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Varela M, Villatoro S, Lorenzo D, Piulats JM, Caminal JM. Optimizing ctDNA: An Updated Review of a Promising Clinical Tool for the Management of Uveal Melanoma. Cancers (Basel) 2024; 16:3053. [PMID: 39272911 PMCID: PMC11394595 DOI: 10.3390/cancers16173053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 08/23/2024] [Accepted: 08/26/2024] [Indexed: 09/15/2024] Open
Abstract
Uveal melanoma (UM) is the most common primary malignant intraocular tumor in adults. Distant metastasis is common, affecting around 50% of patients. Prognostic accuracy relies on molecular characterization of tumor tissue. In these patients, however, conventional biopsy can be challenging due to the difficulty of obtaining sufficient tissue for the analysis due to the small tumor size and/or post-brachytherapy shrinkage. An alternative approach is liquid biopsy, a non-invasive technique that allows for real-time monitoring of tumor dynamics. Liquid biopsy plays an increasingly prominent role in precision medicine, providing valuable information on the molecular profile of the tumor and treatment response. Liquid biopsy can facilitate early detection and can be used to monitor progression and recurrence. ctDNA-based tests are particularly promising due to their ease of integration into clinical practice. In this review, we discuss the application of ctDNA in liquid biopsies for UM. More specifically, we explore the emerging technologies in this field and the advantages and disadvantages of using different bodily fluids for liquid biopsy. Finally, we discuss the current barriers to routine clinical use of this technique.
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Affiliation(s)
- Mar Varela
- Department of Pathology, Hospital Universitari de Bellvitge, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Laboratori Core d'Anàlisi Molecular, Hospital Universitari de Bellvitge-Institut Català d'Oncologia, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Sergi Villatoro
- Department of Pathology, Hospital Universitari de Bellvitge, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Laboratori Core d'Anàlisi Molecular, Hospital Universitari de Bellvitge-Institut Català d'Oncologia, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Daniel Lorenzo
- Ophthalmology Department, Hospital Universitari de Bellvitge, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Josep Maria Piulats
- Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- Medical Oncology Department, Institut Català d'Oncologia, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Josep Maria Caminal
- Ophthalmology Department, Hospital Universitari de Bellvitge, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
- Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
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2
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Lynce F, Mainor C, Donahue RN, Geng X, Jones G, Schlam I, Wang H, Toney NJ, Jochems C, Schlom J, Zeck J, Gallagher C, Nanda R, Graham D, Stringer-Reasor EM, Denduluri N, Collins J, Chitalia A, Tiwari S, Nunes R, Kaltman R, Khoury K, Gatti-Mays M, Tarantino P, Tolaney SM, Swain SM, Pohlmann P, Parsons HA, Isaacs C. Adjuvant nivolumab, capecitabine or the combination in patients with residual triple-negative breast cancer: the OXEL randomized phase II study. Nat Commun 2024; 15:2691. [PMID: 38538574 PMCID: PMC10973408 DOI: 10.1038/s41467-024-46961-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Chemotherapy and immune checkpoint inhibitors have a role in the post-neoadjuvant setting in patients with triple-negative breast cancer (TNBC). However, the effects of nivolumab, a checkpoint inhibitor, capecitabine, or the combination in changing peripheral immunoscore (PIS) remains unclear. This open-label randomized phase II OXEL study (NCT03487666) aimed to assess the immunologic effects of nivolumab, capecitabine, or the combination in terms of the change in PIS (primary endpoint). Secondary endpoints included the presence of ctDNA, toxicity, clinical outcomes at 2-years and association of ctDNA and PIS with clinical outcomes. Forty-five women with TNBC and residual invasive disease after standard neoadjuvant chemotherapy were randomized to nivolumab, capecitabine, or the combination. Here we show that a combination of nivolumab plus capecitabine leads to a greater increase in PIS from baseline to week 6 (91%) compared with nivolumab (47%) or capecitabine (53%) alone (log-rank p = 0.08), meeting the pre-specified primary endpoint. In addition, the presence of circulating tumor DNA (ctDNA) is associated with disease recurrence, with no new safety signals in the combination arm. Our results provide efficacy and safety data on this combination in TNBC and support further development of PIS and ctDNA analyses to identify patients at high risk of recurrence.
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Affiliation(s)
- Filipa Lynce
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Candace Mainor
- MedStar Georgetown University Hospital, Washington, DC, USA
| | - Renee N Donahue
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xue Geng
- Georgetown University, Washington, DC, USA
| | | | - Ilana Schlam
- MedStar Washington Hospital Center, Washington, DC, USA
- Tufts Medical Center, Boston, MA, USA
| | | | - Nicole J Toney
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Caroline Jochems
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey Schlom
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jay Zeck
- MedStar Georgetown University Hospital, Washington, DC, USA
| | | | | | - Deena Graham
- Hackensack University Medical Center, Hackensack, NJ, USA
| | | | | | - Julie Collins
- MedStar Georgetown University Hospital, Washington, DC, USA
- AstraZeneca, Arlington, VA, USA
| | - Ami Chitalia
- MedStar Washington Hospital Center, Washington, DC, USA
| | - Shruti Tiwari
- MedStar Washington Hospital Center, Washington, DC, USA
| | - Raquel Nunes
- Johns Hopkins Sidney Kimmel Cancer Center, Baltimore, MD, USA
- AstraZeneca, Arlington, VA, USA
| | | | - Katia Khoury
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Paolo Tarantino
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sara M Tolaney
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Paula Pohlmann
- MedStar Georgetown University Hospital, Washington, DC, USA
| | - Heather A Parsons
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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3
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Galant N, Nicoś M, Kuźnar-Kamińska B, Krawczyk P. Variant Allele Frequency Analysis of Circulating Tumor DNA as a Promising Tool in Assessing the Effectiveness of Treatment in Non-Small Cell Lung Carcinoma Patients. Cancers (Basel) 2024; 16:782. [PMID: 38398173 PMCID: PMC10887123 DOI: 10.3390/cancers16040782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Despite the different possible paths of treatment, lung cancer remains one of the leading causes of death in oncological patients. New tools guiding the therapeutic process are under scientific investigation, and one of the promising indicators of the effectiveness of therapy in patients with NSCLC is variant allele frequency (VAF) analysis. VAF is a metric characterized as the measurement of the specific variant allele proportion within a genomic locus, and it can be determined using methods based on NGS or PCR. It can be assessed using not only tissue samples but also ctDNA (circulating tumor DNA) isolated from liquid biopsy. The non-invasive characteristic of liquid biopsy enables a more frequent collection of material and increases the potential of VAF analysis in monitoring therapy. Several studies have been performed on patients with NSCLC to evaluate the possibility of VAF usage. The research carried out so far demonstrates that the evaluation of VAF dynamics may be useful in monitoring tumor progression, remission, and recurrence during or after treatment. Moreover, the use of VAF analysis appears to be beneficial in making treatment decisions. However, several issues require better understanding and standardization before VAF testing can be implemented in clinical practice. In this review, we discuss the difficulties in the application of ctDNA VAF analysis in clinical routine, discussing the diagnostic and methodological challenges in VAF measurement in liquid biopsy. We highlight the possible applications of VAF-based measurements that are under consideration in clinical trials in the monitoring of personalized treatments for patients with NSCLC.
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Affiliation(s)
- Natalia Galant
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
| | - Marcin Nicoś
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
| | - Barbara Kuźnar-Kamińska
- Department of Pulmonology, Allergology and Respiratory Oncology, Poznan University of Medical Sciences, 61-710 Poznan, Poland;
| | - Paweł Krawczyk
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
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Friedlaender A, Perol M, Banna GL, Parikh K, Addeo A. Oncogenic alterations in advanced NSCLC: a molecular super-highway. Biomark Res 2024; 12:24. [PMID: 38347643 PMCID: PMC10863183 DOI: 10.1186/s40364-024-00566-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/17/2024] [Indexed: 02/15/2024] Open
Abstract
Lung cancer ranks among the most common cancers world-wide and is the first cancer-related cause of death. The classification of lung cancer has evolved tremendously over the past two decades. Today, non-small cell lung cancer (NSCLC), particularly lung adenocarcinoma, comprises a multitude of molecular oncogenic subsets that change both the prognosis and management of disease.Since the first targeted oncogenic alteration identified in 2004, with the epidermal growth factor receptor (EGFR), there has been unprecedented progress in identifying and targeting new molecular alterations. Almost two decades of experience have allowed scientists to elucidate the biological function of oncogenic drivers and understand and often overcome the molecular basis of acquired resistance mechanisms. Today, targetable molecular alterations are identified in approximately 60% of lung adenocarcinoma patients in Western populations and 80% among Asian populations. Oncogenic drivers are largely enriched among non-smokers, east Asians, and younger patients, though each alteration has its own patient phenotype.The current landscape of druggable molecular targets includes EGFR, anaplastic lymphoma kinase (ALK), v-raf murine sarcoma viral oncogene homolog B (BRAF), ROS proto-oncogene 1 (ROS1), Kirstin rat sarcoma virus (KRAS), human epidermal receptor 2 (HER2), c-MET proto-oncogene (MET), neurotrophic receptor tyrosine kinase (NTRK), rearranged during transfection (RET), neuregulin 1 (NRG1). In addition to these known targets, others including Phosphoinositide 3-kinases (PI3K) and fibroblast growth factor receptor (FGFR) have garnered significant attention and are the subject of numerous ongoing trials.In this era of personalized, precision medicine, it is of paramount importance to identify known or potential oncogenic drivers in each patient. The development of targeted therapy is mirrored by diagnostic progress. Next generation sequencing offers high-throughput, speed and breadth to identify molecular alterations in entire genomes or targeted regions of DNA or RNA. It is the basis for the identification of the majority of current druggable alterations and offers a unique window into novel alterations, and de novo and acquired resistance mechanisms.In this review, we discuss the diagnostic approach in advanced NSCLC, focusing on current oncogenic driver alterations, through their pathophysiology, management, and future perspectives. We also explore the shortcomings and hurdles encountered in this rapidly evolving field.
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Affiliation(s)
- Alex Friedlaender
- Clinique Générale Beaulieu, Geneva, Switzerland
- Oncology Department, University Hospital Geneva, Rue Gentil Perret 4. 1205, Geneva, Switzerland
| | - Maurice Perol
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - Giuseppe Luigi Banna
- Portsmouth Hospitals University NHS Trust, Portsmouth, UK
- Faculty of Science and Health, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | | | - Alfredo Addeo
- Oncology Department, University Hospital Geneva, Rue Gentil Perret 4. 1205, Geneva, Switzerland.
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5
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Lynce F, Mainor C, Donahue RN, Geng X, Jones G, Schlam I, Wang H, Toney NJ, Jochems C, Schlom J, Zeck J, Gallagher C, Nanda R, Graham D, Stringer-Reasor EM, Denduluri N, Collins J, Chitalia A, Tiwari S, Nunes R, Kaltman R, Khoury K, Gatti-Mays M, Tarantino P, Tolaney SM, Swain SM, Pohlmann P, Parsons HA, Isaacs C. Adjuvant nivolumab, capecitabine or the combination in patients with residual triple-negative breast cancer: the OXEL randomized phase II study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.04.23297559. [PMID: 38105958 PMCID: PMC10723519 DOI: 10.1101/2023.12.04.23297559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Chemotherapy and immune checkpoint inhibitors have a role in the post-neoadjuvant setting in patients with triple-negative breast cancer (TNBC). However, the effects of nivolumab, a checkpoint inhibitor, capecitabine, or the combination in changing peripheral immunoscore (PIS) remains unclear. This open-label randomized phase II OXEL study (NCT03487666) aimed to assess the immunologic effects of nivolumab, capecitabine, or the combination in terms of the change in PIS (primary endpoint). Secondary endpoints include the presence of ctDNA, toxicity, clinical outcomes at 2-years and association of ctDNA and PIS with clinical outcomes. Forty-five women with TNBC and residual invasive disease after standard neoadjuvant chemotherapy were randomized to nivolumab, capecitabine, or the combination. Here we show that a combination of nivolumab plus capecitabine leads to a greater increase in PIS from baseline to week 6 (91%) compared with nivolumab (47%) or capecitabine (53%) alone (log-rank p = 0.08), meeting the pre-specified primary endpoint. In addition, the presence of circulating tumor DNA (ctDNA) was associated with disease recurrence, with no new safety signals in the combination arm. Our results provide efficacy and safety data on this combination in TNBC and support further development of PIS and ctDNA analyses to identify patients at high risk of recurrence.
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Affiliation(s)
- Filipa Lynce
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Candace Mainor
- MedStar Georgetown University Hospital, Washington, DC, USA
| | - Renee N. Donahue
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xue Geng
- Georgetown University, Washington, DC
| | - Greg Jones
- NeoGenomics, Research Triangle Park, NC, USA
| | - Ilana Schlam
- MedStar Washington Hospital Center, Washington, DC, USA
- Tufts Medical Center, Boston, MA, USA
| | | | - Nicole J. Toney
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Caroline Jochems
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey Schlom
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jay Zeck
- MedStar Georgetown University Hospital, Washington, DC, USA
| | | | | | - Deena Graham
- Hackensack University Medical Center, Hackensack, NJ, USA
| | | | | | - Julie Collins
- MedStar Georgetown University Hospital, Washington, DC, USA
| | - Ami Chitalia
- MedStar Washington Hospital Center, Washington, DC, USA
| | - Shruti Tiwari
- MedStar Washington Hospital Center, Washington, DC, USA
| | - Raquel Nunes
- Johns Hopkins Sidney Kimmel Cancer Center, Baltimore, MD, USA
| | | | - Katia Khoury
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Paolo Tarantino
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sara M. Tolaney
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Paula Pohlmann
- MedStar Georgetown University Hospital, Washington, DC, USA
| | - Heather A. Parsons
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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6
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Blaquier JB, Ortiz-Cuaran S, Ricciuti B, Mezquita L, Cardona AF, Recondo G. Tackling Osimertinib Resistance in EGFR-Mutant Non-Small Cell Lung Cancer. Clin Cancer Res 2023; 29:3579-3591. [PMID: 37093192 DOI: 10.1158/1078-0432.ccr-22-1912] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/11/2023] [Accepted: 04/12/2023] [Indexed: 04/25/2023]
Abstract
The current landscape of targeted therapies directed against oncogenic driver alterations in non-small cell lung cancer (NSCLC) is expanding. Patients with EGFR-mutant NSCLC can derive significant benefit from EGFR tyrosine kinase inhibitor (TKI) therapy, including the third-generation EGFR TKI osimertinib. However, invariably, all patients will experience disease progression with this therapy mainly due to the adaptation of cancer cells through primary or secondary molecular mechanisms of resistance. The comprehension and access to tissue and cell-free DNA next-generation sequencing have fueled the development of innovative therapeutic strategies to prevent and overcome resistance to osimertinib in the clinical setting. Herein, we review the biological and clinical implications of molecular mechanisms of osimertinib resistance and the ongoing development of therapeutic strategies to overcome or prevent resistance.
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Affiliation(s)
- Juan Bautista Blaquier
- Thoracic Oncology Unit, Medical Oncology, Center for Medical Education and Clinical Research (CEMIC), Buenos Aires, Argentina
| | - Sandra Ortiz-Cuaran
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, France
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Laura Mezquita
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Andrés Felipe Cardona
- Foundation for Clinical and Applied Cancer Research-FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
- Direction of Research and Education, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Cancer-CTIC, Bogotá, Colombia
| | - Gonzalo Recondo
- Thoracic Oncology Unit, Medical Oncology, Center for Medical Education and Clinical Research (CEMIC), Buenos Aires, Argentina
- Medical Oncology Department, Bradford Hill Clinical Research Center, Santiago, Chile
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Tébar-Martínez R, Martín-Arana J, Gimeno-Valiente F, Tarazona N, Rentero-Garrido P, Cervantes A. Strategies for improving detection of circulating tumor DNA using next generation sequencing. Cancer Treat Rev 2023; 119:102595. [PMID: 37390697 DOI: 10.1016/j.ctrv.2023.102595] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/02/2023]
Abstract
Cancer has become a global health issue and liquid biopsy has emerged as a non-invasive tool for various applications. In cancer, circulating tumor DNA (ctDNA) can be detected from cell-free DNA (cfDNA) obtained from plasma and has potential for early diagnosis, treatment, resistance, minimal residual disease detection, and tumoral heterogeneity identification. However, the low frequency of ctDNA requires techniques for accurate analysis. Multitarget assay such as Next Generation Sequencing (NGS) need improvement to achieve limits of detection that can identify the low frequency variants present in the cfDNA. In this review, we provide a general overview of the use of cfDNA and ctDNA in cancer, and discuss techniques developed to optimize NGS as a tool for ctDNA detection. We also summarize the results obtained using NGS strategies in both investigational and clinical contexts.
