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Yaung SJ, Woestmann C, Ju C, Ma XM, Gattam S, Zhou Y, Xi L, Pal S, Balasubramanyam A, Tikoo N, Heussel CP, Thomas M, Kriegsmann M, Meister M, Schneider MA, Herth FJ, Wehnl B, Diehn M, Alizadeh AA, Palma JF, Muley T. Early Assessment of Chemotherapy Response in Advanced Non-Small Cell Lung Cancer with Circulating Tumor DNA. Cancers (Basel) 2022; 14:cancers14102479. [PMID: 35626082 PMCID: PMC9139958 DOI: 10.3390/cancers14102479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/12/2022] [Accepted: 05/15/2022] [Indexed: 11/16/2022] Open
Abstract
Monitoring treatment efficacy early during therapy could enable a change in treatment to improve patient outcomes. We report an early assessment of response to treatment in advanced NSCLC using a plasma-only strategy to measure changes in ctDNA levels after one cycle of chemotherapy. Plasma samples were collected from 92 patients with Stage IIIB-IV NSCLC treated with first-line chemo- or chemoradiation therapies in an observational, prospective study. Retrospective ctDNA analysis was performed using next-generation sequencing with a targeted 198-kb panel designed for lung cancer surveillance and monitoring. We assessed whether changes in ctDNA levels after one or two cycles of treatment were associated with clinical outcomes. Subjects with ≤50% decrease in ctDNA level after one cycle of chemotherapy had a lower 6-month progression-free survival rate (33% vs. 58%, HR 2.3, 95% CI 1.2 to 4.2, log-rank p = 0.009) and a lower 12-month overall survival rate (25% vs. 70%, HR 4.3, 95% CI 2.2 to 9.7, log-rank p < 0.001). Subjects with ≤50% decrease in ctDNA level after two cycles of chemotherapy also had shorter survival. Using non-invasive liquid biopsies to measure early changes in ctDNA levels in response to chemotherapy may help identify non-responders before standard-of-care imaging in advanced NSCLC.
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Affiliation(s)
- Stephanie J. Yaung
- Roche Sequencing Solutions, Inc., Pleasanton, CA 94588, USA; (X.M.M.); (L.X.); (J.F.P.)
- Correspondence: ; Tel.: +1-925-523-8824
| | | | - Christine Ju
- Roche Molecular Systems, Inc., Pleasanton, CA 94588, USA; (C.J.); (S.G.); (Y.Z.); (S.P.); (A.B.)
| | - Xiaoju Max Ma
- Roche Sequencing Solutions, Inc., Pleasanton, CA 94588, USA; (X.M.M.); (L.X.); (J.F.P.)
| | - Sandeep Gattam
- Roche Molecular Systems, Inc., Pleasanton, CA 94588, USA; (C.J.); (S.G.); (Y.Z.); (S.P.); (A.B.)
| | - Yiyong Zhou
- Roche Molecular Systems, Inc., Pleasanton, CA 94588, USA; (C.J.); (S.G.); (Y.Z.); (S.P.); (A.B.)
| | - Liu Xi
- Roche Sequencing Solutions, Inc., Pleasanton, CA 94588, USA; (X.M.M.); (L.X.); (J.F.P.)
| | - Subrata Pal
- Roche Molecular Systems, Inc., Pleasanton, CA 94588, USA; (C.J.); (S.G.); (Y.Z.); (S.P.); (A.B.)
| | - Aarthi Balasubramanyam
- Roche Molecular Systems, Inc., Pleasanton, CA 94588, USA; (C.J.); (S.G.); (Y.Z.); (S.P.); (A.B.)
| | - Nalin Tikoo
- Alector, Inc., South San Francisco, CA 94080, USA;
| | - Claus Peter Heussel
- Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik, University Hospital, 69126 Heidelberg, Germany;
- Diagnostic and Interventional Radiology, University Hospital, 69120 Heidelberg, Germany
- Translational Lung Research Centre (TLRC) Heidelberg, Member of the German Centre for Lung Research (DZL), 69120 Heidelberg, Germany; (M.T.); (M.M.); (M.A.S.); (F.J.H.); (T.M.)
| | - Michael Thomas
- Translational Lung Research Centre (TLRC) Heidelberg, Member of the German Centre for Lung Research (DZL), 69120 Heidelberg, Germany; (M.T.); (M.M.); (M.A.S.); (F.J.H.); (T.M.)
