - Jianxing He
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Disease, Guangzhou, 510120, China.,Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
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214
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Extracellular vesicle-derived DNA for performing EGFR genotyping of NSCLC patients. Mol Cancer 2018; 17:15. [PMID: 29374476 PMCID: PMC5787306 DOI: 10.1186/s12943-018-0772-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/23/2018] [Indexed: 12/18/2022] Open
Abstract
Tumor cells shed an abundance of extracellular vesicles (EVs) to body fluids containing bioactive molecules including DNA, RNA, and protein. Investigations in the field of tumor-derived EVs open a new horizon in understanding cancer biology and its potential as cancer biomarkers as well as platforms for personalized medicine. This study demonstrates that successfully isolated EVs from plasma and bronchoalveolar lavage fluid (BALF) of non-small cell lung cancer (NSCLC) patients contain DNA that can be used for EGFR genotyping through liquid biopsy. In both plasma and BALF samples, liquid biopsy results using EV DNA show higher accordance with conventional tissue biopsy compared to the liquid biopsy of cfDNA. Especially, liquid biopsy with BALF EV DNA is tissue-specific and extremely sensitive compared to using cfDNA. Furthermore, use of BALF EV DNA also demonstrates higher efficiency in comparison to tissue rebiopsy for detecting p.T790 M mutation in the patients who developed resistance to EGFR-TKIs. These finding demonstrate possibility of liquid biopsy using EV DNA potentially replacing the current diagnostic methods for more accurate, cheaper, and faster results.
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215
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Abraham J, Singh S, Joshi S. Liquid biopsy - emergence of a new era in personalized cancer care. ACTA ACUST UNITED AC 2018. [DOI: 10.1186/s41241-018-0053-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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216
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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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217
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Barris DM, Weiner SB, Dubin RA, Fremed M, Zhang X, Piperdi S, Zhang W, Maqbool S, Gill J, Roth M, Hoang B, Geller D, Gorlick R, Weiser DA. Detection of circulating tumor DNA in patients with osteosarcoma. Oncotarget 2018; 9:12695-12704. [PMID: 29560102 PMCID: PMC5849166 DOI: 10.18632/oncotarget.24268] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/09/2018] [Indexed: 12/30/2022] Open
Abstract
Identification and quantification of somatic alterations in plasma-derived, circulating tumor DNA (ctDNA) is gaining traction as a non-invasive and cost effective method of disease monitoring in cancer patients, particularly to evaluate response to treatment and monitor for disease recurrence. To our knowledge, genetic analysis of ctDNA in osteosarcoma has not yet been studied. To determine whether somatic alterations can be detected in ctDNA and perhaps applied to patient management in this disease, we collected germline, tumor, and serial plasma samples from pediatric, adolescent, and young adult patients with osteosarcoma and used targeted Next Generation Sequencing (NGS) to identify somatic single nucleotide variants (SNV), insertions and deletions (INDELS), and structural variants (SV) in 7 genes commonly mutated in osteosarcoma. We demonstrate that patient-specific somatic alterations identified through comparison of tumor-germline pairs can be detected and quantified in cell-free DNA of osteosarcoma patients.
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Affiliation(s)
- David M Barris
- Department of Genetics and Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Shoshana B Weiner
- Department of Genetics and Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert A Dubin
- Computational Genomics Core, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Michael Fremed
- Department of Genetics and Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Xusheng Zhang
- Computational Genomics Core, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sajida Piperdi
- Department of Pediatrics, Montefiore Medical Center, Bronx, NY, USA
| | - Wendong Zhang
- Department of Pediatrics, Montefiore Medical Center, Bronx, NY, USA
| | - Shahina Maqbool
- Department of Genetics and Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jonathan Gill
- Division of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael Roth
- Division of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bang Hoang
- Department of Orthopedic Surgery, Montefiore Medical Center, Bronx, NY, USA
| | - David Geller
- Department of Orthopedic Surgery, Montefiore Medical Center, Bronx, NY, USA
| | - Richard Gorlick
- Division of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Daniel A Weiser
- Division of Hematology/Oncology, Children's Hospital at Montefiore, Bronx, NY, USA.,Departments of Pediatrics and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
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218
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Ai B, Liu H, Huang Y, Peng P. Circulating cell-free DNA as a prognostic and predictive biomarker in non-small cell lung cancer. Oncotarget 2018; 7:44583-44595. [PMID: 27323821 PMCID: PMC5190120 DOI: 10.18632/oncotarget.10069] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 05/29/2016] [Indexed: 01/15/2023] Open
Abstract
Circulating cell-free DNA (cfDNA), which can be obtained from plasma or serum by non-invasive procedures, has showed great potential to predict treatment response and survival for cancer patients. Several studies have assessed the prognostic and predictive value of cfDNA in non-small cell lung cancer (NSCLC). However, these studies were often small and reported varying results. To address this issue, a meta-analysis was carried out. A total of 22 studies involving 2518 patients were subjected to the final analysis. Our results indicated that NSCLC patients with higher cfDNA concentration had shorter median progression-free survival (PFS) and overall survival (OS) time. In addition, high levels of cfDNA were significantly associated with poor PFS (hazard ratio or HR, 1.32; 95% CI, 1.02-1.71) and OS (HR, 1.64; 95% CI, 1.26-2.15). With respect to tumor specific mutations, we failed to reveal significant differences for PFS (HR, 1.30; 95% CI, 0.66-2.56) and OS (HR, 1.05; 95% CI, 0.49-2.25) when NSCLC patients were grouped according to KRAS genotype detected in cfDNA. However, NSCLC patients which harbored EGFR activating mutation in cfDNA had a greater chance of response to EGFR-TKIs (odds ratio or OR, 1.96; 95% CI, 1.59-2.42). No significant publication bias was detected in this study. In conclusion, cfDNA could act as a prognostic and predictive biomarker for patients with NSCLC.
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Affiliation(s)
- Bo Ai
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan 430030, People's Republic of China
| | - Huiquan Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan 430030, People's Republic of China
| | - Yu Huang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan 430030, People's Republic of China
| | - Ping Peng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, Wuhan 430030, People's Republic of China
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219
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Qian X, Liu J, Sun Y, Wang M, Lei H, Luo G, Liu X, Xiong C, Liu D, Liu J, Tang Y. Circulating cell-free DNA has a high degree of specificity to detect exon 19 deletions and the single-point substitution mutation L858R in non-small cell lung cancer. Oncotarget 2018; 7:29154-65. [PMID: 27081078 PMCID: PMC5045385 DOI: 10.18632/oncotarget.8684] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/28/2016] [Indexed: 01/06/2023] Open
Abstract
Detection of an epidermal growth factor receptor (EGFR) mutation in circulating cell-free DNA (cfDNA) is a noninvasive method to collect genetic information to guide treatment of lung cancer with tyrosine-kinase inhibitors (TKIs). However, the association between cfDNA and detection of EGFR mutations in tumor tissue remains unclear. Here, a meta-analysis was performed to determine whether cfDNA could serve as a substitute for tissue specimens for the detection of EGFR mutations. The pooled sensitivity, specificity, and areas under the curve of cfDNA were 0.60, 0.94, and 0.9208 for the detection of EGFR mutations, 0.64, 0.99, and 0.9583 for detection of the exon 19 deletion, and 0.57, 0.99, and 0.9605 for the detection of the L858R mutation, respectively. Our results showed that cfDNA has a high degree of specificity to detect exon 19 deletions and L858R mutation. Due to its high specificity and noninvasive characteristics, cfDNA analysis presents a promising method to screen for mutations in NSCLC and predict patient response to EGFR-TKI treatment, dynamically assess treatment outcome, and facilitate early detection of resistance mutations.
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Affiliation(s)
- Xin Qian
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Jia Liu
- Department of Orthopedic, Lanzhou University First Hospital, Lanzhou, 730000, Gansu, P.R. China
| | - Yuhui Sun
- Department of Emergency Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Meifang Wang
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Huaiding Lei
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Guoshi Luo
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Xianjun Liu
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Chang Xiong
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Dan Liu
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Jie Liu
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
| | - Yijun Tang
- Department of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China.,Institute of Respiratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, P.R. China
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220
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Goldman JW, Noor ZS, Remon J, Besse B, Rosenfeld N. Are liquid biopsies a surrogate for tissue EGFR testing? Ann Oncol 2018; 29:i38-i46. [PMID: 29462257 DOI: 10.1093/annonc/mdx706] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Molecular profiling has changed the treatment landscape in advanced non-small-cell lung cancer. Accurately identifying the tumours that harbour sensitizing EGFR mutations, the most common targetable molecular alteration, as well as those with acquired resistance mutations (e.g. T790M) on treatment is a high clinical priority. The current clinical gold standard is genotyping of tumour specimens. However, the practical utility of this approach is limited by the lack of available tissue and the potential complications associated with biopsies. With the advent of newer sequencing assays, it has become feasible to assess tumour genomics via a blood sample, termed a 'liquid biopsy'. In this review, we summarize the available techniques for liquid biopsies and their applicability for detecting sensitizing and resistance EGFR mutations and how these results may be used for making treatment decisions.