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Affiliation(s)
- Roberto Tébar-Martínez
- Department of Medical Oncology, INCLIVA Health Research Institute, University of Valencia, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain; Precision Medicine Unit, INCLIVA Health Research Institute, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain.
| | - Jorge Martín-Arana
- Department of Medical Oncology, INCLIVA Health Research Institute, University of Valencia, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain; Bioinformatics Unit, INCLIVA Health Research Institute, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain.
| | - Francisco Gimeno-Valiente
- Cancer Evolution and Genome Instability Laboratory, University College of London Cancer Institute, 72 Huntley St, WC1E 6DD London, United Kingdom.
| | - Noelia Tarazona
- Department of Medical Oncology, INCLIVA Health Research Institute, University of Valencia, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain; Health Institute Carlos III, CIBERONC, C/ Sinesio Delgado, 4, 28029 Madrid, Spain.
| | - Pilar Rentero-Garrido
- Precision Medicine Unit, INCLIVA Health Research Institute, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain.
| | - Andrés Cervantes
- Department of Medical Oncology, INCLIVA Health Research Institute, University of Valencia, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain; Health Institute Carlos III, CIBERONC, C/ Sinesio Delgado, 4, 28029 Madrid, Spain.
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Dao J, Conway PJ, Subramani B, Meyyappan D, Russell S, Mahadevan D. Using cfDNA and ctDNA as Oncologic Markers: A Path to Clinical Validation. Int J Mol Sci 2023; 24:13219. [PMID: 37686024 PMCID: PMC10487653 DOI: 10.3390/ijms241713219] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
The detection of circulating tumor DNA (ctDNA) in liquid biopsy samples as an oncological marker is being used in clinical trials at every step of clinical management. As ctDNA-based liquid biopsy kits are developed and used in clinics, companies work towards increased convenience, accuracy, and cost over solid biopsies and other oncological markers. The technology used to differentiate ctDNA and cell-free DNA (cfDNA) continues to improve with new tests and methodologies being able to detect down to mutant allele frequencies of 0.001% or 1/100,000 copies. Recognizing this development in technology, the FDA has recently given pre-market approval and breakthrough device designations to multiple companies. The purpose of this review is to look at the utility of measuring total cfDNA, techniques used to differentiate ctDNA from cfDNA, and the utility of different ctDNA-based liquid biopsy kits using relevant articles from PubMed, clinicaltrials.gov, FDA approvals, and company newsletters. Measuring total cfDNA could be a cost-effective, viable prognostic marker, but various factors do not favor it as a monitoring tool during chemotherapy. While there may be a place in the clinic for measuring total cfDNA in the future, the lack of standardization means that it is difficult to move forward with large-scale clinical validation studies currently. While the detection of ctDNA has promising standardized liquid biopsy kits from various companies with large clinical trials ongoing, their applications in screening and minimal residual disease can suffer from lower sensitivity. However, researchers are working towards solutions to these issues with innovations in technology, multi-omics, and sampling. With great promise, further research is needed before liquid biopsies can be recommended for everyday clinical management.
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Affiliation(s)
- Jonathan Dao
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Patrick J. Conway
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Baskaran Subramani
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Devi Meyyappan
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
| | - Sammy Russell
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Daruka Mahadevan
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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9
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Mahmood K, Jampani P, Clarke JM, Wolf S, Wang X, Wahidi MM, Giovacchini CX, Dorry M, Shofer SL, Shier J, Jones G, Antonia SJ, Nixon AB. High Yield of Pleural Cell-Free DNA for Diagnosis of Oncogenic Mutations in Lung Adenocarcinoma. Chest 2023; 164:252-261. [PMID: 36693563 PMCID: PMC10331627 DOI: 10.1016/j.chest.2023.01.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 01/08/2023] [Accepted: 01/13/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Pleural cytology is currently used to assess targetable mutations in patients with advanced lung adenocarcinoma. However, it is fraught with low diagnostic yield. RESEARCH QUESTION Can pleural cell-free DNA (cfDNA) be used to assess targetable mutations in lung adenocarcinoma patients with malignant pleural effusions (MPE)? STUDY DESIGN AND METHODS Patients with lung adenocarcinoma MPE were recruited prospectively between January 2017 and September 2021. Oncogenic mutations were assessed by treating providers using pleural fluid cytology or lung cancer biopsies. Pleural and plasma cfDNA were used to assess the mutations using next-generation sequencing (NGS). RESULTS Fifty-four pleural fluid samples were collected from 42 patients. The diagnostic yield to detect oncogenic mutations for pleural cfDNA, pleural cytology, biopsy, and plasma cfDNA was 49/54 (90.7%), 16/33 (48.5%), 22/25 (88%), and 24/32 (75%), respectively, P < .001. The agreement of mutations in positive samples between pleural cfDNA and pleural cytology was 100%, whereas the agreement of pleural cfDNA with biopsies was 89.4%. The median concentration (interquartile range) of pleural cfDNA was higher than plasma: 28,444 (4,957-67,051) vs 2,966.5 (2,167-5,025) copies of amplifiable DNA per mL, P < .01. Median of 5 mL (interquartile range, 4.5-5) of pleural fluid supernatant was adequate for cfDNA testing. INTERPRETATION The diagnostic yield of pleural cfDNA NGS for oncogenic mutations in lung adenocarcinoma patients is comparable to tumor biopsies and higher than pleural cytology and plasma cfDNA. The pleural cfDNA can be longitudinally collected, can be readily incorporated in clinical workflow, and may decrease the need for additional biopsies.
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Affiliation(s)
- Kamran Mahmood
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Duke University, Durham, NC.
| | - Parvathi Jampani
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, NC
| | - Jeffrey M Clarke
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, NC
| | - Steven Wolf
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC
| | - Xiaofei Wang
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC
| | - Momen M Wahidi
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Duke University, Durham, NC
| | - Coral X Giovacchini
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Duke University, Durham, NC
| | - Michael Dorry
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Duke University, Durham, NC
| | - Scott L Shofer
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Duke University, Durham, NC
| | - Jessica Shier
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Duke University, Durham, NC
| | | | - Scott J Antonia
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, NC
| | - Andrew B Nixon
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, NC
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10
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Santonja A, Cooper WN, Eldridge MD, Edwards PAW, Morris JA, Edwards AR, Zhao H, Heider K, Couturier D, Vijayaraghavan A, Mennea P, Ditter E, Smith CG, Boursnell C, Manzano García R, Rueda OM, Beddowes E, Biggs H, Sammut S, Rosenfeld N, Caldas C, Abraham JE, Gale D. Comparison of tumor-informed and tumor-naïve sequencing assays for ctDNA detection in breast cancer. EMBO Mol Med 2023; 15:e16505. [PMID: 37161793 PMCID: PMC10245040 DOI: 10.15252/emmm.202216505] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 05/11/2023] Open
Abstract
Analysis of circulating tumor DNA (ctDNA) to monitor cancer dynamics and detect minimal residual disease has been an area of increasing interest. Multiple methods have been proposed but few studies have compared the performance of different approaches. Here, we compare detection of ctDNA in serial plasma samples from patients with breast cancer using different tumor-informed and tumor-naïve assays designed to detect structural variants (SVs), single nucleotide variants (SNVs), and/or somatic copy-number aberrations, by multiplex PCR, hybrid capture, and different depths of whole-genome sequencing. Our results demonstrate that the ctDNA dynamics and allele fractions (AFs) were highly concordant when analyzing the same patient samples using different assays. Tumor-informed assays showed the highest sensitivity for detection of ctDNA at low concentrations. Hybrid capture sequencing targeting between 1,347 and 7,491 tumor-identified mutations at high depth was the most sensitive assay, detecting ctDNA down to an AF of 0.00024% (2.4 parts per million, ppm). Multiplex PCR targeting 21-47 tumor-identified SVs per patient detected ctDNA down to 0.00047% AF (4.7 ppm) and has potential as a clinical assay.
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Affiliation(s)
- Angela Santonja
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Wendy N Cooper
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Matthew D Eldridge
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Paul A W Edwards
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
- Department of PathologyUniversity of CambridgeCambridgeUK
| | - James A Morris
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Abigail R Edwards
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
| | - Hui Zhao
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Katrin Heider
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Dominique‐Laurent Couturier
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
- MRC Biostatistics UnitUniversity of CambridgeCambridgeUK
| | - Aadhitthya Vijayaraghavan
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Paulius Mennea
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Emma‐Jane Ditter
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Christopher G Smith
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Chris Boursnell
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Raquel Manzano García
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Oscar M Rueda
- MRC Biostatistics UnitUniversity of CambridgeCambridgeUK
| | - Emma Beddowes
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Heather Biggs
- Department of OncologyUniversity of CambridgeCambridgeUK
- Precision Breast Cancer Institute, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's HospitalCambridgeUK
| | - Stephen‐John Sammut
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
- Department of OncologyUniversity of CambridgeCambridgeUK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
- Department of OncologyUniversity of CambridgeCambridgeUK
- Precision Breast Cancer Institute, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's HospitalCambridgeUK
| | - Jean E Abraham
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
- Department of OncologyUniversity of CambridgeCambridgeUK
- Precision Breast Cancer Institute, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's HospitalCambridgeUK
| | - Davina Gale
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
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11
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Filis P, Kyrochristos I, Korakaki E, Baltagiannis EG, Thanos D, Roukos DH. Longitudinal ctDNA profiling in precision oncology and immunο-oncology. Drug Discov Today 2023; 28:103540. [PMID: 36822363 DOI: 10.1016/j.drudis.2023.103540] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/13/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023]
Abstract
Serial analysis of circulating tumor DNA (ctDNA) over the disease course is emerging as a prognostic, predictive and patient-monitoring biomarker. In the metastatic setting, several multigene ctDNA assays have been approved or recommended by regulatory organizations for personalized targeted therapy, especially for lung cancer. By contrast, in nonmetastatic disease, detection of ctDNA resulting from minimal residual disease (MRD) following multimodal treatment with curative intent presents major technical challenges. Several studies using tumor genotyping-informed serial ctDNA profiling have provided promising findings on the sensitivity and specificity of ctDNA in predicting the risk of recurrence. We discuss progress, limitations and future perspectives relating to the use of ctDNA as a biomarker to guide targeted therapy in metastatic disease, as well as the use of ctDNA MRD detection to guide adjuvant treatment in the nonmetastatic setting.
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Affiliation(s)
- Panagiotis Filis
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Medical Oncology, Medical School, University of Ioannina, 45110 Ioannina, Greece
| | - Ioannis Kyrochristos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, D-80539 Munich, Germany
| | - Efterpi Korakaki
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Physiology, Medical School, University of Ioannina, Ioannina 45110, Greece
| | - Evangelos G Baltagiannis
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Surgery, University Hospital of Ioannina, Ioannina 45500, Greece
| | - Dimitris Thanos
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Dimitrios H Roukos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Systems Biology, Biomedical Research Foundation of the Academy of Athens (BRFAA), 11527 Athens, Greece.
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12
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Armakolas A, Kotsari M, Koskinas J. Liquid Biopsies, Novel Approaches and Future Directions. Cancers (Basel) 2023; 15:1579. [PMID: 36900369 PMCID: PMC10000663 DOI: 10.3390/cancers15051579] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/22/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Cancer is among the leading causes of death worldwide. Early diagnosis and prognosis are vital to improve patients' outcomes. The gold standard of tumor characterization leading to tumor diagnosis and prognosis is tissue biopsy. Amongst the constraints of tissue biopsy collection is the sampling frequency and the incomplete representation of the entire tumor bulk. Liquid biopsy approaches, including the analysis of circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), circulating miRNAs, and tumor-derived extracellular vesicles (EVs), as well as certain protein signatures that are released in the circulation from primary tumors and their metastatic sites, present a promising and more potent candidate for patient diagnosis and follow up monitoring. The minimally invasive nature of liquid biopsies, allowing frequent collection, can be used in the monitoring of therapy response in real time, allowing the development of novel approaches in the therapeutic management of cancer patients. In this review we will describe recent advances in the field of liquid biopsy markers focusing on their advantages and disadvantages.
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Affiliation(s)
- Athanasios Armakolas
- Physiology Laboratory, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- B' Department of Medicine, Hippokration Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Maria Kotsari
- Physiology Laboratory, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - John Koskinas
- B' Department of Medicine, Hippokration Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece
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13
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van Dorp J, Pipinikas C, Suelmann BBM, Mehra N, van Dijk N, Marsico G, van Montfoort ML, Hackinger S, Braaf LM, Amarante T, van Steenis C, McLay K, Daletzakis A, van den Broek D, van de Kamp MW, Hendricksen K, de Feijter JM, Boellaard TN, Meijer RP, van der Heijden AG, Rosenfeld N, van Rhijn BWG, Jones G, van der Heijden MS. High- or low-dose preoperative ipilimumab plus nivolumab in stage III urothelial cancer: the phase 1B NABUCCO trial. Nat Med 2023; 29:588-592. [PMID: 36732628 DOI: 10.1038/s41591-022-02199-y] [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: 07/05/2022] [Accepted: 12/22/2022] [Indexed: 02/04/2023]
Abstract
Cohort 1 of the phase 1B NABUCCO trial showed high pathological complete response (pCR) rates with preoperative ipilimumab plus nivolumab in stage III urothelial cancer (UC). In cohort 2, the aim was dose adjustment to optimize responses. Additionally, we report secondary endpoints, including efficacy and tolerability, in cohort 2 and the association of presurgical absence of circulating tumor DNA (ctDNA) in urine and plasma with clinical outcome in both cohorts. Thirty patients received two cycles of either ipilimumab 3 mg kg-1 plus nivolumab 1 mg kg-1 (cohort 2A) or ipilimumab 1 mg kg-1 plus nivolumab 3 mg kg-1 (cohort 2B), both followed by nivolumab 3 mg kg-1. We observed a pCR in six (43%) patients in cohort 2A and a pCR in one (7%) patient in cohort 2B. Absence of urinary ctDNA correlated with pCR in the bladder (ypT0Nx) but not with progression-free survival (PFS). Absence of plasma ctDNA correlated with pCR (odds ratio: 45.0; 95% confidence interval (CI): 4.9-416.5) and PFS (hazard ratio: 10.4; 95% CI: 2.9-37.5). Our data suggest that high-dose ipilimumab plus nivolumab is required in stage III UC and that absence of ctDNA in plasma can predict PFS. ClinicalTrials.gov registration: NCT03387761 .
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Affiliation(s)
- Jeroen van Dorp
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Dutch Uro-Oncology Study Group, Bilthoven, The Netherlands
| | | | - Britt B M Suelmann
- Dutch Uro-Oncology Study Group, Bilthoven, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Niven Mehra
- Dutch Uro-Oncology Study Group, Bilthoven, The Netherlands
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nick van Dijk
- Dutch Uro-Oncology Study Group, Bilthoven, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Maurits L van Montfoort
- Dutch Uro-Oncology Study Group, Bilthoven, The Netherlands
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Linde M Braaf
- Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - Antonios Daletzakis
- Department of Biometrics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maaike W van de Kamp
- Dutch Uro-Oncology Study Group, Bilthoven, The Netherlands
- Department of Surgical Oncology (Urology), Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kees Hendricksen
- Dutch Uro-Oncology Study Group, Bilthoven, The Netherlands
- Department of Surgical Oncology (Urology), Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jeantine M de Feijter
- Dutch Uro-Oncology Study Group, Bilthoven, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Thierry N Boellaard
- Dutch Uro-Oncology Study Group, Bilthoven, The Netherlands
- Department of Radiology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Richard P Meijer
- Dutch Uro-Oncology Study Group, Bilthoven, The Netherlands
- Department of Urological Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Antoine G van der Heijden
- Dutch Uro-Oncology Study Group, Bilthoven, The Netherlands
- Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nitzan Rosenfeld
- Inivata Ltd., Babraham Research Park, Cambridge, UK
- Cancer Research UK Cambridge Institute, Cambridge, UK
- Cancer Research UK Major Centre Cambridge, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Bas W G van Rhijn
- Dutch Uro-Oncology Study Group, Bilthoven, The Netherlands
- Department of Surgical Oncology (Urology), Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Urology, Caritas St. Josef Medical Centre, University of Regensburg, Regensburg, Germany
| | - Greg Jones
- Inivata Ltd., Babraham Research Park, Cambridge, UK.
| | - Michiel S van der Heijden
- Dutch Uro-Oncology Study Group, Bilthoven, The Netherlands.
