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Macias RIR, Kanzaki H, Berasain C, Avila MA, Marin JJG, Hoshida Y. The Search for Risk, Diagnostic, and Prognostic Biomarkers of Cholangiocarcinoma and Their Biological and Clinicopathologic Significance. THE AMERICAN JOURNAL OF PATHOLOGY 2024:S0002-9440(24)00277-3. [PMID: 39103092 DOI: 10.1016/j.ajpath.2024.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/01/2024] [Accepted: 06/20/2024] [Indexed: 08/07/2024]
Abstract
Cholangiocarcinomas (CCAs) are a heterogeneous group of malignant tumors that originate from the biliary tract. They are usually diagnosed in advanced stages, leading to a dismal prognosis for affected patients. As CCA often arises as a sporadic cancer in individuals lacking specific risk factors or with heterogeneous backgrounds, and there are no defined high-risk groups, the implementation of effective surveillance programs for CCA is problematic. The identification and validation of new biomarkers useful for risk stratification, diagnosis, prognosis, and prediction of treatment response remains an unmet need for patients with CCA, even though numerous studies have been conducted lately to try to discover and validate CCA biomarkers. In this review, we overview the available information about the different types of biomarkers that have been investigated in recent years using minimally invasive biospecimens (blood, serum/plasma, bile, and urine) and their potential usefulness in diagnosis, prognosis, and risk stratification. It is widely accepted that early detection of CCA will impact patients' outcomes, by improving survival rates, quality of life, and the possibility of less invasive and/or curative treatments; however, challenges to its translation and clinical application for patients with CCA need to be resolved.
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Affiliation(s)
- Rocio I R Macias
- Experimental Hepatology and Drug Targeting Group, University of Salamanca, IBSAL, Salamanca, Spain; Center for the Study of Liver and Gastrointestinal Diseases, Carlos III National Institute of Health, Madrid, Spain.
| | - Hiroaki Kanzaki
- Division of Digestive and Liver Diseases, Department of Internal Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Carmen Berasain
- Center for the Study of Liver and Gastrointestinal Diseases, Carlos III National Institute of Health, Madrid, Spain; Hepatology Laboratory, Solid Tumors Program, Center for Applied Medical Research, Cancer Center University of Navarra, Pamplona, Spain
| | - Matias A Avila
- Center for the Study of Liver and Gastrointestinal Diseases, Carlos III National Institute of Health, Madrid, Spain; Hepatology Laboratory, Solid Tumors Program, Center for Applied Medical Research, Cancer Center University of Navarra, Pamplona, Spain
| | - Jose J G Marin
- Experimental Hepatology and Drug Targeting Group, University of Salamanca, IBSAL, Salamanca, Spain; Center for the Study of Liver and Gastrointestinal Diseases, Carlos III National Institute of Health, Madrid, Spain
| | - Yujin Hoshida
- Division of Digestive and Liver Diseases, Department of Internal Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas.
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Zhu S, Wu R, Liu X, Xie B, Xie C, Li S, Wu Z, Zhang Z, Tang Z, Gu L. Clinical application of ctDNA in early diagnosis, treatment and prognosis of patients with non-small cell lung cancer. Future Oncol 2024:1-12. [PMID: 39073412 DOI: 10.1080/14796694.2024.2376513] [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: 11/21/2023] [Accepted: 07/02/2024] [Indexed: 07/30/2024] Open
Abstract
Lung cancer is one of the most common malignancies worldwide, with non-small cell lung cancer (NSCLC) being the most common type. As understanding of precise treatment options for NSCLC deepens, circulating tumor DNA (ctDNA) has emerged as a potential biomarker that has become a research hotspot and may represent a new approach for the individualized diagnosis and treatment of NSCLC. This article reviews the applications of ctDNA for the early screening of patients with NSCLC, guiding targeted therapy and immunotherapy, evaluating chemotherapy and postoperative efficacy, assessing prognosis and monitoring recurrence. With the in-depth study of the pathogenesis of NSCLC, plasma ctDNA may become an indispensable part of the precise treatment of NSCLC, which has great clinical application prospects.
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Affiliation(s)
- Shenyu Zhu
- Department of Thoracic Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Key Lab of Brain Injury & Brain Protection, Ganzhou, China
| | - Rongqian Wu
- Department of Endocrinology and Metabolism, Gaoxin Hospital of The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiangjin Liu
- Department of Thoracic Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Bin Xie
- First Clinical Medical College, The Gannan Medical University, Ganzhou, China
| | - Chunfa Xie
- Department of Thoracic Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Key Lab of Brain Injury & Brain Protection, Ganzhou, China
| | - Shulin Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Key Lab of Brain Injury & Brain Protection, Ganzhou, China
| | - Zhicheng Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Key Lab of Brain Injury & Brain Protection, Ganzhou, China
| | - Zuxiong Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Key Lab of Brain Injury & Brain Protection, Ganzhou, China
| | - Zhixian Tang
- Department of Thoracic Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Key Lab of Brain Injury & Brain Protection, Ganzhou, China
| | - Liang Gu
- Department of Thoracic Surgery, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Ganzhou Key Lab of Brain Injury & Brain Protection, Ganzhou, China
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Delzenne G, Boileau M, Jamme P, Farchi O, Mortier L. Relevance of detection of RAF fusion transcripts in pan-negative melanoma in routine practice. Melanoma Res 2024; 34:182-185. [PMID: 38329225 DOI: 10.1097/cmr.0000000000000955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Pan-negative melanomas account for 30% of melanomas. In case of immunotherapy failure, therapeutic options are limited. Oncogene fusions represent a target of interest in many solid cancers. In melanoma, the frequency of oncogene fusion is not well documented and not routinely investigated. We conducted a single-center retrospective study. The objective was to determine the frequency of oncogene fusion detected by RNA sequencing, in patients with advanced or metastatic pan-negative melanoma. In parallel, an extended molecular alteration search was performed using extended targeted next-generation sequencing. We identified 59 patients with advanced pan-negative melanoma between January 2021 and January 2023. It was a cutaneous melanoma in 71.1% of the cases, a mucous melanoma in 15.2% of the cases. We identified nine patients with a RAF fusion, including seven BRAF gene fusion and two RAF1 fusion. Of the other molecular alterations, NF1 mutation was the most frequent molecular alteration identified. Among the nine patients with RAF fusions, all the patients initially received treatment with anti-PD1 ± anti-CTLA4 immunotherapy. After immunotherapy failure, five patients benefited from second-line targeted therapy (two with BRAF and MEK inhibitors combination, three MEK inhibitors alone). The response rate was 20%. In a population of pan-negative melanoma, we detected 15.2% of RAF fusion. Fusion detection allowed the introduction of a second line of targeted therapy, in the absence of a validated therapeutic option in 55.5% of cases. This study suggests the relevance of detecting RAF fusion in a selected population.
