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Wang D, Rausch C, Buerger SA, Tschuri S, Rothenberg-Thurley M, Schulz M, Hasenauer J, Ziemann F, Metzeler KH, Marr C. Modeling early treatment response in AML from cell-free tumor DNA. iScience 2023; 26:108271. [PMID: 38047080 PMCID: PMC10690559 DOI: 10.1016/j.isci.2023.108271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/03/2023] [Accepted: 10/17/2023] [Indexed: 12/05/2023] Open
Abstract
Monitoring disease response after intensive chemotherapy for acute myeloid leukemia (AML) currently requires invasive bone marrow biopsies, imposing a significant burden on patients. In contrast, cell-free tumor DNA (ctDNA) in peripheral blood, carrying tumor-specific mutations, offers a less-invasive assessment of residual disease. However, the relationship between ctDNA levels and bone marrow blast kinetics remains unclear. We explored this in 10 AML patients with NPM1 and IDH2 mutations undergoing initial chemotherapy. Comparison of mathematical mixed-effect models showed that (1) inclusion of blast cell death in the bone marrow, (2) transition of ctDNA to peripheral blood, and (3) ctDNA decay in peripheral blood describes kinetics of blast cells and ctDNA best. The fitted model allows prediction of residual bone marrow blast content from ctDNA, and its scaling factor, representing clonal heterogeneity, correlates with relapse risk. Our study provides precise insights into blast and ctDNA kinetics, offering novel avenues for AML disease monitoring.
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Affiliation(s)
- Dantong Wang
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany
- Center for Mathematics, Technische Universität München, Garching 85748, Germany
| | - Christian Rausch
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
- German Cancer Consortium (DKTK), partner sites Munich/Dresden, Germany
| | - Simon A. Buerger
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
| | - Sebastian Tschuri
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
| | - Maja Rothenberg-Thurley
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
| | - Melanie Schulz
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany
- Center for Mathematics, Technische Universität München, Garching 85748, Germany
| | - Jan Hasenauer
- Center for Mathematics, Technische Universität München, Garching 85748, Germany
- Computational Health Center, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany
- Faculty of Mathematics and Natural Sciences, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Frank Ziemann
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
- German Cancer Consortium (DKTK), partner sites Munich/Dresden, Germany
| | - Klaus H. Metzeler
- Department of Hematology and Cell Therapy, University Hospital Leipzig (UHL) 04103, Germany
| | - Carsten Marr
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany
- Center for Mathematics, Technische Universität München, Garching 85748, Germany
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Pasca S, Guo MZ, Wang S, Stokvis K, Shedeck A, Pallavajjala A, Shams C, Pallavajjala R, DeZern AE, Varadhan R, Gocke CD, Jones RJ, Gondek LP. Cell-free DNA measurable residual disease as a predictor of postallogeneic hematopoietic cell transplant outcomes. Blood Adv 2023; 7:4660-4670. [PMID: 37276081 PMCID: PMC10448421 DOI: 10.1182/bloodadvances.2023010416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/25/2023] [Accepted: 05/25/2023] [Indexed: 06/07/2023] Open
Abstract
The measurable residual disease (MRD) assessment provides an attractive predictor of allogeneic hematopoietic cell transplnat (alloHCT) outcomes. Cell-free DNA (cfDNA) has been applied to diagnosis, early detection, and disease burden monitoring in various tumors, but its utility as an MRD test in myeloid malignancies has not been systematically evaluated. We sought to determine the differential sensitivity between bone marrow (BM) and cfDNA MRD and to assess the effect of cfDNA MRD on alloHCT outcomes. The technical and clinical validation cohorts, including 82 patients participating in clinical trials (Bone Marrow Transplant Clinical Trials Network-0201 and 0402), were used. Ultradeep error-corrected targeted sequencing was performed on plasma and BM-derived DNA. We demonstrated that 94.6% (range, 93.9-95.3) of cfDNA was derived from hematopoietic tissue. The mutant allele fraction was congruent between BM and cfDNA (rho = 0.8; P < .0001); however, cfDNA seemed to be more sensitive in detecting clones with a variant allele frequency (VAF) of <0.26%. cfDNA-MRD clearance by day 90 after alloHCT (D90) was associated with improved relapse-free survival (RFS, median survival not reached vs 5.5 months; P < .0001) and overall survival (OS, median survival not reached vs 7.3 months; P < .0001) when compared with patients with persistent MRD. Irrespective of pre-alloHCT MRD, D90 cfDNA MRD was associated with inferior 2-year OS (16.7% vs 84.8%; P < .0001) and RFS (16.7% vs 80.7%; P < .0001). cfDNA seems to be an accurate, minimally invasive alternative to BM aspirates in MRD assessment and confers important prognostic implications in patients with myeloid malignancies undergoing alloHCT.
