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Foffano L, Vida R, Piacentini A, Molteni E, Cucciniello L, Da Ros L, Silvia B, Cereser L, Roncato R, Gerratana L, Puglisi F. Is ctDNA ready to outpace imaging in monitoring early and advanced breast cancer? Expert Rev Anticancer Ther 2024; 24:679-691. [PMID: 38855809 DOI: 10.1080/14737140.2024.2362173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
INTRODUCTION Circulating tumor DNA (ctDNA) and radiological imaging are increasingly recognized as crucial elements in breast cancer management. While radiology remains the cornerstone for screening and monitoring, ctDNA holds distinctive advantages in anticipating diagnosis, recurrence, or progression, providing concurrent biological insights complementary to imaging results. AREAS COVERED This review delves into the current evidence on the synergistic relationship between ctDNA and imaging in breast cancer. It presents data on the clinical validity and utility of ctDNA in both early and advanced settings, providing insights into emerging liquid biopsy techniques like epigenetics and fragmentomics. Simultaneously, it explores the present and future landscape of imaging methodologies, particularly focusing on radiomics. EXPERT OPINION Numerous are the current technical, strategic, and economic challenges preventing the clinical integration of ctDNA analysis in the breast cancer monitoring. Understanding these complexities and devising targeted strategies is pivotal to effectively embedding this methodology into personalized patient care.
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Affiliation(s)
- Lorenzo Foffano
- Department of Medicine, University of Udine, Udine, Italy
- Department of Medical Oncology, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Riccardo Vida
- Department of Medicine, University of Udine, Udine, Italy
- Department of Medical Oncology, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | | | - Elisabetta Molteni
- Department of Medicine, University of Udine, Udine, Italy
- Weill Cornell Medicine, Department of Medicine, Division of Hematology-Oncology, New York, NY, USA
| | - Linda Cucciniello
- Department of Medicine, University of Udine, Udine, Italy
- Department of Medical Oncology, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Lucia Da Ros
- Department of Medical Oncology, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Buriolla Silvia
- Department of Oncology, Santa Maria della Misericordia University Hospital, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Lorenzo Cereser
- Department of Medicine, University of Udine, Udine, Italy
- Azienda Sanitaria-Universitaria Friuli Centrale (ASUFC), University Hospital S. Maria della Misericordia, Udine, Italy
| | | | - Lorenzo Gerratana
- Department of Medicine, University of Udine, Udine, Italy
- Department of Medical Oncology, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Fabio Puglisi
- Department of Medicine, University of Udine, Udine, Italy
- Department of Medical Oncology, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
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Fu Y, Xu Y, Liu W, Zhang J, Wang F, Jian Q, Huang G, Zou C, Xie X, Kim AH, Mathios D, Pang F, Li F, Wang K, Shen J, Yin J. Tumor-informed deep sequencing of ctDNA detects minimal residual disease and predicts relapse in osteosarcoma. EClinicalMedicine 2024; 73:102697. [PMID: 39022798 PMCID: PMC11252770 DOI: 10.1016/j.eclinm.2024.102697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Background Current surveillance modalities of osteosarcoma relapse exhibit limited sensitivity and specificity. Although circulating tumor DNA (ctDNA) has been established as a biomarker of minimal residual disease (MRD) in many solid tumors, a sensitive ctDNA detection technique has not been thoroughly explored for longitudinal MRD detection in osteosarcoma. Methods From August 2019 to June 2023, 59 patients diagnosed with osteosarcoma at the First Affiliated Hospital of Sun Yat-sen University were evaluated in this study. Tumor-informed MRD panels were developed through whole exome sequencing (WES) of tumor tissues. Longitudinal blood samples were collected during treatment and subjected to multiplex PCR-based next-generation sequencing (NGS). Kaplan-Meier curves and Log-rank tests were used to compare outcomes, and Cox regression analysis was performed to identify prognostic factors. Findings WES analysis of 83 patients revealed substantial mutational heterogeneity, with non-recurrent mutated genes accounting for 58.1%. Tumor-informed MRD panels were successfully obtained for 85.5% of patients (71/83). Among 59 patients with successful MRD panel customization and available