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Fu R, Xiong Y, Cai M, Li F, Chen R, Wu Y, Zhong W. Evaluation of molecular residual disease in operable non-small cell lung cancer with gene fusions, MET exon skipping or de novo MET amplification. Front Med 2024:10.1007/s11684-024-1060-z. [PMID: 38805102 DOI: 10.1007/s11684-024-1060-z] [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: 09/27/2023] [Accepted: 01/17/2024] [Indexed: 05/29/2024]
Abstract
Gene fusions and MET alterations are rare and difficult to detect in plasma samples. The clinical detection efficacy of molecular residual disease (MRD) based on circulating tumor DNA (ctDNA) in patients with non-small cell lung cancer (NSCLC) with these mutations remains unknown. This prospective, non-intervention study recruited 49 patients with operable NSCLC with actionable gene fusions (ALK, ROS1, RET, and FGFR1), MET exon 14 skipping or de novo MET amplification. We analyzed 43 tumor tissues and 111 serial perioperative plasma samples using 1021- and 338-gene panels, respectively. Detectable MRD correlated with a significantly higher recurrence rate (P < 0.001), yielding positive predictive values of 100% and 90.9%, and negative predictive values of 82.4% and 86.4% at landmark and longitudinal time points, respectively. Patients with detectable MRD showed reduced disease-free survival (DFS) compared to those with undetectable MRD (P < 0.001). Patients who harbored tissue-derived fusion/MET alterations in their MRD had reduced DFS compared to those who did not (P = 0.05). To our knowledge, this is the first comprehensive study on ctDNA-MRD clinical detection efficacy in operable NSCLC patients with gene fusions and MET alterations. Patients with detectable tissue-derived fusion/MET alterations in postoperative MRD had worse clinical outcomes.
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Affiliation(s)
- Rui Fu
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | | | - Miao Cai
- Geneplus-Beijing, Beijing, 102206, China
| | - Fang Li
- Geneplus-Beijing, Beijing, 102206, China
| | | | - Yilong Wu
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Wenzhao Zhong
- School of Medicine, South China University of Technology, Guangzhou, 510006, China.
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China.
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Kim B, Kim Y, Cho JY, Lee KA. Identification of Potential Genomic Alterations Using Pan-Cancer Cell-Free DNA Next-Generation Sequencing in Patients With Gastric Cancer. Ann Lab Med 2024; 44:164-173. [PMID: 37903652 PMCID: PMC10628753 DOI: 10.3343/alm.2023.0187] [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: 05/03/2023] [Revised: 06/27/2023] [Accepted: 09/12/2023] [Indexed: 11/01/2023] Open
Abstract
Background Molecular cancer profiling may lead to appropriate trials for molecularly targeted therapies. Cell-free DNA (cfDNA) is a promising diagnostic and/or prognostic biomarker in gastric cancer (GC). We characterized somatic genomic alterations in cfDNA of patients with GC. Methods Medical records and cfDNA data of 81 patients diagnosed as having GC were reviewed. Forty-nine and 32 patients were tested using the Oncomine Pan-Cancer Cell-Free Assay on the Ion Torrent platform and AlphaLiquid 100 kit on the Illumina platform, respectively. Results Tier I or II alterations were detected in 64.2% (52/81) of patients. Biomarkers for potential targeted therapy were detected in 55.6% of patients (45/81), and clinical trials are underway. ERBB2 amplification is actionable and was detected in 4.9% of patients (4/81). Among biomarkers showing potential for possible targeted therapy, TP53 mutation (38.3%, 35 variants in 31 patients, 31/81) and FGFR2 amplification (6.2%, 5/81) were detected the most. Conclusions Next-generation sequencing of cfDNA is a promising technique for the molecular profiling of GC. Evidence suggests that cfDNA analysis can provide accurate and reliable information on somatic genomic alterations in patients with GC, potentially replacing tissue biopsy as a diagnostic and prognostic tool. Through cfDNA analysis for molecular profiling, it may be possible to translate the molecular classification into therapeutic targets and predictive biomarkers, leading to personalized treatment options for patients with GC in the future.