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Affiliation(s)
- Sergiu Pasca
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Matthew Z. Guo
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Shiyu Wang
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Kristin Stokvis
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Audra Shedeck
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Aparna Pallavajjala
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Cynthia Shams
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Roshni Pallavajjala
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Amy E. DeZern
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Ravi Varadhan
- Division of Biostatistics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christopher D. Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Richard J. Jones
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Lukasz P. Gondek
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
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Fu H, Shen J, Zhou H, Zhang F, Li H, Ma Z, Huang W, Chen L, Chen Y, Liu T. Mutation profiling of circulating tumor DNA identifies distinct mutation patterns in non-Hodgkin lymphoma. Eur J Haematol 2022; 108:298-309. [PMID: 34997652 DOI: 10.1111/ejh.13736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Circulating tumor DNA (ctDNA) is emerging as a versatile biomarker for noninvasive genotyping and response monitoring in specific B-cell lymphomas; however, few studies have been conducted to explore ctDNA-based mutation profiling across non-Hodgkin lymphomas (NHLs) and genomic changes after initiation of chemotherapy. METHODS A targeted sequencing of 362 genes was performed to detect the mutation profiles in paired blood and tissue samples from 42 NHL patients. Genomic alterations were explored in 11 diffuse large B-cell lymphoma (DLBCL) patients using paired blood samples collected pre- and post-R-CHOP chemotherapy. RESULTS The frequencies of PIM1, MYD88, MYC, ZNF292, JAK, and MAF mutations were higher in aggressive than in indolent B-cell lymphoma and NK/T subtypes. Tumor mutation burden in blood samples was higher in aggressive than in indolent B-cell lymphomas and higher in patients who progressed than in those who responded to treatments. Our data also revealed significant enhance of concordance index through integrating mutated genes that were significantly associated with prognosis into International Prognostic Index-based prognostic model. Moreover, acquisition of mutations such as PCLO_p.L1220Tfs*3 was associated with resistance to R-CHOP in DLBCL patients. CONCLUSIONS Our findings illustrated distinct mutation patterns across various NHL subtypes and suggested the association of genomic alterations in ctDNA with treatment outcomes.
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Affiliation(s)
- Haiying Fu
- Department of Hematology, The Third Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, The Third People's Hospital of Fujian Province, Fuzhou, China
| | - Jianzhen Shen
- Department of Hematology, Fujian Medical University Union Hospital, Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fuzhou, China
| | - Huarong Zhou
- Department of Hematology, Fujian Medical University Union Hospital, Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fuzhou, China
| | - Feng Zhang
- Department of Hematology, Fujian Medical University Union Hospital, Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fuzhou, China
| | - Hongping Li
- Research and Development Division, Oriomics Biotech Inc, Hangzhou, China
| | - Zhiming Ma
- Research and Development Division, Oriomics Biotech Inc, Hangzhou, China
| | - Wanling Huang
- Department of Hematology, Fujian Medical University Union Hospital, Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fuzhou, China
| | - Lushan Chen
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yi Chen
- Department of Hematology, Fujian Medical University Union Hospital, Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fuzhou, China
| | - Tingbo Liu
- Department of Hematology, Fujian Medical University Union Hospital, Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fuzhou, China
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Olmedillas-López S, Olivera-Salazar R, García-Arranz M, García-Olmo D. Current and Emerging Applications of Droplet Digital PCR in Oncology: An Updated Review. Mol Diagn Ther 2021; 26:61-87. [PMID: 34773243 DOI: 10.1007/s40291-021-00562-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2021] [Indexed: 12/14/2022]
Abstract