blood samples, 13 patients exhibited positive ctDNA detection after surgery. Patients with negative post-operative ctDNA had better event-free survival (EFS) compared to those with positive ctDNA, at 1-6 months after surgery, after adjuvant chemotherapy, and more than 6 months after surgery (p < 0.05). In both univariate and multivariate Cox regression analysis, ctDNA results emerged as a significant predictor of EFS (p < 0.05). ctDNA detection preceded positive imaging in 5 patients, with an average lead time of 92.6 days. Thirty-nine patients remained disease-free, with ctDNA results consistently negative or turning negative during follow-up. Interpretation Our study underscores the applicability of tumor-informed deep sequencing of ctDNA in osteosarcoma MRD surveillance and, to our knowledge, represents the largest cohort to date. ctDNA detection is a significant prognostic factor, enabling the early identification of tumor relapse and progression compared to standard imaging, thus offering valuable insights in guiding osteosarcoma patient management. Funding The Grants of National Natural Science Foundation of China (No. 82072964, 82072965, 82203798, 82203026), the Natural Science Foundation of Guangdong (No. 2023A1515012659, 2023A1515010302), and the Regional Combination Project of Basic and Applied Basic Research Foundation of Guangdong (No. 2020A1515110010).
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Affiliation(s)
- Yiwei Fu
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Yu Xu
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Weihai Liu
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Jiajun Zhang
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Fen Wang
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | | | - Gang Huang
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Changye Zou
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Xianbiao Xie
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Albert H. Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Dimitrios Mathios
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Fei Pang
- OrigiMed, Shanghai, 201124, China
| | - Feng Li
- OrigiMed, Shanghai, 201124, China
| | - Kai Wang
- OrigiMed, Shanghai, 201124, China
| | - Jingnan Shen
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Junqiang Yin
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
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Panet F, Papakonstantinou A, Borrell M, Vivancos J, Vivancos A, Oliveira M. Use of ctDNA in early breast cancer: analytical validity and clinical potential. NPJ Breast Cancer 2024; 10:50. [PMID: 38898045 PMCID: PMC11187121 DOI: 10.1038/s41523-024-00653-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024] Open
Abstract
Circulating free tumor DNA (ctDNA) analysis is gaining popularity in precision oncology, particularly in metastatic breast cancer, as it provides non-invasive, real-time tumor information to complement tissue biopsies, allowing for tailored treatment strategies and improved patient selection in clinical trials. Its use in early breast cancer has been limited so far, due to the relatively low sensitivity of available techniques in a setting characterized by lower levels of ctDNA shedding. However, advances in sequencing and bioinformatics, as well as the use of methylome profiles, have led to an increasing interest in the application of ctDNA analysis in early breast cancer, from screening to curative treatment evaluation and minimal residual disease (MRD) detection. With multiple prospective clinical trials in this setting, ctDNA evaluation may become useful in clinical practice. This article reviews the data regarding the analytical validity of the currently available tests for ctDNA detection and the clinical potential of ctDNA analysis in early breast cancer.
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Affiliation(s)
- François Panet
- Breast Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Lady Davis Institute, Jewish General Hospital, Montréal, QC, Canada
| | - Andri Papakonstantinou
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
- Department of Breast, Endocrine Tumors and Sarcomas, Karolinska Comprehensive Cancer Center, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Borrell
- Breast Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron Hospital, Barcelona, Spain
| | - Joan Vivancos
- Cancer Genomics Group, Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ana Vivancos
- Cancer Genomics Group, Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Mafalda Oliveira
- Breast Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.
- Medical Oncology Department, Vall d'Hebron Hospital, Barcelona, Spain.