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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14
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Kemper M, Krekeler C, Menck K, Lenz G, Evers G, Schulze AB, Bleckmann A. Liquid Biopsies in Lung Cancer. Cancers (Basel) 2023; 15:1430. [PMID: 36900221 PMCID: PMC10000706 DOI: 10.3390/cancers15051430] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023] Open
Abstract
As lung cancer has the highest cancer-specific mortality rates worldwide, there is an urgent need for new therapeutic and diagnostic approaches to detect early-stage tumors and to monitor their response to the therapy. In addition to the well-established tissue biopsy analysis, liquid-biopsy-based assays may evolve as an important diagnostic tool. The analysis of circulating tumor DNA (ctDNA) is the most established method, followed by other methods such as the analysis of circulating tumor cells (CTCs), microRNAs (miRNAs), and extracellular vesicles (EVs). Both PCR- and NGS-based assays are used for the mutational assessment of lung cancer, including the most frequent driver mutations. However, ctDNA analysis might also play a role in monitoring the efficacy of immunotherapy and its recent accomplishments in the landscape of state-of-the-art lung cancer therapy. Despite the promising aspects of liquid-biopsy-based assays, there are some limitations regarding their sensitivity (risk of false-negative results) and specificity (interpretation of false-positive results). Hence, further studies are needed to evaluate the usefulness of liquid biopsies for lung cancer. Liquid-biopsy-based assays might be integrated into the diagnostic guidelines for lung cancer as a tool to complement conventional tissue sampling.
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Affiliation(s)
- Marcel Kemper
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Carolin Krekeler
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Kerstin Menck
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Georg Lenz
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Georg Evers
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Arik Bernard Schulze
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
| | - Annalen Bleckmann
- Department of Medicine A for Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany
- West German Cancer Center, University Hospital Muenster, 48149 Muenster, Germany
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15
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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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16
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Lipsyc-Sharf M, de Bruin EC, Santos K, McEwen R, Stetson D, Patel A, Kirkner GJ, Hughes ME, Tolaney SM, Partridge AH, Krop IE, Knape C, Feger U, Marsico G, Howarth K, Winer EP, Lin NU, Parsons HA. Circulating Tumor DNA and Late Recurrence in High-Risk Hormone Receptor-Positive, Human Epidermal Growth Factor Receptor 2-Negative Breast Cancer. J Clin Oncol 2022; 40:2408-2419. [PMID: 35658506 PMCID: PMC9467679 DOI: 10.1200/jco.22.00908] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PURPOSE To examine the prevalence and dynamics of circulating tumor DNA (ctDNA) and its association with metastatic recurrence in patients with high-risk early-stage hormone receptor-positive breast cancer (HR+ BC) more than 5 years from diagnosis. METHODS We enrolled 103 patients with high-risk stage II-III HR+ BC diagnosed more than 5 years prior without clinical evidence of recurrence. We performed whole-exome sequencing (WES) on primary tumor tissue to identify somatic mutations tracked via a personalized, tumor-informed ctDNA test to detect minimal residual disease (MRD). We collected plasma at the time of consent and at routine visits every 6-12 months. Patients were followed for clinical recurrence. RESULTS In total, 85 of 103 patients had sufficient tumor tissue; of them, 83 of 85 (97.6%) patients had successful whole-exome sequencing. Personalized ctDNA assays were designed targeting a median of 36 variants to test 219 plasma samples. The median time from diagnosis to first sample was 8.4 years. The median follow-up was 10.4 years from diagnosis and 2.0 years from first sample. The median number of plasma samples per patient was two. Eight patients (10%) had positive MRD testing at any time point. Six patients (7.2%) developed distant metastatic recurrence, all of whom were MRD-positive before overt clinical recurrence, with median ctDNA lead time of 12.4 months. MRD was not identified in one patient (1.2%) with local recurrence. Two of eight MRD-positive patients had not had clinical recurrence at last follow-up. CONCLUSION In this prospective study, in patients with high-risk HR+ BC in the late adjuvant setting, ctDNA was identified a median of 1 year before all cases of distant metastasis. Future studies will determine if ctDNA-guided intervention in patients with HR+ BC can alter clinical outcomes.
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Affiliation(s)
- Marla Lipsyc-Sharf
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Harvard Medical School, Boston, MA
| | | | | | | | | | - Ashka Patel
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Sara M Tolaney
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Harvard Medical School, Boston, MA
| | - Ann H Partridge
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Harvard Medical School, Boston, MA
| | - Ian E Krop
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Harvard Medical School, Boston, MA.,Present affiliation: Yale University, New Haven, CT
| | | | - Ute Feger
- Inivata Inc, Research Triangle Park, NC
| | | | | | - Eric P Winer
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Harvard Medical School, Boston, MA.,Present affiliation: Yale University, New Haven, CT
| | - Nancy U Lin
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Harvard Medical School, Boston, MA
| | - Heather A Parsons
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.,Harvard Medical School, Boston, MA
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17
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Gale D, Heider K, Ruiz-Valdepenas A, Hackinger S, Perry M, Marsico G, Rundell V, Wulff J, Sharma G, Knock H, Castedo J, Cooper W, Zhao H, Smith CG, Garg S, Anand S, Howarth K, Gilligan D, Harden SV, Rassl DM, Rintoul RC, Rosenfeld N. Residual ctDNA after treatment predicts early relapse in patients with early-stage non-small cell lung cancer. Ann Oncol 2022; 33:500-510. [PMID: 35306155 PMCID: PMC9067454 DOI: 10.1016/j.annonc.2022.02.007] [Citation(s) in RCA: 136] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/02/2022] [Accepted: 02/14/2022] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Identification of residual disease in patients with localized non-small cell lung cancer (NSCLC) following treatment with curative intent holds promise to identify patients at risk of relapse. New methods can detect circulating tumour DNA (ctDNA) in plasma to fractional concentrations as low as a few parts per million, and clinical evidence is required to inform their use. PATIENTS AND METHODS We analyzed 363 serial plasma samples from 88 patients with early-stage NSCLC (48.9%/28.4%/22.7% at stage I/II/III), predominantly adenocarcinomas (62.5%), treated with curative intent by surgery (n = 61), surgery and adjuvant chemotherapy/radiotherapy (n = 8), or chemoradiotherapy (n = 19). Tumour exome sequencing identified somatic mutations and plasma was analyzed using patient-specific RaDaR™ assays with up to 48 amplicons targeting tumour-specific variants unique to each patient. RESULTS ctDNA was detected before treatment in 24%, 77% and 87% of patients with stage I, II and III disease, respectively, and in 26% of all longitudinal samples. The median tumour fraction detected was 0.042%, with 63% of samples <0.1% and 36% of samples <0.01%. ctDNA detection had clinical specificity >98.5% and preceded clinical detection of recurrence of the primary tumour by a median of 212.5 days. ctDNA was detected after treatment in 18/28 (64.3%) of patients who had clinical recurrence of their primary tumour. Detection within the landmark timepoint 2 weeks to 4 months after treatment end occurred in 17% of patients, and was associated with shorter recurrence-free survival [hazard ratio (HR): 14.8, P <0.00001] and overall survival (HR: 5.48, P <0.0003). ctDNA was detected 1-3 days after surgery in 25% of patients yet was not associated with disease recurrence. Detection before treatment was associated with shorter overall survival and recurrence-free survival (HR: 2.97 and 3.14, P values 0.01 and 0.003, respectively). CONCLUSIONS ctDNA detection after initial treatment of patients with early-stage NSCLC using sensitive patient-specific assays has potential to identify patients who may benefit from further therapeutic intervention.
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Affiliation(s)
- D Gale
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - K Heider
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - A Ruiz-Valdepenas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - S Hackinger
- Inivata Ltd, The Glenn Berge Building, Babraham Research Park, Babraham, Cambridge, UK
| | - M Perry
- Inivata Ltd, The Glenn Berge Building, Babraham Research Park, Babraham, Cambridge, UK
| | - G Marsico
- Inivata Ltd, The Glenn Berge Building, Babraham Research Park, Babraham, Cambridge, UK
| | - V Rundell
- Cambridge Clinical Trials Unit - Cancer Theme, Cambridge, UK
| | - J Wulff
- Cambridge Clinical Trials Unit - Cancer Theme, Cambridge, UK
| | - G Sharma
- Inivata Ltd, The Glenn Berge Building, Babraham Research Park, Babraham, Cambridge, UK
| | - H Knock
- Cambridge Clinical Trials Unit - Cancer Theme, Cambridge, UK
| | - J Castedo
- Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK; Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - W Cooper
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - H Zhao
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - C G Smith
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - S Garg
- Cancer Molecular Diagnostics Laboratory, Clifford Allbutt Building, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - S Anand
- Cancer Molecular Diagnostics Laboratory, Clifford Allbutt Building, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - K Howarth
- Inivata Ltd, The Glenn Berge Building, Babraham Research Park, Babraham, Cambridge, UK
| | - D Gilligan
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK; Addenbrooke's Hospital, Cambridge, UK
| | | | - D M Rassl
- Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK; Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - R C Rintoul
- Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK; Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK.
| | - N Rosenfeld
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK; Inivata Ltd, The Glenn Berge Building, Babraham Research Park, Babraham, Cambridge, UK.
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18
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Knapp B, Mezquita L, Devarakonda S, Aldea M, Waqar SN, Pepin K, Ward JP, Botticella A, Howarth K, Knape C, Morris C, Govindan R, Besse B, Morgensztern D. Exploring the Feasibility of Utilizing Limited Gene Panel Circulating Tumor DNA Clearance as a Biomarker in Patients With Locally Advanced Non-Small Cell Lung Cancer. Front Oncol 2022; 12:856132. [PMID: 35419282 PMCID: PMC9000093 DOI: 10.3389/fonc.2022.856132] [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: 01/16/2022] [Accepted: 02/28/2022] [Indexed: 12/25/2022] Open
Abstract
Introduction Circulating tumor DNA (ctDNA) testing may identify patients at high risk for recurrence following chemoradiation (CRT) for locally advanced non-small cell lung cancer (LA-NSCLC). We evaluated the feasibility of ctDNA testing on a readily available commercial fixed-gene panel to predict outcomes in patients with LA-NSCLC. Methods Plasma of 43 patients was collected at CRT initiation (pre-CRT), completion (post-CRT1), quarterly follow up for 12 months (post-CRT2, 3, 4, 5 respectively) after CRT, and at disease progression. ctDNA analysis was performed using InVisionFirst®-Lung to detect mutations in 36 cancer-related genes. ctDNA clearance was defined as absence of pre-CRT variants at post-CRT1. Patients without detectable pre-CRT variants or no post-CRT1 samples were excluded. Results Twenty eight of 43 patients (65%) had detectable variants pre-CRT. Nineteen of 43 patients (44%) had detectable pre-CRT variants and post-CRT1 samples and were included in analysis. Median age at diagnosis was 65 years (43-82), and most patients had stage IIIB disease (10/19, 53%). Two patients died from non-cancer related causes before post-CRT2 and were excluded from further analysis. All three patients who did not clear ctDNA had tumor relapse with a median time to relapse of 74 days (30-238), while 50% (7/14) of those who cleared ctDNA have remained disease free. Progression free survival was longer in patients who cleared ctDNA compared to those who did not (median 567 vs 74 d, p = 0.01). Conclusions Although it is feasible to use ctDNA testing on a limited gene panel to identify patients with LA-NSCLC who are at high risk for disease recurrence following CRT, further studies will be necessary to optimize these assays before they can be used to inform clinical care in patients with lung cancer.
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Affiliation(s)
- Brendan Knapp
- Department of Medicine, Division of General Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Laura Mezquita
- Medical Oncology Department, Gustave Roussy Cancer Campus, Villejuif, France
| | - Siddhartha Devarakonda
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, United States
| | - Mihaela Aldea
- Medical Oncology Department, Gustave Roussy Cancer Campus, Villejuif, France
| | - Saiama N Waqar
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, United States
| | - Kym Pepin
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, United States
| | - Jeffrey P Ward
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, United States
| | - Angela Botticella
- Radiation Oncology Department, Gustave Roussy Cancer Campus, Villejuif, France
| | - Karen Howarth
- Department of Clinical Genomics, Inivata Limited, Cambridge, United Kingdom
| | - Charlene Knape
- Inivata Inc, Research Triangle Park, Durham, NC, United States
| | - Clive Morris
- Department of Clinical Genomics, Inivata Limited, Cambridge, United Kingdom
| | - Ramaswamy Govindan
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, United States
| | - Benjamin Besse
- Medical Oncology Department, Gustave Roussy Cancer Campus, Villejuif, France
| | - Daniel Morgensztern
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, United States
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19
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Cai J, Jiang H, Li S, Yan X, Wang M, Li N, Zhu C, Dong H, Wang D, Xu Y, Xie H, Wu S, Lou J, Zhao J, Li Q. The Landscape of Actionable Genomic Alterations by Next-Generation Sequencing in Tumor Tissue Versus Circulating Tumor DNA in Chinese Patients With Non-Small Cell Lung Cancer. Front Oncol 2022; 11:751106. [PMID: 35273907 PMCID: PMC8902245 DOI: 10.3389/fonc.2021.751106] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 12/30/2021] [Indexed: 12/24/2022] Open
Abstract
Background Circulating tumor DNA (ctDNA) sequence analysis shows great potential in the management of non-small cell lung cancer (NSCLC) and the prediction of drug sensitivity or resistance in many cancers. Here, we drew and compared the somatic mutational profile using ctDNA and tumor tissue sequence analysis in lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC), and assess its potential clinical value. Methods In this study, 221 tumor tissues and 174 plasma samples from NSCLC patients were analyzed by hybridization capture-based next-generation sequencing (NGS) panel including 95 cancer-associated genes. Tumor response assessments were applied to 137 patients with advanced-stage (III and IV) NSCLC who first received targeted agents. Results Twenty significantly mutated genes were identified such as TP53, EGFR, RB1, KRAS, PIK3CA, CD3EAP, CTNNB1, ERBB2, APC, BRAF, TERT, FBXW7, and HRAS. Among them, TP53 was the most frequently mutated gene and had a higher mutation probability in male (p = 0.00124) and smoking (p < 0.0001) patients. A total of 48.35% (191/395) of NSCLC patients possessed at least one actionable alteration according to the OncoKB database. Although the sensitivity of genomic profiling from ctDNA was lower than that from tumor tissue DNA, the mutational landscape of target genes from ctDNA is similar to that from tumor tissue DNA, which led to 61.22% (30/49) of mutational concordance in NSCLC. Additionally, the mutational concordance between tissue DNA and ctDNA in LUAD differs from that in LUSC, which is 63.83% versus 46.67%, indicating that NSCLC subtypes influence the specificity of mutation detection in plasma-derived ctDNA. Lastly, patients with EGFR and TP53 co-alterations showed similar responses to Gefitinib and Icotinib, and the co-occurring TP53 mutation was most likely to be a poor prognostic factor for patients receiving Gefitinib, indicating that the distributions and types of TP53 mutations may contribute to the efficacy and prognosis of molecular targeted therapy. Conclusions As a promising alternative for tumor genomic profiling, ctDNA analysis is more credible in LUAD than in LUSC. Genomic subtyping has strong potential in prognostication and therapeutic decision-making for NSCLC patients, which indicated the necessity for the utility of target NGS in guiding clinical management.
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Affiliation(s)
- Jun Cai
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, China
| | - Huihui Jiang
- Zhangjiang Center for Translational Medicine, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
| | - Shuqing Li
- Department of General Surgery, Yucheng Hospital of Traditional Chinese Medicine, Dezhou City, China
| | - Xiaoxia Yan
- Zhangjiang Center for Translational Medicine, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
| | - Meng Wang
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, China
| | - Na Li
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, China
| | - Cuimin Zhu
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, China
| | - Hui Dong
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, China
| | - Dongjuan Wang
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, China
| | - Yue Xu
- Zhangjiang Center for Translational Medicine, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
| | - Hui Xie
- Zhangjiang Center for Translational Medicine, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
| | - Shouxin Wu
- Zhangjiang Center for Translational Medicine, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
| | - Jingwei Lou
- Zhangjiang Center for Translational Medicine, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
| | - Jiangman Zhao
- Zhangjiang Center for Translational Medicine, Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
| | - Qingshan Li
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, China
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20
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Flach S, Howarth K, Hackinger S, Pipinikas C, Ellis P, McLay K, Marsico G, Forshew T, Walz C, Reichel CA, Gires O, Canis M, Baumeister P. Liquid BIOpsy for MiNimal RESidual DiSease Detection in Head and Neck Squamous Cell Carcinoma (LIONESS)-a personalised circulating tumour DNA analysis in head and neck squamous cell carcinoma. Br J Cancer 2022; 126:1186-1195. [PMID: 35132238 PMCID: PMC9023460 DOI: 10.1038/s41416-022-01716-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 12/11/2021] [Accepted: 01/21/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) remain a substantial burden to global health. Cell-free circulating tumour DNA (ctDNA) is an emerging biomarker but has not been studied sufficiently in HNSCC. METHODS We conducted a single-centre prospective cohort study to investigate ctDNA in patients with p16-negative HNSCC who received curative-intent primary surgical treatment. Whole-exome sequencing was performed on formalin-fixed paraffin-embedded (FFPE) tumour tissue. We utilised RaDaRTM, a highly sensitive personalised assay using deep sequencing for tumour-specific variants, to analyse serial pre- and post-operative plasma samples for evidence of minimal residual disease and recurrence. RESULTS In 17 patients analysed, personalised panels were designed to detect 34 to 52 somatic variants. Data show ctDNA detection in baseline samples taken prior to surgery in 17 of 17 patients. In post-surgery samples, ctDNA could be detected at levels as low as 0.0006% variant allele frequency. In all cases with clinical recurrence to date, ctDNA was detected prior to progression, with lead times ranging from 108 to 253 days. CONCLUSIONS This study illustrates the potential of ctDNA as a biomarker for detecting minimal residual disease and recurrence in HNSCC and demonstrates the feasibility of personalised ctDNA assays for the detection of disease prior to clinical recurrence.