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Affiliation(s)
- J W Goldman
- David Geffen School of Medicine at University of California Los Angeles, Los Angeles, USA
| | - Z S Noor
- David Geffen School of Medicine at University of California Los Angeles, Los Angeles, USA
| | - J Remon
- Department of Oncology Medicine, Gustave Roussy, Villejuif
| | - B Besse
- Department of Oncology Medicine, Gustave Roussy, Villejuif
- University Paris-Sud, Orsay, France
| | - N Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge
- Cancer Research UK Major Centre - Cambridge, Cambridge, UK
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221
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Veldore VH, Choughule A, Routhu T, Mandloi N, Noronha V, Joshi A, Dutt A, Gupta R, Vedam R, Prabhash K. Validation of liquid biopsy: plasma cell-free DNA testing in clinical management of advanced non-small cell lung cancer. LUNG CANCER (AUCKLAND, N.Z.) 2018; 9:1-11. [PMID: 29379323 PMCID: PMC5757203 DOI: 10.2147/lctt.s147841] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Plasma cell-free tumor DNA, or circulating tumor DNA (ctDNA), from liquid biopsy is a potential source of tumor genetic material, in the absence of tissue biopsy, for EGFR testing. Our validation study reiterates the clinical utility of ctDNA next generation sequencing (NGS) for EGFR mutation testing in non-small cell lung cancer (NSCLC). A total of 163 NSCLC cases were included in the validation, of which 132 patients had paired tissue biopsy and ctDNA. We chose to validate ctDNA using deep sequencing with custom designed bioinformatics methods that could detect somatic mutations at allele frequencies as low as 0.01%. Benchmarking allele specific real time PCR as one of the standard methods for tissue-based EGFR mutation testing, the ctDNA NGS test was validated on all the plasma derived cell-free DNA samples. We observed a high concordance (96.96%) between tissue biopsy and ctDNA for oncogenic driver mutations in Exon 19 and Exon 21 of the EGFR gene. The sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy of the assay were 91.1%, 100% 100%, 95.6%, and 97%, respectively. A false negative rate of 3% was observed. A subset of mutations was also verified on droplet digital PCR. Sixteen percent EGFR mutation positivity was observed in patients where only liquid biopsy was available, thus creating options for targeted therapy. This is the first and largest study from India, demonstrating successful validation of circulating cell-free DNA as a clinically useful material for molecular testing in NSCLC.
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Affiliation(s)
| | | | | | | | | | - Amit Joshi
- Tata Memorial Centre, Parel, Mumbai, India
| | - Amit Dutt
- The Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, India
| | - Ravi Gupta
- MedGenome Labs Private Ltd,, Bangalore, India
| | - Ramprasad Vedam
- MedGenome Labs Private Ltd,, Bangalore, India
- Ramprasad Vedam, MedGenome Labs Private Ltd., 3 Floor, Narayana Netralaya Building, NH City, 258/A, Bommasandra Industrial Area, Bommasandra, Bangalore 560099, India, Email
| | - Kumar Prabhash
- Tata Memorial Centre, Parel, Mumbai, India
- Correspondence: Kumar Prabhash, Department of Medical Oncology, Tata Memorial Hospital, Dr E Borges Road, Parel, Mumbai 400 012, India, Email
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222
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Mamdani H, Ahmed S, Armstrong S, Mok T, Jalal SI. Blood-based tumor biomarkers in lung cancer for detection and treatment. Transl Lung Cancer Res 2017; 6:648-660. [PMID: 29218268 DOI: 10.21037/tlcr.2017.09.03] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The therapeutic landscape of lung cancer has expanded significantly over the past decade. Advancements in molecularly targeted therapies, strategies to discover and treat resistance mutations, and development of personalized cancer treatments in the context of tumor heterogeneity and dynamic tumor biology have made it imperative to obtain tumor samples on several different occasions through the course of patient treatment. While this approach is critical to the delivery of optimal cancer treatment, it is fraught with a number of barriers including the need for invasive procedures with associated complications, access to limited amount of tissue, logistical delays in obtaining the biopsy, high healthcare cost, and in many cases inability to obtain tissue because of technically difficult location of the tumor. Given multiple limitations of obtaining tissue samples, the use of blood-based biomarkers ("liquid biopsies") may enable earlier diagnosis of cancer, lower costs by avoiding complex invasive procedures, tailoring molecular targeted treatments, improving patient convenience, and ultimately supplement clinical oncologic decision-making. In this paper, we review various blood-based biomarkers including circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), tumor derived exosomes, tumor educated platelets (TEPs), and microRNA; and highlight current evidence for their use in detection and treatment of lung cancer.
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Affiliation(s)
- Hirva Mamdani
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Shahid Ahmed
- Division of Hematology/Oncology, Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
| | - Samantha Armstrong
- Internal Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tony Mok
- Department of Clinical Oncology, Chinese University of Hong Kong, Hong Kong, China
| | - Shadia I Jalal
- Division of Hematology/Oncology, Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
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223
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Mayo-de-Las-Casas C, Garzón Ibáñez M, Jordana-Ariza N, García-Peláez B, Balada-Bel A, Villatoro S, Malapelle U, Karachaliou N, Troncone G, Rosell R, Molina-Vila MA. An update on liquid biopsy analysis for diagnostic and monitoring applications in non-small cell lung cancer. Expert Rev Mol Diagn 2017; 18:35-45. [PMID: 29172773 DOI: 10.1080/14737159.2018.1407243] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Collection of tumor samples is not always feasible in non-small cell lung cancer (NSCLC) patients, and circulating free DNA (cfDNA) extracted from blood represents a viable alternative. Different sensitive platforms have been developed for genetic cfDNA testing, some of which are already in clinical use. However, several difficulties remain, particularly the lack of standardization of these methodologies. Areas covered: Here, the authors present a review of the literature to update the applicability of cfDNA for diagnosis and monitoring of NSCLC patients. Expert commentary: Detection of somatic alterations in cfDNA is already in use in clinical practice and provides valuable information for patient management. Monitoring baseline alterations and emergence of resistance mutations is one of the most important clinical applications and can be used to non-invasively track disease evolution. Today, different technologies are available for cfDNA analysis, including whole-genome or exome sequencing and targeted methods that focus on a selection of genes of interest in a specific disease. In the case of Next Generation Sequencing (NGS) approaches, in depth coverage of candidate mutation loci can be achieved by selecting a limited number of targeted genes.
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Affiliation(s)
| | | | | | | | - Ariadna Balada-Bel
- a Pangaea Oncology , Quirón Dexeus University Hospital , Barcelona , Spain
| | - Sergio Villatoro
- a Pangaea Oncology , Quirón Dexeus University Hospital , Barcelona , Spain
| | - Umberto Malapelle
- b Department of Public Health , University of Naples Federico II , Naples , Italy
| | - Niki Karachaliou
- c Dr Rosell Oncology Institute , University Hospital Sagrat Cor , Barcelona , Spain
| | - Giancarlo Troncone
- b Department of Public Health , University of Naples Federico II , Naples , Italy
| | - Rafael Rosell
- d Cancer Biology and Precision Medicine Program, Catalan Institute of Oncology , Germans Trias i Pujol Health Sciences Institute and Hospital , Badalona , Spain
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224
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Li X, Zhou C. Comparison of cross-platform technologies for EGFR T790M testing in patients with non-small cell lung cancer. Oncotarget 2017; 8:100801-100818. [PMID: 29246024 PMCID: PMC5725066 DOI: 10.18632/oncotarget.19007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/19/2017] [Indexed: 12/14/2022] Open
Abstract
Somatic mutations in the gene encoding epidermal growth factor receptor (EGFR) play an important role in determining targeted treatment modalities in non-small cell lung cancer (NSCLC). The EGFR T790M mutation emerges in approximately 50% of cases who acquire resistance to tyrosine kinase inhibitors. Detecting EGFR T790M mutation in tumor tissue is challenging due to heterogeneity of the tumor, low abundance of the mutation and difficulty for re-biopsy in patients with advanced disease. Alternatively, circulating tumor DNA (ctDNA) has been proposed as a non-invasive method for mutational analysis. The presence of EGFR mutations in ctDNA predicts response to the EGFR TKIs in the first-line setting. Molecular testing is now considered a standard care for NSCLC. The advent of standard commercially available kits and targeted mutational analysis has revolutionized the accuracy of mutation detection platforms for detection of EGFR mutations. Our review provides an overview of various commonly used platforms for detecting EGFR T790M mutation in tumor tissue and plasma.
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Affiliation(s)
- Xuefei Li
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Pulmonary Cancer institute, Tongji University School of Medicine, Shanghai, P. R. China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University, Tongji University Medical School Cancer Institute, Shanghai, P. R. China
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225
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Sung JS, Chong HY, Kwon NJ, Kim HM, Lee JW, Kim B, Lee SB, Park CW, Choi JY, Chang WJ, Choi YJ, Lee SY, Kang EJ, Park KH, Kim YH. Detection of somatic variants and EGFR mutations in cell-free DNA from non-small cell lung cancer patients by ultra-deep sequencing using the ion ampliseq cancer hotspot panel and droplet digital polymerase chain reaction. Oncotarget 2017; 8:106901-106912. [PMID: 29290998 PMCID: PMC5739783 DOI: 10.18632/oncotarget.22456] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/17/2017] [Indexed: 12/18/2022] Open
Abstract
Highly sensitive genotyping assays can detect mutations in cell-free DNA (cfDNA) from cancer patients, reflecting the biology of each patient’s cancer. Because circulating tumor DNA comprises a small, variable fraction of DNA circulating in the blood, sensitive parallel multiplexing tests are required to determine mutation profiles. We prospectively examined the clinical utility of ultra-deep sequencing analysis of cfDNA from 126 non-small cell lung cancer (NSCLC) patients using the Ion AmpliSeq Cancer Hotspot Panel v2 (ICP) and validated these findings with droplet digital polymerase chain reaction (ddPCR). ICP results were compared with tumor tissue genotyping (TTG) results and clinical outcomes. A total of 853 variants were detected, with a median of four variants per patient. Overall concordance of ICP and TTG analyses was 90% for EGFR exon 19 deletion and 88% for the L858R mutation. Of 34 patients with a well-defined EGFR activating mutation defined based on the results of ICP and TTG, 31 (81.6%) showed long-term disease control with EGFR TKI treatment. Of 56 patients treated with an EGFR tyrosine kinase inhibitor (TKI), the presence of the de novo T790M mutation was confirmed in 28 (50%). Presence of this de novo mutation did not have a negative effect on EGFR TKI treatment. Ultra-deep sequencing analysis of cfDNA using ICP combined with confirmatory ddPCR was effective at defining driver genetic changes in NSCLC patients. Comprehensive analysis of tumor DNA and cfDNA can increase the specificity of molecular diagnosis, which could translate into tailored treatment.