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Affiliation(s)
- Boyeon Kim
- Division of Biotechnology, Invites BioCore Co. Ltd., Yongin, Korea
- Genome Service Development, Invites Genomics Co. Ltd., Jeju, Korea
| | - Yoonjung Kim
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Yong Cho
- Division of Medical Oncology, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
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Li C, Shao J, Li P, Feng J, Li J, Wang C. Circulating tumor DNA as liquid biopsy in lung cancer: Biological characteristics and clinical integration. Cancer Lett 2023; 577:216365. [PMID: 37634743 DOI: 10.1016/j.canlet.2023.216365] [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: 02/15/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023]
Abstract
Lung cancer maintains high morbidity and mortality rate globally despite significant advancements in diagnosis and treatment in the era of precision medicine. Pathological analysis of tumor tissue, the current gold standard for lung cancer diagnosis, is intrusive and intrinsically confined to evaluating the limited amount of tissues that could be physically extracted. However, tissue biopsy has several limitations, including the invasiveness of the procedure and difficulty in obtaining samples for patients at advanced stages., there Additionally,has been no major breakthrough in tumor biomarkers with high specificity and sensitivity, particularly for early-stage lung cancer. Liquid biopsy has been considered a feasible auxiliary tool for tearly dianosis, evaluating treatment responses and monitoring prognosis of lung cancer. Circulating tumor DNA (ctDNA), an ideal biomarker of liquid biopsy, has emerged as one of the most reliable tools for monitoring tumor processes at molecular levels. Herein, this review focuses on tumor heterogeneity to elucidate the superiority of liquid biopsy and retrospectively discussdeciphersolution. We systematically elaborate ctDNA biological characteristics, introduce methods for ctDNA detection, and discuss the current role of plasma ctDNA in lung cancer management. Finally, we summarize the drawbacks of ctDNA analysis and highlight its potential clinical application in lung cancer.
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Affiliation(s)
- Changshu Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jun Shao
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Peiyi Li
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiaming Feng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jingwei Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Chengdi Wang
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China.
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4
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Li J, Xiao Z, Wang D, Jia L, Nie S, Zeng X, Hu W. The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells. Mol Cancer 2023; 22:141. [PMID: 37649123 PMCID: PMC10466891 DOI: 10.1186/s12943-023-01844-5] [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: 05/02/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.
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Affiliation(s)
- Jiangping Li
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Zhiwen Xiao
- Department of Otolaryngology Head and Neck Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, People's Republic of China
| | - Donghui Wang
- Department of Radiation Oncology, The Third Affiliated Hospital Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
| | - Lei Jia
- International Health Medicine Innovation Center, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Shihong Nie
- Department of Radiation Oncology, West China Hospital, Sichuan University, Cancer Center, Chengdu, 610041, People's Republic of China
| | - Xingda Zeng
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wei Hu
- Division of Vascular Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China
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Webster J, Dang HX, Chauhan PS, Feng W, Shiang A, Harris PK, Pachynski RK, Chaudhuri AA, Maher CA. PACT: a pipeline for analysis of circulating tumor DNA. Bioinformatics 2023; 39:btad489. [PMID: 37549060 PMCID: PMC10415172 DOI: 10.1093/bioinformatics/btad489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/26/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023] Open
Abstract
MOTIVATION Detection of genomic alterations in circulating tumor DNA (ctDNA) is currently used for active clinical monitoring of cancer progression and treatment response. While methods for analysis of small mutations are more developed, strategies for detecting structural variants (SVs) in ctDNA are limited. Additionally, reproducibly calling small-scale mutations, copy number alterations, and SVs in ctDNA is challenging due to the lack to unified tools for these different classes of variants. RESULTS We developed a unified pipeline for the analysis of ctDNA [Pipeline for the Analysis of ctDNA (PACT)] that accurately detects SVs and consistently outperformed similar tools when applied to simulated, cell line, and clinical data. We provide PACT in the form of a Common Workflow Language pipeline which can be run by popular workflow management systems in high-performance computing environments. AVAILABILITY AND IMPLEMENTATION PACT is freely available at https://github.com/ChrisMaherLab/PACT.