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Affiliation(s)
- Guillaume Delzenne
- Service de Dermatologie, Hôpital C. Huriez, CHU de Lille
- Department of Medicine, Université de Lille
| | - Marie Boileau
- Service de Dermatologie, Hôpital C. Huriez, CHU de Lille
- Department of Medicine, Université de Lille
| | - Philippe Jamme
- Service de Dermatologie, Hôpital C. Huriez, CHU de Lille
- Department of Medicine, Université de Lille
| | - Olivier Farchi
- Department of Medicine, Université de Lille
- Service de Biochimie et de Biologie Moléculaire Hormonologie Metabolism Nutrition Oncology, Centre de Biologie et Pathologie, CHU de Lille, Lille, France
| | - Laurent Mortier
- Service de Dermatologie, Hôpital C. Huriez, CHU de Lille
- Department of Medicine, Université de Lille
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Kasi PM, Lee JK, Pasquina LW, Decker B, Vanden Borre P, Pavlick DC, Allen JM, Parachoniak C, Quintanilha JCF, Graf RP, Schrock AB, Oxnard GR, Lovly CM, Tukachinsky H, Subbiah V. Circulating Tumor DNA Enables Sensitive Detection of Actionable Gene Fusions and Rearrangements Across Cancer Types. Clin Cancer Res 2024; 30:836-848. [PMID: 38060240 PMCID: PMC10870120 DOI: 10.1158/1078-0432.ccr-23-2693] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/03/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023]
Abstract
PURPOSE Genomic rearrangements can generate potent oncogenic drivers or disrupt tumor suppressor genes. This study examines the landscape of fusions and rearrangements detected by liquid biopsy (LBx) of circulating tumor DNA (ctDNA) across different cancer types. EXPERIMENTAL DESIGN LBx from 53,842 patients with 66 solid tumor types were profiled using FoundationOneLiquid CDx, a hybrid-capture sequencing platform that queries 324 cancer-related genes. Tissue biopsies (TBx) profiled using FoundationOneCDx were used as a comparator. RESULTS Among all LBx, 7,377 (14%) had ≥1 pathogenic rearrangement detected. A total of 3,648 (6.8%) LBx had ≥1 gain-of-function (GOF) oncogene rearrangement, and 4,428 (8.2%) LBx had ≥1 loss-of-function rearrangement detected. Cancer types with higher prevalence of GOF rearrangements included those with canonical fusion drivers: prostate cancer (19%), cholangiocarcinoma (6.4%), bladder (5.5%), and non-small cell lung cancer (4.4%). Although the prevalence of driver rearrangements was lower in LBx than TBx overall, the frequency of detection was comparable in LBx with a tumor fraction (TF) ≥1%. Rearrangements in FGFR2, BRAF, RET, and ALK, were detected across cancer types, but tended to be clonal variants in some cancer types and potential acquired resistance variants in others. CONCLUSIONS In contrast to some prior literature, this study reports detection of a wide variety of rearrangements in ctDNA. The prevalence of driver rearrangements in tissue and LBx was comparable when TF ≥1%. LBx presents a viable alternative when TBx is not available, and there may be less value in confirmatory testing when TF is sufficient.
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Affiliation(s)
- Pashtoon M. Kasi
- Weill Cornell Medicine, Englander Institute of Precision Medicine, New York Presbyterian Hospital, New York, New York
| | | | | | | | | | | | | | | | | | - Ryon P. Graf
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | | | | | | | | | - Vivek Subbiah
- The University of Texas MD Anderson Cancer Center, Houston, Texas
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Ranghiero A, Frascarelli C, Cursano G, Pescia C, Ivanova M, Vacirca D, Rappa A, Taormina SV, Barberis M, Fusco N, Rocco EG, Venetis K. Circulating tumour DNA testing in metastatic breast cancer: Integration with tissue testing. Cytopathology 2023; 34:519-529. [PMID: 37640801 DOI: 10.1111/cyt.13295] [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: 06/16/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]
Abstract
Breast cancer biomarker profiling predominantly relies on tissue testing (surgical and/or biopsy samples). However, the field of liquid biopsy, particularly the analysis of circulating tumour DNA (ctDNA), has witnessed remarkable progress and continues to evolve rapidly. The incorporation of ctDNA-based testing into clinical practice is creating new opportunities for patients with metastatic breast cancer (MBC). ctDNA offers advantages over conventional tissue analyses, as it reflects tumour heterogeneity and enables multiple serial biopsies in a minimally invasive manner. Thus, it serves as a valuable complement to standard tumour tissues and, in certain instances, may even present a potential alternative approach. In the context of MBC, ctDNA testing proves highly informative in the detection of disease progression, monitoring treatment response, assessing actionable biomarkers, and identifying mechanisms of resistance. Nevertheless, ctDNA does exhibit inherent limitations, including its generally low abundance, necessitating timely blood samplings and rigorous management of the pre-analytical phase. The development of highly sensitive assays and robust bioinformatic tools has paved the way for reliable ctDNA analyses. The time has now come to establish how ctDNA and tissue analyses can be effectively integrated into the diagnostic workflow of MBC to provide patients with the most comprehensive and accurate profiling. In this manuscript, we comprehensively analyse the current methodologies employed in ctDNA analysis and explore the potential benefits arising from the integration of tissue and ctDNA testing for patients diagnosed with MBC.