In the era of personalized medicine and targeted therapies for the management of patients with cancer, ultrasensitive detection methods for tumor genotyping, such as next-generation sequencing or droplet digital polymerase chain reaction (ddPCR), play a significant role. In the search for less invasive strategies for diagnosis, prognosis and disease monitoring, the number of publications regarding liquid biopsy approaches using ddPCR has increased substantially in recent years. There is a long list of malignancies in which ddPCR provides a reliable and accurate tool for detection of nucleic acid-based markers derived from cell-free DNA, cell-free RNA, circulating tumor cells, extracellular vesicles or exosomes when isolated from whole blood, plasma and serum, helping to anticipate tumor relapse or unveil intratumor heterogeneity and clonal evolution in response to treatment. This updated review describes recent developments in ddPCR platforms and provides a general overview about the major applications of liquid biopsy in blood, including its utility for molecular response and minimal residual disease monitoring in hematological malignancies or the therapeutic management of patients with colorectal or lung cancer, particularly for the selection and monitoring of treatment with tyrosine kinase inhibitors. Although plasma is the main source of genetic material for tumor genomic profiling, liquid biopsy by ddPCR is being investigated in a wide variety of biologic fluids, such as cerebrospinal fluid, urine, stool, ocular fluids, sputum, saliva, bronchoalveolar lavage, pleural effusion, mucin, peritoneal fluid, fine needle aspirate, bile or pancreatic juice. The present review focuses on these "alternative" sources of genetic material and their analysis by ddPCR in different kinds of cancers.
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Affiliation(s)
- Susana Olmedillas-López
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.
| | - Rocío Olivera-Salazar
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain
| | - Mariano García-Arranz
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.,Department of Surgery, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain
| | - Damián García-Olmo
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.,Department of Surgery, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain.,Department of Surgery, Fundación Jiménez Díaz University Hospital (FJD), 28040, Madrid, Spain
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Ji H, Long X, Gu J, Jin J, Mao X, Wang Z, Ma H, Chen L. Longitudinal Monitoring of Plasma Circulating Tumour DNA Enables the Prediction of Early Relapse in Patients with Non-Hodgkin Lymphoma: A Case Series. Diagnostics (Basel) 2021; 11:diagnostics11112055. [PMID: 34829401 PMCID: PMC8618087 DOI: 10.3390/diagnostics11112055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 01/09/2023] Open
Abstract
Growing evidence now suggests that circulating tumour DNA (ctDNA) has great potential as a non-invasive biomarker for disease monitoring, since ctDNA carries tumour-specific modifications. In particular, monitoring ctDNA has important implications for identifying patients with haematological malignancies at clinical risk of disease progression. We hereby describe three patients with B-cell non-Hodgkin lymphoma and investigate the clinical value of sequential ctDNA profiling for the early detection of tumour relapse. Somatic mutations in diagnostic tumour biopsy samples of these three patients were identified by applying high-throughput next-generation sequencing. Droplet digital PCR probes and primers were designed and tested for each hotspot mutation. Serial ctDNA analysis was subsequently conducted among these three patients. We found that the longitudinal monitoring of plasma ctDNA could predict for at least one month in advance compared with flow cytometry, cytology and conventional imaging modalities. Therefore, our results support liquid biopsy based on ctDNA as a non-invasive complementary modality to other detection methods for detecting early relapse and contribute to more precise management for non-Hodgkin lymphoma patients.
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Affiliation(s)
- Hongyan Ji
- Department of Haematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.J.); (X.L.); (J.G.); (J.J.); (X.M.); (Z.W.)
| | - Xiaolu Long
- Department of Haematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.J.); (X.L.); (J.G.); (J.J.); (X.M.); (Z.W.)
| | - Jia Gu
- Department of Haematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.J.); (X.L.); (J.G.); (J.J.); (X.M.); (Z.W.)
| | - Jin Jin
- Department of Haematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.J.); (X.L.); (J.G.); (J.J.); (X.M.); (Z.W.)
| | - Xia Mao
- Department of Haematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.J.); (X.L.); (J.G.); (J.J.); (X.M.); (Z.W.)
| | - Zhiqiong Wang
- Department of Haematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.J.); (X.L.); (J.G.); (J.J.); (X.M.); (Z.W.)
| | - Heng Ma
- FNA Cytology Examining Room, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China;
| | - Liting Chen
- Department of Haematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.J.); (X.L.); (J.G.); (J.J.); (X.M.); (Z.W.)