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Affiliation(s)
- Jae Sook Sung
- Cancer Research Institute, Korea University, Seoul, Republic of Korea
| | | | | | | | - Jong Won Lee
- Cancer Research Institute, Korea University, Seoul, Republic of Korea
| | - Boyeon Kim
- Cancer Research Institute, Korea University, Seoul, Republic of Korea
| | - Saet Byeol Lee
- Cancer Research Institute, Korea University, Seoul, Republic of Korea
| | | | - Jung Yoon Choi
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Won Jin Chang
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Yoon Ji Choi
- Division of Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sung Yong Lee
- Department of Internal Medicine, Guro Hospital, Korea University, Seoul, Republic of Korea
| | - Eun Joo Kang
- Department of Internal Medicine, Guro Hospital, Korea University, Seoul, Republic of Korea
| | - Kyong Hwa Park
- Cancer Research Institute, Korea University, Seoul, Republic of Korea.,Division of Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Yeul Hong Kim
- Cancer Research Institute, Korea University, Seoul, Republic of Korea.,Division of Oncology/Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
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226
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Pi C, Zhang MF, Peng XX, Zhang YC, Xu CR, Zhou Q. Liquid biopsy in non-small cell lung cancer: a key role in the future of personalized medicine? Expert Rev Mol Diagn 2017; 17:1089-1096. [PMID: 29057681 DOI: 10.1080/14737159.2017.1395701] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Liquid biopsies, especially the analysis of circulating tumor DNA (ctDNA), as a novel and non-invasive method for the diagnosis and monitoring of non-small cell lung cancer (NSCLC) have already been implemented in clinical settings. The majority of ctDNA is released from apoptotic or necrotic tumor cells, thus reflecting the genetic profile of a tumor. Numerous studies have reported a high concordance in mutation profiles derived from liquid biopsy and tissue biopsy, especially in driver genes. Liquid biopsy could overcome the clonal heterogeneity of tumour biopsy, as it provides a single snapshot of a tumour tissue. Moreover, non-invasiveness is the biggest advantage for liquid biopsy, and the procedure can be repeatedly performed during the treatment for the purpose of monitoring. Therefore, ctDNA could act as a potential complementary method for tissue biopsies in diagnosis, prognostic, treatment response and resistance. Areas covered: This review summarizes the recent advancements in liquid biopsy with a focus on NSCLC, including its applications and technologies associated with assessing ctDNA. The authors conclude the review by discussing the challenges associated with liquid biopsy. Expert commentary: The analysis of ctDNA represents a promising method for liquid biopsy, which will be a novel and potentially complementary method in diagnosis, treatment and prognostic in NSCLC at all stages.
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Affiliation(s)
- Can Pi
- a Guangdong Lung Cancer Institute , Guangdong General Hospital and Guangdong Academy of Medical Sciences , Guangdong , PR China.,b The Second School of Clinical Medicine , Southern Medical University , Guangdong , PR China
| | - Ming-Feng Zhang
- a Guangdong Lung Cancer Institute , Guangdong General Hospital and Guangdong Academy of Medical Sciences , Guangdong , PR China.,b The Second School of Clinical Medicine , Southern Medical University , Guangdong , PR China
| | - Xiao-Xiao Peng
- a Guangdong Lung Cancer Institute , Guangdong General Hospital and Guangdong Academy of Medical Sciences , Guangdong , PR China.,c School of Medicine , South China University of Technology , Guangzhou , China
| | - Yi-Chen Zhang
- a Guangdong Lung Cancer Institute , Guangdong General Hospital and Guangdong Academy of Medical Sciences , Guangdong , PR China.,b The Second School of Clinical Medicine , Southern Medical University , Guangdong , PR China
| | - Chong-Rui Xu
- a Guangdong Lung Cancer Institute , Guangdong General Hospital and Guangdong Academy of Medical Sciences , Guangdong , PR China
| | - Qing Zhou
- a Guangdong Lung Cancer Institute , Guangdong General Hospital and Guangdong Academy of Medical Sciences , Guangdong , PR China.,b The Second School of Clinical Medicine , Southern Medical University , Guangdong , PR China
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227
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Liquid Biopsy and Therapeutic Targets: Present and Future Issues in Thoracic Oncology. Cancers (Basel) 2017; 9:cancers9110154. [PMID: 29125548 PMCID: PMC5704172 DOI: 10.3390/cancers9110154] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/06/2017] [Accepted: 11/08/2017] [Indexed: 02/06/2023] Open
Abstract
The practice of liquid biopsy (LB) has revolutionized the care of patients with metastatic lung cancer. Many oncologists now use this approach in daily practice, applying precise procedures for the detection of activating or resistance mutations in EGFR. These tests are performed with plasma DNA and have been approved as companion diagnostic test for patients treated with tyrosine kinase inhibitors. ALK is another important target in lung cancer since it leads to treatment of patients who are positive for a rearrangement in ALK identified with tumor tissue. By analogy with EGFR, LB for detection of genomic alterations in ALK (rearrangements or mutations) has been rapidly adopted in the clinic. However, this promising approach has some limitations and has not yet been disseminated as much as the blood test targeting EGFR. In addition to these two therapeutic targets LB can be used for evaluation of the genomic status of other genes of interest of patients with lung cancer (ROS1, RET, NTRK MET, BRAF, HER2, etc.). LB can be performed to evaluate a specific target or for a more or less complex panel of genes. Considering the number of potential targets for clinical trials, techniques of next-generation sequencing of circulating DNA are on the rise. This review will provide an update on the contribution of LB to care of patients with metastatic lung cancer, including the present limits of this approach, and will consider certain perspectives.
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228
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Bouhlel L, Hofman V, Maschi C, Ilié M, Allégra M, Marquette CH, Audigier-Valette C, Thariat J, Hofman P. The liquid biopsy: a tool for a combined diagnostic and theranostic approach for care of a patient with late-stage lung carcinoma presenting with bilateral ocular metastases. Expert Rev Anticancer Ther 2017; 17:1087-1092. [PMID: 29069959 DOI: 10.1080/14737140.2017.1398089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Liquid biopsies (LB) are used routinely in clinical practice in two situations for late stage non-small-cell lung cancer (NSCLC) patients, (i) at the initial diagnosis when looking for activating mutations in EGFR in the absence of analyzable tissue DNA and, (ii) during tumor progression on a tyrosine kinase inhibitor treatment to look for the resistance mutation T790M in EGFR. LB is not presently recommended in daily practice for the diagnosis of NSCLC. Areas covered: We report the diagnosis of a NSCLC in a patient with bilateral ocular metastases after detection of a deletion in exon 19 of EGFR when using plasma DNA. Without histological analysis, the origin of the primary ocular metastasis was uncertain. In this context, a LB showing an activating mutation in EGFR and circulating tumor cells positive for TTF1 led to the diagnosis of NSCLC and targeted therapy. Expert commentary: When no tumor tissue sample is available a LB can be used to diagnose for metastatic NSCLC, when a mutation in EGFR is identified. While a tissue biopsy is the gold standard approach for the diagnosis of a NSCLC and for identification of activating mutations, LB can exceptionally provide both a diagnosis of the primitive tumor and indicate appropriate therapy based on a molecular analysis.
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Affiliation(s)
- Linda Bouhlel
- a Department of Oncology , Antoine Lacassagne Comprehensive Cancer Centre , Nice , France
| | - Véronique Hofman
- b FHU OncoAge, Laboratory of Clinical and Experimental Pathology , CHU of Nice , Nice , France.,c Hospital-Integrated Biobank (BB-0033-00025) , CHU of Nice , Nice , France
| | - Célia Maschi
- d Department of Ophtalmology , CHU of Nice , Nice , France
| | - Marius Ilié
- b FHU OncoAge, Laboratory of Clinical and Experimental Pathology , CHU of Nice , Nice , France.,c Hospital-Integrated Biobank (BB-0033-00025) , CHU of Nice , Nice , France
| | - Maryline Allégra
- b FHU OncoAge, Laboratory of Clinical and Experimental Pathology , CHU of Nice , Nice , France.,c Hospital-Integrated Biobank (BB-0033-00025) , CHU of Nice , Nice , France
| | | | | | - Juliette Thariat
- g Radiation Oncology Department , Antoine Lacassagne Comprehensive Cancer Center , Nice , France
| | - Paul Hofman
- b FHU OncoAge, Laboratory of Clinical and Experimental Pathology , CHU of Nice , Nice , France.,c Hospital-Integrated Biobank (BB-0033-00025) , CHU of Nice , Nice , France
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Singh AP, Cheng H, Guo X, Levy B, Halmos B. Circulating Tumor DNA in Non–Small-Cell Lung Cancer: A Primer for the Clinician. JCO Precis Oncol 2017; 1:1-13. [DOI: 10.1200/po.17.00054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Circulating tumor DNA (ctDNA) consists of short, double-stranded DNA fragments that are released into the circulation by tumor cells. With the advent of newer molecular platforms, ctDNA can be detected with high sensitivity and specificity in plasma. The assay’s noninvasive nature, ability to reflect intratumoral heterogeneity, short turnaround time, and ability to obtain serial samples make it an attractive option compared with traditional tissue biopsy tumor sequencing. Currently, this technology is mostly being used for the detection of EGFR mutations in patients with advanced non–small-cell lung cancer where tissue is inadequate to detect EGFR mutations that drive acquired resistance, most notably EGFR T790M. Emerging uses include the incorporation of ctDNA testing into primary diagnosis, treatment monitoring, detection of minimal residual disease, and detection of early-stage disease in screening populations. This review summarizes both validated and evolving uses of ctDNA testing in non–small-cell lung cancer in the context of oncologists’ daily practice and some of its potential challenges in the era of targeted therapy and immunotherapy.