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Klocker EV, Hasenleithner S, Bartsch R, Gampenrieder SP, Egle D, Singer CF, Rinnerthaler G, Hubalek M, Schmitz K, Bago-Horvath Z, Petzer A, Heibl S, Heitzer E, Balic M, Gnant M. Clinical applications of next-generation sequencing-based ctDNA analyses in breast cancer: defining treatment targets and dynamic changes during disease progression. Mol Oncol 2024. [PMID: 38867388 DOI: 10.1002/1878-0261.13671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/03/2024] [Accepted: 05/17/2024] [Indexed: 06/14/2024] Open
Abstract
The advancements in the detection and characterization of circulating tumor DNA (ctDNA) have revolutionized precision medicine and are likely to transform standard clinical practice. The non-invasive nature of this approach allows for molecular profiling of the entire tumor entity, while also enabling real-time monitoring of the effectiveness of cancer therapies as well as the identification of resistance mechanisms to guide targeted therapy. Although the field of ctDNA studies offers a wide range of applications, including in early disease, in this review we mainly focus on the role of ctDNA in the dynamic molecular characterization of unresectable locally advanced and metastatic BC (mBC). Here, we provide clinical practice guidance for the rapidly evolving field of molecular profiling of mBC, outlining the current landscape of liquid biopsy applications and how to choose the right ctDNA assay. Additionally, we underline the importance of exploring the clinical relevance of novel molecular alterations that potentially represent therapeutic targets in mBC, along with mutations where targeted therapy is already approved. Finally, we present a potential roadmap for integrating ctDNA analysis into clinical practice.
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Affiliation(s)
- Eva Valentina Klocker
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Samantha Hasenleithner
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Austria
| | - Rupert Bartsch
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Austria
| | - Simon P Gampenrieder
- Third Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Oncologic Center, Paracelsus Medical University Salzburg, Austria
| | - Daniel Egle
- Department of Gynecology, Breast Cancer Center Tirol, Medical University of Innsbruck, Austria
| | - Christian F Singer
- Department of Gynecology, Breast Cancer Center Vienna, Medical University of Vienna, Austria
| | - Gabriel Rinnerthaler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Michael Hubalek
- Department of Gynecology, Breast Health Center Schwaz, Austria
| | - Katja Schmitz
- Institute of Pathology, University Medical Center Göttingen, Germany
- Tyrolpath Obrist Brunhuber GmbH and Krankenhaus St. Vinzenz, Zams, Austria
| | | | - Andreas Petzer
- Department of Internal Medicine I for Hematology with Stem Cell Transplantation, Hemostaseology and Medical Oncology, Barmherzige Schwestern, Elisabethinen, Ordensklinikum Linz GmbH, Austria
| | - Sonja Heibl
- Department of Internal Medicine IV, Klinikum Wels-Grieskirchen GmbH, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Christian Doppler Laboratory for Liquid Biopsies for early Detection of Cancer, Medical University of Graz, Austria
| | - Marija Balic
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
- Division of Hematology and Medical Oncology, University of Pittsburgh School of Medicine, PA, USA
| | - Michael Gnant
- Comprehensive Cancer Center, Medical University of Vienna, Austria
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5
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Nader-Marta G, Monteforte M, Agostinetto E, Cinquini M, Martins-Branco D, Langouo M, Llombart-Cusac A, Cortés J, Ignatiadis M, Torri V, Apolone G, Cappelletti V, Pruneri G, de Azambuja E, Di Cosimo S. Circulating tumor DNA for predicting recurrence in patients with operable breast cancer: a systematic review and meta-analysis. ESMO Open 2024; 9:102390. [PMID: 38460249 PMCID: PMC10940943 DOI: 10.1016/j.esmoop.2024.102390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND The incorporation of circulating tumor DNA (ctDNA) into the management of operable breast cancer (BC) has been hampered by the heterogeneous results from different studies. We aimed to assess the prognostic value of ctDNA in patients with operable (non metastatic) BC. MATERIALS AND METHODS A systematic search of databases (PubMed/Medline, Embase, and CENTRAL) and conference proceedings was conducted to identify studies reporting the association of ctDNA detection with disease-free survival (DFS) and overall survival (OS) in patients with stage I-III BC. Log-hazard ratios (HRs) were pooled at each timepoint of ctDNA assessment (baseline, after neoadjuvant therapy, and follow-up). ctDNA assays were classified as primary tumor-informed and non tumor-informed. RESULTS Of the 3174 records identified, 57 studies including 5779 patients were eligible. In univariate analyses, ctDNA detection was associated with worse DFS at baseline [HR 2.98, 95% confidence interval (CI) 1.92-4.63], after neoadjuvant therapy (HR 7.69, 95% CI 4.83-12.24), and during follow-up (HR 14.04, 95% CI 7.55-26.11). Similarly, ctDNA detection at all timepoints was associated with worse OS (at baseline: HR 2.76, 95% CI 1.60-4.77; after neoadjuvant therapy: HR 2.72, 95% CI 1.44-5.14; and during follow-up: HR 9.19, 95% CI 3.26-25.90). Similar DFS and OS results were observed in multivariate analyses. Pooled HRs were numerically higher when ctDNA was detected at the end of neoadjuvant therapy or during follow-up and for primary tumor-informed assays. ctDNA detection sensitivity and specificity for BC recurrence ranged from 0.31 to 1.0 and 0.7 to 1.0, respectively. The mean lead time from ctDNA detection to overt recurrence was 10.81 months (range 0-58.9 months). CONCLUSIONS ctDNA detection was associated with worse DFS and OS in patients with operable BC, particularly when detected after treatment and using primary tumor-informed assays. ctDNA detection has a high specificity for anticipating BC relapse.