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany
| | - Mark Kriegsmann
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany;
| | - Michael Meister
- Translational Lung Research Centre (TLRC) Heidelberg, Member of the German Centre for Lung Research (DZL), 69120 Heidelberg, Germany; (M.T.); (M.M.); (M.A.S.); (F.J.H.); (T.M.)
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany
| | - Marc A. Schneider
- Translational Lung Research Centre (TLRC) Heidelberg, Member of the German Centre for Lung Research (DZL), 69120 Heidelberg, Germany; (M.T.); (M.M.); (M.A.S.); (F.J.H.); (T.M.)
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany
| | - Felix J. Herth
- Translational Lung Research Centre (TLRC) Heidelberg, Member of the German Centre for Lung Research (DZL), 69120 Heidelberg, Germany; (M.T.); (M.M.); (M.A.S.); (F.J.H.); (T.M.)
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany
| | - Birgit Wehnl
- Roche Diagnostics GmbH, 82377 Penzberg, Germany;
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.A.A.)
| | - Ash A. Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; (M.D.); (A.A.A.)
| | - John F. Palma
- Roche Sequencing Solutions, Inc., Pleasanton, CA 94588, USA; (X.M.M.); (L.X.); (J.F.P.)
| | - Thomas Muley
- Translational Lung Research Centre (TLRC) Heidelberg, Member of the German Centre for Lung Research (DZL), 69120 Heidelberg, Germany; (M.T.); (M.M.); (M.A.S.); (F.J.H.); (T.M.)
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany
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Sanz-Garcia E, Zhao E, Bratman SV, Siu LL. Monitoring and adapting cancer treatment using circulating tumor DNA kinetics: Current research, opportunities, and challenges. SCIENCE ADVANCES 2022; 8:eabi8618. [PMID: 35080978 PMCID: PMC8791609 DOI: 10.1126/sciadv.abi8618] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Circulating tumor DNA (ctDNA) has emerged as a biomarker with wide-ranging applications in cancer management. While its role in guiding precision medicine in certain tumors via noninvasive detection of susceptibility and resistance alterations is now well established, recent evidence has pointed to more generalizable use in treatment monitoring. Quantitative changes in ctDNA levels over time (i.e., ctDNA kinetics) have shown potential as an early indicator of therapeutic efficacy and could enable treatment adaptation. However, ctDNA kinetics are complex and heterogeneous, affected by tumor biology, host physiology, and treatment factors. This review outlines the current preclinical and clinical knowledge of ctDNA kinetics in cancer and how early on-treatment changes in ctDNA levels could be applied in clinical research to collect evidence to support implementation in daily practice.
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Affiliation(s)
- Enrique Sanz-Garcia
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Eric Zhao
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Scott V. Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Lillian L. Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Corresponding author.
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Longitudinal Circulating Tumor DNA Analysis in Blood and Saliva for Prediction of Response to Osimertinib and Disease Progression in EGFR-Mutant Lung Adenocarcinoma. Cancers (Basel) 2021; 13:cancers13133342. [PMID: 34283064 PMCID: PMC8268167 DOI: 10.3390/cancers13133342] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/24/2021] [Accepted: 06/29/2021] [Indexed: 01/19/2023] Open
Abstract
Background: We assessed whether serial ctDNA monitoring of plasma and saliva predicts response and resistance to osimertinib in EGFR-mutant lung adenocarcinoma. Three ctDNA technologies-blood-based droplet-digital PCR (ddPCR), next-generation sequencing (NGS), and saliva-based EFIRM liquid biopsy (eLB)-were employed to investigate their complementary roles. Methods: Plasma and saliva samples were collected from patients enrolled in a prospective clinical trial of osimertinib and local ablative therapy upon progression (NCT02759835). Plasma was analyzed by ddPCR and NGS. Saliva was analyzed by eLB. Results: A total of 25 patients were included. We analyzed 534 samples by ddPCR (n = 25), 256 samples by NGS (n = 24) and 371 samples by eLB (n = 22). Among 20 patients who progressed, ctDNA progression predated RECIST 1.1 progression by a median of 118 days (range: 61-272 days) in 11 (55%) patients. Of nine patients without ctDNA progression by ddPCR, two patients had an increase in mutant EGFR by eLB and two patients were found to have ctDNA progression by NGS. Levels of ctDNA measured by ddPCR and NGS at early time points, but not volumetric tumor burden, were associated with PFS. EGFR/ERBB2/MET/KRAS amplifications, EGFR C797S, PIK3CA E545K, PTEN V9del, and CTNNB1 S45P were key resistance mechanisms identified by NGS. Conclusion: Serial assessment of ctDNA in plasma and saliva predicts response and resistance to osimertinib, with each assay having supplementary roles.