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Affiliation(s)
- Susanne Flach
- Department of Otorhinolaryngology, Head and Neck Surgery, Hospital of the Ludwig-Maximilians-University (LMU) of Munich, Marchioninistrasse 15, 81377, Munich, Germany.
| | | | | | | | - Pete Ellis
- Inivata Ltd, Babraham Research Park, Cambridge, UK
| | | | | | - Tim Forshew
- Inivata Ltd, Babraham Research Park, Cambridge, UK
| | - Christoph Walz
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Christoph A Reichel
- Department of Otorhinolaryngology, Head and Neck Surgery, Hospital of the Ludwig-Maximilians-University (LMU) of Munich, Marchioninistrasse 15, 81377, Munich, Germany
| | - Olivier Gires
- Department of Otorhinolaryngology, Head and Neck Surgery, Hospital of the Ludwig-Maximilians-University (LMU) of Munich, Marchioninistrasse 15, 81377, Munich, Germany.,Clinical Cooperation Group "Personalised Radiotherapy in Head and Neck Cancer", German Research Centre for Environmental Health GmbH, Neuherberg, Munich, Germany
| | - Martin Canis
- Department of Otorhinolaryngology, Head and Neck Surgery, Hospital of the Ludwig-Maximilians-University (LMU) of Munich, Marchioninistrasse 15, 81377, Munich, Germany.,Clinical Cooperation Group "Personalised Radiotherapy in Head and Neck Cancer", German Research Centre for Environmental Health GmbH, Neuherberg, Munich, Germany
| | - Philipp Baumeister
- Department of Otorhinolaryngology, Head and Neck Surgery, Hospital of the Ludwig-Maximilians-University (LMU) of Munich, Marchioninistrasse 15, 81377, Munich, Germany.,Clinical Cooperation Group "Personalised Radiotherapy in Head and Neck Cancer", German Research Centre for Environmental Health GmbH, Neuherberg, Munich, Germany
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21
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Reddy T, Esmail A, Chang JC, Ghobrial RM, Abdelrahim M. Utility of Cell-Free DNA Detection in Transplant Oncology. Cancers (Basel) 2022; 14:cancers14030743. [PMID: 35159010 PMCID: PMC8833373 DOI: 10.3390/cancers14030743] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/20/2022] [Accepted: 01/29/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Transplant oncology is an emerging field in cancer treatment that applies transplant medicine, surgery, and oncology to improve cancer patient survival and quality of life. This review aims to provide a comprehensive overview of the history and emergence of cfDNA technology, its applications to specifically monitor tumor burden at pre-and post-liver transplant stages, and evaluate transplant rejection. The use of ctDNA to evaluate transplant rejection has been extensively studied in non-hepatocellular carcinoma (HCC) diseases. Emerging studies have also investigated the use of ctDNA detection in evaluating HCC tumor burden pre-and post-surgery as well as transplant rejection. However, extensive studies still need to be conducted to evaluate the role of ctDNA detection in the medical management of transplant oncology patients. Abstract Transplant oncology is an emerging field in cancer treatment that applies transplant medicine, surgery, and oncology to improve cancer patient survival and quality of life. A critical concept that must be addressed to ensure the successful application of transplant oncology to patient care is efficient monitoring of tumor burden pre-and post-transplant and transplant rejection. Cell-free DNA (cfDNA) detection has emerged as a vital tool in revolutionizing the management of cancer patients who undergo organ transplantation. The advances in cfDNA technology have provided options to perform a pre-transplant evaluation of minimal residual disease (MRD) and post-transplant evaluation of cancer recurrence and transplant rejection. This review aims to provide a comprehensive overview of the history and emergence of cfDNA technology, its applications to specifically monitor tumor burden at pre-and post-transplant stages, and evaluate transplant rejection.
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Affiliation(s)
- Tejaswini Reddy
- Section of GI Oncology, Department of Medical Oncology, Houston Methodist Cancer Center, Houston, TX 77030, USA; (T.R.); (A.E.)
- Texas A&M Health Science Center, College of Medicine, Bryan, TX 77807, USA
- Houston Methodist Research Institute, Houston, TX 77030, USA;
| | - Abdullah Esmail
- Section of GI Oncology, Department of Medical Oncology, Houston Methodist Cancer Center, Houston, TX 77030, USA; (T.R.); (A.E.)
- Houston Methodist Research Institute, Houston, TX 77030, USA;
| | - Jenny C. Chang
- Houston Methodist Research Institute, Houston, TX 77030, USA;
- Section of Breast, Department of Medical Oncology, Houston Methodist Cancer Center, Houston, TX 77030, USA
| | - Rafik Mark Ghobrial
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA;
- Sherrie and Alan Conover Center for Liver Disease and Transplantation, JC Walter Jr Center for Transplantation, Houston, TX 77030, USA
| | - Maen Abdelrahim
- Section of GI Oncology, Department of Medical Oncology, Houston Methodist Cancer Center, Houston, TX 77030, USA; (T.R.); (A.E.)
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA;
- Cockrell Center of Advanced Therapeutics Phase I program, Houston Methodist Research Institute, Houston, TX 77030, USA
- Correspondence:
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22
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Fernandes MGO, Cruz-Martins N, Machado JC, Costa JL, Hespanhol V. The value of cell-free circulating tumour DNA profiling in advanced non-small cell lung cancer (NSCLC) management. Cancer Cell Int 2021; 21:675. [PMID: 34915883 PMCID: PMC8680243 DOI: 10.1186/s12935-021-02382-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/30/2021] [Indexed: 01/04/2023] Open
Abstract
AbstractLiquid biopsy (LB) has boosted a remarkable change in the management of cancer patients by contributing to tumour genomic profiling. Plasma circulating cell-free tumour DNA (ctDNA) is the most widely searched tumour-related element for clinical application. Specifically, for patients with lung cancer, LB has revealed valuable to detect the diversity of targetable genomic alterations and to detect and monitor the emergence of resistance mechanisms. Furthermore, its non-invasive nature helps to overcome the difficulty in obtaining tissue samples, offering a comprehensive view about tumour diversity. However, the use of the LB to support diagnostic and therapeutic decisions still needs further clarification. In this sense, this review aims to provide a critical view of the clinical importance of plasma ctDNA analysis, the most widely applied LB, and its limitations while anticipating concepts that will intersect the present and future of LB in non-small cell lung cancer patients.
Graphical Abstract
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23
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Liquid Biopsy for EGFR Mutation Analysis in Advanced Non-Small-Cell Lung Cancer Patients: Thoughts Drawn from a Real-Life Experience. Biomedicines 2021; 9:biomedicines9101299. [PMID: 34680416 PMCID: PMC8533402 DOI: 10.3390/biomedicines9101299] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/16/2021] [Accepted: 09/19/2021] [Indexed: 01/15/2023] Open
Abstract
Background: Liquid biopsy analysis for EGFR detection in cell-free DNA (cfDNA) from NSCLC patients has become routine. The aim of this study was to explore its applicability in clinical practice. Methods: We collected data of EGFR-mutated NSCLC patients with liquid biopsy analysis. Data included test timing, concomitant tissue re-biopsy, therapy change, histology, stage, smoking habits, gender and age. All analyses were performed via a real-time PCR method to analyze EGFR mutations at exons 18, 19, 20 and 21. Variant allele frequency was performed for patients with available sequential EGFR mutation analysis in cfDNA. Overall survival was analyzed through the Kaplan–Meier method. We designed flow charts to show the real-life application of liquid biopsy. Results: We found that liquid biopsy is used in treatment-naïve patients as an alternative to EGFR detection in tumor tissue, and in patients with positive or negative EGFR from tumor biopsy. The majority of liquid biopsy analyses were performed in NSCLC patients who were disease progressive during TKI therapy. The presence of EGFR mutation in cfDNA was associated with a worse prognosis. In two patients, VAF of EGFR mutations in cfDNA was concordant with tumor volume changes. Conclusion: These findings suggest that liquid biopsy for EGFR detection can continue to be useful.
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24
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Deveson IW, Gong B, Lai K, LoCoco JS, Richmond TA, Schageman J, Zhang Z, Novoradovskaya N, Willey JC, Jones W, Kusko R, Chen G, Madala BS, Blackburn J, Stevanovski I, Bhandari A, Close D, Conroy J, Hubank M, Marella N, Mieczkowski PA, Qiu F, Sebra R, Stetson D, Sun L, Szankasi P, Tan H, Tang LY, Arib H, Best H, Burgher B, Bushel PR, Casey F, Cawley S, Chang CJ, Choi J, Dinis J, Duncan D, Eterovic AK, Feng L, Ghosal A, Giorda K, Glenn S, Happe S, Haseley N, Horvath K, Hung LY, Jarosz M, Kushwaha G, Li D, Li QZ, Li Z, Liu LC, Liu Z, Ma C, Mason CE, Megherbi DB, Morrison T, Pabón-Peña C, Pirooznia M, Proszek PZ, Raymond A, Rindler P, Ringler R, Scherer A, Shaknovich R, Shi T, Smith M, Song P, Strahl M, Thodima VJ, Tom N, Verma S, Wang J, Wu L, Xiao W, Xu C, Yang M, Zhang G, Zhang S, Zhang Y, Shi L, Tong W, Johann DJ, Mercer TR, Xu J. Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology. Nat Biotechnol 2021; 39:1115-1128. [PMID: 33846644 PMCID: PMC8434938 DOI: 10.1038/s41587-021-00857-z] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/15/2021] [Indexed: 02/08/2023]
Abstract
Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation of the analytical performance of five industry-leading ctDNA assays. We evaluated each stage of the ctDNA sequencing workflow with simulations, synthetic DNA spike-in experiments and proficiency testing on standardized, cell-line-derived reference samples. Above 0.5% variant allele frequency, ctDNA mutations were detected with high sensitivity, precision and reproducibility by all five assays, whereas, below this limit, detection became unreliable and varied widely between assays, especially when input material was limited. Missed mutations (false negatives) were more common than erroneous candidates (false positives), indicating that the reliable sampling of rare ctDNA fragments is the key challenge for ctDNA assays. This comprehensive evaluation of the analytical performance of ctDNA assays serves to inform best practice guidelines and provides a resource for precision oncology.
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Affiliation(s)
- Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Binsheng Gong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Kevin Lai
- Bioinformatics, Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | - Todd A Richmond
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
| | | | - Zhihong Zhang
- Research and Development, Burning Rock Biotech, Shanghai, China
| | | | - James C Willey
- Departments of Medicine, Pathology, and Cancer Biology, College of Medicine and Life Sciences, University of Toledo Health Sciences Campus, Toledo, OH, USA
| | | | | | - Guangchun Chen
- Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bindu Swapna Madala
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - James Blackburn
- Cancer Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Igor Stevanovski
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | | | - Devin Close
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
| | | | - Michael Hubank
- NIHR Biomedical Research Centre, Royal Marsden Hospital, Sutton, Surrey, UK
| | | | | | - Fujun Qiu
- Research and Development, Burning Rock Biotech, Shanghai, China
| | - Robert Sebra
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Lihyun Sun
- Elim Biopharmaceuticals, Inc., Hayward, CA, USA
| | - Philippe Szankasi
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
| | - Haowen Tan
- Primbio Genes Biotechnology, East Lake High-tech Development Zone, Wuhan, Hubei, China
| | - Lin-Ya Tang
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA
| | - Hanane Arib
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hunter Best
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
- Departments of Pathology and Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Pierre R Bushel
- National Institute of Environmental Health Sciences, Research Triangle Park, Morrisville, NC, USA
| | - Fergal Casey
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
| | - Simon Cawley
- Clinical Sequencing Division, Thermo Fisher Scientific, South San Francisco, CA, USA
| | - Chia-Jung Chang
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Jonathan Choi
- Roche Sequencing Solutions, Inc., Pleasanton, CA, USA
| | - Jorge Dinis
- Roche Sequencing Solutions, Inc., Pleasanton, CA, USA
| | | | - Agda Karina Eterovic
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA
| | - Liang Feng
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
| | | | - Kristina Giorda
- Marketing, Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | | | | | | | - Li-Yuan Hung
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mirna Jarosz
- NGS Products and Services, Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Garima Kushwaha
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
| | - Dan Li
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Quan-Zhen Li
- Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhiguang Li
- Intramural Research Program, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Liang-Chun Liu
- Clinical Diagnostic Division, Thermo Fisher Scientific, Fremont, CA, USA
| | - Zhichao Liu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Charles Ma
- Cancer Genetics, Inc., Rutherford, NJ, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Dalila B Megherbi
- CMINDS Research Center, Department of Electrical and Computer Engineering, College of Engineering, University of Massachusetts Lowell, Lowell, MA, USA
| | | | | | - Mehdi Pirooznia
- Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paula Z Proszek
- NIHR Biomedical Research Centre, Royal Marsden Hospital, Sutton, Surrey, UK
| | | | - Paul Rindler
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
| | | | - Andreas Scherer
- Institute for Molecular Medicine Finland (FIMM), Nordic EMBL Partnership for Molecular Medicine, HiLIFE Unit, Biomedicum Helsinki 2U (D302b), University of Helsinki, Helsinki, Finland
- EATRIS ERIC- European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
| | | | - Tieliu Shi
- Center for Bioinformatics and Computational Biology and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Melissa Smith
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ping Song
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA
| | - Maya Strahl
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Nikola Tom
- EATRIS ERIC- European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Jiashi Wang
- Research and Development, Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Leihong Wu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Wenzhong Xiao
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Chang Xu
- Research and Development, QIAGEN Sciences, Inc., Frederick, MD, USA
| | - Mary Yang
- Department of Information Science, University of Arkansas at Little Rock, Little Rock, AR, USA
| | | | - Sa Zhang
- Clinical Laboratory, Burning Rock Biotech, Guangzhou, China
| | - Yilin Zhang
- Elim Biopharmaceuticals, Inc., Hayward, CA, USA
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
- Fudan-Gospel Joint Research Center for Precision Medicine, Fudan University, Shanghai, China
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Donald J Johann
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - Timothy R Mercer
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Queensland, QLD, Australia.
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
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Di Capua D, Bracken-Clarke D, Ronan K, Baird AM, Finn S. The Liquid Biopsy for Lung Cancer: State of the Art, Limitations and Future Developments. Cancers (Basel) 2021; 13:cancers13163923. [PMID: 34439082 PMCID: PMC8391249 DOI: 10.3390/cancers13163923] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary During the development and progression of lung tumors, processes such as necrosis and vascular invasion shed tumor cells or cellular components into various fluid compartments. Liquid biopsies consist of obtaining a bodily fluid, typically peripheral blood, in order to isolate and investigate these shed tumor constituents. Circulating tumor cells (CTCs) are one such constituent, which can be isolated from blood and can act as a diagnostic aid and provide valuable prognostic information. Liquid-based biopsies may also have a potential future role in lung cancer screening. Circulating tumor DNA (ctDNA) is found in small quantities in blood and, with the recent development of sensitive molecular and sequencing technologies, can be used to directly detect actionable genetic alterations or monitor for resistance mutations and guide clinical management. While potential benefits of liquid biopsies are promising, they are not without limitations. In this review, we summarize the current state and limitations of CTCs and ctDNA and possible future directions. Abstract Lung cancer is a leading cause of cancer-related deaths, contributing to 18.4% of cancer deaths globally. Treatment of non-small cell lung carcinoma has seen rapid progression with targeted therapies tailored to specific genetic drivers. However, identifying genetic alterations can be difficult due to lack of tissue, inaccessible tumors and the risk of complications for the patient with serial tissue sampling. The liquid biopsy provides a minimally invasive method which can obtain circulating biomarkers shed from the tumor and could be a safer alternative to tissue biopsy. While tissue biopsy remains the gold standard, liquid biopsies could be very beneficial where serial sampling is required, such as monitoring disease progression or development of resistance mutations to current targeted therapies. Liquid biopsies also have a potential role in identifying patients at risk of relapse post treatment and as a component of future lung cancer screening protocols. Rapid developments have led to multiple platforms for isolating circulating tumor cells (CTCs) and detecting circulating tumor DNA (ctDNA); however, standardization is lacking, especially in lung carcinoma. Additionally, clonal hematopoiesis of uncertain clinical significance must be taken into consideration in genetic sequencing, as it introduces the potential for false positives. Various biomarkers have been investigated in liquid biopsies; however, in this review, we will concentrate on the current use of ctDNA and CTCs, focusing on the clinical relevance, current and possible future applications and limitations of each.
