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Chen K, He Y, Wang W, Yuan X, Carbone DP, Yang F. Development of new techniques and clinical applications of liquid biopsy in lung cancer management. Sci Bull (Beijing) 2024; 69:1556-1568. [PMID: 38641511 DOI: 10.1016/j.scib.2024.03.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/12/2023] [Accepted: 01/17/2024] [Indexed: 04/21/2024]
Abstract
Lung cancer is an exceedingly malignant tumor reported as having the highest morbidity and mortality of any cancer worldwide, thus posing a great threat to global health. Despite the growing demand for precision medicine, current methods for early clinical detection, treatment and prognosis monitoring in lung cancer are hampered by certain bottlenecks. Studies have found that during the formation and development of a tumor, molecular substances carrying tumor-related genetic information can be released into body fluids. Liquid biopsy (LB), a method for detecting these tumor-related markers in body fluids, maybe a way to make progress in these bottlenecks. In recent years, LB technology has undergone rapid advancements. Therefore, this review will provide information on technical updates to LB and its potential clinical applications, evaluate its effectiveness for specific applications, discuss the existing limitations of LB, and present a look forward to possible future clinical applications. Specifically, this paper will introduce technical updates from the prospectives of engineering breakthroughs in the detection of membrane-based LB biomarkers and other improvements in sequencing technology. Additionally, it will summarize the latest applications of liquid biopsy for the early detection, diagnosis, treatment, and prognosis of lung cancer. We will present the interconnectedness of clinical and laboratory issues and the interplay of technology and application in LB today.
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Affiliation(s)
- Kezhong Chen
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China
| | - Yue He
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China
| | - Wenxiang Wang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China
| | - Xiaoqiu Yuan
- Peking University Health Science Center, Beijing 100191, China
| | - David P Carbone
- Thoracic Oncology Center, Ohio State University, Columbus 43026, USA.
| | - Fan Yang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China.
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Andersson D, Kebede FT, Escobar M, Österlund T, Ståhlberg A. Principles of digital sequencing using unique molecular identifiers. Mol Aspects Med 2024; 96:101253. [PMID: 38367531 DOI: 10.1016/j.mam.2024.101253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 02/19/2024]
Abstract
Massively parallel sequencing technologies have long been used in both basic research and clinical routine. The recent introduction of digital sequencing has made previously challenging applications possible by significantly improving sensitivity and specificity to now allow detection of rare sequence variants, even at single molecule level. Digital sequencing utilizes unique molecular identifiers (UMIs) to minimize sequencing-induced errors and quantification biases. Here, we discuss the principles of UMIs and how they are used in digital sequencing. We outline the properties of different UMI types and the consequences of various UMI approaches in relation to experimental protocols and bioinformatics. Finally, we describe how digital sequencing can be applied in specific research fields, focusing on cancer management where it can be used in screening of asymptomatic individuals, diagnosis, treatment prediction, prognostication, monitoring treatment efficacy and early detection of treatment resistance as well as relapse.
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Affiliation(s)
- Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Firaol Tamiru Kebede
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Mandy Escobar
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Tobias Österlund
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 413 90, Gothenburg, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 413 90, Gothenburg, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden.
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Otsuji R, Fujioka Y, Hata N, Kuga D, Hatae R, Sangatsuda Y, Nakamizo A, Mizoguchi M, Yoshimoto K. Liquid Biopsy for Glioma Using Cell-Free DNA in Cerebrospinal Fluid. Cancers (Basel) 2024; 16:1009. [PMID: 38473369 DOI: 10.3390/cancers16051009] [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: 12/25/2023] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Glioma is one of the most common primary central nervous system (CNS) tumors, and its molecular diagnosis is crucial. However, surgical resection or biopsy is risky when the tumor is located deep in the brain or brainstem. In such cases, a minimally invasive approach to liquid biopsy is beneficial. Cell-free DNA (cfDNA), which directly reflects tumor-specific genetic changes, has attracted attention as a target for liquid biopsy, and blood-based cfDNA monitoring has been demonstrated for other extra-cranial cancers. However, it is still challenging to fully detect CNS tumors derived from cfDNA in the blood, including gliomas, because of the unique structure of the blood-brain barrier. Alternatively, cerebrospinal fluid (CSF) is an ideal source of cfDNA and is expected to contribute significantly to the liquid biopsy of gliomas. Several successful studies have been conducted to detect tumor-specific genetic alterations in cfDNA from CSF using digital PCR and/or next-generation sequencing. This review summarizes the current status of CSF-based cfDNA-targeted liquid biopsy for gliomas. It highlights how the approaches differ from liquid biopsies of other extra-cranial cancers and discusses the current issues and prospects.
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Affiliation(s)
- Ryosuke Otsuji
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yutaka Fujioka
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Nobuhiro Hata
- Department of Neurosurgery, Oita University Faculty of Medicine, Yufu 879-5593, Japan
| | - Daisuke Kuga
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Ryusuke Hatae
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Akira Nakamizo
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Department of Neurosurgery, National Hospital Organization Kyushu Medical Center, Clinical Research Institute, Fukuoka 810-8563, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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4
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Zavarykina TM, Lomskova PK, Pronina IV, Khokhlova SV, Stenina MB, Sukhikh GT. Circulating Tumor DNA Is a Variant of Liquid Biopsy with Predictive and Prognostic Clinical Value in Breast Cancer Patients. Int J Mol Sci 2023; 24:17073. [PMID: 38069396 PMCID: PMC10706922 DOI: 10.3390/ijms242317073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
This paper introduces the reader to the field of liquid biopsies and cell-free nucleic acids, focusing on circulating tumor DNA (ctDNA) in breast cancer (BC). BC is the most common type of cancer in women, and progress with regard to treatment has been made in recent years. Despite this, there remain a number of unresolved issues in the treatment of BC; in particular, early detection and diagnosis, reliable markers of response to treatment and for the prediction of recurrence and metastasis, especially for unfavorable subtypes, are needed. It is also important to identify biomarkers for the assessment of drug resistance and for disease monitoring. Our work is devoted to ctDNA, which may be such a marker. Here, we describe its main characteristics and potential applications in clinical oncology. This review considers the results of studies devoted to the analysis of the prognostic and predictive roles of various methods for the determination of ctDNA in BC patients. Currently known epigenetic changes in ctDNA with clinical significance are reviewed. The possibility of using ctDNA as a predictive and prognostic marker for monitoring BC and predicting the recurrence and metastasis of cancer is also discussed, which may become an important part of a precision approach to the treatment of BC.