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Noh JM, Kim YJ, Lee HY, Choi C, Ahn WG, Lee T, Pyo H, Park JH, Park D, Park WY. Targeted Liquid Biopsy Using Irradiation to Facilitate the Release of Cell-Free DNA from a Spatially Aimed Tumor Tissue. Cancer Res Treat 2021; 54:40-53. [PMID: 34044476 PMCID: PMC8756125 DOI: 10.4143/crt.2021.151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/24/2021] [Indexed: 11/22/2022] Open
Abstract
Purpose We investigated the feasibility of using an anatomically localized, target-enriched liquid biopsy (TLB) in mouse models of lung cancer. Materials and Methods After irradiating xenograft mouse with human lung cancer cell lines, H1299 (NRAS proto-oncogene, GTPase [NRAS] Q61K) and HCC827 (epidermal growth factor receptor [EGFR] E746–750del), circulating (cell-free) tumor DNA (ctDNA) levels were monitored with quantitative polymerase chain reaction on human long interspersed nuclear element-1 and cell line-specific mutations. We checked dose-dependency at 6, 12, or 18 Gy to each tumor-bearing mouse leg using 6-MV photon beams. We also analyzed ctDNA of lung cancer patients by LiquidSCAN, a targeted deep sequencing to validated the clinical performances of TLB method. Results Irradiation could enhance the detection sensitivity of NRAS Q61K in the plasma sample of H1299-xenograft mouse to 4.5-fold. While cell-free DNA (cfDNA) level was not changed at 6 Gy, ctDNA level was increased upon irradiation. Using double-xenograft mouse with H1299 and HCC827, ctDNA polymerase chain reaction analysis with local irradiation in each region could specify mutation type matched to transplanted cell types, proposing an anatomically localized, TLB. Furthermore, when we performed targeted deep sequencing of cfDNA to monitor ctDNA level in 11 patients with lung cancer who underwent radiotherapy, the average ctDNA level was increased within a week after the start of radiotherapy. Conclusion TLB using irradiation could temporarily amplify ctDNA release in xenograft mouse and lung cancer patients, which enables us to develop theragnostic method for cancer patients with accurate ctDNA detection.
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Affiliation(s)
- Jae Myoung Noh
- Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yeon Jeong Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Ho Yun Lee
- Department of Radiology and Center for Imaging Science, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Changhoon Choi
- Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Won-Gyun Ahn
- Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Taeseob Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.,GENINUS Inc, Seoul, Korea
| | - Hongryull Pyo
- Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jee Hyun Park
- Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Donghyun Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.,GENINUS Inc, Seoul, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
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Wang X, Zhang Y, Niu C, Wang S, Li L, Guo Y, Zhu L, Jin X, Gao H, Xu W, Zhu P, Lan Q, Du M, Cheng X, Gao Y, Dong L. Establishment of primary reference measurement procedures and reference materials for EGFR variant detection in non-small cell lung cancer. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:2114-2123. [PMID: 33870958 DOI: 10.1039/d1ay00328c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Circulating tumor DNA (ctDNA)-based mutation detection is promising to change the clinical practice of genotype-directed therapy for cancer. A growing number of non-invasive tests for cancer screening and monitoring that involve the detection of ctDNA have been commercialized. Primary reference measurement procedures (PRMPs) and reference materials (RMs) are urgently needed to assess the non-invasive tests. In this study, a PRMP based on digital PCR (dPCR) and ctDNA RMs for quantification of the frequently occurring variant in epidermal growth factor receptor (EGFR L858R, T790M, and 19Del) in non-small cell lung cancer (NSCLC) were established. The candidate dPCR PRMP showed high specificity (false positive rate 0-0.003%), good repeatability (coefficient of variance (CV), 2-3% for 104 copies/reaction), and high interlaboratory reproducibility (3-10%). A good linearity (0.97 < slope < 1.03, R2 ≥ 0.9999) between the measured mutant (MU) value and prepared value was observed for all assays over the fractional abundance (FA) range, between 25% and 0.05%. The limit of quantification (LoQ) was determined to be 34 L858R, 23 T790M, and 34 19Del copies/reaction, corresponding to a FA of 0.2%. An inter-laboratory study of using the EGFR ctDNA RMs and dPCR assays demonstrated that the participating laboratories produced consistent concentrations of MU and wild-type (WT), as well as FA. This study demonstrates that dPCR can act as a potential PRMP for EGFR mutation for validation of NSCLC genotyping tests and ctDNA quantitative tests. The PRMP and RMs established here could improve interlaboratory repeatability and reproducibility, which supports rapid translation and application of non-invasive tests into clinical practice.