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Affiliation(s)
- Jace Webster
- McDonnell Genome Institute, Washington University in St. Louis, MO 63108, United States
| | - Ha X Dang
- McDonnell Genome Institute, Washington University in St. Louis, MO 63108, United States
- Siteman Cancer Center, Washington University in St. Louis, MO 63110, United States
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Pradeep S Chauhan
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Wenjia Feng
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Alex Shiang
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63110, United States
| | | | - Russell K Pachynski
- Siteman Cancer Center, Washington University in St. Louis, MO 63110, United States
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Aadel A Chaudhuri
- Siteman Cancer Center, Washington University in St. Louis, MO 63110, United States
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63110, United States
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, United States
- Department of Biomedical Engineering, Washington University in St. Louis, MO 63130, United States
- Department of Computer Science and Engineering, Washington University in St. Louis, MO 63130, United States
| | - Christopher A Maher
- McDonnell Genome Institute, Washington University in St. Louis, MO 63108, United States
- Siteman Cancer Center, Washington University in St. Louis, MO 63110, United States
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States
- Department of Biomedical Engineering, Washington University in St. Louis, MO 63130, United States
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Lee D, Lee W, Kim HP, Kim M, Ahn HK, Bang D, Kim KH. Accurate Detection of Urothelial Bladder Cancer Using Targeted Deep Sequencing of Urine DNA. Cancers (Basel) 2023; 15:2868. [PMID: 37345205 DOI: 10.3390/cancers15102868] [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: 03/29/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
Patients with hematuria are commonly given an invasive cystoscopy test to detect bladder cancer (BC). To avoid the risks associated with cystoscopy, several urine-based methods for BC detection have been developed, the most prominent of which is the deep sequencing of urine DNA. However, the current methods for urine-based BC detection have significant levels of false-positive signals. In this study, we report on uAL100, a method to precisely detect BC tumor DNA in the urine without tumor samples. Using urine samples from 43 patients with BC and 21 healthy donors, uAL100 detected BC with 83.7% sensitivity and 100% specificity. The mutations identified in the urine DNA by uAL100 for BC detection were highly associated with BC tumorigenesis and progression. We suggest that uAL100 has improved accuracy compared to other urine-based methods for early BC detection and can reduce unnecessary cystoscopy tests for patients with hematuria.
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Affiliation(s)
- Dongin Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | | | | | - Myong Kim
- Department of Urology, Ewha Womans University Seoul Hospital, Seoul 07804, Republic of Korea
| | - Hyun Kyu Ahn
- Department of Urology, Ewha Womans University Seoul Hospital, Seoul 07804, Republic of Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Kwang Hyun Kim
- Department of Urology, Ewha Womans University Seoul Hospital, Seoul 07804, Republic of Korea
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Legason ID, Ogwang MD, Chamba C, Mkwizu E, El Mouden C, Mwinula H, Chirande L, Schuh A, Chiwanga F. A protocol to clinically evaluate liquid biopsies as a tool to speed up diagnosis of children and young adults with aggressive infection-related lymphoma in East Africa "(AI-REAL)". BMC Cancer 2022; 22:484. [PMID: 35501771 PMCID: PMC9059110 DOI: 10.1186/s12885-022-09553-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 04/17/2022] [Indexed: 11/16/2022] Open
Abstract
Background The capacity for invasive tissue biopsies followed by histopathology diagnosis in sub-Saharan Africa is severely limited. Consequently, many cancer patients are diagnosed late and outcomes are poor. Here, we propose to evaluate circulating tumour (ct) DNA analysis (“liquid biopsy”), a less invasive and faster approach to diagnose endemic EBV-driven lymphomas (EBVL) in East Africa. Methods We will evaluate the clinical utility of an already validated ctDNA test prospectively in a head-to-head comparison against histopathology. The primary endpoint is the time from presentation to the specialist centre to a final diagnosis of EBV- Lymphoma. Secondary endpoints include the sensitivity and specificity of liquid biopsy and health economic benefits over histopathology. One hundred forty-six patients will be recruited over 18 months. Patients will be eligible if they are 3–30 years of age and have provided written consent or assent as per IRB guidelines. Tissue and venous blood samples will be processed as per established protocols. Clinical data will be captured securely and in real-time into a REDCap database. The time from presentation to diagnosis will be documented. The sensitivity and specificity of the methods can be estimated within 5% error margin with 95% confidence level using 73 cases and 73 controls. Health-economic assessment will include micro-costing of ctDNA test and histopathology. All results will be reviewed in a multidisciplinary tumour board. Discussion The study evaluates the clinical utility of ctDNA in improving the speed of diagnostic pathways for EBVL in sub-Saharan Africa. Our results would provide proof-of-principle that ctDNA can be used as a diagnostic tool in areas without access to regular pathology, that transfer of the tool is feasible, and that it leads to an earlier and faster diagnosis. The potential clinical and economic impact of this proposal is thus significant. If successful, this study will provide appropriate, and cost-effective diagnostic tools that will promote earlier diagnosis of EBVL and potentially other cancers in countries with restricted healthcare resources. Trial registration Pan African Clinical Trials Registry: PACTR202204822312651, registered on 14th-April-2022.