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Affiliation(s)
- Tatiana M. Zavarykina
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Polina K. Lomskova
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
| | - Irina V. Pronina
- Institute of General Pathology and Pathophysiology, Moscow 125315, Russia;
| | - Svetlana V. Khokhlova
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Marina B. Stenina
- “N.N. Blokhin National Medical Research Center of Oncology of Ministry of Health of the Russian Federation, Moscow 115522, Russia;
| | - Gennady T. Sukhikh
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
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5
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Trivedi R, Bhat KP. Liquid biopsy: creating opportunities in brain space. Br J Cancer 2023; 129:1727-1746. [PMID: 37752289 PMCID: PMC10667495 DOI: 10.1038/s41416-023-02446-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/10/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
In recent years, liquid biopsy has emerged as an alternative method to diagnose and monitor tumors. Compared to classical tissue biopsy procedures, liquid biopsy facilitates the repetitive collection of diverse cellular and acellular analytes from various biofluids in a non/minimally invasive manner. This strategy is of greater significance for high-grade brain malignancies such as glioblastoma as the quantity and accessibility of tumors are limited, and there are collateral risks of compromised life quality coupled with surgical interventions. Currently, blood and cerebrospinal fluid (CSF) are the most common biofluids used to collect circulating cells and biomolecules of tumor origin. These liquid biopsy analytes have created opportunities for real-time investigations of distinct genetic, epigenetic, transcriptomics, proteomics, and metabolomics alterations associated with brain tumors. This review describes different classes of liquid biopsy biomarkers present in the biofluids of brain tumor patients. Moreover, an overview of the liquid biopsy applications, challenges, recent technological advances, and clinical trials in the brain have also been provided.
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Affiliation(s)
- Rakesh Trivedi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Krishna P Bhat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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Verlicchi A, Canale M, Chiadini E, Cravero P, Urbini M, Andrikou K, Pasini L, Flospergher M, Burgio MA, Crinò L, Ulivi P, Delmonte A. The Clinical Significance of Circulating Tumor DNA for Minimal Residual Disease Identification in Early-Stage Non-Small Cell Lung Cancer. Life (Basel) 2023; 13:1915. [PMID: 37763318 PMCID: PMC10532754 DOI: 10.3390/life13091915] [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: 07/07/2023] [Revised: 08/18/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Lung cancer (LC) is the deadliest malignancy worldwide. In an operable stage I-III patient setting, the detection of minimal residual disease (MRD) after curative treatment could identify patients at higher risk of relapse. In this context, the study of circulating tumor DNA (ctDNA) is emerging as a useful tool to identify patients who could benefit from an adjuvant treatment, and patients who could avoid adverse events related to a more aggressive clinical management. On the other hand, ctDNA profiling presents technical, biological and standardization challenges before entering clinical practice as a decisional tool. In this paper, we review the latest advances regarding the role of ctDNA in identifying MRD and in predicting patients' prognosis, with a particular focus on clinical trials investigating the potential of ctDNA, the technical challenges to address and the biological parameters that influence the MRD detection.
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Affiliation(s)
- Alberto Verlicchi
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Matteo Canale
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Elisa Chiadini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Paola Cravero
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Milena Urbini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Kalliopi Andrikou
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Luigi Pasini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Michele Flospergher
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Marco Angelo Burgio
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Lucio Crinò
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Paola Ulivi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Angelo Delmonte
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
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Takahashi K, Takeda Y, Ono Y, Isomoto H, Mizukami Y. Current status of molecular diagnostic approaches using liquid biopsy. J Gastroenterol 2023; 58:834-847. [PMID: 37470859 PMCID: PMC10423147 DOI: 10.1007/s00535-023-02024-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/08/2023] [Indexed: 07/21/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive and lethal cancers, and developing an efficient and reliable approach for its early-stage diagnosis is urgently needed. Precancerous lesions of PDAC, such as pancreatic intraepithelial neoplasia (PanIN) and intraductal papillary mucinous neoplasms (IPMN), arise through multiple steps of driver gene alterations in KRAS, TP53, CDKN2A, SMAD4, or GNAS. Hallmark mutations play a role in tumor initiation and progression, and their detection in bodily fluids is crucial for diagnosis. Recently, liquid biopsy has gained attention as an approach to complement pathological diagnosis, and in addition to mutation signatures in cell-free DNA, cell-free RNA, and extracellular vesicles have been investigated as potential diagnostic and prognostic markers. Integrating such molecular information to revise the diagnostic criteria for pancreatic cancer can enable a better understanding of the pathogenesis underlying inter-patient heterogeneity, such as sensitivity to chemotherapy and disease outcomes. This review discusses the current diagnostic approaches and clinical applications of genetic analysis in pancreatic cancer and diagnostic attempts by liquid biopsy and molecular analyses using pancreatic juice, duodenal fluid, and blood samples. Emerging knowledge in the rapidly advancing liquid biopsy field is promising for molecular profiling and diagnosing pancreatic diseases with significant diversity.