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Affiliation(s)
- Daniel Di Capua
- Department of Histopathology, St. James’s Hospital, D08NHY1 Dublin, Ireland;
| | - Dara Bracken-Clarke
- Department of Medical Oncology, St. James’ Hospital, D08NHY1 Dublin, Ireland;
| | - Karine Ronan
- Faculty of Medicine, University College Dublin, D04V1W8 Dublin, Ireland;
| | - Anne-Marie Baird
- School of Medicine, Trinity Translational Medicine Institute, Trinity College, D02PN40 Dublin, Ireland;
| | - Stephen Finn
- Department of Histopathology, St. James’s Hospital, D08NHY1 Dublin, Ireland;
- Correspondence:
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26
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Foley JF, Elgart B, Alex Merrick B, Phadke DP, Cook ME, Malphurs JA, Solomon GG, Shah RR, Fessler MB, Miller FW, Gerrish KE. Whole genome sequencing of low input circulating cell-free DNA obtained from normal human subjects. Physiol Rep 2021; 9:e14993. [PMID: 34350716 PMCID: PMC8339531 DOI: 10.14814/phy2.14993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 11/29/2022] Open
Abstract
Cell-free DNA circulates in plasma at low levels as a normal by-product of cellular apoptosis. Multiple clinical pathologies, as well as environmental stressors can lead to increased circulating cell-free DNA (ccfDNA) levels. Plasma DNA studies frequently employ targeted amplicon deep sequencing platforms due to limited concentrations (ng/ml) of ccfDNA in the blood. Here, we report whole genome sequencing (WGS) and read distribution across chromosomes of ccfDNA extracted from two human plasma samples from normal, healthy subjects, representative of limited clinical samples at <1 ml. Amplification was sufficiently robust with ~90% of the reference genome (GRCh38.p2) exhibiting 10X coverage. Chromosome read coverage was uniform and directly proportional to the number of reads for each chromosome across both samples. Almost 99% of the identified genomic sequence variants were known annotated dbSNP variants in the hg38 reference genome. A high prevalence of C>T and T>C mutations was present along with a strong concordance of variants shared between the germline genome databases; gnomAD (81.1%) and the 1000 Genome Project (93.6%). This study demonstrates isolation and amplification procedures from low input ccfDNA samples that can detect sequence variants across the whole genome from amplified human plasma ccfDNA that can translate to multiple clinical research disciplines.
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Affiliation(s)
- Julie F. Foley
- Division of National Toxicology ProgramNIEHSDurhamNorth CarolinaUSA
| | | | - B. Alex Merrick
- Division of National Toxicology ProgramNIEHSDurhamNorth CarolinaUSA
| | | | - Molly E. Cook
- Division of Intramural ResearchNIEHSDurhamNorth CarolinaUSA
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27
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Longitudinal Circulating Tumor DNA Analysis in Blood and Saliva for Prediction of Response to Osimertinib and Disease Progression in EGFR-Mutant Lung Adenocarcinoma. Cancers (Basel) 2021; 13:cancers13133342. [PMID: 34283064 PMCID: PMC8268167 DOI: 10.3390/cancers13133342] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/24/2021] [Accepted: 06/29/2021] [Indexed: 01/19/2023] Open
Abstract
Background: We assessed whether serial ctDNA monitoring of plasma and saliva predicts response and resistance to osimertinib in EGFR-mutant lung adenocarcinoma. Three ctDNA technologies-blood-based droplet-digital PCR (ddPCR), next-generation sequencing (NGS), and saliva-based EFIRM liquid biopsy (eLB)-were employed to investigate their complementary roles. Methods: Plasma and saliva samples were collected from patients enrolled in a prospective clinical trial of osimertinib and local ablative therapy upon progression (NCT02759835). Plasma was analyzed by ddPCR and NGS. Saliva was analyzed by eLB. Results: A total of 25 patients were included. We analyzed 534 samples by ddPCR (n = 25), 256 samples by NGS (n = 24) and 371 samples by eLB (n = 22). Among 20 patients who progressed, ctDNA progression predated RECIST 1.1 progression by a median of 118 days (range: 61-272 days) in 11 (55%) patients. Of nine patients without ctDNA progression by ddPCR, two patients had an increase in mutant EGFR by eLB and two patients were found to have ctDNA progression by NGS. Levels of ctDNA measured by ddPCR and NGS at early time points, but not volumetric tumor burden, were associated with PFS. EGFR/ERBB2/MET/KRAS amplifications, EGFR C797S, PIK3CA E545K, PTEN V9del, and CTNNB1 S45P were key resistance mechanisms identified by NGS. Conclusion: Serial assessment of ctDNA in plasma and saliva predicts response and resistance to osimertinib, with each assay having supplementary roles.
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28
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Finkle JD, Boulos H, Driessen TM, Lo C, Blidner RA, Hafez A, Khan AA, Lozac'hmeur A, McKinnon KE, Perera J, Zhu W, Dowlati A, White KP, Tell R, Beaubier N. Validation of a liquid biopsy assay with molecular and clinical profiling of circulating tumor DNA. NPJ Precis Oncol 2021; 5:63. [PMID: 34215841 PMCID: PMC8253837 DOI: 10.1038/s41698-021-00202-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/28/2021] [Indexed: 11/09/2022] Open
Abstract
Liquid biopsy is a valuable precision oncology tool that is increasingly used as a non-invasive approach to identify biomarkers, detect resistance mutations, monitor disease burden, and identify early recurrence. The Tempus xF liquid biopsy assay is a 105-gene, hybrid-capture, next-generation sequencing (NGS) assay that detects single-nucleotide variants, insertions/deletions, copy number variants, and chromosomal rearrangements. Here, we present extensive validation studies of the xF assay using reference standards, cell lines, and patient samples that establish high sensitivity, specificity, and accuracy in variant detection. The Tempus xF assay is highly concordant with orthogonal methods, including ddPCR, tumor tissue-based NGS assays, and another commercial plasma-based NGS assay. Using matched samples, we developed a dynamic filtering method to account for germline mutations and clonal hematopoiesis, while significantly decreasing the number of false-positive variants reported. Additionally, we calculated accurate circulating tumor fraction estimates (ctFEs) using the Off-Target Tumor Estimation Routine (OTTER) algorithm for targeted-panel sequencing. In a cohort of 1,000 randomly selected cancer patients who underwent xF testing, we found that ctFEs correlated with disease burden and clinical outcomes. These results highlight the potential of serial testing to monitor treatment efficacy and disease course, providing strong support for incorporating liquid biopsy in the management of patients with advanced disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Wei Zhu
- Tempus Labs, Chicago, IL, USA
| | - Afshin Dowlati
- University Hospitals Seidman Cancer Center, Cleveland, OH, USA
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29
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Nteliopoulos G, Page K, Hills A, Howarth K, Emmett W, Green E, Martinson LJ, Fernadez-Garcia D, Hastings R, Guttery DS, Kenny L, Stebbing J, Cleator S, Rehman F, Gleason KLT, Sanela A, Ion C, Rushton AJ, Rosenfeld N, Coombes RC, Shaw JA. Comparison of two targeted ultra-deep sequencing technologies for analysis of plasma circulating tumour DNA in endocrine-therapy-resistant breast cancer patients. Breast Cancer Res Treat 2021; 188:465-476. [PMID: 34097174 PMCID: PMC8260509 DOI: 10.1007/s10549-021-06220-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/30/2021] [Indexed: 12/15/2022]
Abstract
PURPOSE There is growing interest in the application of circulating tumour DNA (ctDNA) as a sensitive tool for monitoring tumour evolution and guiding targeted therapy in patients with cancer. However, robust comparisons of different platform technologies are still required. Here we compared the InVisionSeq™ ctDNA Assay with the Oncomine™ Breast cfDNA Assay to assess their concordance and feasibility for the detection of mutations in plasma at low (< 0.5%) variant allele fraction (VAF). METHODS Ninety-six plasma samples from 50 patients with estrogen receptor (ER)-positive metastatic breast cancer (mBC) were profiled using the InVision Assay. Results were compared to the Oncomine assay in 30 samples from 26 patients, where there was sufficient material and variants were covered by both assays. Longitudinal samples were analysed for 8 patients with endocrine resistance. RESULTS We detected alterations in 59/96 samples from 34/50 patients analysed with the InVision assay, most frequently affecting ESR1, PIK3CA and TP53. Complete or partial concordance was found in 28/30 samples analysed by both assays, and VAF values were highly correlated. Excellent concordance was found for most genes, and most discordant calls occurred at VAF < 1%. In longitudinal samples from progressing patients with endocrine resistance, we detected consistent alterations in sequential samples, most commonly in ESR1 and PIK3CA. CONCLUSION This study shows that both ultra-deep next-generation sequencing (NGS) technologies can detect genomic alternations even at low VAFs in plasma samples of mBC patients. The strong agreement of the technologies indicates sufficient reproducibility for clinical use as prognosic and predictive biomarker.
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Affiliation(s)
- Georgios Nteliopoulos
- Department of Surgery and Cancer, Division of Cancer, Imperial College London, London, UK
| | - Karen Page
- Department of Genetics and Genome Biology and Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Allison Hills
- Department of Surgery and Cancer, Division of Cancer, Imperial College London, London, UK
| | | | | | | | - Luke J Martinson
- Department of Genetics and Genome Biology and Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Daniel Fernadez-Garcia
- Department of Genetics and Genome Biology and Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Robert Hastings
- Department of Genetics and Genome Biology and Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - David S Guttery
- Department of Genetics and Genome Biology and Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Laura Kenny
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Justin Stebbing
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Susan Cleator
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Farah Rehman
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Kelly L T Gleason
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Andrijac Sanela
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Charlotte Ion
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Amelia J Rushton
- Department of Surgery and Cancer, Division of Cancer, Imperial College London, London, UK
| | | | - R Charles Coombes
- Department of Surgery and Cancer, Division of Cancer, Imperial College London, London, UK
| | - Jacqueline A Shaw
- Department of Genetics and Genome Biology and Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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30
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Xia Y, Ying S, Jin R, Wu H, Shen Y, Yin T, Yan F, Zhang W, Lan F, Zhang B, Zhu C, Li C, Li W, Shen H. Application of a classifier combining bronchial transcriptomics and chest computed tomography features facilitates the diagnostic evaluation of lung cancer in smokers and nonsmokers. Int J Cancer 2021; 149:1290-1301. [PMID: 33963762 DOI: 10.1002/ijc.33675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 12/24/2022]
Abstract
Lung cancer screening by computed tomography (CT) reduces mortality but exhibited high false-positive rates. We established a diagnostic classifier combining chest CT features with bronchial transcriptomics. Patients with CT-detected suspected lung cancer were enrolled. The sample collected by bronchial brushing was used for RNA sequencing. The e1071 and pROC packages in R software was applied to build the model. Eventually, a total of 283 patients, including 183 with lung cancer and 100 with benign lesions, were included into final analysis. When incorporating transcriptomic data with radiological characteristics, the advanced model yielded 0.903 AUC with 81.1% NPV. Moreover, the classifier performed well regardless of lesion size, location, stage, histologic type or smoking status. Pathway analysis showed enhanced epithelial differentiation, tumor metastasis, and impaired immunity were predominant in smokers with cancer, whereas tumorigenesis played a central role in nonsmokers with cancer. Apoptosis and oxidative stress contributed critically in metastatic lung cancer; by contrast, immune dysfunction was pivotal in locally advanced lung cancer. Collectively, we devised a minimal-to-noninvasive, efficient diagnostic classifier for smokers and nonsmokers with lung cancer, which provides evidence for different mechanisms of cancer development and metastasis associated with smoking. A negative classifier result will help the physician make conservative diagnostic decisions.
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Affiliation(s)
- Yang Xia
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Songmin Ying
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Rui Jin
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Hao Wu
- Department of Human Genetics, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ye Shen
- Hangzhou Mitigenomics Technology Co, Ltd, Hangzhou, China
| | - Tong Yin
- Hangzhou Mitigenomics Technology Co, Ltd, Hangzhou, China
| | - Fugui Yan
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Zhang
- Hangzhou Mitigenomics Technology Co, Ltd, Hangzhou, China
| | - Fen Lan
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Bin Zhang
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Chen Zhu
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Chen Li
- Department of Human Genetics, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wen Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Huahao Shen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
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Bekaii-Saab TS, Bridgewater J, Normanno N. Practical considerations in screening for genetic alterations in cholangiocarcinoma. Ann Oncol 2021; 32:1111-1126. [PMID: 33932504 DOI: 10.1016/j.annonc.2021.04.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/06/2021] [Accepted: 04/18/2021] [Indexed: 12/14/2022] Open
Abstract
Cholangiocarcinoma (CCA) encompasses diverse epithelial tumors historically associated with poor outcomes due to an aggressive disease course, late diagnosis, and limited benefit of standard chemotherapy for advanced disease. Comprehensive molecular profiling has revealed a diverse landscape of genomic alterations as oncogenic drivers in CCA. TP53 mutations, CDKN2A/B loss, and KRAS mutations are the most common genetic alterations in CCA. However, intrahepatic CCA (iCCA) and extrahepatic CCA (eCCA) differ substantially in the frequency of many alterations. This includes actionable alterations, such as isocitrate dehydrogenase 1 (IDH1) mutations and a large variety of FGFR2 rearrangements, which are found in up to 29% and ∼10% of patients with iCCA, respectively, but are rare in eCCA. FGFR2 rearrangements are currently the only genetic alteration in CCA for which a targeted therapy, the fibroblast growth factor receptor 1-3 inhibitor pemigatinib, has been approved. However, favorable phase III results for IDH1-targeted therapy with ivosidenib in iCCA have been published, and numerous other alterations are actionable by targeted therapies approved in other indications. Recent advances in next-generation sequencing (NGS) have led to the development of assays that allow comprehensive genomic profiling of large gene panels within 2-3 weeks, including in vitro diagnostic tests approved in the United States. These assays vary regarding acceptable source material (tumor tissue or peripheral whole blood), genetic source for library construction (DNA or RNA), target selection technology, gene panel size, and type of detectable genomic alterations. While some large commercial laboratories offer rapid and comprehensive genomic profiling services based on proprietary assay platforms, clinical centers may use commercial genomic profiling kits designed for clinical research to develop their own customized laboratory-developed tests. Large-scale genomic profiling based on NGS allows for a detailed and precise molecular diagnosis of CCA and provides an important opportunity for improved targeted treatment plans tailored to the individual patient's genetic signature.
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Affiliation(s)
| | - J Bridgewater
- University College London Cancer Institute, London, UK
| | - N Normanno
- Istituto Nazionale Tumori 'Fondazione Giovanni Pascale' IRCCS, Naples, Italy
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32
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Park S, Olsen S, Ku BM, Lee MS, Jung HA, Sun JM, Lee SH, Ahn JS, Park K, Choi YL, Ahn MJ. High concordance of actionable genomic alterations identified between circulating tumor DNA-based and tissue-based next-generation sequencing testing in advanced non-small cell lung cancer: The Korean Lung Liquid Versus Invasive Biopsy Program. Cancer 2021; 127:3019-3028. [PMID: 33826761 DOI: 10.1002/cncr.33571] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/13/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Because of the growing number of actionable biomarkers in non-small cell lung cancer (NSCLC), sufficient tissue availability for testing is becoming a greater challenge. Liquid biopsy offers a potential solution by complementing standard tissue-based methods. In this study, the authors analyzed the concordance of actionable genomic alterations sequenced from circulating tumor DNA (ctDNA; Guardant360) and tissue (Oncomine Focus Assay). METHODS From September 2015 to May 2018, 421 paired plasma and tissue samples from patients with advanced NSCLC who had previously undergone tissue testing by standard methods were collected. Both types of samples were available for 287 patients (262 in cohort 1 [treatment-naive] and 25 in cohort 2 [treatment failure]), and only 1 sample type was available for 134 patients (50 in cohort 3 [plasma only] and 84 in cohort 4 [tissue only]). RESULTS In cohort 1, 198 samples (77.6%) showed concordance between tissue and plasma next-generation sequencing (NGS). Among the discordant cases, plasma testing detected additional genomic alterations in 11 patients (4.2%). In 50 patients without tissue-based NGS results (cohort 3), the ctDNA-based test detected genomic alterations in 20 samples (40.0%). The median allele frequency (AF) of mutations identified with ctDNA-based NGS (0.74%) was lower than that identified with the tissue-based NGS test (13.90%). Clinical responses to matched targeted therapy occurred, regardless of the ctDNA AF. Upfront ctDNA-based testing identified 60.4% of patients with genomic alterations. In addition, ctDNA-based testing uncovered 12.0% more actionable alterations when it was performed after tissue-based NGS testing. CONCLUSIONS The results indicate that a ctDNA-based test identifies additional patients with actionable genomic alterations and could, therefore, be used to complement traditional tissue-based testing for NSCLC. LAY SUMMARY Circulating tumor DNA (ctDNA)-based next-generation sequencing (NGS) testing is becoming essential as the number of actionable genomic biomarker increases for the treatment selection of non-small cell lung cancer. This study demonstrates the additive value of ctDNA-based testing in addition to tissue-based NGS and standard of care-based biomarker testing for detecting additional patients with actionable genomic alterations. Clinical responses have also been observed in patients with a low allele frequency detected by ctDNA-based NGS testing.