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Affiliation(s)
- Xia Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
| | - Yongzhuo Zhang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
| | - Chunyan Niu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
| | - Shangjun Wang
- Nanjing Institute of Measurement and Testing Technology, Nanjing 210049, People's Republic of China
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing 100084, People's Republic of China
| | - Lingxiang Zhu
- Human Genetic Resource Center, National Research Institute for Health and Family Planning, Beijing 100081, People's Republic of China
| | - Xiaohua Jin
- Human Genetic Resource Center, National Research Institute for Health and Family Planning, Beijing 100081, People's Republic of China
| | - Huafang Gao
- Human Genetic Resource Center, National Research Institute for Health and Family Planning, Beijing 100081, People's Republic of China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China
| | - Pengyu Zhu
- Chinese Academy of Inspection and Quarantine, Beijing 100176, People's Republic of China
| | - Qingkuo Lan
- Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin 300381, People's Republic of China
| | - Meihong Du
- Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing Center for Physical & Chemical Analysis, Beijing 100093, People's Republic of China
| | - Xiaoyan Cheng
- Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing Center for Physical & Chemical Analysis, Beijing 100093, People's Republic of China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
| | - Lianhua Dong
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
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Dong L, Wang X, Wang S, Du M, Niu C, Yang J, Li L, Zhang G, Fu B, Gao Y, Wang J. Interlaboratory assessment of droplet digital PCR for quantification of BRAF V600E mutation using a novel DNA reference material. Talanta 2019; 207:120293. [PMID: 31594564 DOI: 10.1016/j.talanta.2019.120293] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/13/2022]
Abstract
Droplet digital PCR (ddPCR) has attracted much attention in the detection of genetic signatures of cancer present at low levels in circulating tumor DNA (ctDNA) in blood. A growing number of laboratory-developed liquid biopsy tests based on such technology have become commercially available for clinical settings. To obtain consistent and comparable results, an international standard is necessary for validation of the analytical performance. In this study, a novel and SI-traceable "ctDNA" reference material (RM) carrying BRAF V600E was prepared by gravimetrically mixing a 152 bp PCR amplicon and sonicated wild-type genomic DNA. The ddPCR performance was evaluated by analyzing serial "ctDNA" dilutions using a competitive MGB assay. The mutant frequency concordance (k) between ddPCR and the gravimetrical value was 1.03 in the range from 53.9% to 0.1%. The limit of blank (LoB), detection (LoD) and quantification (LoQ) of ddPCR assay were determined to be 0.01%, 0.02% and 0.1%, respectively. Results from the interlaboratory study, using challenging low levels of BRAF V600E ctDNA RMs, demonstrated that the participating laboratories had the appropriate technical competency to perform accurate ddPCR-based low level of ratio measurements. However, a systematic error caused by uncorrected droplet volume in Naica Crystal ddPCR platform was found by using the ctDNA RM. Between-laboratory consistency in copy number measurement was greatly improved when a correct droplet volume was applied for the ddPCR measurement by using the ctDNA RM. This confirms that the "ctDNA" RM is fit for the validation of ddPCR systems for ctDNA quantification. This would also support translation of tests for circulating tumor DNA by ddPCR into routine use.
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Affiliation(s)
- Lianhua Dong
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, PR China.
| | - Xia Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, PR China
| | - Shangjun Wang
- Nanjing Institute of Measurement and Testing Technology, Nanjing, 210049, PR China
| | - Meihong Du
- Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing Center for Physical & Chemical Analysis, Beijing, 100093, PR China
| | - Chunyan Niu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, PR China
| | - Jiayi Yang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, PR China
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Ganlin Zhang
- Oncology Department, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, PR China
| | - Boqiang Fu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, PR China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, PR China
| | - Jing Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, PR China.