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Affiliation(s)
- Alberto Ranghiero
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Chiara Frascarelli
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Giulia Cursano
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Carlo Pescia
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- School of Pathology, University of Milan, Milan, Italy
| | - Mariia Ivanova
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Davide Vacirca
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Alessandra Rappa
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Massimo Barberis
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Elena Guerini Rocco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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Hafstað V, Häkkinen J, Persson H. Fast and sensitive validation of fusion transcripts in whole-genome sequencing data. BMC Bioinformatics 2023; 24:359. [PMID: 37741966 PMCID: PMC10518092 DOI: 10.1186/s12859-023-05489-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND In cancer, genomic rearrangements can create fusion genes that either combine protein-coding sequences from two different partner genes or place one gene under the control of the promoter of another gene. These fusion genes can act as oncogenic drivers in tumor development and several fusions involving kinases have been successfully exploited as drug targets. Expressed fusions can be identified in RNA sequencing (RNA-Seq) data, but fusion prediction software often has a high fraction of false positive fusion transcript predictions. This is problematic for both research and clinical applications. RESULTS We describe a method for validation of fusion transcripts detected by RNA-Seq in matched whole-genome sequencing (WGS) data. Our pipeline uses discordant read pairs to identify supported fusion events and analyzes soft-clipped read alignments to determine genomic breakpoints. We have tested it on matched RNA-Seq and WGS data for both tumors and cancer cell lines and show that it can be used to validate both new predicted gene fusions and experimentally validated fusion events. It was considerably faster and more sensitive than using BreakDancer and Manta, software that is instead designed to detect many different types of structural variants on a genome-wide scale. CONCLUSIONS We have developed a fast and very sensitive pipeline for validation of gene fusions detected by RNA-Seq in matched WGS data. It can be used to identify high-quality gene fusions for further bioinformatic and experimental studies, including validation of genomic breakpoints and studies of the mechanisms that generate fusions. In a clinical setting, it could help find expressed gene fusions for personalized therapy.
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Affiliation(s)
- Völundur Hafstað
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden
| | - Jari Häkkinen
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden
| | - Helena Persson
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University Cancer Centre, Lund, Sweden.
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Rose KM, Huelster HL, Meeks JJ, Faltas BM, Sonpavde GP, Lerner SP, Ross JS, Spiess PE, Grass GD, Jain RK, Kamat AM, Vosoughi A, Wang L, Wang X, Li R. Circulating and urinary tumour DNA in urothelial carcinoma - upper tract, lower tract and metastatic disease. Nat Rev Urol 2023; 20:406-419. [PMID: 36977797 DOI: 10.1038/s41585-023-00725-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2023] [Indexed: 03/30/2023]
Abstract
Precision medicine has transformed the way urothelial carcinoma is managed. However, current practices are limited by the availability of tissue samples for genomic profiling and the spatial and temporal molecular heterogeneity observed in many studies. Among rapidly advancing genomic sequencing technologies, non-invasive liquid biopsy has emerged as a promising diagnostic tool to reproduce tumour genomics, and has shown potential to be integrated in several aspects of clinical care. In urothelial carcinoma, liquid biopsies such as plasma circulating tumour DNA (ctDNA) and urinary tumour DNA (utDNA) have been investigated as a surrogates for tumour biopsies and might bridge many shortfalls currently faced by clinicians. Both ctDNA and utDNA seem really promising in urothelial carcinoma diagnosis, staging and prognosis, response to therapy monitoring, detection of minimal residual disease and surveillance. The use of liquid biopsies in patients with urothelial carcinoma could further advance precision medicine in this population, facilitating personalized patient monitoring through non-invasive assays.
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Affiliation(s)
- Kyle M Rose
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Heather L Huelster
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Joshua J Meeks
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - Bishoy M Faltas
- Department of Hematology/Oncology, Weill-Cornell Medicine, New York, NY, USA
| | - Guru P Sonpavde
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Seth P Lerner
- Department of Urology, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc, Cambridge, MA, USA
- Departments of Urology and Pathology, Upstate Medical University, Syracuse, NY, USA
| | - Philippe E Spiess
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - G Daniel Grass
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Rohit K Jain
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Ashish M Kamat
- Department of Urology, MD Anderson Cancer Center, Houston, TX, USA
| | - Aram Vosoughi
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Liang Wang
- Department of Tumour Biology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Xuefeng Wang
- Department of Biostatistics/Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Roger Li
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA.
- Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, FL, USA.