- Correspondence:
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Laurenzana I, Trino S, Lamorte D, Girasole M, Dinarelli S, De Stradis A, Grieco V, Maietti M, Traficante A, Statuto T, Villani O, Musto P, Sgambato A, De Luca L, Caivano A. Analysis of Amount, Size, Protein Phenotype and Molecular Content of Circulating Extracellular Vesicles Identifies New Biomarkers in Multiple Myeloma. Int J Nanomedicine 2021; 16:3141-3160. [PMID: 33994784 PMCID: PMC8114829 DOI: 10.2147/ijn.s303391] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/11/2021] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION Extracellular vesicles (EVs) are naturally secreted cellular lipid bilayer particles, which carry a selected molecular content. Owing to their systemic availability and their role in tumor pathogenesis, circulating EVs (cEVs) can be a valuable source of new biomarkers useful for tumor diagnosis, prognostication and monitoring. However, a precise approach for isolation and characterization of cEVs as tumor biomarkers, exportable in a clinical setting, has not been conclusively established. METHODS We developed a novel and laboratory-made procedure based on a bench centrifuge step which allows the isolation of serum cEVs suitable for subsequent characterization of their size, amount and phenotype by nanoparticle tracking analysis, microscopy and flow cytometry, and for nucleic acid assessment by digital PCR. RESULTS Applied to blood from healthy subjects (HSs) and tumor patients, our approach permitted from a small volume of serum (i) the isolation of a great amount of EVs enriched in small vesicles free from protein contaminants; (ii) a suitable and specific cell origin identification of EVs, and (iii) nucleic acid content assessment. In clonal plasma cell malignancy, like multiple myeloma (MM), our approach allowed us to identify specific MM EVs, and to characterize their size, concentration and microRNA content allowing significant discrimination between MM and HSs. Finally, EV associated biomarkers correlated with MM clinical parameters. CONCLUSION Overall, our cEV based procedure can play an important role in malignancy biomarker discovery and then in real-time tumor monitoring using minimal invasive samples. From a practical point of view, it is smart (small sample volume), rapid (two hours), easy (no specific expertise required) and requirements are widely available in clinical laboratories.
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Affiliation(s)
- Ilaria Laurenzana
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Stefania Trino
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Daniela Lamorte
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Marco Girasole
- Institute for the Study of the Structure of Matter, National Research Council (CNR), Rome, Italy
| | - Simone Dinarelli
- Institute for the Study of the Structure of Matter, National Research Council (CNR), Rome, Italy
| | - Angelo De Stradis
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Vitina Grieco
- Laboratory of Clinical Research and Advanced Diagnostics, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Maddalena Maietti
- Unit of Clinical Pathology, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Antonio Traficante
- Unit of Clinical Pathology, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Teodora Statuto
- Laboratory of Clinical Research and Advanced Diagnostics, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Oreste Villani
- Hematology and Stem Cell Transplantation Unit, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Pellegrino Musto
- Hematology and Stem Cell Transplantation Unit, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Alessandro Sgambato
- Scientific Direction, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Luciana De Luca
- Laboratory of Clinical Research and Advanced Diagnostics, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Antonella Caivano
- Laboratory of Clinical Research and Advanced Diagnostics, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
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Ogawa M, Yokoyama K, Imoto S, Tojo A. Role of Circulating Tumor DNA in Hematological Malignancy. Cancers (Basel) 2021; 13:2078. [PMID: 33923024 PMCID: PMC8123338 DOI: 10.3390/cancers13092078] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 04/23/2021] [Indexed: 02/07/2023] Open
Abstract
With the recent advances in noninvasive approaches for cancer diagnosis and surveillance, the term "liquid biopsy" has become more familiar to clinicians, including hematologists. Liquid biopsy provides a variety of clinically useful genetic data. In this era of personalized medicine, genetic information is critical to early diagnosis, aiding risk stratification, directing therapeutic options, and monitoring disease relapse. The validity of circulating tumor DNA (ctDNA)-mediated liquid biopsies has received increasing attention. This review summarizes the current knowledge of liquid biopsy ctDNA in hematological malignancies, focusing on the feasibility, limitations, and key areas of clinical application. We also highlight recent advances in the minimal residual disease monitoring of leukemia using ctDNA. This article will be useful to those involved in the clinical practice of hematopoietic oncology.