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Affiliation(s)
- G Nader-Marta
- Academic Trials Promoting Team (ATPT), Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (U.L.B), Brussels, Belgium.
| | - M Monteforte
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - E Agostinetto
- Academic Trials Promoting Team (ATPT), Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (U.L.B), Brussels, Belgium. https://twitter.com/ElisaAgostinett
| | - M Cinquini
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - D Martins-Branco
- Academic Trials Promoting Team (ATPT), Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (U.L.B), Brussels, Belgium. https://twitter.com/DMBranco
| | - M Langouo
- Medical Oncology Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (U.L.B), Brussels, Belgium
| | - A Llombart-Cusac
- Medica Scientia Innovation Research (MEDSIR), Barcelona, Spain; Medica Scientia Innovation Research (MEDSIR), Ridgewood, New Jersey, USA; Arnau de Vilanova Hospital; Universidad Católica de Valencia, Valencia, Spain
| | - J Cortés
- Medica Scientia Innovation Research (MEDSIR), Barcelona, Spain; Medica Scientia Innovation Research (MEDSIR), Ridgewood, New Jersey, USA; International Breast Cancer Center (IBCC), Pangaea Oncology, Quiron Group, Barcelona, Spain; Department of Medicine, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Madrid, Spain. https://twitter.com/JavierCortesMD
| | - M Ignatiadis
- Academic Trials Promoting Team (ATPT), Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (U.L.B), Brussels, Belgium; Medical Oncology Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (U.L.B), Brussels, Belgium. https://twitter.com/MIgnatiadis
| | - V Torri
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy. https://twitter.com/ValterTorri
| | - G Apolone
- Scientific Directorate, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - V Cappelletti
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - G Pruneri
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; University of Milan, School of Medicine, Milan, Italy. https://twitter.com/PruneriG
| | - E de Azambuja
- Academic Trials Promoting Team (ATPT), Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (U.L.B), Brussels, Belgium; Medical Oncology Department, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (HUB), Université Libre de Bruxelles (U.L.B), Brussels, Belgium. https://twitter.com/E_de_Azambuja
| | - S Di Cosimo
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy. https://twitter.com/serenadicosimo
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Hu Q, Chen L, Li K, Liu R, Sun L, Han T. Circulating tumor DNA: current implementation issues and future challenges for clinical utility. Clin Chem Lab Med 2023; 0:cclm-2023-1157. [PMID: 38109307 DOI: 10.1515/cclm-2023-1157] [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: 10/16/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
Over the past decades, liquid biopsy, especially circulating tumor DNA (ctDNA), has received tremendous attention as a noninvasive detection approach for clinical applications, including early diagnosis of cancer and relapse, real-time therapeutic efficacy monitoring, potential target selection and investigation of drug resistance mechanisms. In recent years, the application of next-generation sequencing technology combined with AI technology has significantly improved the accuracy and sensitivity of liquid biopsy, enhancing its potential in solid tumors. However, the increasing integration of such promising tests to improve therapy decision making by oncologists still has complexities and challenges. Here, we propose a conceptual framework of ctDNA technologies and clinical utilities based on bibliometrics and highlight current challenges and future directions, especially in clinical applications such as early detection, minimal residual disease detection, targeted therapy, and immunotherapy. We also discuss the necessities of developing a dynamic field of translational cancer research and rigorous clinical studies that may support therapeutic strategy decision making in the near future.