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Semenkovich NP, Szymanski JJ, Earland N, Chauhan PS, Pellini B, Chaudhuri AA. Genomic approaches to cancer and minimal residual disease detection using circulating tumor DNA. J Immunother Cancer 2023; 11:e006284. [PMID: 37349125 PMCID: PMC10314661 DOI: 10.1136/jitc-2022-006284] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2023] [Indexed: 06/24/2023] Open
Abstract
Liquid biopsies using cell-free circulating tumor DNA (ctDNA) are being used frequently in both research and clinical settings. ctDNA can be used to identify actionable mutations to personalize systemic therapy, detect post-treatment minimal residual disease (MRD), and predict responses to immunotherapy. ctDNA can also be isolated from a range of different biofluids, with the possibility of detecting locoregional MRD with increased sensitivity if sampling more proximally than blood plasma. However, ctDNA detection remains challenging in early-stage and post-treatment MRD settings where ctDNA levels are minuscule giving a high risk for false negative results, which is balanced with the risk of false positive results from clonal hematopoiesis. To address these challenges, researchers have developed ever-more elegant approaches to lower the limit of detection (LOD) of ctDNA assays toward the part-per-million range and boost assay sensitivity and specificity by reducing sources of low-level technical and biological noise, and by harnessing specific genomic and epigenomic features of ctDNA. In this review, we highlight a range of modern assays for ctDNA analysis, including advancements made to improve the signal-to-noise ratio. We further highlight the challenge of detecting ultra-rare tumor-associated variants, overcoming which will improve the sensitivity of post-treatment MRD detection and open a new frontier of personalized adjuvant treatment decision-making.
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Affiliation(s)
- Nicholas P Semenkovich
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jeffrey J Szymanski
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Noah Earland
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Pradeep S Chauhan
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bruna Pellini
- Department of Thoracic Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Aadel A Chaudhuri
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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Assi T, Khoury R, Ibrahim R, Baz M, Ibrahim T, LE Cesne A. Overview of the role of liquid biopsy in cancer management. Transl Oncol 2023; 34:101702. [PMID: 37267803 DOI: 10.1016/j.tranon.2023.101702] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/04/2023] Open
Abstract
With the emergence of novel targeted therapeutic options in early-stage and advanced-stage malignancies, researchers have shifted their focus on developing personalized treatment plans through molecular profiling. Circulating tumor DNA (ctDNA) is a cell-free DNA (ctDNA) fragment, originating from tumor cells, and circulating in the bloodstream as well as biological fluids. Over the past decade, many techniques were developed for liquid biopsies through next-generation sequencing. This alternative non-invasive biopsy offers several advantages in various types of tumors over traditional tissue biopsy. The process of liquid biopsy is considered minimally invasive and therefore easily repeatable when needed, providing a more dynamic analysis of the tumor cells. Moreover, it has an advantage in patients with tumors that are not candidates for tissue sampling. Besides, it offers a deeper understanding of tumor burden as well as treatment response, thereby enhancing the detection of minimal residual disease and therapeutic guidance for personalized medicine. Despite its many advantages, ctDNA and liquid biopsy do have some limitations. This paper discusses the basis of ctDNA and the current data available on the subject, as well as its clinical utility. We also reflect on the limitations of using ctDNA in addition to its future perspectives in clinical oncology and precision medicine.
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Affiliation(s)
- Tarek Assi
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France.
| | - Rita Khoury
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
| | - Rebecca Ibrahim
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
| | - Maria Baz
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
| | - Tony Ibrahim
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
| | - Axel LE Cesne
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
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10
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Trinidad EM, Juan-Ribelles A, Pisano G, Castel V, Cañete A, Gut M, Heath S, Font de Mora J. Evaluation of circulating tumor DNA by electropherogram analysis and methylome profiling in high-risk neuroblastomas. Front Oncol 2023; 13:1037342. [PMID: 37251933 PMCID: PMC10213460 DOI: 10.3389/fonc.2023.1037342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
Background Liquid biopsy has emerged as a promising, non-invasive diagnostic approach in oncology because the analysis of circulating tumor DNA (ctDNA) reflects the precise status of the disease at diagnosis, progression, and response to treatment. DNA methylation profiling is also a potential solution for sensitive and specific detection of many cancers. The combination of both approaches, DNA methylation analysis from ctDNA, provides an extremely useful and minimally invasive tool with high relevance in patients with childhood cancer. Neuroblastoma is an extracranial solid tumor most common in children and responsible for up to 15% of cancer-related deaths. This high death rate has prompted the scientific community to search for new therapeutic targets. DNA methylation also offers a new source for identifying these molecules. However, the limited blood sample size which can be obtained from children with cancer and the fact that ctDNA content may occasionally be diluted by non-tumor cell-free DNA (cfDNA) complicate optimal quantities of material for high-throughput sequencing studies. Methods In this article, we present an improved method for ctDNA methylome studies of blood-derived plasma from high-risk neuroblastoma patients. We assessed the electropherogram profiles of ctDNA-containing samples suitable for methylome studies, using 10 ng of plasma-derived ctDNA from 126 samples of 86 high-risk neuroblastoma patients, and evaluated several bioinformatic approaches to analyze DNA methylation sequencing data. Results We demonstrated that enzymatic methyl-sequencing (EM-seq) outperformed bisulfite conversion-based method, based on the lower proportion of PCR duplicates and the higher percentage of unique mapping reads, mean coverage, and genome coverage. The analysis of the electropherogram profiles revealed the presence of nucleosomal multimers, and occasionally high molecular weight DNA. We established that 10% content of the mono-nucleosomal peak is sufficient ctDNA for successful detection of copy number variations and methylation profiles. Quantification of mono-nucleosomal peak also showed that samples at diagnosis contained a higher amount of ctDNA than relapse samples. Conclusions Our results refine the use of electropherogram profiles to optimize sample selection for subsequent high-throughput analysis and support the use of liquid biopsy followed by enzymatic conversion of unmethylated cysteines to assess the methylomes of neuroblastoma patients.