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Affiliation(s)
- Ismail D Legason
- AI-REAL Study, St Mary's Hospital Lacor, Gulu& African Field Epidemiology Network, 180, Gulu-Uganda. African Field Epidemiology Network, 12874, Kampala, Uganda.
| | - Martin D Ogwang
- AI-REAL Study, St Mary's Hospital Lacor, Gulu& African Field Epidemiology Network, 180, Gulu-Uganda. African Field Epidemiology Network, 12874, Kampala, Uganda
| | - Clara Chamba
- AI-REAL Study, Muhimbili University of Health and Allied Sciences, Dar es Salam, Tanzania
| | - Elifuraha Mkwizu
- AI-REAL Study, Kilimanjaro Christian Medical Center, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Claire El Mouden
- AI-REAL Study, Muhimbili National Hospital, Dar es Salaam, Tanzania
| | - Hadija Mwinula
- Molecular Diagnostic Center, Department of Oncology, University of Oxford, Oxford, UK
| | - Lulu Chirande
- AI-REAL Study, Muhimbili University of Health and Allied Sciences, Dar es Salam, Tanzania
| | - Anna Schuh
- AI-REAL Study, Muhimbili National Hospital, Dar es Salaam, Tanzania
| | - Faraja Chiwanga
- AI-REAL Study, Muhimbili National Hospital, Dar es Salaam, Tanzania
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Barsan V, Xia Y, Klein D, Gonzalez-Pena V, Youssef S, Inaba Y, Mahmud O, Natarajan S, Agarwal V, Pang Y, Autry R, Pui CH, Inaba H, Evans W, Gawad C. Simultaneous monitoring of disease and microbe dynamics through plasma DNA sequencing in pediatric patients with acute lymphoblastic leukemia. SCIENCE ADVANCES 2022; 8:eabj1360. [PMID: 35442732 PMCID: PMC9020671 DOI: 10.1126/sciadv.abj1360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 01/19/2022] [Indexed: 05/09/2023]
Abstract
Treatment of acute lymphoblastic leukemia (ALL) necessitates continuous risk assessment of leukemic disease burden and infections that arise in the setting of immunosuppression. This study was performed to assess the feasibility of a hybrid capture next-generation sequencing panel to longitudinally measure molecular leukemic disease clearance and microbial species abundance in 20 pediatric patients with ALL throughout induction chemotherapy. This proof of concept helps establish a technical and conceptual framework that we anticipate will be expanded and applied to additional patients with leukemia, as well as extended to additional cancer types. Molecular monitoring can help accelerate the attainment of insights into the temporal biology of host-microbe-leukemia interactions, including how those changes correlate with and alter anticancer therapy efficacy. We also anticipate that fewer invasive bone marrow examinations will be required, as these methods improve with standardization and are validated for clinical use.