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Affiliation(s)
- Aditi P. Singh
- Aditi P. Singh, Haiying Cheng, Xiaoling Guo, and Balazs Halmos, Montefiore Medical Center, Bronx, NY; and Benjamin Levy, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center at Sibley Memorial Hospital, Washington, DC
| | - Haiying Cheng
- Aditi P. Singh, Haiying Cheng, Xiaoling Guo, and Balazs Halmos, Montefiore Medical Center, Bronx, NY; and Benjamin Levy, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center at Sibley Memorial Hospital, Washington, DC
| | - Xiaoling Guo
- Aditi P. Singh, Haiying Cheng, Xiaoling Guo, and Balazs Halmos, Montefiore Medical Center, Bronx, NY; and Benjamin Levy, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center at Sibley Memorial Hospital, Washington, DC
| | - Benjamin Levy
- Aditi P. Singh, Haiying Cheng, Xiaoling Guo, and Balazs Halmos, Montefiore Medical Center, Bronx, NY; and Benjamin Levy, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center at Sibley Memorial Hospital, Washington, DC
| | - Balazs Halmos
- Aditi P. Singh, Haiying Cheng, Xiaoling Guo, and Balazs Halmos, Montefiore Medical Center, Bronx, NY; and Benjamin Levy, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center at Sibley Memorial Hospital, Washington, DC
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230
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Chang Y, Tolani B, Nie X, Zhi X, Hu M, He B. Review of the clinical applications and technological advances of circulating tumor DNA in cancer monitoring. Ther Clin Risk Manag 2017; 13:1363-1374. [PMID: 29066904 PMCID: PMC5644666 DOI: 10.2147/tcrm.s141991] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) released by tumor cells, termed ctDNA, closely reflects the heterogeneity of primary cancers and their metastases. As a noninvasive, real-time monitoring biomarker, ctDNA is a promising tool for detecting driver gene mutations, assessing tumor burden and acquired resistance, and early diagnosis. However, isolation and enrichment of cfDNA is a big challenge due to the high degree of DNA fragmentation and its relatively low abundance in the bloodstream. This review aims to provide insights into the recent technological advances in acquisition of optimal quality cfDNA, the use of preservatives, isolation methods, processing timelines, and detection techniques. It also describes clinical applications of ctDNA in cancer patient management.
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Affiliation(s)
- Yi Chang
- Department of Respiratory Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China
- Thoracic Oncology Program, Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Bhairavi Tolani
- Thoracic Oncology Program, Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Xiuhong Nie
- Department of Respiratory Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Xiuyi Zhi
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Mu Hu
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Biao He
- Thoracic Oncology Program, Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
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231
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Piton N, Lamy A, Sabourin JC. Séquençage des tumeurs : évolutions et révolutions. Cancer Radiother 2017; 21:580-583. [DOI: 10.1016/j.canrad.2017.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 07/22/2017] [Indexed: 11/26/2022]
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232
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Franovic A, Raymond VM, Erlander MG, Reckamp KL. Urine test for EGFR analysis in patients with non-small cell lung cancer. J Thorac Dis 2017; 9:S1323-S1331. [PMID: 29184671 DOI: 10.21037/jtd.2017.06.144] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Precision medicine approaches in oncology are reliant on the accurate genomic characterization of tumors. While tissue remains the mainstay specimen for molecular testing, tumor biopsies are riddled with challenges and limitations due to their invasive and site-specific nature. Tumor inaccessibility and intratumoral heterogeneity, in particular, represent significant obstacles to the identification of actionable genetic alterations and hence effective mono- and combination therapy strategies. Proof-of-concept studies indicate that circulating tumor DNA (ctDNA) released from multiple tumor regions and anatomical locations is more reflective of intra- and intertumoral heterogeneity. Non-invasive liquid biopsy approaches that allow for the analysis of ctDNA are thus being increasingly implemented in routine patient care for the detection and monitoring of cancer-associated mutations. Indeed, the use of plasma testing to screen for epidermal growth factor receptor (EGFR) T790M mutant positive non-small cell lung cancer (NSCLC) patients eligible for treatment with third-generation EGFR inhibitors was recently approved by the U.S. Food and Drug Administration and is incorporated into the most recent version of the National Comprehensive Cancer Center guidelines as an alternative to tissue biopsy. Urine represents another liquid biopsy specimen that is distinguished by its ease of collection, option for home collection, and lack of temporal and volumetric collection restrictions. Importantly, there is an accumulating body of evidence supporting the clinical validity of urinary EGFR mutant testing for the identification and stratification of patients likely to benefit from EGFR-directed therapies and as a means to assess patient response, the presence of residual disease, and emergence of resistant tumor cell populations.
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233
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Duréndez-Sáez E, Azkárate A, Meri M, Calabuig-Fariñas S, Aguilar-Gallardo C, Blasco A, Jantus-Lewintre E, Camps C. New insights in non-small-cell lung cancer: circulating tumor cells and cell-free DNA. J Thorac Dis 2017; 9:S1332-S1345. [PMID: 29184672 DOI: 10.21037/jtd.2017.06.112] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Lung cancer is the second most frequent tumor and the leading cause of death by cancer in both men and women. Increasing knowledge about the cancer genome and tumor environment has led to a new setting in which morphological and molecular characterization is needed to treat patients in the most personalized way in order to achieve better outcomes. Since tumor products can be detected in body fluids, the liquid biopsy, particularly, peripheral blood, has emerged as a new source for lung cancer biomarker's analysis. A variety of tumor components can be used for this purpose. Among them, circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) should be especially considered. Different detection methods for both CTCs and ctDNA have been and are being developed to improve the sensitivity and specificity of these tests. This would lead to better characterization and would solve some clinical doubts at different disease evolution times, e.g., intratumoral or temporal heterogeneity, difficulty in the obtaining a tumor sample, etc., and would also avoid the side effects of very expensive and complicated tumor obtaining interventions. CTCs and ctDNA are useful in different lung cancer settings. Their value has been shown for the early diagnosis, prognosis, prediction of treatment efficacy, monitoring responses and early detection of lung cancer relapse. CTCs have still not been validated for use in clinical settings in non-small-cell lung cancer (NSCLC), while ctDNA has been approved by the Food and Drug Administration (FDA) and European Medical Association (EMA), and the main clinical guidelines used for detect different epidermal growth factor receptor (EGFR) mutations and the monitoring and treatment choice of mutated patients with tyrosine kinase inhibitors (TKIs). This review, describes how ctDNA seem to be winning the race against CTCs from the laboratory bench to clinical practice due to easier obtaining methods, manipulation and its implementation into clinical practice.
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Affiliation(s)
- Elena Duréndez-Sáez
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, Valencia, Spain
| | - Aitor Azkárate
- Department of Oncology, University Hospital Son Espases, Palma de Mallorca, Spain
| | - Marina Meri
- Department of Medical Oncology, Hospital General Universitario de Valencia, Valencia, Spain
| | - Silvia Calabuig-Fariñas
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, Valencia, Spain.,Department of Pathology, Universitat de València, Valencia, Spain.,CIBERONC, Valencia, Spain
| | | | - Ana Blasco
- Department of Medical Oncology, Hospital General Universitario de Valencia, Valencia, Spain.,CIBERONC, Valencia, Spain
| | - Eloisa Jantus-Lewintre
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, Valencia, Spain.,CIBERONC, Valencia, Spain.,Department of Biotechnology, Universitat Politècnica de València, Valencia, Spain
| | - Carlos Camps
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, Valencia, Spain.,Department of Medical Oncology, Hospital General Universitario de Valencia, Valencia, Spain.,CIBERONC, Valencia, Spain.,Department of Medicine, Universitat de València, Valencia, Spain
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234
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Karachaliou N, Sosa AE, Molina MA, Centelles Ruiz M, Rosell R. Possible application of circulating free tumor DNA in non-small cell lung cancer patients. J Thorac Dis 2017; 9:S1364-S1372. [PMID: 29184675 DOI: 10.21037/jtd.2017.09.59] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liquid biopsies have been heralded as a game changer in cancer management. Blood tests offer a minimally invasive, safe and sensitive complementary (or even alternative) approach for tissue biopsies. With lung cancer being the second most commonly diagnosed cancer and the leading cause of cancer deaths worldwide, due to the limitations of tissue sampling, liquid biopsies must urgently materialize in the clinic. In this short review, we will present the current applications of cell-free DNA (cfDNA) in lung cancer management, emphasizing on our own experience and previous work. We will also shortly comment on the challenges and need for a coordinated collaboration combining disciplines and sectors (from academia to health economies) in order to accelerate liquid biopsy development in lung cancer and other cancers.