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Affiliation(s)
- Eva María Trinidad
- Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
| | - Antonio Juan-Ribelles
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
- Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
| | - Giulia Pisano
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
- Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
| | - Victoria Castel
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
- Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
| | - Adela Cañete
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
- Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
- School of Medicine, University of Valencia, Valencia, Spain
| | - Marta Gut
- National Center for Genomic Analysis – Centre for Genomic Regulation (CNAG-CRG), Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Simon Heath
- National Center for Genomic Analysis – Centre for Genomic Regulation (CNAG-CRG), Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jaime Font de Mora
- Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
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11
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Husain H, Pavlick DC, Fendler BJ, Madison RW, Decker B, Gjoerup O, Parachoniak CA, McLaughlin-Drubin M, Erlich RL, Schrock AB, Frampton GM, Das Thakur M, Oxnard GR, Tukachinsky H. Tumor Fraction Correlates With Detection of Actionable Variants Across > 23,000 Circulating Tumor DNA Samples. JCO Precis Oncol 2022; 6:e2200261. [PMID: 36265119 PMCID: PMC9616642 DOI: 10.1200/po.22.00261] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
PURPOSE Profiling of circulating tumor DNA (ctDNA) is increasingly adopted in the management of solid tumors, concurrent with increased availability of more comprehensive ctDNA panels. However, variable ctDNA shed can result in variable assay sensitivity. We studied the relationship between ctDNA tumor fraction (TF) and detection of actionable alterations across cancer types. METHODS A total of 23,482 liquid biopsies (LBx) submitted between September 2020 and October 2021 were sequenced using a hybrid capture panel that reports genomic alterations (GAs) and genomic biomarkers across 324 cancer-related genes. The primary end points were the prevalence of targetable GAs by cancer type and detection in relationship to ctDNA TF. Sensitivity of detection in LBx was assessed in 1,289 patients with available tissue results. RESULTS 94% (n = 22,130) of LBx had detectable ctDNA, with a median TF of 2.2%. LBx profiling detected GAs in National Comprehensive Cancer Network category 1 genes in 37% of lung, 30% of prostate, 36% of breast, and 51% of colon cancer cases. Potential germline GAs flagged on clinical reports were detected in genes including <i>BRCA1/2</i>, <i>PALB2</i>, <i>CHEK2</i>, and <i>ATM.</i> Polyclonal mutations in genes associated with resistance such as <i>AR</i>, <i>ESR1</i>, <i>RB1</i>, and <i>NF1</i> were detected. The sensitivity of LBx to detect driver alterations identified in tissue biopsy from the same patient ranged from 58% to 86% but was consistently at or near 100% in cases with TF ≥ 10%. CONCLUSION Elevated ctDNA shed is associated with both high sensitivity and negative predictive value for detection of actionable GAs. The presence of elevated TF suggests adequate tumor profiling and may reduce the value of subsequent reflex to confirmatory tissue testing in patients with negative LBx results.
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Affiliation(s)
- Hatim Husain
- University of California, San Diego, La Jolla, CA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Hanna Tukachinsky
- Foundation Medicine, Cambridge, MA,Hanna Tukachinsky, PhD, Foundation Medicine, 150 Second St, Cambridge, MA 02141; e-mail:
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12
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Kanai M. Current Clinical Practice of Precision Medicine Using Comprehensive Genomic Profiling Tests in Biliary Tract Cancer in Japan. Curr Oncol 2022; 29:7272-7284. [PMID: 36290850 PMCID: PMC9599999 DOI: 10.3390/curroncol29100573] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022] Open
Abstract
With the recent advances of next generation sequencing technologies, comprehensive genomic profiling (CGP) tests, which are designed to measure more than hundreds of cancer-related genes at a time, have now been widely introduced into daily clinical practice. For the patients whose tumor samples are not fit for tissue-based CGP tests, a blood-based CGP test (liquid biopsy) is available as an alternative option. Three CGP tests, "OncoGuide NCC™Oncopanel System (124 genes)", "FoundationOne®CDx (324 genes)", and "Founda-tionOne®CDx Liquid (324 genes)", are now reimbursed by public insurance in 233 hospitals designated for cancer genomic medicine in Japan. In biliary tract cancer, the prevalence of druggable variants is relatively higher compared to other cancer types and the European Society for Medical Oncology recommends routine use of CGP tests for advanced biliary tract cancer to guide treatment options. The latest National Cancer Center Network guideline lists eight druggable markers (NTRK fusion, MSI-H, TMB-H, BRAF V600E, FGFR2 fusions/rearrangement, IDH1 mutations, RET fusion, and HER2 overexpression) and matched therapies. In Japan, matched therapies for four markers (NTRK, MSI-H, TMB-H, and FGFR2) are reimbursed by public insurance (as of September 2022). The progress of genomic profiling technology will contribute to the improvement of the dismal clinical outcomes of this disease in the future.
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Affiliation(s)
- Masashi Kanai
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
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13
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Liquid Biopsy Analysis as a Tool for TKI-Based Treatment in Non-Small Cell Lung Cancer. Cells 2022; 11:cells11182871. [PMID: 36139444 PMCID: PMC9497234 DOI: 10.3390/cells11182871] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 12/03/2022] Open
Abstract
The treatment of non-small cell lung cancer (NSCLC) has recently evolved with the introduction of targeted therapy based on the use of tyrosine kinase inhibitors (TKIs) in patients with certain gene alterations, including EGFR, ALK, ROS1, BRAF, and MET genes. Molecular targeted therapy based on TKIs has improved clinical outcomes in a large number of NSCLC patients with advanced disease, enabling significantly longer progression-free survival (PFS). Liquid biopsy is an increasingly popular diagnostic tool for treating TKI-based NSCLC. The studies presented in this article show that detection and analysis based on liquid biopsy elements such as circulating tumor cells (CTCs), cell-free DNA (cfDNA), exosomes, and/or tumor-educated platelets (TEPs) can contribute to the appropriate selection and monitoring of targeted therapy in NSCLC patients as complementary to invasive tissue biopsy. The detection of these elements, combined with their molecular analysis (using, e.g., digital PCR (dPCR), next generation sequencing (NGS), shallow whole genome sequencing (sWGS)), enables the detection of mutations, which are required for the TKI treatment. Despite such promising results obtained by many research teams, it is still necessary to carry out prospective studies on a larger group of patients in order to validate these methods before their application in clinical practice.