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Affiliation(s)
- Kenji Takahashi
- Division of Metabolism and Biosystemic Science, Gastroenterology, and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan.
| | - Yohei Takeda
- Division of Medicine and Clinical Science, Department of Multidisciplinary Internal Medicine, Faculty of Medicine, Tottori University, Tottori, Japan
| | - Yusuke Ono
- Division of Metabolism and Biosystemic Science, Gastroenterology, and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | - Hajime Isomoto
- Division of Medicine and Clinical Science, Department of Multidisciplinary Internal Medicine, Faculty of Medicine, Tottori University, Tottori, Japan
| | - Yusuke Mizukami
- Division of Metabolism and Biosystemic Science, Gastroenterology, and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
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Cai P, Yang B, Zhao J, Ye P, Yang D. Detection of KRAS mutation using plasma samples in non-small-cell lung cancer: a systematic review and meta-analysis. Front Oncol 2023; 13:1207892. [PMID: 37483491 PMCID: PMC10357383 DOI: 10.3389/fonc.2023.1207892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Background The aim of this study was to investigate the diagnostic accuracy of KRAS mutation detection using plasma sample of patients with non-small cell lung cancer (NSCLC). Methods Databases of Pubmed, Embase, Cochrane Library, and Web of Science were searched for studies detecting KRAS mutation in paired tissue and plasma samples of patients with NSCLC. Data were extracted from each eligible study and analyzed using MetaDiSc and STATA. Results After database searching and screening of the studies with pre-defined criteria, 43 eligible studies were identified and relevant data were extracted. After pooling the accuracy data from 3341 patients, the pooled sensitivity, specificity and diagnostic odds ratio were 71%, 94%, and 59.28, respectively. Area under curve of summary receiver operating characteristic curve was 0.8883. Subgroup analysis revealed that next-generation sequencing outperformed PCR-based techniques in detecting KRAS mutation using plasma sample of patients with NSCLC, with sensitivity, specificity, and diagnostic odds ratio of 73%, 94%, and 82.60, respectively. Conclusion Compared to paired tumor tissue sample, plasma sample showed overall good performance in detecting KRAS mutation in patients with NSCLC, which could serve as good surrogate when tissue samples are not available.
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Affiliation(s)
- Peiling Cai
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, China
| | - Bofan Yang
- School of Clinical Medicine, Chengdu University, Chengdu, China
| | - Jiahui Zhao
- School of Clinical Medicine, Chengdu University, Chengdu, China
| | - Peng Ye
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, China
| | - Dongmei Yang
- Clinical Laboratory & Clinical Research and Translational Center, Second People’s Hospital of Yibin City-West China Yibin Hospital, Sichuan University, Yibin, China
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Khan SR, Scheffler M, Soomar SM, Rashid YA, Moosajee M, Ahmad A, Raza A, Uddin S. Role of circulating-tumor DNA in the early-stage non-small cell lung carcinoma as a predictive biomarker. Pathol Res Pract 2023; 245:154455. [PMID: 37054576 DOI: 10.1016/j.prp.2023.154455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 04/15/2023]
Abstract
Lung cancer is one of the most common solid malignancies. Tissue biopsy is the standard method for accurately diagnosing lung and many other malignancies over decades. However, molecular profiling of tumors leads to establishing a new horizon in the field of precision medicine, which has now entered the mainstream in clinical practice. In this context, a minimally invasive complementary method has been proposed as a liquid biopsy (LB) which is a blood-based test that is gaining popularity as it provides the opportunity to test genotypes in a unique, less invasive manner. Circulating tumor cells (CTC) captivating the Circulating-tumor DNA (Ct-DNA) are often present in the blood of lung cancer patients and are the fundamental concept behind LB. There are multiple clinical uses of Ct-DNA, including its role in prognostic and therapeutic purposes. The treatment of lung cancer has drastically evolved over time. Therefore, this review article mainly focuses on the current literature on circulating tumor DNA and its clinical implications and future goals in non-small cell lung cancer.
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Affiliation(s)
- Saqib Raza Khan
- Medical Oncology Department, Aga Khan University Hospital, Karachi, Pakistan.
| | - Matthias Scheffler
- Internal Medicine Department, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | | | - Yasmin Abdul Rashid
- Medical Oncology Department, Aga Khan University Hospital, Karachi, Pakistan
| | - Munira Moosajee
- Medical Oncology Department, Aga Khan University Hospital, Karachi, Pakistan
| | - Aamir Ahmad
- Translational Research Institute & Dermatology Institute, Hamad Medical Corporation, Doha, Qatar
| | - Afsheen Raza
- College of Health Sciences, Abu Dhabi University, Abu Dhabi, United Arab Emirates
| | - Shahab Uddin
- Translational Research Institute & Dermatology Institute, Hamad Medical Corporation, Doha, Qatar.
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10
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Caputo V, Ciardiello F, Corte CMD, Martini G, Troiani T, Napolitano S. Diagnostic value of liquid biopsy in the era of precision medicine: 10 years of clinical evidence in cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:102-138. [PMID: 36937316 PMCID: PMC10017193 DOI: 10.37349/etat.2023.00125] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/13/2022] [Indexed: 03/06/2023] Open
Abstract
Liquid biopsy is a diagnostic repeatable test, which in last years has emerged as a powerful tool for profiling cancer genomes in real-time with minimal invasiveness and tailoring oncological decision-making. It analyzes different blood-circulating biomarkers and circulating tumor DNA (ctDNA) is the preferred one. Nevertheless, tissue biopsy remains the gold standard for molecular evaluation of solid tumors whereas liquid biopsy is a complementary tool in many different clinical settings, such as treatment selection, monitoring treatment response, cancer clonal evolution, prognostic evaluation, as well as the detection of early disease and minimal residual disease (MRD). A wide number of technologies have been developed with the aim of increasing their sensitivity and specificity with acceptable costs. Moreover, several preclinical and clinical studies have been conducted to better understand liquid biopsy clinical utility. Anyway, several issues are still a limitation of its use such as false positive and negative results, results interpretation, and standardization of the panel tests. Although there has been rapid development of the research in these fields and recent advances in the clinical setting, many clinical trials and studies are still needed to make liquid biopsy an instrument of clinical routine. This review provides an overview of the current and future clinical applications and opening questions of liquid biopsy in different oncological settings, with particular attention to ctDNA liquid biopsy.