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Affiliation(s)
- Miho Ogawa
- Division of Molecular Therapy, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (M.O.); (A.T.)
| | - Kazuaki Yokoyama
- Department of Hematology/Oncology, Research Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan;
| | - Arinobu Tojo
- Division of Molecular Therapy, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (M.O.); (A.T.)
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8
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Tan X, Yan H, Chen L, Zhang Y, Sun C. Clinical Value of ctDNA in Hematological Malignancies (Lymphomas, Multiple Myeloma, Myelodysplastic Syndrome, and Leukemia): A Meta-Analysis. Front Oncol 2021; 11:632910. [PMID: 33747954 PMCID: PMC7970179 DOI: 10.3389/fonc.2021.632910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/05/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Circulating tumor DNA (ctDNA) has offered a minimally invasive approach for the detection and measurement of cancer. However, its diagnostic and prognostic value in hematological malignancies remains unclear. Materials and methods: Pubmed, Embase, and Cochrane Library were searched for relating literature. Diagnostic accuracy variables and disease progression prediction data were pooled by the Meta-Disc version 1.4 software. Review Manager version 5.4 software was applied for prognostic data analysis. Results: A total of 11 studies met our inclusion criteria. In terms of diagnosis, the pooled sensitivity and specificity were 0.51 (95% confidence intervals (CI) 0.38–0.64) and 0.96 (95% CI 0.88–1.00), respectively. The AUSROC (area under the SROC) curve was 0.89 (95%CI 0.75–1.03). When it comes to the prediction of disease progression, the overall sensitivity and specificity was 0.83 (95% CI 0.67–0.94) and 0.98 (95% CI 0.93–1.00), respectively. Moreover, a significant association also existed between the presence of ctDNA and worse progression-free survival (HR 2.63, 95% CI 1.27–5.43, p = 0.009), as well as overall survival (HR 2.92, 95% CI 1.53–5.57, p = 0.001). Conclusions: The use of ctDNA in clinical practice for hematological malignancies is promising, as it may not only contribute to diagnosis, but could also predict the prognosis of patients so as to guide treatment. In the future, more studies are needed to realize the standardization of sequencing techniques and improve the detection sensitivity of exploration methods.
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Affiliation(s)
- Xiangyu Tan
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Han Yan
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Chen
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuyang Zhang
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunyan Sun
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, Wuhan, China
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9
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Shi Y, Su H, Song Y, Jiang W, Sun X, Qian W, Zhang W, Gao Y, Jin Z, Zhou J, Jin C, Zou L, Qiu L, Li W, Yang J, Hou M, Xiong Y, Zhou H, Du X, Wang X, Peng B. Circulating tumor DNA predicts response in Chinese patients with relapsed or refractory classical hodgkin lymphoma treated with sintilimab. EBioMedicine 2021; 54:102731. [PMID: 32304999 PMCID: PMC7186760 DOI: 10.1016/j.ebiom.2020.102731] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/17/2020] [Accepted: 03/05/2020] [Indexed: 02/08/2023] Open
Abstract
Background Blood-based biomarker such as circulating tumor DNA (ctDNA) has emerged as a promising tool for assessment of response to immunotherapy in solid tumors; But in hematological malignances, evidences are still lacking to support its clinical utility. In current study the feasibility of ctDNA for prediction and monitoring of response to anti-PD-1 therapy in Chinese patients with relapsed or refractory classical Hodgkin lymphoma (r/r cHL) was assessed. Methods A total of 192 plasma samples from 75 patients with r/r cHL were collected at baseline and upon therapeutic evaluation. ctDNA were sequenced by targeting panels capturing frequently mutated genes in cHL and other hematological malignancies and then quantified. Analysis on: 1) Gene mutation profile and association of the gene mutations with progression-free survival; 2) Association of pre- and post-treatment ctDNA variant allelic frequencies with clinical outcome; (3) Correlation of the mutated genes with treatment resistance; were performed. Findings Somatic mutations were detected in 50 out of 61 patients by ctDNA genotyping. The mutations of CHD8 was significantly higher in patients with PFS ≥ 12 months. Baseline ctDNA was significantly higher in responders and a decrease of ctDNA ≥ 40% from baseline indicated superior clinical outcome. Strong agreement between ctDNA dynamic and radiographic response change during therapy was observed in majority of the patients. Furthermore, the mutations of B2M, TNFRSF14 and KDM2B were found to be associated with acquired resistance. Interpretation ctDNA could be an informative biomarker for anti-PD-1 immunotherapy in r/r cHL. Funding This work was supported by Innovent Biologics, Eli Lilly and Companyhttps://doi.org/10.13039/501100002852, China National New Drug Innovation Program (2014ZX09201041-001 and 2017ZX09304015), Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS) (2016-I2M-1-001) and National Key Scientific Program Precision Medicine Research Fund of China (2017YFC0909801). The funders had no role in study design, data collection, data analysis, interpretation or writing.