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14
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Shields MD, Chen K, Dutcher G, Patel I, Pellini B. Making the Rounds: Exploring the Role of Circulating Tumor DNA (ctDNA) in Non-Small Cell Lung Cancer. Int J Mol Sci 2022; 23:ijms23169006. [PMID: 36012272 PMCID: PMC9408840 DOI: 10.3390/ijms23169006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022] Open
Abstract
Advancements in the clinical practice of non-small cell lung cancer (NSCLC) are shifting treatment paradigms towards increasingly personalized approaches. Liquid biopsies using various circulating analytes provide minimally invasive methods of sampling the molecular content within tumor cells. Plasma-derived circulating tumor DNA (ctDNA), the tumor-derived component of cell-free DNA (cfDNA), is the most extensively studied analyte and has a growing list of applications in the clinical management of NSCLC. As an alternative to tumor genotyping, the assessment of oncogenic driver alterations by ctDNA has become an accepted companion diagnostic via both single-gene polymerase chain reactions (PCR) and next-generation sequencing (NGS) for advanced NSCLC. ctDNA technologies have also shown the ability to detect the emerging mechanisms of acquired resistance that evolve after targeted therapy. Furthermore, the detection of minimal residual disease (MRD) by ctDNA for patients with NSCLC after curative-intent treatment may serve as a prognostic and potentially predictive biomarker for recurrence and response to therapy, respectively. Finally, ctDNA analysis via mutational, methylation, and/or fragmentation multi-omic profiling offers the potential for improving early lung cancer detection. In this review, we discuss the role of ctDNA in each of these capacities, namely, for molecular profiling, treatment response monitoring, MRD detection, and early cancer detection of NSCLC.
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Affiliation(s)
- Misty Dawn Shields
- Department of Internal Medicine, Division of Hematology/Oncology, Indiana University School of Medicine, Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
| | - Kevin Chen
- Department of Radiation Oncology, Division of Cancer Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Giselle Dutcher
- Department of Medicine, Division of Solid Tumor Oncology, University Hospitals Seidman Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ishika Patel
- Department of Public Health, University of South Florida, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Bruna Pellini
- Department of Thoracic Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence:
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15
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Imai M, Nakamura Y, Sunami K, Kage H, Komine K, Koyama T, Amano T, Ennishi D, Kanai M, Kenmotsu H, Maeda T, Morita S, Sakai D, Bando H, Makiyama A, Suzuki T, Hirata M, Kohsaka S, Tsuchihara K, Naito Y, Yoshino T. Expert Panel Consensus Recommendations on the Use of Circulating Tumor DNA Assays for Patients with Advanced Solid Tumors. Cancer Sci 2022; 113:3646-3656. [PMID: 35876224 PMCID: PMC9633310 DOI: 10.1111/cas.15504] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 12/01/2022] Open
Abstract
Comprehensive genomic profiling is increasingly used to facilitate precision oncology based on molecular stratification. In addition to conventional tissue comprehensive genomic profiling, comprehensive genomic profiling of circulating tumor DNA has become widely utilized in cancer care owing on its advantages, including less invasiveness, rapid turnaround time, and capturing heterogeneity. However, circulating tumor DNA comprehensive genomic profiling has some limitations, mainly false negatives due to low levels of plasma circulating tumor deoxyribonucleic acid and false positives caused by clonal hematopoiesis. Nevertheless, no guidelines and recommendations fully address these issues. Here, an expert panel committee involving representatives from 12 Designated Core Hospitals for Cancer Genomic Medicine in Japan was organized to develop expert consensus recommendations for the use of circulating tumor deoxyribonucleic acid‐based comprehensive genomic profiling. The aim was to generate guidelines for clinicians and allied healthcare professionals on the optimal use of the circulating tumor DNA assays in advanced solid tumors and to aid the design of future clinical trials that utilize and develop circulating tumor DNA assays to refine precision oncology. Fourteen clinical questions regarding circulating tumor deoxyribonucleic acid comprehensive genomic profiling including the timing of testing and considerations for interpreting results were established by searching and curating associated literatures, and corresponding recommendations were prepared based on the literature for each clinical question. Final consensus recommendations were developed by voting to determine the level of each recommendation by the Committee members.