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Affiliation(s)
- Vincenza Caputo
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Fortunato Ciardiello
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Carminia Maria Della Corte
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Giulia Martini
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Teresa Troiani
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Stefania Napolitano
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
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Abstract
Liquid biopsy provides a noninvasive window to the cancer genome and physiology. In particular, cell-free DNA (cfDNA) is a versatile analyte for guiding treatment, monitoring treatment response and resistance, tracking minimal residual disease, and detecting cancer earlier. Despite certain successes, brain cancer diagnosis is amongst those applications that has so far resisted clinical implementation. Recent approaches have highlighted the clinical gain achievable by exploiting cfDNA biological signatures to boost liquid biopsy or unlock new applications. However, the biology of cfDNA is complex, still partially understood, and affected by a range of intrinsic and extrinsic factors. This guide will provide the keys to read, decode, and harness cfDNA biology: the diverse sources of cfDNA in the bloodstream, the mechanism of cfDNA release from cells, the cfDNA structure, topology, and why accounting for cfDNA biology matters for clinical applications of liquid biopsy.
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Affiliation(s)
- Florent Mouliere
- Amsterdam UMC location Vrije Universiteit Amsterdam, Pathology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
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12
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Palmieri M, Zulato E, Wahl SGF, Guibert N, Frullanti E. Diagnostic accuracy of circulating free DNA testing for the detection of KRAS mutations in non-small cell lung cancer: A systematic review and meta-analysis. Front Genet 2022; 13:1015161. [PMID: 36386815 PMCID: PMC9640997 DOI: 10.3389/fgene.2022.1015161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
Kirsten rat sarcoma viral oncogene homolog (KRAS) gene encodes a GTPase that acts as a molecular switch for intracellular signal transduction, promoting cell growth and proliferation. Mutations in the KRAS gene represent important biomarkers for NSCLC targeted therapy. However, detection of KRAS mutations in tissues has shown some limitations. During the last years, analyses of circulating free DNA (cfDNA) has emerged as an alternative and minimally invasive, approach to investigate tumor molecular changes. Here, we assessed the diagnostic performance of cfDNA analysis, compared to tissues through a meta-analysis and systematic review of existing literature. From 561 candidate papers, we finally identified 40 studies, including 2,805 NSCLC patients. We extracted values relating to the number of true-positive, false-positive, false-negative, and true-negative. Pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio, each with 95% CI, were calculated. A summary receiver operating characteristic curve and the area under curve (AUC) were used to evaluate the overall diagnostic performance. The pooled sensitivity was 0.71 (95% CI 0.68–0.74) and the specificity was 0.93 (95% CI 0.92–0.94). The diagnostic odds ratio was 35.24 (95% CI 24.88–49.91) and the area under the curve was 0.92 (SE = 0.094). These results provide evidence that detection of KRAS mutation using cfDNA testing is of adequate diagnostic accuracy thus offering to the clinicians a new promising screening test for NSCLC patients.
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Affiliation(s)
- Maria Palmieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisabetta Zulato
- Basic and Translational Oncology Unit, Istituto Oncologico Veneto IOV—IRCCS, Padova, Italy
| | - Sissel Gyrid Freim Wahl
- Department of Pathology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Technology and Science, Trondheim, Norway
| | - Nicolas Guibert
- Thoracic Oncology Department, Larrey Hospital, University Hospital of Toulouse, Toulouse, France
- Inserm, Centre de Recherche en Cancérologie de Toulouse, CRCT UMR-1037, Toulouse, France
- University of Toulouse III (Paul Sabatier), Toulouse, France
| | - Elisa Frullanti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- *Correspondence: Elisa Frullanti,
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13
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Methodology established for the detection of circulating tumor DNA by hybridization capture. Biotechniques 2022; 73:151-158. [PMID: 36065956 DOI: 10.2144/btn-2022-0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Roche's AVENIO ctDNA analysis kits and bioinformatics analysis (the AVENIO system) are accessible to all NGS laboratories. We have developed an approach, namely the Sec-Seq system, and compared the accuracy, sensitivity, repeatability and economic cost between the AVENIO system and the Sec-Seq system. Both methods share the comparable accuracy and sensitivity in detecting the variant allele frequency of 0.0005, while the Sec-Seq system shows better accuracy in detecting the variant allele frequency of 0.001. Furthermore, the Sec-Seq system displays a much better detection sensitivity than the AVENIO system. The Sec-Seq system has satisfactory performance in detecting the rare genetic variants in ctDNA with lower economic cost compared with the AVENIO system.