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Affiliation(s)
- Valentin Barsan
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Yuntao Xia
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - David Klein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Veronica Gonzalez-Pena
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sarah Youssef
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yuki Inaba
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ousman Mahmud
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sivaraman Natarajan
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Vibhu Agarwal
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Yakun Pang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robert Autry
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - William Evans
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Charles Gawad
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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Liu H, Yin H, Li G, Li J, Wang X. Aperture: alignment-free detection of structural variations and viral integrations in circulating tumor DNA. Brief Bioinform 2021; 22:6345221. [PMID: 34368852 DOI: 10.1093/bib/bbab290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/18/2021] [Accepted: 07/06/2021] [Indexed: 01/23/2023] Open
Abstract
The identification of structural variations (SVs) and viral integrations in circulating tumor DNA (ctDNA) is a key step in precision oncology that may assist clinicians in treatment selection and monitoring. However, due to the short fragment size of ctDNA, it is challenging to accurately detect low-frequency SVs or SVs involving complex junctions in ctDNA sequencing data. Here, we describe Aperture, a new fast SV caller that applies a unique strategy of $k$-mer-based searching, binary label-based breakpoint detection and candidate clustering to detect SVs and viral integrations with high sensitivity, especially when junctions span repetitive regions. Aperture also employs a barcode-based filter to ensure specificity. Compared with existing methods, Aperture exhibits superior sensitivity and specificity in simulated, reference and real data tests, especially at low dilutions. Additionally, Aperture is able to predict sites of viral integration and identify complex SVs involving novel insertions and repetitive sequences in real patient data. Aperture is freely available at https://github.com/liuhc8/Aperture.
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Affiliation(s)
- Hongchao Liu
- State Key Laboratory of Medical Molecular Biology, Center for Bioinformatics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences,School of Basic Medicine Peking Union Medical College
| | - Huihui Yin
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Guangyu Li
- State Key Laboratory of Medical Molecular Biology, Center for Bioinformatics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences,School of Basic Medicine Peking Union Medical College
| | - Junling Li
- National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xiaoyue Wang
- State Key Laboratory of Medical Molecular Biology, Center for Bioinformatics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences,School of Basic Medicine Peking Union Medical College
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Cell-Free Total Nucleic Acid-Based Genotyping of Aggressive Lymphoma: Comprehensive Analysis of Gene Fusions and Nucleotide Variants by Next-Generation Sequencing. Cancers (Basel) 2021; 13:cancers13123032. [PMID: 34204385 PMCID: PMC8235203 DOI: 10.3390/cancers13123032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary This study aimed to simultaneously demonstrate pathogenic chromosomal translocations and point mutations from both tissue biopsy and peripheral blood (PB) liquid biopsy (LB) samples of aggressive lymphoma patients. Matched samples were analyzed by next-generation sequencing for the same 125 genes. Eight different gene fusions, including the classical BCL2, BCL6, and MYC genes were detected in the corresponding samples with generally good agreement. Besides, mutations of 29 commonly affected genes, such as BCL2, MYD88, NOTCH2, EZH2, and CD79B could be identified in the matched samples at a rate of 16/24 (66.7%). Our prospective study demonstrates a non-invasive approach to identify frequent gene fusions and variants in aggressive lymphomas. In conclusion, PB LB sampling substantially supports the oncogenetic diagnostics of lymphomas, especially at anatomically critical sites (such as the central nervous system). Abstract Chromosomal translocations and pathogenic nucleotide variants both gained special clinical importance in lymphoma diagnostics. Non-invasive genotyping from peripheral blood (PB) circulating free nucleic acid has been effectively used to demonstrate cancer-related nucleotide variants, while gene fusions were not covered in the past. Our prospective study aimed to isolate and quantify PB cell-free total nucleic acid (cfTNA) from patients diagnosed with aggressive lymphoma and to compare with tumor-derived RNA (tdRNA) from the tissue sample of the same patients for both gene fusion and nucleotide variant testing. Matched samples from 24 patients were analyzed by next-generation sequencing following anchored multiplexed polymerase chain reaction (AMP) for 125 gene regions. Eight different gene fusions, including the classical BCL2, BCL6, and MYC genes, were detected in the corresponding tissue biopsy and cfTNA specimens with generally good agreement. Synchronous BCL2 and MYC translocations in double-hit high-grade B-cell lymphomas were obvious from cfTNA. Besides, mutations of 29 commonly affected genes, such as BCL2, MYD88, NOTCH2, EZH2, and CD79B, could be identified in matched cfTNA, and previously described pathogenic variants were detected in 16/24 cases (66.7%). In 3/24 cases (12.5%), only the PB sample was informative. Our prospective study demonstrates a non-invasive approach to identify frequent gene fusions and variants in aggressive lymphomas. cfTNA was found to be a high-value representative reflecting the complexity of the lymphoma aberration landscape.