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Affiliation(s)
- Yuankai Shi
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China.
| | - Hang Su
- The 307th Hospital of Chinese People's Liberation Army, Beijing, China
| | - Yongping Song
- The affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Wenqi Jiang
- Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiuhua Sun
- Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Wenbin Qian
- The First Affiliated Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Wei Zhang
- Peking Union Medical College Hospital, Beijing, China
| | - Yuhuan Gao
- Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhengming Jin
- The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jianfeng Zhou
- Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chuan Jin
- Cancer Hospital Affiliated to Guangzhou Medical University, Guangzhou, China
| | - Liqun Zou
- West China Hospital, Sichuan University, Chengdu, China
| | - Lugui Qiu
- Blood Institute of Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Wei Li
- The First Hospital of Jilin University, Changchun, China
| | | | - Ming Hou
- Qilu Hospital of Shandong University, Jinan, China
| | - Yan Xiong
- Innovent Biologics (Suzhou) Co., Ltd, China
| | - Hui Zhou
- Innovent Biologics (Suzhou) Co., Ltd, China
| | | | - Xiong Wang
- Innovent Biologics (Suzhou) Co., Ltd, China
| | - Bo Peng
- Innovent Biologics (Suzhou) Co., Ltd, China
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10
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Salinas RD, Durgin JS, O'Rourke DM. Potential of Glioblastoma-Targeted Chimeric Antigen Receptor (CAR) T-Cell Therapy. CNS Drugs 2020; 34:127-145. [PMID: 31916100 DOI: 10.1007/s40263-019-00687-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Despite the established efficacy of chimeric antigen receptor (CAR) T-cell therapy in hematologic malignancies, translating CAR T therapy to solid tumors has remained investigational. Glioblastoma, the most aggressive and lethal form of primary brain tumor, has recently been among the malignancies being trialed clinically with CAR T cells. Glioblastoma in particular holds several unique features that have hindered clinical translation, including its vast intertumoral and intratumoral heterogeneity, associated immunosuppressive environment, and lack of clear experimental models to predict response and analyze resistant phenotypes. Here, we review the history of CAR T therapy development, its current progress in treating glioblastoma, as well as the current challenges and future directions in establishing CAR T therapy as a viable alternative to the current standard of care. Tremendous efforts are currently ongoing to identify novel CAR targets and target combinations for glioblastoma, to modify T cells to enhance their efficacy and to enable them to resist tumor-mediated immunosuppression, and to utilize adjunct therapies such as lymphodepletion, checkpoint inhibition, and bi-specific engagers to improve CAR T persistence. Furthermore, new preclinical models of CAR T therapy are being developed that better reflect the clinical features seen in human trials. Current clinical trials that rapidly incorporate key preclinical findings to patient translation are emerging.