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Shi W, Xu X, Huang R, Yu Q, Zhang P, Xie S, Zheng H, Lu R. Plasma C-MYC level manifesting as an indicator in progression of breast cancer. Biomark Med 2019; 13:917-929. [PMID: 31144531 DOI: 10.2217/bmm-2019-0073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Aim: To investigate whether plasma C-MYC level could be an indicator in clinical progression of breast cancer. Materials & methods: Plasma level of C-MYC expression was detected by quantitative real time PCR and the level of c-myc protein in breast cancer tissues was detected by immunohistochemistry. The expression level of C-MYC mRNA in supernatant of cancer cells culture was measured compared with the nonbreast cancer cells. Results: Plasma C-MYC level was significantly higher in patients with breast cancer than that in the controls, which associated with clinical stages, lymph node status, etc. Receiver operating characteristic curve analysis showed the sensitivity and specificity of plasma C-MYC level for diagnosis of breast cancer were 63.6 and 81.8%, respectively. The expression of c-myc protein in breast cancer tissues was associated with plasma C-MYC level, even C-MYC level in supernatant of cancer cells was elevated. Conclusion: Plasma C-MYC level might be a potential indicator in progression of breast cancer.
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Affiliation(s)
- Weizhong Shi
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Clinical Laboratory, Shanghai Proton & Heavy Ion Center, Shanghai, PR China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Xiaofeng Xu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Clinical Laboratory, Shanghai Proton & Heavy Ion Center, Shanghai, PR China
| | - Ren Huang
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Clinical Laboratory, Shanghai Proton & Heavy Ion Center, Shanghai, PR China
| | - Qi Yu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Clinical Laboratory, Shanghai Proton & Heavy Ion Center, Shanghai, PR China
| | - Peiru Zhang
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Clinical Laboratory, Shanghai Proton & Heavy Ion Center, Shanghai, PR China
| | - Suhong Xie
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Hui Zheng
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Renquan Lu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, PR China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
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8
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Zaini J, Syahruddin E, Yunus M, Andarini SL, Hudoyo A, Masykura N, Yasril R, Ridwanuloh A, Hidajat H, Nurwidya F, Suharsono S, Utomo ARH. Evaluation of PCR-HRM, RFLP, and direct sequencing as simple and cost-effective methods to detect common EGFR mutations in plasma cell-free DNA of non-small cell lung cancer patients. Cancer Rep (Hoboken) 2019; 2:e1159. [PMID: 32721094 DOI: 10.1002/cnr2.1159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Lung cancer patients with mutations in epidermal growth factor receptor (EGFR) gene are treated with tyrosine kinase inhibitor (TKI). AIMS We aimed to evaluate polymerase chain reaction (PCR)-high-resolution melting (HRM), restriction fragment length polymorphism (RFLP), and direct sequencing (DS) to detect EGFR mutations in cell-free DNA (cfDNA) before and after TKI treatment in real-world settings of a developing country. METHODS Paired cytology and plasma samples were collected from 116 treatment-naïve lung cancer patients. DNA from both plasma and cytology specimens was isolated and analyzed using PCR-HRM (to detect exon 19 insertion/deletion), RFLP (to genotypes L858R and L861Q), and DS (to detect uncommon mutations G719A, G719C, or G719S [G719Xaa] in exon 18 and T790M and insertion mutations in exon 20). RESULTS EGFR genotypes were obtained in all 116 (100%) cfDNA and 110/116 (94.82%) of cytological specimens of treatment-naïve patient (baseline samples). EGFR-activating mutations were detected in 46/110 (40.6%) plasma samples, and 69/110 (63.2%) mutations were found in routine cytology samples. Using cytological EGFR genotypes as reference, we found that sensitivity and specificity of baseline plasma EGFR testing varied from 9.1% to 39.39% and 83.12% to 96.55%, respectively. In particular, the sensitivity and specificity of this assay in detecting baseline T790M mutations in exon 20 were 30% and 89.58%, respectively. Three months after TKI treatment, plasma T790M and insertion exon 20 mutations appeared in 5.4% and 2.7% patients, respectively. CONCLUSIONS Despite low sensitivity, combined DS, RFLP, and PCR-HRM was able to detect EGFR mutations in plasma cfDNA with high specificity. Moreover, TKI resistance exon 20 insertions mutation was detected as early as 3 months post TKI treatment.