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Affiliation(s)
- Niki Karachaliou
- Instituto Oncológico Dr Rosell (IOR), University Hospital Sagrat Cor, Barcelona, Spain.,Coyote Research Group, Pangaea Oncology, Laboratory of Molecular Biology, Quirón-Dexeus University Institute, Barcelona, Spain
| | - Aaron E Sosa
- Instituto Oncológico Dr Rosell (IOR), University Hospital Sagrat Cor, Barcelona, Spain
| | - Miguel Angel Molina
- Pangaea Oncology, Laboratory of Molecular Biology, Quirón-Dexeus University Institute, Barcelona, Spain
| | | | - Rafael Rosell
- Instituto Oncológico Dr Rosell (IOR), University Hospital Sagrat Cor, Barcelona, Spain.,Coyote Research Group, Pangaea Oncology, Laboratory of Molecular Biology, Quirón-Dexeus University Institute, Barcelona, Spain.,Institut d'Investigació en Ciències Germans Trias i Pujol, Badalona, Spain.,Institut Català d'Oncologia, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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235
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Liquid biopsy genotyping in lung cancer: ready for clinical utility? Oncotarget 2017; 8:18590-18608. [PMID: 28099915 PMCID: PMC5392351 DOI: 10.18632/oncotarget.14613] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 01/04/2017] [Indexed: 01/08/2023] Open
Abstract
Liquid biopsy is a blood test that detects evidence of cancer cells or tumor DNA in the circulation. Despite complicated collection methods and the requirement for technique-dependent platforms, it has generated substantial interest due, in part, to its potential to detect driver oncogenes such as epidermal growth factor receptor (EGFR) mutants in lung cancer. This technology is advancing rapidly and is being incorporated into numerous EGFR tyrosine kinase inhibitor (EGFR-TKI) development programs. It appears ready for integration into clinical care. Recent studies have demonstrated that biological fluids such as saliva and urine can also be used for detecting EGFR mutant DNA through application other user-friendly techniques. This review focuses on the clinical application of liquid biopsies to lung cancer genotyping, including EGFR and other targets of genotype-directed therapy and compares multiple platforms used for liquid biopsy.
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236
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Mao X, Zhang Y, Xie F, Zheng X, Sun J. Can peripheral blood be used as surrogate in detecting epidermal growth factor receptor mutation status in advanced non-small cell lung cancer patients? A meta-analysis. Oncotarget 2017; 8:78057-78067. [PMID: 29100447 PMCID: PMC5652836 DOI: 10.18632/oncotarget.20291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 06/01/2017] [Indexed: 12/25/2022] Open
Abstract
Background Apply peripheral blood as a surrogate for detecting epidermal growth factor receptor mutation status in tumor, also called liquid biopsy, has been reported to be a feasible method in patients with advanced non-small lung cancer. But the diagnostic yield varies in different studies. Methods A meta-analysis was carried out to evaluate the sensitivity and specificity of peripheral blood in detection epidermal growth factor receptor mutation status in advanced non-small lung cancer patients. Publications up to October 2016 were searched using PubMed, Embase and Web of Science databases. Sensitivity, specificity and other parameters were pooled using the bivariate mixed-effects regression model. Results Fifteen studies meeting the inclusion criteria were included. The pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio and diagnostic odds ratio were 0.69 (95% CI: 0.59~0.78), 0.97 (95% CI: 0.94~0.99), 23.1 (95% CI: 11.6~46.1), 0.32 (95% CI: 0.23~0.44), 73 (95% CI: 33~159), respectively. The summary receiver operating characteristic curve was 0.93 (95% CI: 0.91–0.95). Discussion Detecting epidermal growth factor receptor mutation in peripheral blood is a reliable and non-invasive method in patients with advanced non-small lung cancer. More sensitive detection methods are required to increase the sensitivity of liquid biopsy of ctDNA.
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Affiliation(s)
- Xiaowei Mao
- Department of Endoscopy and Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Yujun Zhang
- Department of Endoscopy and Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Fangfang Xie
- Department of Endoscopy and Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Xiaoxuan Zheng
- Department of Endoscopy and Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Jiayuan Sun
- Department of Endoscopy and Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, PR China
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237
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Yu HA, Spira A, Horn L, Weiss J, West H, Giaccone G, Evans T, Kelly RJ, Desai B, Krivoshik A, Moran D, Poondru S, Jie F, Aoyama K, Keating A, Oxnard GR. A Phase I, Dose Escalation Study of Oral ASP8273 in Patients with Non-small Cell Lung Cancers with Epidermal Growth Factor Receptor Mutations. Clin Cancer Res 2017; 23:7467-7473. [PMID: 28954786 DOI: 10.1158/1078-0432.ccr-17-1447] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/18/2017] [Accepted: 09/20/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Acquired EGFR T790M mutations are the most frequently identified resistance mechanism to EGFR tyrosine kinase inhibitors (TKI) in patients with EGFR-mutant lung cancers. ASP8273 is a third-generation EGFR TKI with antitumor activity in preclinical models of EGFR-mutant lung cancer that targets mutant EGFR, including EGFR T790M.Experimental Design: In this multicohort, phase I study (NCT02113813), escalating doses of ASP8273 (25-500 mg) were administered once daily to non-small cell lung cancer (NSCLC) patients with disease progression after prior treatment with an EGFR TKI. EGFR T790M was required for all cohorts, except the dose escalation cohort. Primary endpoints were safety/tolerability; secondary endpoints were determination of the RP2D, pharmacokinetic profile, and preliminary antitumor activity of ASP8273. Evaluation of the use of EGFR mutations in circulating free DNA (cfDNA) as a biomarker of ASP8273 treatment effects was an exploratory endpoint.Results: A total of 110 patients were treated with ASP8273 across dose escalation (n = 36), response-expansion (n = 36), RP2D (300 mg; n = 19) and food-effect (n = 19) cohorts. The most common treatment-emergent adverse events included diarrhea, nausea, fatigue, constipation, vomiting, and hyponatremia. Across all doses, in patients with EGFR T790M, the response rate was 30.7% (n = 27/88; 95% CI, 19.5%-44.5%), and median progression-free survival was 6.8 months (95% CI, 5.5-10.1 months). EGFR mutations in cfDNA, both the activating mutation and EGFR T790M, became undetectable in most patients in the setting of clinical response and reemerged upon disease progression.Conclusions: ASP8273 was well tolerated and promoted antitumor activity in patients with EGFR-mutant lung cancer with disease progression on prior EGFR TKI therapy. Clin Cancer Res; 23(24); 7467-73. ©2017 AACR.
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Affiliation(s)
- Helena A Yu
- Memorial Sloan Kettering Cancer Center, New York, New York.
| | | | - Leora Horn
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Jared Weiss
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina
| | - Howard West
- Swedish Cancer Institute, Seattle, Washington
| | | | - Tracey Evans
- Abramson Cancer Center, Philadelphia, Pennsylvania
| | - Ronan J Kelly
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Bethesda, Maryland
| | - Bhardwaj Desai
- Astellas Pharma Global Development, Northbrook, Illinois
| | | | - Diarmuid Moran
- Astellas Pharma Global Development, Northbrook, Illinois
| | | | - Fei Jie
- Astellas Pharma Global Development, Northbrook, Illinois
| | | | - Anne Keating
- Astellas Pharma Global Development, Northbrook, Illinois
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238
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Zhao J, Dinkel J, Warth A, Penzel R, Reinmuth N, Schnabel P, Muley T, Meister M, Zabeck H, Steins M, Yang JY, Zhou Q, Schlemmer HP, Herth FJF, Kauczor HU, Heussel CP. CT characteristics in pulmonary adenocarcinoma with epidermal growth factor receptor mutation. PLoS One 2017; 12:e0182741. [PMID: 28949965 PMCID: PMC5614426 DOI: 10.1371/journal.pone.0182741] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 07/24/2017] [Indexed: 12/12/2022] Open
Abstract
Comprehensively investigate the association of CT morphology and clinical findings of adenocarcinoma with EGFR mutation status. Retrospectively included 282 patients who was pathologically proved as lung adenocarcinoma with known EGFR mutation status (mutations: 138 patients, female: 86, median age: 66 years; wildtype: 144 patients, female: 67, median age: 62 years) and their pre-treatment CT scans were analyzed. CT findings and clinical information were collected. Univariate and multivariable logistic regression analysis were performed. Adjusted for age, gender and smoking history of two groups, significantly more patients with pleural tags, pleural and liver metastases were found in the EGFR mutated group (P = 0.007, 0.004, and 0.043, respectively). Multivariable logistic regression analysis found that the model included age, gender, smoking history, air bronchogram, pleural tags, pleural and liver metastasis had a moderate predictive value for EGFR mutation status (AUC = 0.741, P < .0001). Exon-19 deletion was associated with air bronchogram which adjusted for age, gender and smoking history (P = 0.007, OR: 2.91, 95%CI: 1.25–7.79). The evidence of pleural tags, pleural and liver metastases go along with a higher probability of EGFR mutation in adenocarcinoma patients and air bronchogram is positively associated with Exon-19 deletion mutation.