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Affiliation(s)
- Ryan D Salinas
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Joseph S Durgin
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Donald M O'Rourke
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Glioblastoma Translational Center of Excellence, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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11
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Prognostic impact of circulating tumor DNA status post–allogeneic hematopoietic stem cell transplantation in AML and MDS. Blood 2019; 133:2682-2695. [DOI: 10.1182/blood-2018-10-880690] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/07/2019] [Indexed: 12/11/2022] Open
Abstract
Abstract
This study was performed to assess the utility of tumor-derived fragmentary DNA, or circulating tumor DNA (ctDNA), for identifying high-risk patients for relapse of acute myeloid leukemia and myelodysplastic syndrome (AML/MDS) after undergoing myeloablative allogeneic hematopoietic stem cell transplantation (alloSCT). We retrospectively collected tumor and available matched serum samples at diagnosis and 1 and 3 months post-alloSCT from 53 patients with AML/MDS. After identifying driver mutations in 51 patients using next-generation sequencing, we designed at least 1 personalized digital polymerase chain reaction assay per case. Diagnostic ctDNA and matched tumor DNA exhibited excellent correlations with variant allele frequencies. Sixteen patients relapsed after a median of 7 months post-alloSCT. Both mutation persistence (MP) in bone marrow (BM) at 1 and 3 months post-alloSCT and corresponding ctDNA persistence (CP) in the matched serum (MP1 and MP3; CP1 and CP3, respectively) were comparably associated with higher 3-year cumulative incidence of relapse (CIR) rates (MP1 vs non-MP1, 72.9% vs 13.8% [P = .0012]; CP1 vs non-CP1, 65.6% vs 9.0% [P = .0002]; MP3 vs non-MP3, 80% vs 11.6% [P = .0002]; CP3 vs non-CP3, 71.4% vs 8.4% [P < .0001]). We subsequently evaluated whether subset analysis of patients with 3 genes associated with clonal hematopoiesis, DNMT3A, TET2, and ASXL1 (DTA), could also be helpful in relapse prediction. As a result, CP based on DTA gene mutations also had the prognostic effect on CIR. These results, for the first time, support the utility of ctDNA as a noninvasive prognostic biomarker in patients with AML/MDS undergoing alloSCT.
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12
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Lu H, Yang H, Wu L, Liao W, He X, Li E, Wu R, Shi S, Yang Z. A novel prognostic model for diagnosing atypical bile duct hyperplasia in patients with intrahepatic lithiasis. Medicine (Baltimore) 2019; 98:e15364. [PMID: 31027122 PMCID: PMC6831388 DOI: 10.1097/md.0000000000015364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 12/18/2022] Open
Abstract
There is no specific method for the preoperative diagnosis of atypical bile duct hyperplasia, which is a precursor of cholangiocarcinoma. This study aimed to create a new model for diagnosing atypical bile duct hyperplasia based on routine laboratory tests in patients with intrahepatic lithiasis.The new diagnostic model was developed with a derivation cohort that included 375 patients with intrahepatic lithiasis. Clinical and pathological data were retrospectively collected. Prognostic factors were evaluated with univariate and logistic regression analyses. The validation cohort included 136 patients who were retrospectively screened to quantify the model's predictive value.Age and Carbohydrate Antigen 19-9 (CA-199) were revealed to be diagnostic indicators of atypical bile duct hyperplasia in patients with intrahepatic lithiasis. The new diagnostic model was created with the formula: -6.612 + (0.002 × CA-199) + (0.072 × Age). The area under the receiver operating curve of the model was 0.721. With 0.25 as the cutoff point, the sensitivity and specificity of this model in the derivation cohort were 13.9% and 95.9%, respectively. In the validation cohort, these values were 28.5% and 88.7%, respectively. The novel model has an acceptable and stable ability to predict atypical hyperplasia in the intrahepatic bile duct.This novel model provides a simple system for diagnosing atypical bile duct hyperplasia before surgery in patients with intrahepatic lithiasis.