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Shields MD, Chen K, Dutcher G, Patel I, Pellini B. Making the Rounds: Exploring the Role of Circulating Tumor DNA (ctDNA) in Non-Small Cell Lung Cancer. Int J Mol Sci 2022; 23:ijms23169006. [PMID: 36012272 PMCID: PMC9408840 DOI: 10.3390/ijms23169006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022] Open
Abstract
Advancements in the clinical practice of non-small cell lung cancer (NSCLC) are shifting treatment paradigms towards increasingly personalized approaches. Liquid biopsies using various circulating analytes provide minimally invasive methods of sampling the molecular content within tumor cells. Plasma-derived circulating tumor DNA (ctDNA), the tumor-derived component of cell-free DNA (cfDNA), is the most extensively studied analyte and has a growing list of applications in the clinical management of NSCLC. As an alternative to tumor genotyping, the assessment of oncogenic driver alterations by ctDNA has become an accepted companion diagnostic via both single-gene polymerase chain reactions (PCR) and next-generation sequencing (NGS) for advanced NSCLC. ctDNA technologies have also shown the ability to detect the emerging mechanisms of acquired resistance that evolve after targeted therapy. Furthermore, the detection of minimal residual disease (MRD) by ctDNA for patients with NSCLC after curative-intent treatment may serve as a prognostic and potentially predictive biomarker for recurrence and response to therapy, respectively. Finally, ctDNA analysis via mutational, methylation, and/or fragmentation multi-omic profiling offers the potential for improving early lung cancer detection. In this review, we discuss the role of ctDNA in each of these capacities, namely, for molecular profiling, treatment response monitoring, MRD detection, and early cancer detection of NSCLC.
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Affiliation(s)
- Misty Dawn Shields
- Department of Internal Medicine, Division of Hematology/Oncology, Indiana University School of Medicine, Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
| | - Kevin Chen
- Department of Radiation Oncology, Division of Cancer Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Giselle Dutcher
- Department of Medicine, Division of Solid Tumor Oncology, University Hospitals Seidman Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ishika Patel
- Department of Public Health, University of South Florida, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Bruna Pellini
- Department of Thoracic Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence:
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15
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Paulson V, Konnick EQ, Lockwood CH. When Tissue Is the Issue. Clin Lab Med 2022; 42:485-496. [DOI: 10.1016/j.cll.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Pre-PCR Mutation-Enrichment Methods for Liquid Biopsy Applications. Cancers (Basel) 2022; 14:cancers14133143. [PMID: 35804916 PMCID: PMC9264780 DOI: 10.3390/cancers14133143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 01/25/2023] Open
Abstract
Liquid biopsy is having a remarkable impact on healthcare- and disease-management in the context of personalized medicine. Circulating free DNA (cfDNA) is one of the most instructive liquid-biopsy-based biomarkers and harbors valuable information for diagnostic, predictive, and prognostic purposes. When it comes to cancer, circulating DNA from the tumor (ctDNA) has a wide range of applications, from early cancer detection to the early detection of relapse or drug resistance, and the tracking of the dynamic genomic make-up of tumor cells. However, the detection of ctDNA remains technically challenging, due, in part, to the low frequency of ctDNA among excessive circulating cfDNA originating from normal tissues. During the past three decades, mutation-enrichment methods have emerged to boost sensitivity and enable facile detection of low-level mutations. Although most developed techniques apply mutation enrichment during or following initial PCR, there are a few techniques that allow mutation selection prior to PCR, which provides advantages. Pre-PCR enrichment techniques can be directly applied to genomic DNA and diminish the influence of PCR errors that can take place during amplification. Moreover, they have the capability for high multiplexity and can be followed by established mutation detection and enrichment technologies without changes to their established procedures. The first approaches for pre-PCR enrichment were developed by employing restriction endonucleases directly on genomic DNA in the early 1990s. However, newly developed pre-PCR enrichment methods provide higher sensitivity and versatility. This review describes the available pre-PCR enrichment methods and focuses on the most recently developed techniques (NaME-PrO, UVME, and DEASH/MAESTRO), emphasizing their applications in liquid biopsies.
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17
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Kwon M, Ku BM, Olsen S, Park S, Lefterova M, Odegaard J, Jung HA, Sun JM, Lee SH, Ahn JS, Park K, Ahn MJ. Longitudinal monitoring by next-generation sequencing of plasma cell-free DNA in ALK rearranged NSCLC patients treated with ALK tyrosine kinase inhibitors. Cancer Med 2022; 11:2944-2956. [PMID: 35437925 PMCID: PMC9359877 DOI: 10.1002/cam4.4663] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 12/11/2022] Open
Abstract
Background Patients with ALK‐rearranged non‐small cell lung cancer (ALK+ NSCLC) inevitably acquire resistance to ALK inhibitors. Longitudinal monitoring of cell‐free plasma DNA (cfDNA) next‐generation sequencing (NGS) could predict the response and resistance to tyrosine kinase inhibitor (TKI) therapy in ALK+ NSCLC. Methods Patients with ALK+ NSCLC determined by standard tissue testing and planned to undergo TKI therapy were prospectively recruited. Plasma was collected at pretreatment, 2 months‐post therapy, and at progression for cfDNA‐NGS analysis, Guardant 360. Results Among 92 patients enrolled, circulating tumor DNA (ctDNA) was detected in 69 baseline samples (75%): 43 ALK fusions (62.3%) and two ALK mutations without fusion (2.8%). Two patients showed ALK‐resistance mutations after ceritinib; G1202R, and co‐occurring G1202R and T1151R. Eight patients developed ALK resistance mutations after crizotinib therapy; L1196M (n = 5), G1269A (n = 1), G1202R (n = 1), and co‐occurring F1174L, G1202R, and G1269A (n = 1). Absence of ctDNA at baseline was significantly associated with longer progression‐free survival (PFS; median 36.1 vs. 11.4 months, p = 0.0049) and overall survival (OS; not reached vs. 29.3 months, p = 0.0200). ctDNA clearance at 2 months (n = 29) was associated with significantly longer PFS (25.4 vs. 11.6 months, p = 0.0012) and OS (not reached vs. 26.1 months, p = 0.0307) than those without clearance (n = 22). Patients with co‐occurring TP53 alterations and ALK fusions at baseline (n = 16) showed significantly shorter PFS (7.28 vs. 13.0 months, p = 0.0307) than those without TP53 alterations (n = 25). Conclusions cfDNA‐NGS facilitates detection of ALK fusions and resistance mutations, assessment of prognosis, and monitoring dynamic changes of genomic alterations in ALK+ NSCLC treated with ALK‐TKI.