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Affiliation(s)
- Sehhoon Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Steve Olsen
- Department of Medical and Clinical Affairs, Guardant Health AMEA, Singapore, Singapore
| | - Bo Mi Ku
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Min-Sang Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyun-Ae Jung
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jong-Mu Sun
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jin Seok Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Keunchil Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Yoon-La Choi
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Myung-Ju Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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Provencio M, Pérez-Barrios C, Barquin M, Calvo V, Franco F, Sánchez E, Sánchez R, Marsden D, Cristóbal Sánchez J, Martin Acosta P, Laza-Briviesca R, Cruz-Bermúdez A, Romero A. Next-generation sequencing for tumor mutation quantification using liquid biopsies. Clin Chem Lab Med 2021; 58:306-313. [PMID: 31469650 DOI: 10.1515/cclm-2019-0745] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 08/05/2019] [Indexed: 11/15/2022]
Abstract
Background Non-small cell lung cancer (NSCLC) patients benefit from targeted therapies both in first- and second-line treatment. Nevertheless, molecular profiling of lung cancer tumors after first disease progression is seldom performed. The analysis of circulating tumor DNA (ctDNA) enables not only non-invasive biomarker testing but also monitoring tumor response to treatment. Digital PCR (dPCR), although a robust approach, only enables the analysis of a limited number of mutations. Next-generation sequencing (NGS), on the other hand, enables the analysis of significantly greater numbers of mutations. Methods A total of 54 circulating free DNA (cfDNA) samples from 52 NSCLC patients and two healthy donors were analyzed by NGS using the Oncomine™ Lung cfDNA Assay kit and dPCR. Results Lin's concordance correlation coefficient and Pearson's correlation coefficient between mutant allele frequencies (MAFs) assessed by NGS and dPCR revealed a positive and linear relationship between the two data sets (ρc = 0.986; 95% confidence interval [CI] = 0.975-0.991; r = 0.987; p < 0.0001, respectively), indicating an excellent concordance between both measurements. Similarly, the agreement between NGS and dPCR for the detection of the resistance mutation p.T790M was almost perfect (K = 0.81; 95% CI = 0.62-0.99), with an excellent correlation in terms of MAFs (ρc = 0.991; 95% CI = 0.981-0.992 and Pearson's r = 0.998; p < 0.0001). Importantly, cfDNA sequencing was successful using as low as 10 ng cfDNA input. Conclusions MAFs assessed by NGS were highly correlated with MAFs assessed by dPCR, demonstrating that NGS is a robust technique for ctDNA quantification using clinical samples, thereby allowing for dynamic genomic surveillance in the era of precision medicine.
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Affiliation(s)
- Mariano Provencio
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Clara Pérez-Barrios
- Molecular Oncology Laboratory, Biomedical Sciences Research Institute, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
- Laboratory Medicine Department, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Miguel Barquin
- Molecular Oncology Laboratory, Biomedical Sciences Research Institute, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Virginia Calvo
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Fabio Franco
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Estela Sánchez
- Molecular Oncology Laboratory, Biomedical Sciences Research Institute, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Ricardo Sánchez
- Laboratorio de Hematología Traslacional, Servicio de Hematología, Instituto de Investigación Hospital 12 de Octubre (I+12), Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Daniel Marsden
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Juan Cristóbal Sánchez
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Paloma Martin Acosta
- Pathology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Raquel Laza-Briviesca
- Molecular Oncology Laboratory, Biomedical Sciences Research Institute, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Alberto Cruz-Bermúdez
- Molecular Oncology Laboratory, Biomedical Sciences Research Institute, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Atocha Romero
- Molecular Oncology Laboratory, Biomedical Sciences Research Institute, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
- Medical Oncology Department, Puerta de Hierro Hospital, C/ Manuel de Falla 1, Majadahonda, Madrid 28222, Spain
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34
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Lafata KJ, Corradetti MN, Gao J, Jacobs CD, Weng J, Chang Y, Wang C, Hatch A, Xanthopoulos E, Jones G, Kelsey CR, Yin FF. Radiogenomic Analysis of Locally Advanced Lung Cancer Based on CT Imaging and Intratreatment Changes in Cell-Free DNA. Radiol Imaging Cancer 2021; 3:e200157. [PMID: 34114913 PMCID: PMC8344351 DOI: 10.1148/rycan.2021200157] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/18/2021] [Accepted: 04/06/2021] [Indexed: 12/13/2022]
Abstract
The radiologic appearance of locally advanced lung cancer may be linked to molecular changes of the disease during treatment, but characteristics of this phenomenon are poorly understood. Radiomics, liquid biopsy of cell-free DNA (cfDNA), and next-generation sequencing of circulating tumor DNA (ctDNA) encode tumor-specific radiogenomic expression patterns that can be probed to study this problem. Preliminary findings are reported from a radiogenomic analysis of CT imaging, cfDNA, and ctDNA in 24 patients (median age, 64 years; range, 49-74 years) with stage III lung cancer undergoing chemoradiation on a prospective pilot study (NCT00921739) between September 2009 and September 2014. Unsupervised clustering of radiomic signatures resulted in two clusters that were associated with ctDNA TP53 mutations (P = .03) and changes in cfDNA concentration after 2 weeks of chemoradiation (P = .02). The radiomic features dissimilarity (hazard ratio [HR] = 0.56; P = .05), joint entropy (HR = 0.56; P = .04), sum entropy (HR = 0.53; P = .02), and normalized inverse difference (HR = 1.77; P = .05) were associated with overall survival. These results suggest heterogeneous and low-attenuating disease without a detectable ctDNA TP53 mutation was associated with early surges of cfDNA concentration in response to therapy and a generally better prognosis. Keywords: CT-Quantitative, Radiation Therapy, Lung, Computer Applications-3D, Oncology, Tumor Response, Outcomes Analysis Clinical trial registration no. NCT00921739 Supplemental material is available for this article. © RSNA, 2021.
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Affiliation(s)
- Kyle J. Lafata
- From the Departments of Radiation Oncology (K.J.L., M.N.C., C.D.J.,
J.W., Y.C., C.W., C.R.K., F.F.Y.), Radiology (K.J.L.), Biostatistics and
Bioinformatics (J.G.), and Medicine (A.H.), Duke University School of Medicine,
2301 Erwin Rd, Durham, NC 27710; Department of Electrical and Computer
Engineering, Duke University Pratt School of Engineering, Durham, NC (K.J.L.);
Radiology Medical Group of Napa, Napa, Calif (M.N.C.); Department of Radiation
Oncology, Columbia University School of Medicine, New York, NY (E.X.); and
Inivata, Cambridge, England (G.J.)
| | - Michael N. Corradetti
- From the Departments of Radiation Oncology (K.J.L., M.N.C., C.D.J.,
J.W., Y.C., C.W., C.R.K., F.F.Y.), Radiology (K.J.L.), Biostatistics and
Bioinformatics (J.G.), and Medicine (A.H.), Duke University School of Medicine,
2301 Erwin Rd, Durham, NC 27710; Department of Electrical and Computer
Engineering, Duke University Pratt School of Engineering, Durham, NC (K.J.L.);
Radiology Medical Group of Napa, Napa, Calif (M.N.C.); Department of Radiation
Oncology, Columbia University School of Medicine, New York, NY (E.X.); and
Inivata, Cambridge, England (G.J.)
| | - Junheng Gao
- From the Departments of Radiation Oncology (K.J.L., M.N.C., C.D.J.,
J.W., Y.C., C.W., C.R.K., F.F.Y.), Radiology (K.J.L.), Biostatistics and
Bioinformatics (J.G.), and Medicine (A.H.), Duke University School of Medicine,
2301 Erwin Rd, Durham, NC 27710; Department of Electrical and Computer
Engineering, Duke University Pratt School of Engineering, Durham, NC (K.J.L.);
Radiology Medical Group of Napa, Napa, Calif (M.N.C.); Department of Radiation
Oncology, Columbia University School of Medicine, New York, NY (E.X.); and
Inivata, Cambridge, England (G.J.)
| | - Corbin D. Jacobs
- From the Departments of Radiation Oncology (K.J.L., M.N.C., C.D.J.,
J.W., Y.C., C.W., C.R.K., F.F.Y.), Radiology (K.J.L.), Biostatistics and
Bioinformatics (J.G.), and Medicine (A.H.), Duke University School of Medicine,
2301 Erwin Rd, Durham, NC 27710; Department of Electrical and Computer
Engineering, Duke University Pratt School of Engineering, Durham, NC (K.J.L.);
Radiology Medical Group of Napa, Napa, Calif (M.N.C.); Department of Radiation
Oncology, Columbia University School of Medicine, New York, NY (E.X.); and
Inivata, Cambridge, England (G.J.)
| | - Jingxi Weng
- From the Departments of Radiation Oncology (K.J.L., M.N.C., C.D.J.,
J.W., Y.C., C.W., C.R.K., F.F.Y.), Radiology (K.J.L.), Biostatistics and
Bioinformatics (J.G.), and Medicine (A.H.), Duke University School of Medicine,
2301 Erwin Rd, Durham, NC 27710; Department of Electrical and Computer
Engineering, Duke University Pratt School of Engineering, Durham, NC (K.J.L.);
Radiology Medical Group of Napa, Napa, Calif (M.N.C.); Department of Radiation
Oncology, Columbia University School of Medicine, New York, NY (E.X.); and
Inivata, Cambridge, England (G.J.)
| | - Yushi Chang
- From the Departments of Radiation Oncology (K.J.L., M.N.C., C.D.J.,
J.W., Y.C., C.W., C.R.K., F.F.Y.), Radiology (K.J.L.), Biostatistics and
Bioinformatics (J.G.), and Medicine (A.H.), Duke University School of Medicine,
2301 Erwin Rd, Durham, NC 27710; Department of Electrical and Computer
Engineering, Duke University Pratt School of Engineering, Durham, NC (K.J.L.);
Radiology Medical Group of Napa, Napa, Calif (M.N.C.); Department of Radiation
Oncology, Columbia University School of Medicine, New York, NY (E.X.); and
Inivata, Cambridge, England (G.J.)
| | - Chunhao Wang
- From the Departments of Radiation Oncology (K.J.L., M.N.C., C.D.J.,
J.W., Y.C., C.W., C.R.K., F.F.Y.), Radiology (K.J.L.), Biostatistics and
Bioinformatics (J.G.), and Medicine (A.H.), Duke University School of Medicine,
2301 Erwin Rd, Durham, NC 27710; Department of Electrical and Computer
Engineering, Duke University Pratt School of Engineering, Durham, NC (K.J.L.);
Radiology Medical Group of Napa, Napa, Calif (M.N.C.); Department of Radiation
Oncology, Columbia University School of Medicine, New York, NY (E.X.); and
Inivata, Cambridge, England (G.J.)
| | - Ace Hatch
- From the Departments of Radiation Oncology (K.J.L., M.N.C., C.D.J.,
J.W., Y.C., C.W., C.R.K., F.F.Y.), Radiology (K.J.L.), Biostatistics and
Bioinformatics (J.G.), and Medicine (A.H.), Duke University School of Medicine,
2301 Erwin Rd, Durham, NC 27710; Department of Electrical and Computer
Engineering, Duke University Pratt School of Engineering, Durham, NC (K.J.L.);
Radiology Medical Group of Napa, Napa, Calif (M.N.C.); Department of Radiation
Oncology, Columbia University School of Medicine, New York, NY (E.X.); and
Inivata, Cambridge, England (G.J.)
| | - Eric Xanthopoulos
- From the Departments of Radiation Oncology (K.J.L., M.N.C., C.D.J.,
J.W., Y.C., C.W., C.R.K., F.F.Y.), Radiology (K.J.L.), Biostatistics and
Bioinformatics (J.G.), and Medicine (A.H.), Duke University School of Medicine,
2301 Erwin Rd, Durham, NC 27710; Department of Electrical and Computer
Engineering, Duke University Pratt School of Engineering, Durham, NC (K.J.L.);
Radiology Medical Group of Napa, Napa, Calif (M.N.C.); Department of Radiation
Oncology, Columbia University School of Medicine, New York, NY (E.X.); and
Inivata, Cambridge, England (G.J.)
| | - Greg Jones
- From the Departments of Radiation Oncology (K.J.L., M.N.C., C.D.J.,
J.W., Y.C., C.W., C.R.K., F.F.Y.), Radiology (K.J.L.), Biostatistics and
Bioinformatics (J.G.), and Medicine (A.H.), Duke University School of Medicine,
2301 Erwin Rd, Durham, NC 27710; Department of Electrical and Computer
Engineering, Duke University Pratt School of Engineering, Durham, NC (K.J.L.);
Radiology Medical Group of Napa, Napa, Calif (M.N.C.); Department of Radiation
Oncology, Columbia University School of Medicine, New York, NY (E.X.); and
Inivata, Cambridge, England (G.J.)
| | - Chris R. Kelsey
- From the Departments of Radiation Oncology (K.J.L., M.N.C., C.D.J.,
J.W., Y.C., C.W., C.R.K., F.F.Y.), Radiology (K.J.L.), Biostatistics and
Bioinformatics (J.G.), and Medicine (A.H.), Duke University School of Medicine,
2301 Erwin Rd, Durham, NC 27710; Department of Electrical and Computer
Engineering, Duke University Pratt School of Engineering, Durham, NC (K.J.L.);
Radiology Medical Group of Napa, Napa, Calif (M.N.C.); Department of Radiation
Oncology, Columbia University School of Medicine, New York, NY (E.X.); and
Inivata, Cambridge, England (G.J.)
| | - Fang-Fang Yin
- From the Departments of Radiation Oncology (K.J.L., M.N.C., C.D.J.,
J.W., Y.C., C.W., C.R.K., F.F.Y.), Radiology (K.J.L.), Biostatistics and
Bioinformatics (J.G.), and Medicine (A.H.), Duke University School of Medicine,
2301 Erwin Rd, Durham, NC 27710; Department of Electrical and Computer
Engineering, Duke University Pratt School of Engineering, Durham, NC (K.J.L.);
Radiology Medical Group of Napa, Napa, Calif (M.N.C.); Department of Radiation
Oncology, Columbia University School of Medicine, New York, NY (E.X.); and
Inivata, Cambridge, England (G.J.)
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Chibuk J, Flory A, Kruglyak KM, Leibman N, Nahama A, Dharajiya N, van den Boom D, Jensen TJ, Friedman JS, Shen MR, Clemente-Vicario F, Chorny I, Tynan JA, Lytle KM, Holtvoigt LE, Murtaza M, Diaz LA, Tsui DWY, Grosu DS. Horizons in Veterinary Precision Oncology: Fundamentals of Cancer Genomics and Applications of Liquid Biopsy for the Detection, Characterization, and Management of Cancer in Dogs. Front Vet Sci 2021; 8:664718. [PMID: 33834049 PMCID: PMC8021921 DOI: 10.3389/fvets.2021.664718] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 02/23/2021] [Indexed: 12/14/2022] Open
Abstract
Cancer is the leading cause of death in dogs, in part because many cases are identified at an advanced stage when clinical signs have developed, and prognosis is poor. Increased understanding of cancer as a disease of the genome has led to the introduction of liquid biopsy testing, allowing for detection of genomic alterations in cell-free DNA fragments in blood to facilitate earlier detection, characterization, and management of cancer through non-invasive means. Recent discoveries in the areas of genomics and oncology have provided a deeper understanding of the molecular origins and evolution of cancer, and of the "one health" similarities between humans and dogs that underlie the field of comparative oncology. These discoveries, combined with technological advances in DNA profiling, are shifting the paradigm for cancer diagnosis toward earlier detection with the goal of improving outcomes. Liquid biopsy testing has already revolutionized the way cancer is managed in human medicine - and it is poised to make a similar impact in veterinary medicine. Multiple clinical use cases for liquid biopsy are emerging, including screening, aid in diagnosis, targeted treatment selection, treatment response monitoring, minimal residual disease detection, and recurrence monitoring. This review article highlights key scientific advances in genomics and their relevance for veterinary oncology, with the goal of providing a foundational introduction to this important topic for veterinarians. As these technologies migrate from human medicine into veterinary medicine, improved awareness and understanding will facilitate their rapid adoption, for the benefit of veterinary patients.