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Affiliation(s)
- Jing Zhao
- Department of Diagnostic and Interventional Radiology, University Hospital of Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), Heidelberg, Germany
- Department of Diagnostic and Interventional Radiology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- * E-mail: (Zhao J); (Yang J.Y)
| | - Julien Dinkel
- Department of Diagnostic and Interventional Radiology, University Hospital of Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), Heidelberg, Germany
| | - Arne Warth
- Translational Lung Research Center Heidelberg (TLRC), Heidelberg, Germany
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Roland Penzel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Niels Reinmuth
- Airway Center North (ARCN), LungenClinic Grosshansdorf GmbH, Großhansdorf, Germany
| | - Philipp Schnabel
- Translational Lung Research Center Heidelberg (TLRC), Heidelberg, Germany
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Muley
- Translational Lung Research Center Heidelberg (TLRC), Heidelberg, Germany
- Translational Research Unit, Thoraxklinik at University of Heidelberg, Heidelberg, Germany
| | - Michael Meister
- Translational Lung Research Center Heidelberg (TLRC), Heidelberg, Germany
- Translational Research Unit, Thoraxklinik at University of Heidelberg, Heidelberg, Germany
| | - Heike Zabeck
- Department of Thoracic Surgery, Thoraxklinik at University of Heidelberg, Heidelberg, Germany
| | - Martin Steins
- Translational Lung Research Center Heidelberg (TLRC), Heidelberg, Germany
- Department of Thoracic Oncology, Thoraxklinik at University of Heidelberg, Heidelberg, Germany
| | - Jian-yong Yang
- Department of Diagnostic and Interventional Radiology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- * E-mail: (Zhao J); (Yang J.Y)
| | - Qian Zhou
- Clinical Trials Unit, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Heinz-Peter Schlemmer
- Translational Lung Research Center Heidelberg (TLRC), Heidelberg, Germany
- Department of Radiology, German Cancer Research Center (dkfz), Heidelberg, Germany
| | - Felix J. F. Herth
- Translational Lung Research Center Heidelberg (TLRC), Heidelberg, Germany
- Department of Pneumology and Respiratory Critical Care Medicine, Thoraxklinik at University of Heidelberg, Heidelberg, Germany
| | - Hans-Ulrich Kauczor
- Department of Diagnostic and Interventional Radiology, University Hospital of Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), Heidelberg, Germany
| | - Claus Peter Heussel
- Department of Diagnostic and Interventional Radiology, University Hospital of Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), Heidelberg, Germany
- Department of Radiology, German Cancer Research Center (dkfz), Heidelberg, Germany
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239
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Kim JY, Park D, Son DS, Nam SJ, Kim SW, Jung HH, Kim YJ, Park G, Park WY, Lee JE, Park YH. Circulating tumor DNA shows variable clonal response of breast cancer during neoadjuvant chemotherapy. Oncotarget 2017; 8:86423-86434. [PMID: 29156805 PMCID: PMC5689695 DOI: 10.18632/oncotarget.21198] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/23/2017] [Indexed: 01/06/2023] Open
Abstract
Circulating tumor DNA (ctDNA) correlates with tumor burden and provides early detection of treatment response and tumor genetic alterations in breast cancer (BC). In this study, we aimed to identify genetic alterations during the process of tumor clonal evolution and examine if ctDNA level well indicated clinical response to neoadjuvant chemotherapy (NAC) and BC recurrence. We performed targeted ultra-deep sequencing of plasma DNAs, matched germline DNAs and tumor DNAs from locally advanced BC patients. Serial plasma DNAs were collected at diagnosis, after the 1st cycle of NAC and after curative surgery. For the target enrichment, we designed RNA baits covering a total of ∼202kb regions of the human genome including a total of 82 cancer-related genes. For ctDNA, 15 serial samples were collected and 87% of plasma SNVs were detected in 13 BC samples that had somatic alterations in tumor tissues. The TP53 mutation was most commonly detected in primary tumor tissues and plasma followed by BRCA1 and BRCA2. At BC diagnosis, the amount of plasma SNVs did not correlate with clinical stage at diagnosis. With respect to the therapeutic effects of NAC, we found two samples in which ctDNA disappeared after the 1st NAC cycle achieved a pathologic complete response (pCR). In addition, the amount of ctDNA correlated with residual cancer volume detected by breast MRI. This targeted ultra-deep sequencing for ctDNA analysis would be useful for monitoring tumor burden and drug resistance. Most of all, we suggest that ctDNA could be the earliest predictor of NAC response.
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Affiliation(s)
- Ji-Yeon Kim
- Division of Hematology-Oncology, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Donghyun Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Dae-Soon Son
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Seok Jin Nam
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Seok Won Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Hae Hyun Jung
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Korea
| | - Yeon Jeong Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Gahee Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea.,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Korea
| | - Jeong Eon Lee
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Korea
| | - Yeon Hee Park
- Division of Hematology-Oncology, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Korea.,Biomedical Research Institute, Samsung Medical Center, Sungkyunkwan University, Seoul 06351, Korea
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240
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Zhu L, Zhang S, Xun Y, Jiang Y, Xia B, Chen X, Wang L, Jiang H, Ma S. Comparison of the Amplification Refractory Mutation System, Super Amplification Refractory Mutation System, and Droplet Digital PCR for T790 M Mutation Detection in Non-small Cell Lung Cancer after Failure of Tyrosine Kinase Inhibitor Treatment. Pathol Oncol Res 2017; 24:843-851. [PMID: 28868565 DOI: 10.1007/s12253-017-0286-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/07/2017] [Indexed: 01/01/2023]
Abstract
Plasma mutation detection has the advantages of non-invasiveness and accessibility. Here, we evaluated three methods, the amplification refractory mutation system (ARMS), second-generation ARMS (SuperARMS), and droplet digital PCR (ddPCR), to assess their concordance and feasibility for the detection of mutations in plasma samples. Non-small lung cancer patients with stage IIIB/IV that were resistant to epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) treatment were enrolled. Blood samples were collected within 14 days after TKI resistance. Each sample was simultaneously assessed by the three methods. In total, 169 patients were enrolled; 54.4% were female, 72.2% were diagnosed with stage IV disease; and 97.6% had adenocarcinoma. T790 M mutations were detected in 42 (24.8%) of the 169 samples using ARMS, one of which carried the T790 M alone, 22 that also encoded exon 19 deletions, and 19 with L858R mutations. For the SuperARMS assay, 59 (34.9%) samples exhibited the T790 M mutation, and 110 (65.1%) showed no detectable T790 M mutation. ddPCR showed that 61 (36.1%) samples contained the T790 M mutation, whereas 108 (63.9%) were not positive. T790 M abundance ranged from 0.04% to 38.2%. The median T790 M abundance was 0.15% for total samples and 2.98% for T790 M mutation samples. The overall concordance was 78.7% (133/169) among ARMS, SuperARMS, and ddPCR. Compared with patients with stage III disease, patients with stage IV disease exhibited a higher T790 M mutation detection rate (28.7% vs. 14.9% by ARMS; 37.7% vs. 27.7% by SuperARMS; and 41.8% vs. 21.3% by ddPCR). Liquid biopsy showed promise and has the advantages of non-invasiveness and accessibility. T790 M detection based on circulating tumor DNA showed high concordance. Compared with non-digital platforms, ddPCR showed higher sensitivity and provided both frequency and abundance information, which might be important for treatment decisions.
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Affiliation(s)
- Lucheng Zhu
- Department of Oncology, Hangzhou First People's Hospital, Nanjing Medical University, No. 261, Huansha Road, Shangcheng District, Hangzhou, 310006, People's Republic of China.,Department of Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Shirong Zhang
- Hangzhou Translational Medicine Research Center, Hangzhou First People's Hospital, Nanjing Medical University, Nanjing, China. .,Hangzhou First People's Hospital, Nanjing Medical University, No.6, Xiaonv Road, Shangcheng District, Hangzhou, 310006, People's Republic of China.
| | - Yanping Xun
- Hangzhou Translational Medicine Research Center, Hangzhou First People's Hospital, Nanjing Medical University, Nanjing, China
| | - Yanping Jiang
- Hangzhou Translational Medicine Research Center, Hangzhou First People's Hospital, Nanjing Medical University, Nanjing, China
| | - Bing Xia
- Department of Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Xueqin Chen
- Department of Oncology, Hangzhou First People's Hospital, Nanjing Medical University, No. 261, Huansha Road, Shangcheng District, Hangzhou, 310006, People's Republic of China
| | - Limin Wang
- Department of Respiratory, Hangzhou First People's Hospital, Nanjing Medical University, Nanjing, China
| | - Hong Jiang
- Department of Thoracic Surgery, Hangzhou First People's Hospital, Nanjing Medical University, Nanjing, China
| | - Shenglin Ma
- Hangzhou First People's Hospital, Nanjing Medical University, No.261, Huansha Road, Shangcheng District, Hangzhou, 310006, People's Republic of China.
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Schwaederlé MC, Patel SP, Husain H, Ikeda M, Lanman RB, Banks KC, Talasaz A, Bazhenova L, Kurzrock R. Utility of Genomic Assessment of Blood-Derived Circulating Tumor DNA (ctDNA) in Patients with Advanced Lung Adenocarcinoma. Clin Cancer Res 2017; 23:5101-5111. [PMID: 28539465 PMCID: PMC5581668 DOI: 10.1158/1078-0432.ccr-16-2497] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/07/2017] [Accepted: 05/18/2017] [Indexed: 12/11/2022]
Abstract
Purpose: Genomic alterations in blood-derived circulating tumor DNA (ctDNA) from patients with non-small cell lung adenocarcinoma (NSCLC) were ascertained and correlated with clinical characteristics and therapeutic outcomes.Experimental Design: Comprehensive plasma ctDNA testing was performed in 88 consecutive patients; 34 also had tissue next-generation sequencing; 29, other forms of genotyping; and 25 (28.4%) had no tissue molecular tests because of inadequate tissue or biopsy contraindications.Results: Seventy-two patients (82%) had ≥1 ctDNA alteration(s); among these, 75% carried alteration(s) potentially actionable by FDA-approved (61.1%) or experimental drug(s) in clinical trials (additional 13.9%). The most frequent alterations were in the TP53 (44.3% of patients), EGFR (27.3%), MET (14.8%), KRAS (13.6%), and ALK (6.8%) genes. The concordance rate for EGFR alterations was 80.8% (100% vs. 61.5%; ≤1 vs. >1 month between ctDNA and tissue tests; P = 0.04) for patients with any detectable ctDNA alterations. Twenty-five patients (28.4%) received therapy matching ≥1 ctDNA alteration(s); 72.3% (N = 16/22) of the evaluable matched patients achieved stable disease ≥6 months (SD) or partial response (PR). Five patients with ctDNA-detected EGFR T790M were subsequently treated with a third generation EGFR inhibitor; all five achieved SD ≥ 6 months/PR. Patients with ≥1 alteration with ≥5% variant allele fraction (vs. < 5%) had a significantly shorter median survival (P = 0.012).Conclusions: ctDNA analysis detected alterations in the majority of patients, with potentially targetable aberrations found at expected frequencies. Therapy matched to ctDNA alterations demonstrated appreciable therapeutic efficacy, suggesting clinical utility that warrants future prospective studies. Clin Cancer Res; 23(17); 5101-11. ©2017 AACR.