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Affiliation(s)
- Jamal Zaini
- Department of Pulmonology and Respiratory Medicine Faculty of Medicine, Universitas Indonesia and Persahabatan Hospital, Jakarta, Indonesia
| | - Elisna Syahruddin
- Department of Pulmonology and Respiratory Medicine Faculty of Medicine, Universitas Indonesia and Persahabatan Hospital, Jakarta, Indonesia
| | - Muhammad Yunus
- Department of Biotechnology, Institut Pertanian Bogor, Bogor, Indonesia.,Cancer Diagnostic Research, Stem Cell and Cancer Institute, Jakarta, Indonesia
| | - Sita Laksmi Andarini
- Department of Pulmonology and Respiratory Medicine Faculty of Medicine, Universitas Indonesia and Persahabatan Hospital, Jakarta, Indonesia
| | - Achmad Hudoyo
- Department of Pulmonology and Respiratory Medicine Faculty of Medicine, Universitas Indonesia and Persahabatan Hospital, Jakarta, Indonesia
| | - Najmiatul Masykura
- Cancer Diagnostic Research, Stem Cell and Cancer Institute, Jakarta, Indonesia
| | - Refniwita Yasril
- Department of Pulmonology and Respiratory Medicine Faculty of Medicine, Universitas Indonesia and Persahabatan Hospital, Jakarta, Indonesia
| | - Asep Ridwanuloh
- Biotechnology Research Center, Indonesian Research Institute (LIPI), Cibinong, Indonesia
| | - Heriawaty Hidajat
- Anatomic Pathology Laboratory, Persahabatan Hospital, Jakarta, Indonesia
| | - Fariz Nurwidya
- Department of Pulmonology and Respiratory Medicine Faculty of Medicine, Universitas Indonesia and Persahabatan Hospital, Jakarta, Indonesia
| | - Sony Suharsono
- Department of Biotechnology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Ahmad R H Utomo
- Cancer Diagnostic Research, Stem Cell and Cancer Institute, Jakarta, Indonesia.,Molecular Genetic Testing Services, Kalbe Genomics Laboratory Jakarta, Jakarta, Indonesia
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9
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Cabanero M, Tsao MS. Circulating tumour DNA in EGFR-mutant non-small-cell lung cancer. ACTA ACUST UNITED AC 2018; 25:S38-S44. [PMID: 29910646 DOI: 10.3747/co.25.3761] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The advent of targeted therapy in non-small-cell lung cancer (nsclc) has made the routine molecular diagnosis of EGFR mutations crucial for optimal patient management. Obtaining tumour tissue for biomarker testing, especially in the setting of re-biopsy, can present many challenges. A potential alternative source of tumour dna is circulating cell-free tumour-derived dna (ctdna). Although ctdna is present in low quantities in plasma, the convenience of sample acquisition and the increasing reliability of detection methods make this approach a promising one. The various performance characteristics of both digital and nondigital platforms are still variable, and a standardized approach is needed that will make those platforms reliable clinical tools for the detection of EGFR sensitizing mutations and resistance mutations, including the T790M resistance mutation. Information derived from ctdna can be used to assess tumour burden, to identify genomic-based resistance mechanisms, and to track dynamic changes during therapy.
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Affiliation(s)
- M Cabanero
- Princess Margaret Cancer Centre, University Health Network, and.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON
| | - M S Tsao
- Princess Margaret Cancer Centre, University Health Network, and.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON
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10
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O'Leary B, Hrebien S, Morden JP, Beaney M, Fribbens C, Huang X, Liu Y, Bartlett CH, Koehler M, Cristofanilli M, Garcia-Murillas I, Bliss JM, Turner NC. Early circulating tumor DNA dynamics and clonal selection with palbociclib and fulvestrant for breast cancer. Nat Commun 2018; 9:896. [PMID: 29497091 PMCID: PMC5832789 DOI: 10.1038/s41467-018-03215-x] [Citation(s) in RCA: 282] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/29/2018] [Indexed: 01/06/2023] Open
Abstract
CDK4/6 inhibition substantially improves progression-free survival (PFS) for women with advanced estrogen receptor-positive breast cancer, although there are no predictive biomarkers. Early changes in circulating tumor DNA (ctDNA) level may provide early response prediction, but the impact of tumor heterogeneity is unknown. Here we use plasma samples from patients in the randomized phase III PALOMA-3 study of CDK4/6 inhibitor palbociclib and fulvestrant for women with advanced breast cancer and show that relative change in PIK3CA ctDNA level after 15 days treatment strongly predicts PFS on palbociclib and fulvestrant (hazard ratio 3.94, log-rank p = 0.0013). ESR1 mutations selected by prior hormone therapy are shown to be frequently sub clonal, with ESR1 ctDNA dynamics offering limited prediction of clinical outcome. These results suggest that early ctDNA dynamics may provide a robust biomarker for CDK4/6 inhibitors, with early ctDNA dynamics demonstrating divergent response of tumor sub clones to treatment.