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Affiliation(s)
- Minsuk Kwon
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Department of Hematology-Oncology, Ajou University School of Medicine, Suwon, South Korea
| | - Bo Mi Ku
- 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
| | - Sehhoon Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Martina Lefterova
- Department of Medical and Clinical Affairs, Guardant Health AMEA, Singapore, Singapore
| | - Justin Odegaard
- Department of Medical and Clinical Affairs, Guardant Health AMEA, Singapore, Singapore
| | - 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
| | - 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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18
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Nuclease-Assisted, Multiplexed Minor-Allele Enrichment: Application in Liquid Biopsy of Cancer. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2394:433-451. [PMID: 35094339 DOI: 10.1007/978-1-0716-1811-0_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The use of next-generation sequencing (NGS) to profile genomic variation of individual cancer species is revolutionizing the practice of clinical oncology. In liquid biopsy of cancer, sequencing of circulating-free DNA (cfDNA) is gradually applied to all stages of cancer diagnosis and treatment, serving as complement or replacement of tissue biopsies. However, analysis of cfDNA obtained from blood draws still faces technical obstacles due in part to an excess of wild-type DNA originating from normal tissues and hematopoietic cells. The resulting low-level mutation abundance often falls below routine NGS detection sensitivity and limits reliable mutation identification that meets clinical sensitivity and specificity standards. Despite sample preparation advances that reduce sequencing error rates via use of unique molecular identifiers (molecular barcodes) and error-suppression algorithms, excessive amounts of sequencing are still required to detect mutations at allelic frequency levels below 1%. This requirement reduces throughput and increases cost.In this chapter, we describe a sensitive multiplex mutation detection method that enriches mutation-containing DNA during sample preparation, prior to sequencing, thereby increasing signal-to-noise ratios and providing low-level mutation detection without excessive sequencing depth. We couple targeted next-generation sequencing with wild-type DNA removal using Nuclease-assisted Minor-allele Enrichment using Probe Overlap, NaME-PrO, a recently developed method to eliminate wild-type sequences from multiple targets simultaneously. A step by step guide to library preparation and data analysis are provided as well as some precautions during the sample handling.
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19
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Song P, Wu LR, Yan YH, Zhang JX, Chu T, Kwong LN, Patel AA, Zhang DY. Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics. Nat Biomed Eng 2022; 6:232-245. [PMID: 35102279 PMCID: PMC9336539 DOI: 10.1038/s41551-021-00837-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 05/27/2021] [Indexed: 12/15/2022]
Abstract
Cell-free DNA (cfDNA) in the circulating blood plasma of patients with cancer contains tumour-derived DNA sequences that can serve as biomarkers for guiding therapy, for the monitoring of drug resistance, and for the early detection of cancers. However, the analysis of cfDNA for clinical diagnostic applications remains challenging because of the low concentrations of cfDNA, and because cfDNA is fragmented into short lengths and is susceptible to chemical damage. Barcodes of unique molecular identifiers have been implemented to overcome the intrinsic errors of next-generation sequencing, which is the prevailing method for highly multiplexed cfDNA analysis. However, a number of methodological and pre-analytical factors limit the clinical sensitivity of the cfDNA-based detection of cancers from liquid biopsies. In this Review, we describe the state-of-the-art technologies for cfDNA analysis, with emphasis on multiplexing strategies, and discuss outstanding biological and technical challenges that, if addressed, would substantially improve cancer diagnostics and patient care.
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Affiliation(s)
- Ping Song
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Lucia Ruojia Wu
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | | | - Tianqing Chu
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
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20
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Cisneros-Villanueva M, Hidalgo-Pérez L, Rios-Romero M, Cedro-Tanda A, Ruiz-Villavicencio CA, Page K, Hastings R, Fernandez-Garcia D, Allsopp R, Fonseca-Montaño MA, Jimenez-Morales S, Padilla-Palma V, Shaw JA, Hidalgo-Miranda A. Cell-free DNA analysis in current cancer clinical trials: a review. Br J Cancer 2022; 126:391-400. [PMID: 35027672 PMCID: PMC8810765 DOI: 10.1038/s41416-021-01696-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/06/2021] [Accepted: 12/23/2021] [Indexed: 12/13/2022] Open
Abstract
Cell-free DNA (cfDNA) analysis represents a promising method for the diagnosis, treatment selection and clinical follow-up of cancer patients. Although its general methodological feasibility and usefulness has been demonstrated, several issues related to standardisation and technical validation must be addressed for its routine clinical application in cancer. In this regard, most cfDNA clinical applications are still limited to clinical trials, proving its value in several settings. In this paper, we review the current clinical trials involving cfDNA/ctDNA analysis and highlight those where it has been useful for patient stratification, treatment follow-up or development of novel approaches for early diagnosis. Our query included clinical trials, including the terms 'cfDNA', 'ctDNA', 'liquid biopsy' AND 'cancer OR neoplasm' in the FDA and EMA public databases. We identified 1370 clinical trials (FDA = 1129, EMA = 241) involving liquid-biopsy analysis in cancer. These clinical trials show promising results for the early detection of cancer and confirm cfDNA as a tool for real-time monitoring of acquired therapy resistance, accurate disease-progression surveillance and improvement of treatment, situations that result in a better quality of life and extended overall survival for cancer patients.