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Affiliation(s)
- Mitsuho Imai
- Translational Research Support Section, National Cancer Center Hospital East.,Genomics Unit, Keio University School of Medicine
| | - Yoshiaki Nakamura
- Translational Research Support Section, National Cancer Center Hospital East.,Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East
| | - Kuniko Sunami
- Department of Laboratory Medicine, National Cancer Center Hospital
| | - Hidenori Kage
- Department of Next-Generation Precision Medicine Development Laboratory, Graduate School of Medicine, The University of Tokyo
| | - Keigo Komine
- Department of Medical Oncology, Tohoku University Hospital
| | - Takafumi Koyama
- Department of Experimental Therapeutics, National Cancer Center Hospital
| | - Toraji Amano
- Clinical Research and Medical Innovation Center, Hokkaido University Hospital
| | - Daisuke Ennishi
- Center for Comprehensive Genomic Medicine, Okayama University Hospital
| | - Masashi Kanai
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University
| | | | - Takahiro Maeda
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences
| | - Sachi Morita
- Department of Clinical Oncology and Chemotherapy, Nagoya University Hospital
| | - Daisuke Sakai
- Center for Cancer Genomics and Personalized Medicine, Osaka University Hospital
| | - Hideaki Bando
- Translational Research Support Section, National Cancer Center Hospital East.,Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East
| | | | - Tatsuya Suzuki
- Department of Hematology, National Cancer Center Hospital
| | - Makoto Hirata
- Department of Genetic Medicine and Services, National Cancer Center Hospital
| | - Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Research Institute
| | - Katsuya Tsuchihara
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Japan
| | - Yoichi Naito
- Department of General Internal medicine/Experimental Therapeutics/Medical Oncology, National Cancer Center Hospital East
| | - Takayuki Yoshino
- Translational Research Support Section, National Cancer Center Hospital East.,Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East
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16
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Chan HT, Chin YM, Low SK. Circulating Tumor DNA-Based Genomic Profiling Assays in Adult Solid Tumors for Precision Oncology: Recent Advancements and Future Challenges. Cancers (Basel) 2022; 14:3275. [PMID: 35805046 PMCID: PMC9265547 DOI: 10.3390/cancers14133275] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/30/2022] [Accepted: 07/02/2022] [Indexed: 12/04/2022] Open
Abstract
Genomic profiling using tumor biopsies remains the standard approach for the selection of approved molecular targeted therapies. However, this is often limited by its invasiveness, feasibility, and poor sample quality. Liquid biopsies provide a less invasive approach while capturing a contemporaneous and comprehensive tumor genomic profile. Recent advancements in the detection of circulating tumor DNA (ctDNA) from plasma samples at satisfactory sensitivity, specificity, and detection concordance to tumor tissues have facilitated the approval of ctDNA-based genomic profiling to be integrated into regular clinical practice. The recent approval of both single-gene and multigene assays to detect genetic biomarkers from plasma cell-free DNA (cfDNA) as companion diagnostic tools for molecular targeted therapies has transformed the therapeutic decision-making procedure for advanced solid tumors. Despite the increasing use of cfDNA-based molecular profiling, there is an ongoing debate about a 'plasma first' or 'tissue first' approach toward genomic testing for advanced solid malignancies. Both approaches present possible advantages and disadvantages, and these factors should be carefully considered to personalize and select the most appropriate genomic assay. This review focuses on the recent advancements of cfDNA-based genomic profiling assays in advanced solid tumors while highlighting the major challenges that should be tackled to formulate evidence-based guidelines in recommending the 'right assay for the right patient at the right time'.
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Affiliation(s)
- Hiu Ting Chan
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
| | - Yoon Ming Chin
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
- Cancer Precision Medicine, Inc., Kawasaki 213-0012, Japan
| | - Siew-Kee Low
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
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17
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Werner TV, Kock S, Weber I, Kayser G, Werner M, Lassmann S. Validation of a DNA-Based Next-Generation Sequencing Test for Molecular Diagnostic Variant and Fusion Detection in Formalin-Fixed, Paraffin-Embedded Tissue Specimens and Liquid Biopsy Plasma/Cell-Free DNA Samples. J Mol Diagn 2022; 24:784-802. [PMID: 35787794 DOI: 10.1016/j.jmoldx.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 03/26/2022] [Accepted: 04/06/2022] [Indexed: 11/26/2022] Open
Abstract
This study evaluated two DNA-based next-generation sequencing approaches for detection of single-nucleotide variants (SNVs) and fusions in formalin-fixed, paraffin-embedded (FFPE) tissue specimens and liquid biopsies (AVENIO Targeted and Surveillance Panels). Reference standards (n = 7 with SNVs and structural variants) and real-world FFPE tissue specimens (n = 26 lung, colorectal, pancreas, ovary, breast, prostate, melanoma, and soft tissue cancer cases with n = 27 samples), liquid biopsies [n = 29 cases with n = 40 plasma/cell-free DNA (cfDNA) samples], and one pleural effusion (lung cancer) were analyzed by the AVENIO workflow for known SNVs (BRAF, BRCA1/2, CTNNB1, EGFR, KRAS, MET exon 14 skipping, NRAS, PIK3CA, and TP53), insertions and deletions (ERBB2 and KIT), and fusions (ALK and ROS1). Detection of SNVs, insertions and deletions, and fusions was reliable in 24 of 26 FFPE tissue specimen cases and at 1% allele frequency in 5 of 5 cfDNA reference standards and 37 of 40 plasma/cfDNA samples. Pitfalls were identified for the AVENIO workflow in calling and listing of clinically relevant variants, requiring additional manual inspection. Moreover, laboratory workflows are distinct for FFPE tissue specimens and liquid biopsies as well as time-consuming for sample quality control assays. In summary, the DNA-based next-generation sequencing approaches may be suitable for routine molecular pathology diagnostics on careful data interpretation and further optimization of the technical and laboratory workflows.
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Affiliation(s)
- Tamara V Werner
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany; German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg, Germany
| | - Sylvia Kock
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Isabel Weber
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Gian Kayser
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Martin Werner
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany; German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg, Germany
| | - Silke Lassmann
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany; German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg, Germany.
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18
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Vasseur D, Sassi H, Bayle A, Tagliamento M, Besse B, Marzac C, Arbab A, Auger N, Cotteret S, Aldea M, Blanc-Durand F, Géraud A, Gazzah A, Loriot Y, Hollebecque A, Martín-Romano P, Ngo-Camus M, Nicotra C, Ponce S, Sakkal M, Caron O, Smolenschi C, Micol JB, Italiano A, Rouleau E, Lacroix L. Next-Generation Sequencing on Circulating Tumor DNA in Advanced Solid Cancer: Swiss Army Knife for the Molecular Tumor Board? A Review of the Literature Focused on FDA Approved Test. Cells 2022; 11:cells11121901. [PMID: 35741030 PMCID: PMC9221453 DOI: 10.3390/cells11121901] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/01/2022] [Accepted: 06/10/2022] [Indexed: 11/16/2022] Open
Abstract
FDA-approved next-generation sequencing assays based on cell-free DNA offers new opportunities in a molecular-tumor-board context thanks to the noninvasiveness of liquid biopsy, the diversity of analyzed parameters and the short turnaround time. It gives the opportunity to study the heterogeneity of the tumor, to elucidate complex resistance mechanisms and to adapt treatment strategies. However, lowering the limit of detection and increasing the panels' size raise new questions in terms of detection of incidental germline alterations, occult malignancies and clonal hematopoiesis of indeterminate potential mutations. In this review, after a technological discussion and description of the common problematics encountered, we establish recommendations in properly using these FDA-approved tests in a molecular-tumor-board context.