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Affiliation(s)
- Ben O'Leary
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Rd, London, SW3 6JB, UK
- Breast Unit, Royal Marsden Hospital, London, SW3 6JJ, UK
| | - Sarah Hrebien
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Rd, London, SW3 6JB, UK
| | - James P Morden
- The Institute of Cancer Research Clinical Trials and Statistics Unit, London, SM2 5NG, UK
| | - Matthew Beaney
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Rd, London, SW3 6JB, UK
| | - Charlotte Fribbens
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Rd, London, SW3 6JB, UK
- Breast Unit, Royal Marsden Hospital, London, SW3 6JJ, UK
| | - Xin Huang
- Pfizer, 235 E 42nd St, New York, NY, 10017, USA
| | - Yuan Liu
- Pfizer, 235 E 42nd St, New York, NY, 10017, USA
| | | | | | - Massimo Cristofanilli
- Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, 675 N St. Clair, Chicago, IL, 60611, USA
| | - Isaac Garcia-Murillas
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Rd, London, SW3 6JB, UK
| | - Judith M Bliss
- The Institute of Cancer Research Clinical Trials and Statistics Unit, London, SM2 5NG, UK
| | - Nicholas C Turner
- Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Rd, London, SW3 6JB, UK.
- Breast Unit, Royal Marsden Hospital, London, SW3 6JJ, UK.
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11
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Wang H, Stoecklein NH, Lin PP, Gires O. Circulating and disseminated tumor cells: diagnostic tools and therapeutic targets in motion. Oncotarget 2018; 8:1884-1912. [PMID: 27683128 PMCID: PMC5352105 DOI: 10.18632/oncotarget.12242] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 09/20/2016] [Indexed: 12/16/2022] Open
Abstract
Enumeration of circulating tumor cells (CTCs) in peripheral blood with the gold standard CellSearchTM has proven prognostic value for tumor recurrence and progression of metastatic disease. Therefore, the further molecular characterization of isolated CTCs might have clinical relevance as liquid biopsy for therapeutic decision-making and to monitor disease progression. The direct analysis of systemic cancer appears particularly important in view of the known disparity in expression of therapeutic targets as well as epithelial-to-mesenchymal transition (EMT)-based heterogeneity between primary and systemic tumor cells, which all substantially complicate monitoring and therapeutic targeting at present. Since CTCs are the potential precursor cells of metastasis, their in-depth molecular profiling should also provide a useful resource for target discovery. The present review will discuss the use of systemically spread cancer cells as liquid biopsy and focus on potential target antigens.
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Affiliation(s)
- Hongxia Wang
- Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Nikolas H Stoecklein
- Department of General, Visceral and Pediatric Surgery, Medical Faculty, University Hospital of the Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | | | - Olivier Gires
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University of Munich, Munich, Germany.,Clinical Cooperation Group Personalized Radiotherapy of Head and Neck Tumors, Helmholtz, Germany
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12
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Burgener JM, Rostami A, De Carvalho DD, Bratman SV. Cell-free DNA as a post-treatment surveillance strategy: current status. Semin Oncol 2017; 44:330-346. [DOI: 10.1053/j.seminoncol.2018.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 01/18/2018] [Accepted: 01/31/2018] [Indexed: 02/06/2023]
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13
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Iijima Y, Hirotsu Y, Amemiya K, Higashi S, Miyashita Y, Omata M. Rapid decrease of circulating tumor DNA predicted the treatment effect of nivolumab in a lung cancer patient within only 5 days. Respir Med Case Rep 2017. [PMID: 28649487 PMCID: PMC5470530 DOI: 10.1016/j.rmcr.2017.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A 77-year-old Japanese man presented to our hospital with a 1-month history of low back pain and was diagnosed as having stage IV EGFR mutation-positive lung adenocarcinoma. After treatment with EGFR tyrosine kinase inhibitor and cytotoxic chemotherapy, nivolumab was started as fourth-line therapy. Remarkable regression of the primary tumor was observed, suggesting high anti-tumor activity of nivolumab. We retrospectively investigated the change in circulating tumor DNA (ctDNA) variant allele fractions in serial plasma samples before and after the nivolumab therapy. Targeted sequencing analysis showed tumor-derived TP53R249S and EGFRL858R mutations detectable in plasma, and the timing of decrease was only 5 days, much earlier than the appearance of radiological changes. Overall, these results suggest that ctDNA might reflect tumor burden and might be a surrogate marker of the therapeutic efficacy of immune checkpoint therapy.