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Affiliation(s)
- M Cisneros-Villanueva
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - L Hidalgo-Pérez
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - M Rios-Romero
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - A Cedro-Tanda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - C A Ruiz-Villavicencio
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - K Page
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - R Hastings
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - D Fernandez-Garcia
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - R Allsopp
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - M A Fonseca-Montaño
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - S Jimenez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - V Padilla-Palma
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - J A Shaw
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - A Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico.
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21
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Kitamura S, Satoh K, Oono Y. Detection and characterization of genome-wide mutations in M1 vegetative cells of gamma-irradiated Arabidopsis. PLoS Genet 2022; 18:e1009979. [PMID: 35051177 PMCID: PMC8775353 DOI: 10.1371/journal.pgen.1009979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/04/2021] [Indexed: 11/20/2022] Open
Abstract
Radiation-induced mutations have been detected by whole-genome sequencing analyses of self-pollinated generations of mutagenized plants. However, large DNA alterations and mutations in non-germline cells were likely missed. In this study, in order to detect various types of mutations in mutagenized M1 plants, anthocyanin pigmentation was used as a visible marker of mutations. Arabidopsis seeds heterozygous for the anthocyanin biosynthetic genes were irradiated with gamma-rays. Anthocyanin-less vegetative sectors resulting from a loss of heterozygosity were isolated from the gamma-irradiated M1 plants. The whole-genome sequencing analysis of the sectors detected various mutations, including structural variations (SVs) and large deletions (≥100 bp), both of which have been less characterized in the previous researches using gamma-irradiated plant genomes of M2 or later generations. Various types of rejoined sites were found in SVs, including no-insertion/deletion (indel) sites, only-deletion sites, only-insertion sites, and indel sites, but the rejoined sites with 0–5 bp indels represented most of the SVs. Examinations of the junctions of rearrangements (SVs and large deletions), medium deletions (10–99 bp), and small deletions (2–9 bp) revealed unique features (i.e., frequency of insertions and microhomology) at the rejoined sites. These results suggest that they were formed preferentially via different processes. Additionally, mutations that occurred in putative single M1 cells were identified according to the distribution of their allele frequency. The estimated mutation frequencies and spectra of the M1 cells were similar to those of previously analyzed M2 cells, with the exception of the greater proportion of rearrangements in the M1 cells. These findings suggest there are no major differences in the small mutations (<100 bp) between vegetative and germline cells. Thus, this study generated valuable information that may help clarify the nature of gamma-irradiation-induced mutations and their occurrence in cells that develop into vegetative or reproductive tissues. Mutations that occur in plant genome are not only related to plant evolution and speciation in nature, and also useful to identify novel gene functions and to develop new cultivars. Ionizing radiations induce various types of mutations throughout genomes in individual cells of an irradiated/mutagenized plant. However, current knowledge on radiation-induced genome-wide mutations in plants relied on the analyses of self-pollinated generations (M2 or later generations) of the mutagenized plants (M1 generation). Thus, mutations that are hardly transmitted to the next generation and those occurred in non-germline cells could not be investigated. Here, using anthocyanin pigmentation as a visible marker to reduce the genomic complexity in M1 plants, we achieved reliable detection of radiation-induced genome-wide mutations. We demonstrated that rearrangements, which were hardly detected in previous analyses using M2 genomes, occurred substantially often in gamma-irradiated M1 cells. We also revealed that mutation profile of the M1 cells was comparable with that of M2 genomes reported in previous analyses, except for the higher proportion of rearrangements in the M1 genome. Together with unique features at rejoined sites of rearrangements, medium deletions, and small deletions in the M1 genome, our findings are helpful to know the nature of genome-wide mutations induced by gamma-irradiation.
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Affiliation(s)
- Satoshi Kitamura
- Project “Ion Beam Mutagenesis”, Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology, Takasaki, Japan
- * E-mail:
| | - Katsuya Satoh
- Project “Ion Beam Mutagenesis”, Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology, Takasaki, Japan
| | - Yutaka Oono
- Project “Ion Beam Mutagenesis”, Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology, Takasaki, Japan
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22
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Lin PH, Wang MY, Lo C, Tsai LW, Yen TC, Huang TY, Huang WC, Yang K, Chen CK, Fan SC, Kuo SH, Huang CS. Circulating Tumor DNA as a Predictive Marker of Recurrence for Patients With Stage II-III Breast Cancer Treated With Neoadjuvant Therapy. Front Oncol 2021; 11:736769. [PMID: 34868925 PMCID: PMC8632818 DOI: 10.3389/fonc.2021.736769] [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: 07/05/2021] [Accepted: 10/25/2021] [Indexed: 12/22/2022] Open
Abstract
Background Patients with stage II to III breast cancer have a high recurrence rate. The early detection of recurrent breast cancer remains a major unmet need. Circulating tumor DNA (ctDNA) has been proven to be a marker of disease progression in metastatic breast cancer. We aimed to evaluate the prognostic value of ctDNA in the setting of neoadjuvant therapy (NAT). Methods Plasma was sampled at the initial diagnosis (defined as before NAT) and after breast surgery and neoadjuvant therapy(defined as after NAT). We extracted ctDNA from the plasma and performed deep sequencing of a target gene panel. ctDNA positivity was marked by the detection of alterations, such as mutations and copy number variations. Results A total of 95 patients were enrolled in this study; 60 patients exhibited ctDNA positivity before NAT, and 31 patients exhibited ctDNA positivity after NAT. A pathologic complete response (pCR) was observed in 13 patients, including one ER(+)Her2(-) patient, six Her2(+) patients and six triple-negative breast cancer (TNBC) patients. Among the entire cohort, multivariate analysis showed that N3 classification and ctDNA positivity after NAT were independent risk factors that predicted recurrence (N3, hazard ratio (HR) 3.34, 95% confidence interval (CI) 1.26 – 8.87, p = 0.016; ctDNA, HR 4.29, 95% CI 2.06 – 8.92, p < 0.0001). The presence of ctDNA before NAT did not affect the rate of recurrence-free survival. For patients with Her2(+) or TNBC, patients who did not achieve pCR were associated with a trend of higher recurrence (p = 0.105). Advanced nodal status and ctDNA positivity after NAT were significant risk factors for recurrence (N2 – 3, HR 3.753, 95% CI 1.146 – 12.297, p = 0.029; ctDNA, HR 3.123, 95% CI 1.139 – 8.564, p = 0.027). Two patients who achieved pCR had ctDNA positivity after NAT; one TNBC patient had hepatic metastases six months after surgery, and one Her2(+) breast cancer patient had brain metastasis 13 months after surgery. Conclusions This study suggested that the presence of ctDNA after NAT is a robust marker for predicting relapse in stage II to III breast cancer patients.