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Affiliation(s)
| | | | | | - Nicole Leibman
- The Cancer Institute, Animal Medical Center, New York, NY, United States
| | | | | | | | | | | | - M. Richard Shen
- RS Technology Ventures LLC., Rancho Santa Fe, CA, United States
| | | | | | | | | | | | - Muhammed Murtaza
- Department of Surgery and Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Luis A. Diaz
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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36
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Ricciuti B, Jones G, Severgnini M, Alessi JV, Recondo G, Lawrence M, Forshew T, Lydon C, Nishino M, Cheng M, Awad M. Early plasma circulating tumor DNA (ctDNA) changes predict response to first-line pembrolizumab-based therapy in non-small cell lung cancer (NSCLC). J Immunother Cancer 2021; 9:e001504. [PMID: 33771889 PMCID: PMC7996662 DOI: 10.1136/jitc-2020-001504] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Currently available biomarkers are imperfect in their ability to predict responses to the multiple first-line treatment options available for patients with advanced non-small cell lung cancer (NSCLC). Having an early pharmacodynamic marker of treatment resistance may help redirect patients onto more effective alternative therapies. We sought to determine if changes in circulating tumor DNA (ctDNA) levels after initiation of first-line pembrolizumab±chemotherapy in NSCLC would enable early prediction of response prior to radiological assessment. METHODS Plasma collected from patients with advanced NSCLC prior to and serially after starting first-line pembrolizumab±platinum doublet chemotherapy was analyzed by next-generation sequencing using enhanced tagged-amplicon sequencing of hotspots and coding regions from 36 genes. Early change in ctDNA allele fraction (AF) was correlated with radiographic responses and long-term clinical outcomes. RESULTS Among 62 patients who received first-line pembrolizumab±platinum/pemetrexed and underwent ctDNA assessment, 45 had detectable ctDNA alterations at baseline. The median change in AF at the first follow-up (at a median of 21 days after treatment initiation) was -90.1% (range -100% to +65%) among patients who subsequently had a radiologic response (n=18), -19.9% (range: -100% to +1884%) among stable disease cases (n=15), and +28.8% (range: -100% to +410%) among progressive disease cases (n=12); p=0.003. In addition, there was a significant correlation between the percent change in ctDNA at the first follow-up and the percent change in tumor target lesions from baseline (R=0.66, p<0.001). AF decrease between the pretreatment and first on-treatment blood draw was associated with significantly higher response rate (60.7% vs 5.8%, p=0.0003), and significantly longer median progression-free survival (8.3 vs 3.4 months, HR: 0.29 (95% CI: 0.14 to 0.60), p=0.0007) and median overall survival (26.2 vs 13.2 months, HR: 0.34 (95% CI: 0.15 to 0.75), p=0.008) compared with cases with an AF increase. CONCLUSION In patients with advanced NSCLC, rapid decreases in ctDNA prior to radiological assessment correlated with clinical benefit. These results suggest a potential role for ctDNA as an early pharmacodynamic biomarker of response or resistance to immunotherapies.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antibodies, Monoclonal, Humanized/adverse effects
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/adverse effects
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Carcinoma, Non-Small-Cell Lung/blood
- Carcinoma, Non-Small-Cell Lung/diagnostic imaging
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Circulating Tumor DNA/blood
- Circulating Tumor DNA/genetics
- Disease Progression
- Early Diagnosis
- Female
- Humans
- Immune Checkpoint Inhibitors/adverse effects
- Immune Checkpoint Inhibitors/therapeutic use
- Lung Neoplasms/blood
- Lung Neoplasms/diagnostic imaging
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Male
- Middle Aged
- Predictive Value of Tests
- Progression-Free Survival
- Retrospective Studies
- Time Factors
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Affiliation(s)
- Biagio Ricciuti
- Medical Oncology, Lowe Center for Thoracic Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Greg Jones
- Inivata, Research Triangle Park, North Carolina, USA
| | - Mariano Severgnini
- Medical Oncology, Lowe Center for Thoracic Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
- Center for Immuno-Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Joao V Alessi
- Medical Oncology, Lowe Center for Thoracic Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Gonzalo Recondo
- Medical Oncology, Lowe Center for Thoracic Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Marissa Lawrence
- Medical Oncology, Lowe Center for Thoracic Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Tim Forshew
- Inivata, Research Triangle Park, North Carolina, USA
| | - Christine Lydon
- Medical Oncology, Lowe Center for Thoracic Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Mizuki Nishino
- Radiology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
- Radiology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Michael Cheng
- Medical Oncology, Lowe Center for Thoracic Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Mark Awad
- Medical Oncology, Lowe Center for Thoracic Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
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Liquid Biomarkers for Pediatric Brain Tumors: Biological Features, Advantages and Perspectives. J Pers Med 2020; 10:jpm10040254. [PMID: 33260839 PMCID: PMC7711550 DOI: 10.3390/jpm10040254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
Tumors of the central nervous system are the most frequent solid tumor type and the major cause for cancer-related mortality in children and adolescents. These tumors are biologically highly heterogeneous and comprise various different entities. Molecular diagnostics are already well-established for pediatric brain tumors and have facilitated a more accurate patient stratification. The availability of targeted, biomarker-driven therapies has increased the necessity of longitudinal monitoring of molecular alterations within tumors for precision medicine-guided therapy. Nevertheless, diagnosis is still primarily based on analyses of the primary tumor and follow-up is usually performed by imaging techniques which lack important information on tumor biology possibly changing the course of the disease. To overcome this shortage of longitudinal information, liquid biopsy has emerged as a promising diagnostic tool representing a less-invasive source of biomarkers for tumor monitoring and therapeutic decision making. Novel ultrasensitive methods for detection of allele variants, genetic alterations with low abundance, have been developed and are promising tools for establishing and integrating liquid biopsy techniques into clinical routine. Pediatric brain tumors harbor multiple molecular alterations with the potential to be used as liquid biomarkers. Consequently, studies have already investigated different types of biomarker in diverse entities of pediatric brain tumors. However, there are still certain pitfalls until liquid biomarkers can be unleashed and implemented into routine clinical care. Within this review, we summarize current knowledge on liquid biopsy markers and technologies in pediatric brain tumors, their advantages and drawbacks, as well as future potential biomarkers and perspectives with respect to clinical implementation in patient care.
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Iacovino M, Ciaramella V, Paragliola F, Suarato G, Busiello G, Sparano F. Use of liquid biopsy in monitoring therapeutic resistance in EGFR oncogene addicted NSCLC. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2020; 1:391-400. [PMID: 36046387 PMCID: PMC9400718 DOI: 10.37349/etat.2020.00024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 11/10/2020] [Indexed: 11/19/2022] Open
Abstract
Liquid biopsy has emerged as a minimally invasive alternative to tumor tissue analysis for the management of lung cancer patients, especially for epidermal growth factor receptor (EGFR) oncogene addicted tumor. In these patients, despite the clear benefits of tyrosine kinase inhibitors therapy, the development of acquired resistance and progressive disease is inevitable in most cases and liquid biopsy is important for molecular characterization at resistance and, being non-invasive, may be useful for disease monitoring. In this review, the authors will focus on the applications of liquid biopsy in EGFR-mutated non small cells lung cancer at diagnosis, during treatment and at progression, describing available data and possible future scenarios.
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Affiliation(s)
- Marialucia Iacovino
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80131 Naples, Italy
| | - Vincenza Ciaramella
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80131 Naples, Italy
| | - Fernando Paragliola
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80131 Naples, Italy
| | - Gabriella Suarato
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80131 Naples, Italy
| | - Gesualdina Busiello
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80131 Naples, Italy
| | - Francesca Sparano
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80131 Naples, Italy
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Chen M, Wu D, Tu S, Yang C, Chen D, Xu Y. CRISPR/Cas9 cleavage triggered ESDR for circulating tumor DNA detection based on a 3D graphene/AuPtPd nanoflower biosensor. Biosens Bioelectron 2020; 173:112821. [PMID: 33221510 DOI: 10.1016/j.bios.2020.112821] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/15/2022]
Abstract
Circulating tumor DNA (ctDNA) plays an important role in the early diagnosis and prognosis of several cancers and is a credible biomarker for predicting the response to therapy. Additionally, the fact that the strategy used to detect ctDNA is non-invasive also adds to the advantages of using ctDNA for predicting disease diagnosis and prognosis. However, low abundance in peripheral blood and the high background of wild-type DNA impair the precise and specific measurement of ctDNA. In this study, we developed a novel 3D GR/AuPtPd nanoflower sensing platform based on CRISPR/Cas9 cleavage-triggered entropy-driven strand displacement reaction (ESDR) for the effective detection of ctDNA. Low levels of ctDNA could be detected using this method as the ESDR amplification does require complicated operation procedures and stringent reaction conditions. By combining the advantages of the site-specific cleavage by "gene magic scissors," Cas9/sgRNA, with those of the rapid amplification kinetics of entropy-driven strand displacement, our method resulted in amplification efficiency as well as high specificity for discriminating single-nucleotide mismatches. The 3D GR/AuPtPd nanoflower-based electrochemical biosensor displayed high specificity and worthy performance in assays with human serum. Therefore, this pioneered method provides a new paradigm for efficient ctDNA detection and shows great potential for use in clinical and diagnostic applications.
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Affiliation(s)
- Mei Chen
- Clinical Laboratory, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, 610500, PR China
| | - Dongming Wu
- Clinical Laboratory, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, 610500, PR China
| | - Shihua Tu
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, Sichuan, 610500, PR China
| | - Chaoyin Yang
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, Sichuan, 610500, PR China
| | - DeJie Chen
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, Sichuan, 610500, PR China
| | - Ying Xu
- Clinical Laboratory, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, 610500, PR China.
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Hon T, Mars K, Young G, Tsai YC, Karalius JW, Landolin JM, Maurer N, Kudrna D, Hardigan MA, Steiner CC, Knapp SJ, Ware D, Shapiro B, Peluso P, Rank DR. Highly accurate long-read HiFi sequencing data for five complex genomes. Sci Data 2020; 7:399. [PMID: 33203859 PMCID: PMC7673114 DOI: 10.1038/s41597-020-00743-4] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023] Open
Abstract
The PacBio® HiFi sequencing method yields highly accurate long-read sequencing datasets with read lengths averaging 10–25 kb and accuracies greater than 99.5%. These accurate long reads can be used to improve results for complex applications such as single nucleotide and structural variant detection, genome assembly, assembly of difficult polyploid or highly repetitive genomes, and assembly of metagenomes. Currently, there is a need for sample data sets to both evaluate the benefits of these long accurate reads as well as for development of bioinformatic tools including genome assemblers, variant callers, and haplotyping algorithms. We present deep coverage HiFi datasets for five complex samples including the two inbred model genomes Mus musculus and Zea mays, as well as two complex genomes, octoploid Fragaria × ananassa and the diploid anuran Rana muscosa. Additionally, we release sequence data from a mock metagenome community. The datasets reported here can be used without restriction to develop new algorithms and explore complex genome structure and evolution. Data were generated on the PacBio Sequel II System. Measurement(s) | DNA • genome • Metagenome | Technology Type(s) | DNA sequencing • PacBio Sequel System | Factor Type(s) | organism that had its genome sequenced | Sample Characteristic - Organism | Mus musculus • Rana muscosa • Fragaria x ananassa • Zea mays |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12855527
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Affiliation(s)
- Ting Hon
- Pacific Biosciences of California Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025, USA
| | - Kristin Mars
- Pacific Biosciences of California Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025, USA
| | - Greg Young
- Pacific Biosciences of California Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025, USA
| | - Yu-Chih Tsai
- Pacific Biosciences of California Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025, USA
| | - Joseph W Karalius
- Pacific Biosciences of California Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025, USA
| | - Jane M Landolin
- Ravel Biotechnology Inc., 953 Indiana St., San Francisco, CA, 94107, USA
| | - Nicholas Maurer
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - David Kudrna
- Arizona Genomics Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Michael A Hardigan
- Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis, CA, 95616-8571, USA
| | - Cynthia C Steiner
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Global, 15600 San Pasqual Valley Road, Escondido, CA, 92027, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis, CA, 95616-8571, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,USDA-ARS, Plant, Soil, and Nutrition Research Unit, Ithaca, NY, 14853, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Paul Peluso
- Pacific Biosciences of California Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025, USA
| | - David R Rank
- Pacific Biosciences of California Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025, USA.
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41
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Iafolla MAJ, Picardo S, Aung K, Hansen AR. Systematic Review and STARD Scoring of Renal Cell Carcinoma Circulating Diagnostic Biomarker Manuscripts. JNCI Cancer Spectr 2020; 4:pkaa050. [PMID: 33134830 PMCID: PMC7583155 DOI: 10.1093/jncics/pkaa050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/14/2020] [Accepted: 06/01/2020] [Indexed: 01/23/2023] Open
Abstract
Background No validated molecular biomarkers exist to help guide diagnosis of renal cell carcinoma (RCC) patients. We seek to evaluate the quality of published RCC circulating diagnostic biomarker manuscripts using the Standards for Reporting of Diagnostic Accuracy Studies (STARD) guidelines. Methods The phrase “(renal cell carcinoma OR renal cancer OR kidney cancer OR kidney carcinoma) AND circulating AND (biomarkers OR cell free DNA OR tumor DNA OR methylated cell free DNA OR methylated tumor DNA)” was searched in Embase, MEDLINE, and PubMed in March 2018. Relevant manuscripts were scored using 41 STARD subcriteria for a maximal score of 26 points. All tests of statistical significance were 2 sided. Results The search identified 535 publications: 27 manuscripts of primary research were analyzed. The median STARD score was 11.5 (range = 7-16.75). All manuscripts had appropriate abstracts, introductions, and distribution of alternative diagnoses. None of the manuscripts stated how indeterminant data were handled or if adverse events occurred from performing the index test or reference standard. Statistically significantly higher STARD scores were present in manuscripts reporting receiver operator characteristic curves (P < .001), larger sample sizes (P = .007), and after release of the original STARD statement (P = .005). Conclusions Most RCC circulating diagnostic biomarker manuscripts poorly adhere to the STARD guidelines. Future studies adhering to STARD guidelines may address this unmet need.
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Affiliation(s)
- Marco A J Iafolla
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,University of Toronto, Toronto, Ontario, Canada.,Division of Oncology, William Osler Health System, Brampton, Ontario, Canada
| | - Sarah Picardo
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,University of Toronto, Toronto, Ontario, Canada
| | - Kyaw Aung
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,University of Toronto, Toronto, Ontario, Canada.,Livestrong Cancer Institute and Dell Medical School, University of Texas at Austin, Austin, TX, USA
| | - Aaron R Hansen
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,University of Toronto, Toronto, Ontario, Canada
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Gobbini E, Swalduz A, Giaj Levra M, Ortiz-Cuaran S, Toffart AC, Pérol M, Moro-Sibilot D, Saintigny P. Implementing ctDNA Analysis in the Clinic: Challenges and Opportunities in Non-Small Cell Lung Cancer. Cancers (Basel) 2020; 12:E3112. [PMID: 33114393 PMCID: PMC7693855 DOI: 10.3390/cancers12113112] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022] Open
Abstract
Tumor genomic profiling has a dramatic impact on the selection of targeted treatment and for the identification of resistance mechanisms at the time of progression. Solid tissue biopsies are sometimes challenging, and liquid biopsies are used as a non-invasive alternative when tissue is limiting. The clinical relevance of tumor genotyping through analysis of ctDNA is now widely recognized at all steps of the clinical evaluation process in metastatic non-small cell lung cancer (NSCLC) patients. ctDNA analysis through liquid biopsy has recently gained increasing attention as well in the management of early and locally advanced, not oncogene-addicted, NSCLC. Its potential applications in early disease detection and the response evaluation to radical treatments are promising. The aim of this review is to summarize the landscape of liquid biopsies in clinical practice and also to provide an overview of the potential perspectives of development focusing on early detection and screening, the assessment of minimal residual disease, and its potential role in predicting response to immunotherapy. In addition to available studies demonstrating the clinical relevance of liquid biopsies, there is a need for standardization and well-designed clinical trials to demonstrate its clinical utility.
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Affiliation(s)
- Elisa Gobbini
- Thoracic Oncology Unit, CHU Grenoble-Alpes, 38700 Grenoble, France or (E.G.); (M.G.L.); (A.-C.T.); (D.M.-S.)
- Univ Lyon, Université Claude Bernard Lyon, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69373 Lyon, France; (S.O.-C.)
| | - Aurélie Swalduz
- Department of Medical Oncology, Centre Léon Bérard, 69373 Lyon, France; (A.S.); (M.P.)
| | - Matteo Giaj Levra
- Thoracic Oncology Unit, CHU Grenoble-Alpes, 38700 Grenoble, France or (E.G.); (M.G.L.); (A.-C.T.); (D.M.-S.)
| | - Sandra Ortiz-Cuaran
- Univ Lyon, Université Claude Bernard Lyon, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69373 Lyon, France; (S.O.-C.)
| | - Anne-Claire Toffart
- Thoracic Oncology Unit, CHU Grenoble-Alpes, 38700 Grenoble, France or (E.G.); (M.G.L.); (A.-C.T.); (D.M.-S.)
| | - Maurice Pérol
- Department of Medical Oncology, Centre Léon Bérard, 69373 Lyon, France; (A.S.); (M.P.)
| | - Denis Moro-Sibilot
- Thoracic Oncology Unit, CHU Grenoble-Alpes, 38700 Grenoble, France or (E.G.); (M.G.L.); (A.-C.T.); (D.M.-S.)
| | - Pierre Saintigny
- Univ Lyon, Université Claude Bernard Lyon, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69373 Lyon, France; (S.O.-C.)