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Nordgård O, Brendsdal Forthun R, Lapin M, Grønberg BH, Kalland KH, Kopperud RK, Thomsen LCV, Tjensvoll K, Gilje B, Gjertsen BT, Hovland R. Liquid Biopsies in Solid Cancers: Implementation in a Nordic Healthcare System. Cancers (Basel) 2021; 13:cancers13081861. [PMID: 33924696 PMCID: PMC8069797 DOI: 10.3390/cancers13081861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary We here review liquid biopsy methods and their use in the diagnostics and treatment of patients with solid cancers. More specifically, circulating tumor DNA, circulating tumor cells, and their current and future clinical applications are considered. Important factors for further integration of liquid biopsy methods in clinical practice are discussed, with a special focus on a Nordic Healthcare system. Abstract Liquid biopsies have emerged as a potential new diagnostic tool, providing detailed information relevant for characterization and treatment of solid cancers. We here present an overview of current evidence supporting the clinical relevance of liquid biopsy assessments. We also discuss the implementation of liquid biopsies in clinical studies and their current and future clinical role, with a special reference to the Nordic healthcare systems. Our considerations are restricted to the most established liquid biopsy specimens: circulating tumor DNA (ctDNA) and circulating tumor cells (CTC). Both ctDNA and CTCs have been used for prognostic stratification, treatment choices, and treatment monitoring in solid cancers. Several recent publications also support the role of ctDNA in early cancer detection. ctDNA seems to provide more robust clinically relevant information in general, whereas CTCs have the potential to answer more basic questions related to cancer biology and metastasis. Epidermal growth factor receptor-directed treatment of non-small-cell lung cancer represents a clinical setting where ctDNA already has entered the clinic. The role of liquid biopsies in treatment decisions, standardization of methods, diagnostic performance and the need for further research, as well as cost and regulatory issues were identified as factors that influence further integration in the clinic. In conclusion, substantial evidence supports the clinical utility of liquid biopsies in cancer diagnostics, but further research is still required for a more general application in clinical practice.
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Affiliation(s)
- Oddmund Nordgård
- Department of Hematology and Oncology, Stavanger University Hospital, 4011 Stavanger, Norway; (M.L.); (K.T.); (B.G.)
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, 4021 Stavanger, Norway
- Correspondence:
| | - Rakel Brendsdal Forthun
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway; (R.B.F.); (R.H.)
- Section of Cancer Genomics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Morten Lapin
- Department of Hematology and Oncology, Stavanger University Hospital, 4011 Stavanger, Norway; (M.L.); (K.T.); (B.G.)
| | - Bjørn Henning Grønberg
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, 7491 Trondheim, Norway;
- Department of Oncology, St. Olav’s Hospital, Trondheim University Hospital, 7030 Trondheim, Norway
| | - Karl Henning Kalland
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (K.H.K.); (R.K.K.); (L.C.V.T.); (B.T.G.)
- Department of Microbiology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Reidun Kristin Kopperud
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (K.H.K.); (R.K.K.); (L.C.V.T.); (B.T.G.)
| | - Liv Cecilie Vestrheim Thomsen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (K.H.K.); (R.K.K.); (L.C.V.T.); (B.T.G.)
| | - Kjersti Tjensvoll
- Department of Hematology and Oncology, Stavanger University Hospital, 4011 Stavanger, Norway; (M.L.); (K.T.); (B.G.)
| | - Bjørnar Gilje
- Department of Hematology and Oncology, Stavanger University Hospital, 4011 Stavanger, Norway; (M.L.); (K.T.); (B.G.)
| | - Bjørn Tore Gjertsen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (K.H.K.); (R.K.K.); (L.C.V.T.); (B.T.G.)
- Department of Internal Medicine, Hematology Section, Haukeland University Hospital, 5021 Bergen, Norway
| | - Randi Hovland
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway; (R.B.F.); (R.H.)