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Affiliation(s)
- Maria C Schwaederlé
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California.
| | - Sandip P Patel
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California
| | - Hatim Husain
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California
| | - Megumi Ikeda
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California
| | - Richard B Lanman
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, California
| | - Kimberly C Banks
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, California
| | - AmirAli Talasaz
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, California
| | - Lyudmila Bazhenova
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California
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Ma M, Shi C, Qian J, Han B. Accuracy and clinical influence of plasma EGFR mutation detection in management of advanced lung adenocarcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:9559-9566. [PMID: 31966832 PMCID: PMC6965937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/15/2017] [Indexed: 06/10/2023]
Abstract
This study aimed to investigate the accuracy of plasma EGFR status detecting according to tissue EGFR status, and further explore the correlation of plasma EGFR status with clinicopathological features and progression-free survival (PFS) in patients with advanced lung adenocarcinoma. 157 patients with advanced lung adenocarcinoma were recruited. Paired tissue and plasma samples were collected before any prior treatments, EGFR gene mutation detection was performed using the amplification refractory mutation system (ARMS) method. EGFR mutations were detected in 81 tissue samples and the mutation rate was 51.6%, while in 50 plasma samples and the mutation rate was 31.8%. The overall concordance rate of EGFR mutations between tissue and plasma samples was 76.4%. And the sensitivity, specificity, positive predictive value and negative predictive value of the EGFR detection using plasma samples were 94.0%, 68.2%, 58.0 and 96.1% respectively. Patients with no-smoking (P = 0.039) and more number of metastatic sites (P = 0.012) presented a higher EGFR mutation frequency in plasma, but no association of plasma EGFR mutation with other clinicopathological features and PFS by targeted therapy was discovered. This study revealed that plasma EGFR mutation detection might be regarded as a good alternative biomarker for lung adenocarcinoma management, especially for patients who were not tolerant with obtainment of tissue samples, but further prognostic value needs to be investigated.
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Affiliation(s)
- Meili Ma
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University Shanghai, China
| | - Chunlei Shi
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University Shanghai, China
| | - Jialin Qian
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University Shanghai, China
| | - Baohui Han
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University Shanghai, China
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Comprehensive Analysis of the Discordance of EGFR Mutation Status between Tumor Tissues and Matched Circulating Tumor DNA in Advanced Non–Small Cell Lung Cancer. J Thorac Oncol 2017; 12:1376-1387. [DOI: 10.1016/j.jtho.2017.05.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 04/11/2017] [Accepted: 05/17/2017] [Indexed: 11/20/2022]
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Singh AP, Li S, Cheng H. Circulating DNA in EGFR-mutated lung cancer. ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:379. [PMID: 29057239 DOI: 10.21037/atm.2017.07.10] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Circulating tumor DNA (ctDNA) consists of short double stranded DNA fragments that are released by tumors including non-small cell lung cancer (NSCLC). With the identification of driver mutations in the epidermal growth factor receptor (EGFR) gene and development of targeted tyrosine kinase inhibitors (TKIs), the clinical outcome of NSCLC patients in this subgroup has improved tremendously. The gold standard to assess EGFR mutation is through tissue biopsy, which can be limited by difficulty in accessing the tumor, inability of patients to tolerate invasive procedures, insufficient sample for molecular testing and inability to capture intratumoral heterogeneity. The great need for rapid and accurate identification of activating EGFR mutations in NSCLC patients paves the road for ctDNA technology. Studies have demonstrated ctDNA to be a reliable complement to tumor genotyping. Platforms like digital polymerase chain reaction (PCR) and next-generation sequencing based analyses have made it possible to identify EGFR mutations in plasma with high sensitivity and specificity. This article will provide an overview on ctDNA in the context of EGFR mutated NSCLC, especially its emerging applications in diagnosis, disease surveillance, treatment monitoring and detection of resistance mechanisms.
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Affiliation(s)
- Aditi P Singh
- Department of Oncology, Montefiore Medical Center, Bronx, NY, USA
| | - Shenduo Li
- Department of Medicine, Jacobi Medical Center, Bronx, NY, USA
| | - Haiying Cheng
- Department of Oncology, Montefiore Medical Center, Bronx, NY, USA
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Han B, Tjulandin S, Hagiwara K, Normanno N, Wulandari L, Laktionov K, Hudoyo A, He Y, Zhang YP, Wang MZ, Liu CY, Ratcliffe M, McCormack R, Reck M. EGFR mutation prevalence in Asia-Pacific and Russian patients with advanced NSCLC of adenocarcinoma and non-adenocarcinoma histology: The IGNITE study. Lung Cancer 2017; 113:37-44. [PMID: 29110846 DOI: 10.1016/j.lungcan.2017.08.021] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Limited understanding exists of epidermal growth factor receptor (EGFR) mutation frequency in less common subgroups of advanced non-small-cell lung cancer (aNSCLC) (e.g. squamous cell carcinoma [SCC]), and to what extent local practices exclude patients from EGFR testing based on their clinical characteristics. MATERIALS AND METHODS IGNITE (non-comparative/-interventional; NCT01788163) was conducted in 90 centres (Asia-Pacific/Russia). Eligible patients: local/metastatic aNSCLC; chemotherapy-naïve, newly-diagnosed/recurrent disease after resection; ineligible for curative treatment. Patients provided a tissue/cytology (all) and a blood plasma (China/Russia/South Korea/Taiwan) sample. Primary endpoint: EGFR mutation frequency in aNSCLC patients (adenocarcinoma [ADC]/non-ADC), as per local practices. RESULTS 3382 patients were enrolled. EGFR mutation frequencies for evaluable tissue/cytology samples in Asia-Pacific and Russian patients: 49.3% (862/1749) and 18.0% (90/500) for ADC tumours; 14.1% (74/525) and 3.7% (15/402) for non-ADC; 9.9% (40/403) and 3.7% (13/349) for SCC. Of Russian patients with SCC tumours harbouring common, activating EGFR mutations, 6/9 were never-/former-smokers. Mutation status concordance between 2581 matched tissue/cytology and plasma samples: 80.5% (sensitivity 46.9%, specificity 95.6%). CONCLUSION EGFR mutation testing should be considered in all Asian aNSCLC patients. Also, as activating EGFR mutations were observed in a small number of Caucasian squamous NSCLC patients, testing here may be appropriate, particularly in those with no/remote smoking history. Circulating free tumour-derived DNA is feasible for mutation analysis employing well-validated and sensitive methods, when tumour samples are unavailable.
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Affiliation(s)
- Baohui Han
- Department of Respiratory Medicine, Shanghai Chest Hospital, Jiao Tong University, 241 Huaihai West Road, Shanghai, 200030, China.