- Department of Medical Oncology, Centre Léon Bérard, 69373 Lyon, France; (A.S.); (M.P.)
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Ergoren MC, Cobanogulları H, Temel SG, Mocan G. Functional coding/non-coding variants in EGFR, ROS1 and ALK genes and their role in liquid biopsy as a personalized therapy. Crit Rev Oncol Hematol 2020; 156:103113. [PMID: 33038629 DOI: 10.1016/j.critrevonc.2020.103113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 02/06/2023] Open
Abstract
Personalized medicine holds promise to tailor the treatment options for patients' unique genetic make-up, behavioral and environmental background. Liquid biopsy is non-invasive technique and precise diagnosis and treatment approach. Significantly, NGS technologies have revolutionized the genomic medicine by novel identifying SNPs, indel mutations in both coding and non-coding regions and also a promising technology to accelerate the early detection and finding new biomarkers for diagnosis and treatment. The number of the bioinformatics tools have been rapidly increasing with the aim of learning more about the detected mutations either they have a pathogenic role or not. EGFR, ROS1 and ALK genes are members of the RTK family. Until now, mutations within these genes have been associated with many cancers and involved in resistance formation to TKIs. This review article summarized the findings about the mostly investigated variations in EGFR, ROS1 and ALK genes and their potential role in liquid biopsy approach.
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Affiliation(s)
- Mahmut Cerkez Ergoren
- Department of Medical Biology, Faculty of Medicine, Near East University, Nicosia, 99138, Cyprus; DESAM Institute, Near East University, 99138, Nicosia, Cyprus.
| | - Havva Cobanogulları
- Department of Medical Biology, Faculty of Medicine, Near East University, Nicosia, 99138, Cyprus; DESAM Institute, Near East University, 99138, Nicosia, Cyprus
| | - Sehime Gulsun Temel
- Department of Medical Genetics, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey; Department of Histology & Embryology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey; Department of Translational Medicine, Institute of Health Sciences, Bursa Uludag University, Bursa, Turkey
| | - Gamze Mocan
- Department of Medical Biology, Faculty of Medicine, Near East University, Nicosia, 99138, Cyprus; Department of Medical Pathology, Faculty of Medicine, Near East University, Nicosia, 99138, Cyprus
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Clinical and analytical validation of FoundationOne Liquid CDx, a novel 324-Gene cfDNA-based comprehensive genomic profiling assay for cancers of solid tumor origin. PLoS One 2020; 15:e0237802. [PMID: 32976510 PMCID: PMC7518588 DOI: 10.1371/journal.pone.0237802] [Citation(s) in RCA: 198] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/30/2020] [Indexed: 12/25/2022] Open
Abstract
As availability of precision therapies expands, a well-validated circulating cell-free DNA (cfDNA)-based comprehensive genomic profiling assay has the potential to provide considerable value as a complement to tissue-based testing to ensure potentially life-extending therapies are administered to patients most likely to benefit. Additional data supporting the clinical validity of cfDNA-based testing is necessary to inform optimal use of these assays in the clinic. The FoundationOne®Liquid CDx assay is a pan-cancer cfDNA-based comprehensive genomic profiling assay that was recently approved by FDA. Validation studies included >7,500 tests and >30,000 unique variants across >300 genes and >30 cancer types. Clinical validity results across multiple tumor types are presented. Additionally, results demonstrated a 95% limit of detection of 0.40% variant allele fraction for select substitutions and insertions/deletions, 0.37% variant allele fraction for select rearrangements, 21.7% tumor fraction for copy number amplifications, and 30.4% TF for copy number losses. The limit of detection for microsatellite instability and blood tumor mutational burden were also determined. The false positive variant rate was 0.013% (approximately 1 in 8,000). Reproducibility of variant calling was 99.59%. In comparison with an orthogonal method, an overall positive percent agreement of 96.3% and negative percent agreement of >99.9% was observed. These study results demonstrate that FoundationOne Liquid CDx accurately and reproducibly detects the major types of genomic alterations in addition to complex biomarkers such as microsatellite instability, blood tumor mutational burden, and tumor fraction. Critically, clinical validity data is presented across multiple cancer types.
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Fu Y, Zhang Y, Khoo BL. Liquid biopsy technologies for hematological diseases. Med Res Rev 2020; 41:246-274. [PMID: 32929726 DOI: 10.1002/med.21731] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/10/2020] [Accepted: 09/02/2020] [Indexed: 12/18/2022]
Abstract
Since the discovery of circulating tumor cells in 1869, technological advances in studying circulating biomarkers from patients' blood have made the diagnosis of nonhematologic cancers less invasive. Technological advances in the detection and analysis of biomarkers provide new opportunities for the characterization of other disease types. When compared with traditional biopsies, liquid biopsy markers, such as exfoliated bladder cancer cells, circulating cell-free DNA (cfDNA), and extracellular vesicles (EV), are considered more convenient than conventional biopsies. Liquid biopsy markers undoubtedly have the potential to influence disease management and treatment dynamics. Our main focuses of this review will be the cell-based, gene-based, and protein-based key liquid biopsy markers (including EV and cfDNA) in disease detection, and discuss the research progress of these biomarkers used in conjunction with liquid biopsy. First, we highlighted the key technologies that have been broadly adopted used in hematological diseases. Second, we introduced the latest technological developments for the specific detection of cardiovascular disease, leukemia, and coronavirus disease. Finally, we concluded with perspectives on these research areas, focusing on the role of microfluidic technology and artificial intelligence in point-of-care medical applications. We believe that the noninvasive capabilities of these technologies have great potential in the development of diagnostics and can influence treatment options, thereby advancing precision disease management.
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Affiliation(s)
- Yatian Fu
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong, China
| | - Yiyuan Zhang
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong, China
| | - Bee Luan Khoo
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong, China
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Ortiz-Cuaran S, Mezquita L, Swalduz A, Aldea M, Mazieres J, Leonce C, Jovelet C, Pradines A, Avrillon V, Chumbi Flores WR, Lacroix L, Loriot Y, Westeel V, Ngo-Camus M, Tissot C, Raynaud C, Gervais R, Brain E, Monnet I, Giroux Leprieur E, Caramella C, Mahier-Aït Oukhatar C, Hoog-Labouret N, de Kievit F, Howarth K, Morris C, Green E, Friboulet L, Chabaud S, Guichou JF, Perol M, Besse B, Blay JY, Saintigny P, Planchard D. Circulating Tumor DNA Genomics Reveal Potential Mechanisms of Resistance to BRAF-Targeted Therapies in Patients with BRAF-Mutant Metastatic Non-Small Cell Lung Cancer. Clin Cancer Res 2020; 26:6242-6253. [PMID: 32859654 DOI: 10.1158/1078-0432.ccr-20-1037] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/11/2020] [Accepted: 08/20/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE The limited knowledge on the molecular profile of patients with BRAF-mutant non-small cell lung cancer (NSCLC) who progress under BRAF-targeted therapies (BRAF-TT) has hampered the development of subsequent therapeutic strategies for these patients. Here, we evaluated the clinical utility of circulating tumor DNA (ctDNA)-targeted sequencing to identify canonical BRAF mutations and genomic alterations potentially related to resistance to BRAF-TT, in a large cohort of patients with BRAF-mutant NSCLC. EXPERIMENTAL DESIGN This was a prospective study of 78 patients with advanced BRAF-mutant NSCLC, enrolled in 27 centers across France. Blood samples (n = 208) were collected from BRAF-TT-naïve patients (n = 47), patients nonprogressive under treatment (n = 115), or patients at disease progression (PD) to BRAF-TT (24/46 on BRAF monotherapy and 22/46 on BRAF/MEK combination therapy). ctDNA sequencing was performed using InVisionFirst-Lung. In silico structural modeling was used to predict the potential functional effect of the alterations found in ctDNA. RESULTS BRAFV600E ctDNA was detected in 74% of BRAF-TT-naïve patients, where alterations in genes related with the MAPK and PI3K pathways, signal transducers, and protein kinases were identified in 29% of the samples. ctDNA positivity at the first radiographic evaluation under treatment, as well as BRAF-mutant ctDNA positivity at PD were associated with poor survival. Potential drivers of resistance to either BRAF-TT monotherapy or BRAF/MEK combination were identified in 46% of patients and these included activating mutations in effectors of the MAPK and PI3K pathways, as well as alterations in U2AF1, IDH1, and CTNNB1. CONCLUSIONS ctDNA sequencing is clinically relevant for the detection of BRAF-activating mutations and the identification of alterations potentially related to resistance to BRAF-TT in BRAF-mutant NSCLC.
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Affiliation(s)
- Sandra Ortiz-Cuaran
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France.
| | - Laura Mezquita
- Department of Cancer Medicine, Gustave Roussy Cancer Campus, Villejuif, France.,Department of Medical Oncology, Hospital Clinic, Laboratory of Translational Genomics and Targeted Therapeutics in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Aurélie Swalduz
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France.,Department of Medical Oncology, Centre Léon Bérard & Université Claude Bernard Lyon I/Université de Lyon, Lyon, France
| | - Mihalea Aldea
- Department of Cancer Medicine, Gustave Roussy Cancer Campus, Villejuif, France
| | - Julien Mazieres
- Department of Respiratory Disease, Larrey Hospital, University Hospital of Toulouse, Paul Sabatier University, Toulouse, France
| | - Camille Leonce
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France
| | - Cecile Jovelet
- Translational Research Laboratory, Gustave Roussy Cancer Campus, Villejuif, France
| | | | - Virginie Avrillon
- Department of Medical Oncology, Centre Léon Bérard & Université Claude Bernard Lyon I/Université de Lyon, Lyon, France
| | | | - Ludovic Lacroix
- Translational Research Laboratory, Gustave Roussy Cancer Campus, Villejuif, France
| | - Yohann Loriot
- Department of Cancer Medicine, Gustave Roussy Cancer Campus, Villejuif, France
| | | | - Maud Ngo-Camus
- Department of Early Drug Development, Gustave Roussy Cancer Campus, Villejuif, France
| | - Claire Tissot
- University Hospital of Saint-Etienne, Saint-Etienne, France
| | | | | | | | - Isabelle Monnet
- Centre Hospitalier Intercommunal de Créteil, Creteil, France
| | | | - Caroline Caramella
- Department of Radiology, Gustave Roussy Cancer Campus, Villejuif, France
| | | | | | | | | | | | | | - Luc Friboulet
- Université Paris-Saclay, Gustave Roussy Cancer Campus, Inserm, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, Villejuif, France
| | - Sylvie Chabaud
- Department of Clinical Research, Centre Léon Bérard, Lyon, France
| | - Jean-François Guichou
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, Montpellier, France
| | - Maurice Perol
- Department of Medical Oncology, Centre Léon Bérard & Université Claude Bernard Lyon I/Université de Lyon, Lyon, France
| | - Benjamin Besse
- Department of Cancer Medicine, Gustave Roussy Cancer Campus, Villejuif, France
| | - Jean-Yves Blay
- Department of Medical Oncology, Centre Léon Bérard & Université Claude Bernard Lyon I/Université de Lyon, Lyon, France
| | - Pierre Saintigny
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France. .,Department of Medical Oncology, Centre Léon Bérard & Université Claude Bernard Lyon I/Université de Lyon, Lyon, France
| | - David Planchard
- Department of Cancer Medicine, Gustave Roussy Cancer Campus, Villejuif, France.
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Tran LS, Nguyen QTT, Nguyen CV, Tran VU, Nguyen THT, Le HT, Nguyen MLT, Le VT, Pham LS, Vo BT, Dang ATH, Nguyen LT, Nguyen TCV, Pham HAT, Tran TT, Nguyen LH, Nguyen TTT, Nguyen KHT, Vu YV, Nguyen NH, Bui VQ, Bui HH, Do TTT, Lam NV, Truong Dinh K, Phan MD, Nguyen HN, Giang H. Ultra-Deep Massive Parallel Sequencing of Plasma Cell-Free DNA Enables Large-Scale Profiling of Driver Mutations in Vietnamese Patients With Advanced Non-Small Cell Lung Cancer. Front Oncol 2020; 10:1351. [PMID: 32850431 PMCID: PMC7418519 DOI: 10.3389/fonc.2020.01351] [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: 03/28/2020] [Accepted: 06/26/2020] [Indexed: 01/15/2023] Open
Abstract
Population-specific profiling of mutations in cancer genes is of critical importance for the understanding of cancer biology in general as well as the establishment of optimal diagnostics and treatment guidelines for that particular population. Although genetic analysis of tumor tissue is often used to detect mutations in cancer genes, the invasiveness and limited accessibility hinders its application in large-scale population studies. Here, we used ultra-deep massive parallel sequencing of plasma cell free DNA (cfDNA) to identify the mutation profiles of 265 Vietnamese patients with advanced non-small cell lung cancer (NSCLC). Compared to a cohort of advanced NSCLC patients characterized by sequencing of tissue samples, cfDNA genomic testing, despite lower mutation detection rates, was able to detect major mutations in tested driver genes that reflected similar mutation composition and distribution pattern, as well as major associations between mutation prevalence and clinical features. In conclusion, ultra-deep sequencing of plasma cfDNA represents an alternative approach for population-wide genetic profiling of cancer genes where recruitment of patients is limited to the accessibility of tumor tissue site.
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Affiliation(s)
| | | | | | | | | | - Ha Thu Le
- Ha Noi Oncology Hospital, Hanoi, Vietnam
| | | | | | - Lam-Son Pham
- Vietnam National Cancer Hospital, Hanoi, Vietnam
| | | | - Anh-Thu Huynh Dang
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | | | | | | | | | | | - Yen-Vi Vu
- Gene Solutions, Ho Chi Minh City, Vietnam
| | | | | | | | | | - Nien Vinh Lam
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | - Hoai-Nghia Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hoa Giang
- Gene Solutions, Ho Chi Minh City, Vietnam
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Liquid Biopsy by Next-Generation Sequencing: a Multimodality Test for Management of Cancer. Curr Hematol Malig Rep 2020; 14:358-367. [PMID: 31346903 DOI: 10.1007/s11899-019-00532-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW While liquid biopsy is still relatively a new concept, the advent of next-generation sequencing (NGS) technologies has recently generated a revolution in the field and will be the focus of this review. RECENT FINDINGS Circulating tumor DNA (ctDNA) derives from tumor cells and provides information about the genetic alterations of tumors. However, ctDNA concentration in plasma can be below the level of detection by conventional methods; therefore, screening for actionable genetic information is challenging. Clinical trials exploring targeted and untargeted sequencing to improve the outcomes of ctDNA detection are showing promising results, having reached a limit of detection as low as 0.001% of ctDNA in a background of normal circulating DNA. Most of the challenges related to the sensitivity of detection of ctDNA have been defeated by dint of NGS-based approaches. Despite all the efforts, these methods are still expensive, time-consuming, and require advanced skills for appropriate interpretation. Nevertheless, the technology is rapidly improving, and the expectations for the implementation of liquid biopsy into the clinical practice in the near future are high.
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Yang SR, Schultheis AM, Yu H, Mandelker D, Ladanyi M, Büttner R. Precision medicine in non-small cell lung cancer: Current applications and future directions. Semin Cancer Biol 2020; 84:184-198. [PMID: 32730814 DOI: 10.1016/j.semcancer.2020.07.009] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/24/2020] [Accepted: 07/13/2020] [Indexed: 12/24/2022]
Abstract
Advances in biomarkers, targeted therapies, and immuno-oncology have transformed the clinical management of patients with advanced NSCLC. For oncogene-driven tumors, there are highly effective targeted therapies against EGFR, ALK, ROS1, BRAF, TRK, RET, and MET. In addition, investigational therapies for KRAS, NRG1, and HER2 have shown promising results and may become standard-of-care in the near future. In parallel, immune-checkpoint therapy has emerged as an indispensable treatment modality, especially for patients lacking actionable oncogenic drivers. While PD-L1 expression has shown modest predictive utility, biomarkers for immune-checkpoint inhibition in NSCLC have remained elusive and represent an area of active investigation. Given the growing importance of biomarkers, optimal utilization of small tissue biopsies and alternative genotyping methods using circulating cell-free DNA have become increasingly integrated into clinical practice. In this review, we will summarize the current landscape and emerging trends in precision medicine for patients with advanced NSCLC with a special focus on predictive biomarker testing.
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Affiliation(s)
- Soo-Ryum Yang
- Memorial Sloan Kettering Cancer Center, Department of Pathology, United States
| | | | - Helena Yu
- Memorial Sloan Kettering Cancer Center, Department of Medicine, United States
| | - Diana Mandelker
- Memorial Sloan Kettering Cancer Center, Department of Pathology, United States
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, Department of Pathology, United States
| | - Reinhard Büttner
- University Hospital of Cologne, Department of Pathology, Germany.
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