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Affiliation(s)
- Qilin Hu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, P.R. China
| | - Lujun Chen
- The General Hospital of Northern Theater Command Training Base for Graduate, China Medical University, Shenyang, P.R. China
| | - Kerui Li
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, P.R. China
| | - Ruotong Liu
- Clinical Medicine, Shenyang Medical College, Shenyang, P.R. China
| | - Lei Sun
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang, P.R. China
| | - Tao Han
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, P.R. China
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7
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Santonja A, Cooper WN, Eldridge MD, Edwards PAW, Morris JA, Edwards AR, Zhao H, Heider K, Couturier D, Vijayaraghavan A, Mennea P, Ditter E, Smith CG, Boursnell C, Manzano García R, Rueda OM, Beddowes E, Biggs H, Sammut S, Rosenfeld N, Caldas C, Abraham JE, Gale D. Comparison of tumor-informed and tumor-naïve sequencing assays for ctDNA detection in breast cancer. EMBO Mol Med 2023; 15:e16505. [PMID: 37161793 PMCID: PMC10245040 DOI: 10.15252/emmm.202216505] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 05/11/2023] Open
Abstract
Analysis of circulating tumor DNA (ctDNA) to monitor cancer dynamics and detect minimal residual disease has been an area of increasing interest. Multiple methods have been proposed but few studies have compared the performance of different approaches. Here, we compare detection of ctDNA in serial plasma samples from patients with breast cancer using different tumor-informed and tumor-naïve assays designed to detect structural variants (SVs), single nucleotide variants (SNVs), and/or somatic copy-number aberrations, by multiplex PCR, hybrid capture, and different depths of whole-genome sequencing. Our results demonstrate that the ctDNA dynamics and allele fractions (AFs) were highly concordant when analyzing the same patient samples using different assays. Tumor-informed assays showed the highest sensitivity for detection of ctDNA at low concentrations. Hybrid capture sequencing targeting between 1,347 and 7,491 tumor-identified mutations at high depth was the most sensitive assay, detecting ctDNA down to an AF of 0.00024% (2.4 parts per million, ppm). Multiplex PCR targeting 21-47 tumor-identified SVs per patient detected ctDNA down to 0.00047% AF (4.7 ppm) and has potential as a clinical assay.
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Affiliation(s)
- Angela Santonja
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Wendy N Cooper
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Matthew D Eldridge
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Paul A W Edwards
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
- Department of PathologyUniversity of CambridgeCambridgeUK
| | - James A Morris
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Abigail R Edwards
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
| | - Hui Zhao
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Katrin Heider
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Dominique‐Laurent Couturier
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
- MRC Biostatistics UnitUniversity of CambridgeCambridgeUK
| | - Aadhitthya Vijayaraghavan
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Paulius Mennea
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Emma‐Jane Ditter
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Christopher G Smith
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Chris Boursnell
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Raquel Manzano García
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Oscar M Rueda
- MRC Biostatistics UnitUniversity of CambridgeCambridgeUK
| | - Emma Beddowes
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Heather Biggs
- Department of OncologyUniversity of CambridgeCambridgeUK
- Precision Breast Cancer Institute, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's HospitalCambridgeUK
| | - Stephen‐John Sammut
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
- Department of OncologyUniversity of CambridgeCambridgeUK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
- Department of OncologyUniversity of CambridgeCambridgeUK
- Precision Breast Cancer Institute, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's HospitalCambridgeUK
| | - Jean E Abraham
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
- Department of OncologyUniversity of CambridgeCambridgeUK
- Precision Breast Cancer Institute, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's HospitalCambridgeUK
| | - Davina Gale
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
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