| | - Sergei Tjulandin
- Department of Clinical Pharmacology and Chemotherapy, N. N. Blokhin Russian Cancer Research Center, 24 Kashirskoye Shosse, Moscow, 115478, Russia
| | - Koichi Hagiwara
- Division of Pulmonary Medicine, Department of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi, 329-0498, Japan
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione Giovanni Pascale", IRCCS, Via Mariano Semmola, Napoli, 80131, Italy
| | - Laksmi Wulandari
- Department of Pulmonology, Dr Soetomo General Hospital, No. 6-8 Surabaya, Jawa Timur, 60285, Indonesia
| | - Konstantin Laktionov
- Department of Clinical Biotechnology, N. N. Blokhin Russian Cancer Research Center, 24 Kashirskoye Shosse, Moscow, 115478, Russia
| | - Achmad Hudoyo
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, University of Indonesia - Persahabatan Hospital, 2nd Floor Jl. Persahabatan Raya No. 1, Rawamangun, Jakarta, 13230, Indonesia
| | - Yong He
- Department of Respiratory Medicine, Daping Hospital, The Third Military Medical University, No.10 Daping Changjiang Branch Road, Chongqing, 400042, China
| | - Yi-Ping Zhang
- Department of Chemotherapy, Zhejiang Cancer Hospital and Key Laboratory Diagnosis and Treatment Technology on Thoracic Oncology, 38 Guangji Road, Hangzhou, Zhejiang, 10022, China
| | - Meng-Zhao Wang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan Street, Dongcheng District, Beijing, 100730, China
| | - Chien Ying Liu
- Division of Thoracic Medicine, Chang Gung Memorial Hospital, Chang Gung University, 199 Tung Hwa North Road, Taipei, 105, Taiwan
| | - Marianne Ratcliffe
- AstraZeneca, Mereside, Alderley Park, Macclesfield, SK10 4TG, United Kingdom
| | - Rose McCormack
- AstraZeneca, Mereside, Alderley Park, Macclesfield, SK10 4TG, United Kingdom
| | - Martin Reck
- Department of Thoracic Oncology, LungenClinic Grosshansdorf, Airway Research Center North (ARCN), Member of the German Centre for Lung Research (DZL), Wöhrendamm 80, Grosshansdorf, 22927, Germany
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Review of the implementation of plasma ctDNA testing on behalf of IQN Path ASBL: a perspective from an EQA providers' survey. VIRCHOWS ARCHIV : AN INTERNATIONAL JOURNAL OF PATHOLOGY 2017. [PMID: 28840321 DOI: 10.1007/s00428-017-2222-z] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
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247
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Review of the implementation of plasma ctDNA testing on behalf of IQN Path ASBL: a perspective from an EQA providers' survey. Virchows Arch 2017; 471:809-813. [PMID: 28840321 PMCID: PMC5711978 DOI: 10.1007/s00428-017-2222-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/06/2017] [Accepted: 08/14/2017] [Indexed: 01/28/2023]
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248
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Li Y, Xu H, Su S, Ye J, Chen J, Jin X, Lin Q, Zhang D, Ye C, Chen C. Clinical validation of a highly sensitive assay to detect EGFR mutations in plasma cell-free DNA from patients with advanced lung adenocarcinoma. PLoS One 2017; 12:e0183331. [PMID: 28829813 PMCID: PMC5568724 DOI: 10.1371/journal.pone.0183331] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/02/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) is a promising biomarker for noninvasive epidermal growth factor receptor (EGFR) mutations detection in lung cancer patients, but the existing methods have limitations in sensitivity or in availability. In this study, we evaluated the performance of a novel assay called ADx-SuperARMS in detecting EGFR mutations in plasma cell-free DNA from patients with advanced lung adenocarcinoma. METHODS A total of 109 patients with metastatic advanced adenocarcinoma were recruited who provided both blood samples and matched tumor tissue samples. EGFR mutation status in plasma samples were tested with ADx-SuperARMS EGFR assay and tumor tissue samples were tested with ADx-ARMS EGFR assay. The clinical sensitivity, specificity, positive prediction value (PPV), and negative prediction value (NPV) of ADx-SuperARMS EGFR assay were calculated by using EGFR mutation status in tumor tissue as standard reference. A receiver operating characteristic (ROC) analysis was implemented and an area under the curve (AUC) was calculated to evaluate sensitivity and specificity of exon 19 deletion (E19Del) and L858R mutation detection. The objective response rate (ORR) were calculated according to the EGFR mutation status determined by ADx-superARMS as well. RESULTS 0.2% analytical sensitivity and 100% specificity of the ADx-SuperARMS EGFR assays for EGFR E19Del, L858R, and T790M mutants were confirmed by using a series of diluted cell line DNA. In the clinical study, EGFR mutations were detected in 45.9% (50/109) of the plasma samples and in 56.9% (62/109) of the matched tumor tissue samples. The sensitivity, specificity, PPV and NPV of the ADx-SuperARMS EGFR assay for plasma EGFR mutation detection were 82.0% (50/61), 100% (48/48), 100% (50/50), and 81.4% (48/59), respectively. In ROC analysis, ADx-SuperARMS achieved sensitivity and specificity of 88% and 99% in E19Dels as well as sensitivity and specificity of 89% and 100% in L858R, respectively. Among the 35 patients who were plasma EGFR mutation positive and treated with first generation of EGFR-tyrosine kinase inhibitors (TKIs), 23 (65.7%) achieved partial response, 11 (31.4%) sustained disease, and 1 (2.9%) progressive disease. The ORR and disease control rate (DCR) were 65.7% and 97.1%, respectively. CONCLUSIONS ADx-SuperARMS EGFR assay is likely to be a highly sensitive and specific method to noninvasively detect plasma EGFR mutations of patients with advanced lung adenocarcinoma. The EGFR mutations detected by ADx-SuperARMS EGFR assay could predict the efficacy of the treatment with first generation of EGFR-TKIs. Hence, EGFR blood testing with ADx-SuperARMS could address the unmet clinical needs.
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Affiliation(s)
- Yuping Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Hanyan Xu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shanshan Su
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Junru Ye
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Junjie Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xuru Jin
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Quan Lin
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Dongqing Zhang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Caier Ye
- Department of Radiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chengshui Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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Jovelet C, Madic J, Remon J, Honoré A, Girard R, Rouleau E, André B, Besse B, Droniou M, Lacroix L. Crystal digital droplet PCR for detection and quantification of circulating EGFR sensitizing and resistance mutations in advanced non-small cell lung cancer. PLoS One 2017; 12:e0183319. [PMID: 28829811 PMCID: PMC5567481 DOI: 10.1371/journal.pone.0183319] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/02/2017] [Indexed: 01/23/2023] Open
Abstract
Over the past years, targeted therapies using tyrosine kinase inhibitors (TKI) have led to an increase in progression-free survival and response rate for a subgroup of non-small cell lung cancer (NSCLC) patients harbouring specific gene abnormalities compared with chemotherapy. However long-lasting tumor regression is rarely achieved, due to the development of resistant tumoral subclones, which requires alternative therapeutic approaches. Molecular profile at progressive disease is a challenge for making adaptive treatment decisions. The aim of this study was to monitor EGFR-mutant tumors over time based on the quantity of mutant DNA circulating in plasma (ctDNA), comparing two different methods, Crystal™ Digital™ PCR and Massive Parallel Sequencing (MPS). In plasma circulating cell free DNA (cfDNA) of 61 advanced NSCLC patients we found an overall correlation of 78% between mutated allelic fraction measured by Crystal Digital PCR and MPS. 7 additional samples with sensitizing mutations and 4 additional samples with the resistance mutation were detected with Crystal Digital PCR, but not with MPS. Monitoring levels of both mutation types over time showed a correlation between levels and trends of mutated ctDNA detected and clinical assessment of disease for the 6 patients tested. In conclusion, Crystal Digital PCR exhibited good performance for monitoring mutational status in plasma cfDNA, and also appeared as better suited to the detection of known mutations than MPS in terms of features such as time to results.
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Affiliation(s)
- Cécile Jovelet
- Plateforme de Génomique-BMO et Centre de Ressources Biologiques, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France
| | - Jordan Madic
- Stilla Technologies, 1 Mail du Professeur Georges Mathé, Villejuif, France
| | - Jordi Remon
- Département de Médecine Oncologique, Institut Gustave Roussy, Villejuif, Faculté de médecine, Université Paris Sud, Le Kremlin-Bicêtre, France
| | - Aurélie Honoré
- Plateforme de Génomique-BMO et Centre de Ressources Biologiques, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France
| | - Romain Girard
- Ecole Polytechnique, Route de Saclay, Palaiseau, France
| | - Etienne Rouleau
- Plateforme de Génomique-BMO et Centre de Ressources Biologiques, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France
- Département de Biologie et Pathologie Médicales, Institut Gustave Roussy, Villejuif, France
| | - Barbara André
- Stilla Technologies, 1 Mail du Professeur Georges Mathé, Villejuif, France
| | - Benjamin Besse
- Département de Médecine Oncologique, Institut Gustave Roussy, Villejuif, Faculté de médecine, Université Paris Sud, Le Kremlin-Bicêtre, France
| | - Magali Droniou
- Stilla Technologies, 1 Mail du Professeur Georges Mathé, Villejuif, France
| | - Ludovic Lacroix
- Plateforme de Génomique-BMO et Centre de Ressources Biologiques, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy, Villejuif, France
- Département de Biologie et Pathologie Médicales, Institut Gustave Roussy, Villejuif, France
- * E-mail:
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Zhu YJ, Zhang HB, Liu YH, Zhang FL, Zhu YZ, Li Y, Bai JP, Liu LR, Qu YC, Qu X, Chen X, Li Y, Zheng GJ. Estimation of cell-free circulating EGFR mutation concentration predicts outcomes in NSCLC patients treated with EGFR-TKIs. Oncotarget 2017; 8:13195-13205. [PMID: 28061461 PMCID: PMC5355088 DOI: 10.18632/oncotarget.14490] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/16/2016] [Indexed: 01/05/2023] Open
Abstract
Detection of circulating tumor DNA using droplet digital polymerase chain reaction (ddPCR) is a highly-sensitive, minimally invasive alternative to serial biopsies for assessment and management of cancer. We used ddPCR to assess the utility of measuring plasma concentrations of common epidermal growth factor receptor (EGFR) mutations (L858R, exon 19 deletion, and T790M) in 57 non-small cell lung cancer (NSCLC) patients treated with EGFR tyrosine kinase inhibitors (EGFR-TKIs). High baseline plasma EGFR mutation (pEGFRmut) concentrations were associated with shorter progression-free survival (8.43 months) than low baseline pEGFRmut (16.23 months; p = 0.0019). By contrast, there were no differences in tumor shrinkage or overall survival between groups. During EGFR-TKI treatment, pEGFRmut levels decreased to zero in 89.58% of patients. Twenty-five of the 27 patients who progressed had basal pEGFRmut, and 18 also had circulating T790M. All 20 patients with dramatic progression (according to a categorization system for EGFR-TKIs failure) had basal pEGFRmut, and 13 had T790M mutation at progression. These results support the use of ddPCR for analysis of plasma EGFR mutations for prediction of PFS and to monitor clinical responses to EGFR-TKIs in NSCLC patients.
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Affiliation(s)
- Yan-Juan Zhu
- Oncology Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, China
| | - Hai-Bo Zhang
- Oncology Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, China
| | - Yi-Hong Liu
- Oncology Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, China
| | - Fu-Li Zhang
- Oncology Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, China
| | - Ya-Zhen Zhu
- Pathology Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, China
| | - Yong Li
- Oncology Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, China
| | - Jian-Ping Bai
- Oncology Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, China
| | - Li-Rong Liu
- Oncology Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, China
| | - Yan-Chun Qu
- Oncology Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, China
| | - Xin Qu
- Oncology Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, China
| | - Xian Chen
- Oncology Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, China
| | - Yan Li
- Oncology Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, China
| | - Guang-Juan Zheng
- Pathology Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, China
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