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Affiliation(s)
- Hongcheng Lu
- Second Affiliated Hospital of Nanchang University, Research Center of Hepatobiliary Disease, Nanchang
| | - Hao Yang
- Second Affiliated Hospital of Nanchang University, Research Center of Hepatobiliary Disease, Nanchang
| | - Linquan Wu
- Second Affiliated Hospital of Nanchang University, Research Center of Hepatobiliary Disease, Nanchang
| | - Wenjun Liao
- Second Affiliated Hospital of Nanchang University, Research Center of Hepatobiliary Disease, Nanchang
| | - Xianping He
- Second Affiliated Hospital of Nanchang University, Research Center of Hepatobiliary Disease, Nanchang
| | - Enliang Li
- Second Affiliated Hospital of Nanchang University, Research Center of Hepatobiliary Disease, Nanchang
| | - Rongshou Wu
- The First Affiliated Hospital of Gannan Medical College, General Surgery, Ganzhou
| | - Shidai Shi
- Ji’an People's Hospital, Hepatobiliary Surgery, Jian
| | - Zhilong Yang
- Jingdezhen People's Hospital, General Surgery, Jingdezhen, Jiangxi, China
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13
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Bilkey GA, Burns BL, Coles EP, Mahede T, Baynam G, Nowak KJ. Optimizing Precision Medicine for Public Health. Front Public Health 2019; 7:42. [PMID: 30899755 PMCID: PMC6416195 DOI: 10.3389/fpubh.2019.00042] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/14/2019] [Indexed: 01/15/2023] Open
Abstract
Advances in precision medicine have presented challenges to traditional public health decision-making paradigms. Historical methods of allocating healthcare funds based on safety, efficacy, and efficiency, are challenged in a healthcare delivery model that focuses on individualized variations in pathology that form the core of precision medicine. Public health policy and decision-making must adapt to this new frontier of healthcare delivery to ensure that the broad public health goals of reducing healthcare disparities and improving the health of populations are achieved, through effective and equitable allocation of healthcare funds. This paper discusses contemporary applications of precision medicine, and the potential impacts of these on public health policy and decision-making, with particular focus on patients living with rare diseases and rare cancers. The authors then reconcile these, presenting precision public health as the bridge between these seemingly competing fields.
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Affiliation(s)
- Gemma A Bilkey
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia.,Office of the Chief Health Officer, Public and Aboriginal Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Belinda L Burns
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Emily P Coles
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Trinity Mahede
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Gareth Baynam
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia.,Genetic Services of Western Australia, King Edward Memorial Hospital, Department of Health, Government of Western Australia, Perth, WA, Australia.,Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Kristen J Nowak
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia.,Faculty of Health and Medical Sciences, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia.,Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre, Perth, WA, Australia
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14
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Bronkhorst AJ, Ungerer V, Holdenrieder S. The emerging role of cell-free DNA as a molecular marker for cancer management. BIOMOLECULAR DETECTION AND QUANTIFICATION 2019; 17:100087. [PMID: 30923679 PMCID: PMC6425120 DOI: 10.1016/j.bdq.2019.100087] [Citation(s) in RCA: 313] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/26/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023]
Abstract
An increasing number of studies demonstrate the potential use of cell-free DNA (cfDNA) as a surrogate marker for multiple indications in cancer, including diagnosis, prognosis, and monitoring. However, harnessing the full potential of cfDNA requires (i) the optimization and standardization of preanalytical steps, (ii) refinement of current analysis strategies, and, perhaps most importantly, (iii) significant improvements in our understanding of its origin, physical properties, and dynamics in circulation. The latter knowledge is crucial for interpreting the associations between changes in the baseline characteristics of cfDNA and the clinical manifestations of cancer. In this review we explore recent advancements and highlight the current gaps in our knowledge concerning each point of contact between cfDNA analysis and the different stages of cancer management.
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Affiliation(s)
| | | | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße. 36, D-80636, Munich, Germany
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15
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Soyano AE, Baldeo C, Kasi PM. Adjunctive Use of Circulating Tumor DNA Testing in Detecting Pancreas Cancer Recurrence. Front Oncol 2019; 9:46. [PMID: 30788289 PMCID: PMC6372543 DOI: 10.3389/fonc.2019.00046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 01/17/2019] [Indexed: 12/14/2022] Open
Abstract
Liquid biopsies (circulating tumor DNA-ctDNA testing) are increasingly being utilized in clinical trials as well as practice for the detection of cancer, monitoring of tumor genomic abnormalities, response to treatment and early detection of relapse/recurrence. Here, we present a challenging case where liquid biopsy was used to confirm an early recurrence of pancreatic cancer where acquisition of tissue was not safe or feasible on more than one occasion.
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Affiliation(s)
- Aixa E Soyano
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
| | - Candice Baldeo
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
| | - Pashtoon M Kasi
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
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