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Affiliation(s)
- Damien Vasseur
- Medical Biology and Pathology Department, Gustave Roussy, F-94805 Villejuif, France; (H.S.); (C.M.); (A.A.); (N.A.); (S.C.); (E.R.); (L.L.)
- AMMICa UAR3655/US23, Gustave Roussy, F-94805 Villejuif, France
- Correspondence:
| | - Hela Sassi
- Medical Biology and Pathology Department, Gustave Roussy, F-94805 Villejuif, France; (H.S.); (C.M.); (A.A.); (N.A.); (S.C.); (E.R.); (L.L.)
| | - Arnaud Bayle
- Drug Development Department (DITEP), Gustave Roussy, F-94805 Villejuif, France; (A.B.); (A.G.); (P.M.-R.); (M.N.-C.); (C.N.); (S.P.); (A.I.)
- Oncostat U1018, Inserm, Université Paris-Saclay, Équipe Labellisée Ligue Contre le Cancer, F-94805 Villejuif, France
| | - Marco Tagliamento
- Medical Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.T.); (B.B.); (M.A.); (A.G.); (Y.L.); (A.H.); (O.C.)
| | - Benjamin Besse
- Medical Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.T.); (B.B.); (M.A.); (A.G.); (Y.L.); (A.H.); (O.C.)
| | - Christophe Marzac
- Medical Biology and Pathology Department, Gustave Roussy, F-94805 Villejuif, France; (H.S.); (C.M.); (A.A.); (N.A.); (S.C.); (E.R.); (L.L.)
| | - Ahmadreza Arbab
- Medical Biology and Pathology Department, Gustave Roussy, F-94805 Villejuif, France; (H.S.); (C.M.); (A.A.); (N.A.); (S.C.); (E.R.); (L.L.)
| | - Nathalie Auger
- Medical Biology and Pathology Department, Gustave Roussy, F-94805 Villejuif, France; (H.S.); (C.M.); (A.A.); (N.A.); (S.C.); (E.R.); (L.L.)
| | - Sophie Cotteret
- Medical Biology and Pathology Department, Gustave Roussy, F-94805 Villejuif, France; (H.S.); (C.M.); (A.A.); (N.A.); (S.C.); (E.R.); (L.L.)
| | - Mihaela Aldea
- Medical Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.T.); (B.B.); (M.A.); (A.G.); (Y.L.); (A.H.); (O.C.)
| | - Félix Blanc-Durand
- Gynecological Cancer Unit, Department of Medicine, Gustave Roussy, F-94805 Villejuif, France;
| | - Arthur Géraud
- Drug Development Department (DITEP), Gustave Roussy, F-94805 Villejuif, France; (A.B.); (A.G.); (P.M.-R.); (M.N.-C.); (C.N.); (S.P.); (A.I.)
| | - Anas Gazzah
- Medical Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.T.); (B.B.); (M.A.); (A.G.); (Y.L.); (A.H.); (O.C.)
| | - Yohann Loriot
- Medical Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.T.); (B.B.); (M.A.); (A.G.); (Y.L.); (A.H.); (O.C.)
| | - Antoine Hollebecque
- Medical Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.T.); (B.B.); (M.A.); (A.G.); (Y.L.); (A.H.); (O.C.)
| | - Patricia Martín-Romano
- Drug Development Department (DITEP), Gustave Roussy, F-94805 Villejuif, France; (A.B.); (A.G.); (P.M.-R.); (M.N.-C.); (C.N.); (S.P.); (A.I.)
| | - Maud Ngo-Camus
- Drug Development Department (DITEP), Gustave Roussy, F-94805 Villejuif, France; (A.B.); (A.G.); (P.M.-R.); (M.N.-C.); (C.N.); (S.P.); (A.I.)
| | - Claudio Nicotra
- Drug Development Department (DITEP), Gustave Roussy, F-94805 Villejuif, France; (A.B.); (A.G.); (P.M.-R.); (M.N.-C.); (C.N.); (S.P.); (A.I.)
| | - Santiago Ponce
- Drug Development Department (DITEP), Gustave Roussy, F-94805 Villejuif, France; (A.B.); (A.G.); (P.M.-R.); (M.N.-C.); (C.N.); (S.P.); (A.I.)
| | - Madona Sakkal
- Dermatology Unit, Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.S.); (C.S.)
| | - Olivier Caron
- Medical Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.T.); (B.B.); (M.A.); (A.G.); (Y.L.); (A.H.); (O.C.)
| | - Cristina Smolenschi
- Dermatology Unit, Oncology Department, Gustave Roussy, F-94805 Villejuif, France; (M.S.); (C.S.)
| | | | - Antoine Italiano
- Drug Development Department (DITEP), Gustave Roussy, F-94805 Villejuif, France; (A.B.); (A.G.); (P.M.-R.); (M.N.-C.); (C.N.); (S.P.); (A.I.)
| | - Etienne Rouleau
- Medical Biology and Pathology Department, Gustave Roussy, F-94805 Villejuif, France; (H.S.); (C.M.); (A.A.); (N.A.); (S.C.); (E.R.); (L.L.)
- AMMICa UAR3655/US23, Gustave Roussy, F-94805 Villejuif, France
| | - Ludovic Lacroix
- Medical Biology and Pathology Department, Gustave Roussy, F-94805 Villejuif, France; (H.S.); (C.M.); (A.A.); (N.A.); (S.C.); (E.R.); (L.L.)
- AMMICa UAR3655/US23, Gustave Roussy, F-94805 Villejuif, France
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