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Affiliation(s)
- Yuki Iijima
- Lung Cancer and Respiratory Disease Center, Yamanashi Prefectural Central Hospital, 1-1-1 Fujimi, Kofu-City, Yamanashi, 400-8506, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Prefectural Central Hospital, 1-1-1 Fujimi, Kofu-City, Yamanashi, 400-8506, Japan
| | - Kenji Amemiya
- Genome Analysis Center, Yamanashi Prefectural Central Hospital, 1-1-1 Fujimi, Kofu-City, Yamanashi, 400-8506, Japan
| | - Seishi Higashi
- Department of Respirology, Hokuto City Shiokawa Hospital, 773, Fujita, Sutama-Town, Hokuto-City, Yamanashi, 408-0114, Japan
| | - Yoshihiro Miyashita
- Lung Cancer and Respiratory Disease Center, Yamanashi Prefectural Central Hospital, 1-1-1 Fujimi, Kofu-City, Yamanashi, 400-8506, Japan
| | - Masao Omata
- The University of Tokyo, 7-3-1 Hongo, Bunkyou-ku, Tokyo, 113-8654, Japan
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14
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Kato K, Uchida J, Kukita Y, Kumagai T, Nishino K, Inoue T, Kimura M, Imamura F. Transient appearance of circulating tumor DNA associated with de novo treatment. Sci Rep 2016; 6:38639. [PMID: 27934896 PMCID: PMC5146655 DOI: 10.1038/srep38639] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/11/2016] [Indexed: 12/18/2022] Open
Abstract
The limitation of circulating tumor DNA (ctDNA) is its inability to detect cancer cell subpopulations with few or no dying cells. Lung cancer patients subjected to the EGFR tyrosine kinase inhibitor (EGFR-TKI) treatment were prospectively collected, and ctDNA levels represented by the activating and T790M mutations were measured. The first data set (21 patients) consisting of samples collected in the period from before initiation of EGFR-TKI to at least 2 weeks after initiation: the ctDNA dynamics generally exhibited a rapid decrease and/or a transient increase. In 4 patients, we detected a transient increase of ctDNA bearing activating mutations not identified in biopsy samples. ctDNA with the same genotypical pattern was identified in 7 out of the 39 patients of the second data set intended to include samples until the onset of disease progression. In 6 of the 7 patients, this unique ctDNA appeared in the early period after treatment initiation, and did not reappear even after disease progression or chemotherapy. In another patient, similar ctDNA appeared upon radiation therapy. The identification of ctDNA with a unique genotype indicates the presence of cancer cell subpopulations that normally contain few or no dying cells, but generate dead cells because of the treatment.
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Affiliation(s)
- Kikuya Kato
- Department of Molecular and Medical Genetics, Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Junji Uchida
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Yoji Kukita
- Department of Molecular and Medical Genetics, Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Toru Kumagai
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Kazumi Nishino
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Takako Inoue
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Madoka Kimura
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Fumio Imamura
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
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Holdenrieder S, Pagliaro L, Morgenstern D, Dayyani F. Clinically Meaningful Use of Blood Tumor Markers in Oncology. BIOMED RESEARCH INTERNATIONAL 2016; 2016:9795269. [PMID: 28042579 PMCID: PMC5155072 DOI: 10.1155/2016/9795269] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 10/17/2016] [Indexed: 02/06/2023]
Abstract
Before the introduction of modern imaging techniques and the recent developments in molecular diagnosis, tumor markers (TMs) were among the few available diagnostic tools for the management of cancer patients. Easily obtained from serum or plasma samples, TMs are minimally invasive and convenient, and the associated costs are low. Single TMs were traditionally used but these have come under scrutiny due to their low sensitivity and specificity when used, for example, in a screening setting. However, recent research has shown superior performance using a combination of multiple TMs as a panel for assessment, or as part of validated algorithms that also incorporate other clinical factors. In addition, newer TMs have been discovered that have an increased sensitivity and specificity profile for defined malignancies. The aim of this review is to provide a concise overview of the appropriate uses of both traditional and newer TMs and their roles in diagnosis, prognosis, and the monitoring of patients in current clinical practice. We also look at the future direction of TMs and their integration with other diagnostic modalities and other emerging serum based biomarkers, such as circulating nucleic acids, to ultimately advance diagnostic performance and improve patient management.
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Affiliation(s)
| | - Lance Pagliaro
- Mayo Clinic, Department of Oncology, Division of Medical Oncology, Rochester, MN, USA
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