- Section of Cancer Genomics, Haukeland University Hospital, 5021 Bergen, Norway
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Hu N, Si Y, Yue J, Sun T, Wang X, Jia Z, Gao S, Li Q, Shao Y, Wang J, Luo Y, Ma F, Xu B, Yuan P. Anlotinib has good efficacy and low toxicity: a phase II study of anlotinib in pre-treated HER-2 negative metastatic breast cancer. Cancer Biol Med 2021; 18:j.issn.2095-3941.2020.0463. [PMID: 33710812 PMCID: PMC8330540 DOI: 10.20892/j.issn.2095-3941.2020.0463] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/15/2020] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE Anlotinib is a novel tyrosine kinase inhibitor blocking angiogenesis. This study was performed to assess the efficacy and safety of anlotinib in patients with metastatic breast cancer. METHODS Patients with HER2-negative breast cancer, who were pre-treated with anthracycline or taxanes in a neoadjuvant, adjuvant, or metastatic setting, and had treatment failure after at least one prior chemotherapy regimen in the metastatic setting were enrolled. Anlotinib was administered at 12 mg daily for 14 days in a 21-day cycle until disease progression or unacceptable toxicity occurred. Simultaneously, 5-10 mL of venous blood was collected to perform circulating tumor DNA (ctDNA) testing every 2 treatment cycles. The primary endpoint was the objective response rate (ORR). Secondary endpoints included the disease control rate (DCR), progression-free survival (PFS), overall survival, safety, and biomarkers. RESULTS Twenty-six eligible patients were enrolled, with a median age of 56 (30-75) years. The median follow-up time was 10.5 months. The ORR was 15.4%, the DCR was 80.8%, and the median PFS was 5.22 months (95% confidence interval 2.86-6.24). Fourteen (53.8%) patients survived for more than 10 months. The changes in the detectable ctDNA variant allele frequency were consistent with the tumor response. The most common treatment-related adverse events were hypertension (57.7%), thyroidstimulating hormone elevation (34.6%), and hand-foot syndrome (23.1%). CONCLUSIONS Anlotinib showed objective efficacy with tolerable toxicity in heavily pre-treated, metastatic HER2-negative breast cancer. The dynamic changes in the ctDNA variant allele fraction may be predictive of the tumor response.
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Affiliation(s)
- Nanlin Hu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yiran Si
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jian Yue
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Tingting Sun
- Nanjing Geneseeq Technology Inc., Nanjing 210032, China
| | - Xue Wang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhuqing Jia
- Cancer Hospital of Huanxing Chaoyang District Beijing, Beijing 100021, China
| | - Songlin Gao
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Qiao Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc., Nanjing 210032, China
| | - Jiayu Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yang Luo
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Peng Yuan
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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Ouyang J, Zhan X, Guo S, Cai S, Lei J, Zeng S, Yu L. Progress and trends on the analysis of nucleic acid and its modification. J Pharm Biomed Anal 2020; 191:113589. [DOI: 10.1016/j.jpba.2020.113589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/18/2020] [Accepted: 08/20/2020] [Indexed: 12/17/2022]
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Cell-free DNA in blood as a noninvasive insight into the sarcoma genome. Mol Aspects Med 2019; 72:100827. [PMID: 31703948 DOI: 10.1016/j.mam.2019.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/02/2019] [Accepted: 10/18/2019] [Indexed: 12/26/2022]
Abstract
Sarcomas are malignant tumors of mesenchymal origin that arise mainly from connective and supportive tissue. Sarcomas include a wide range of histological subtypes, showing a large diversity at the molecular level, from simple to highly complex karyotypes but with few recurrent somatic changes. Therapeutic decisions increasingly rely on the molecular characteristics of the individual tumor. Circulating cell-free DNA (ctDNA) is released into peripheral blood and can be used for the genomic analysis of sarcomas. However, the diversity and heterogeneity of somatic changes observed in sarcomas pose a challenge when choosing an adequate assay for the detection of ctDNA in body fluids. In this review, we provide an overview of different studies on ctDNA from blood in bone and soft tissue sarcomas, including gastrointestinal stromal tumors. We will specifically address the technological challenges that must be considered to achieve the sensitive detection of ctDNA and discuss the clinical applications of ctDNA in the management and treatment of sarcomas.
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