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Affiliation(s)
- Po-Han Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming-Yang Wang
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Chiao Lo
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Li-Wei Tsai
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Tzu-Chun Yen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Thomas Yoyan Huang
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Wei-Chih Huang
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Karen Yang
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Chih-Kai Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Sheng-Chih Fan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Sung-Hsin Kuo
- Department of Medical Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chiun-Sheng Huang
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan.,Department of Surgery, College of Medicine, National Taiwan University, Taipei, Taiwan
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23
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Yang F, Tang J, Zhao Z, Zhao C, Xiang Y. Circulating tumor DNA: a noninvasive biomarker for tracking ovarian cancer. Reprod Biol Endocrinol 2021; 19:178. [PMID: 34861867 PMCID: PMC8641226 DOI: 10.1186/s12958-021-00860-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 11/11/2021] [Indexed: 12/22/2022] Open
Abstract
Ovarian cancer is the fifth leading cause of cancer-related mortality in women worldwide. Despite the development of technologies over decades to improve the diagnosis and treatment of patients with ovarian cancer, the survival rate remains dismal, mainly because most patients are diagnosed at a late stage. Traditional treatment methods and biomarkers such as cancer antigen-125 as a cancer screening tool lack specificity and cannot offer personalized combinatorial therapy schemes. Circulating tumor DNA (ctDNA) is a promising biomarker for ovarian cancer and can be detected using a noninvasive liquid biopsy. A wide variety of ctDNA applications are being elucidated in multiple studies for tracking ovarian carcinoma during diagnostic and prognostic evaluations of patients and are being integrated into clinical trials to evaluate the disease. Furthermore, ctDNA analysis may be used in combination with multiple "omic" techniques to analyze proteins, epigenetics, RNA, nucleosomes, exosomes, and associated immune markers to promote early detection. However, several technical and biological hurdles impede the application of ctDNA analysis. Certain intrinsic features of ctDNA that may enhance its utility as a biomarker are problematic for its detection, including ctDNA lengths, copy number variations, and methylation. Before the development of ctDNA assays for integration in the clinic, such issues are required to be resolved since these assays have substantial potential as a test for cancer screening. This review focuses on studies concerning the potential clinical applications of ctDNA in ovarian cancer diagnosis and discusses our perspective on the clinical research aimed to treat this daunting form of cancer.
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Affiliation(s)
- Fang Yang
- Department of Physiology, Basic Medical College, Southwest Medical University, Luzhou, Sichuan Province, China
| | - Jun Tang
- Department of Physiology, Basic Medical College, Southwest Medical University, Luzhou, Sichuan Province, China
| | - Zihao Zhao
- Department of Physiology, Basic Medical College, Southwest Medical University, Luzhou, Sichuan Province, China
| | - Chunling Zhao
- Department of Physiology, Basic Medical College, Southwest Medical University, Luzhou, Sichuan Province, China
| | - Yuancai Xiang
- Department of Biochemistry and Molecular Biology, Basic Medical College, Southwest Medical University, Luzhou, Sichuan Province, China.
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24
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Palacín-Aliana I, García-Romero N, Asensi-Puig A, Carrión-Navarro J, González-Rumayor V, Ayuso-Sacido Á. Clinical Utility of Liquid Biopsy-Based Actionable Mutations Detected via ddPCR. Biomedicines 2021; 9:906. [PMID: 34440110 PMCID: PMC8389639 DOI: 10.3390/biomedicines9080906] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 01/10/2023] Open
Abstract
Cancer is one of the leading causes of death worldwide and remains a major public health challenge. The introduction of more sensitive and powerful technologies has permitted the appearance of new tumor-specific molecular aberrations with a significant cancer management improvement. Therefore, molecular pathology profiling has become fundamental not only to guide tumor diagnosis and prognosis but also to assist with therapeutic decisions in daily practice. Although tumor biopsies continue to be mandatory in cancer diagnosis and classification, several studies have demonstrated that liquid biopsies could be used as a potential tool for the detection of cancer-specific biomarkers. One of the main advantages is that circulating free DNA (cfDNA) provides information about intra-tumoral heterogeneity, reflecting dynamic changes in tumor burden. This minimally invasive tool has become an accurate and reliable instrument for monitoring cancer genetics. However, implementing liquid biopsies across the clinical practice is still ongoing. The main challenge is to detect genomic alterations at low allele fractions. Droplet digital PCR (ddPCR) is a powerful approach that can overcome this issue due to its high sensitivity and specificity. Here we explore the real-world clinical utility of the liquid biopsy ddPCR assays in the most diagnosed cancer subtypes.
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Affiliation(s)
- Irina Palacín-Aliana
- Atrys Health, 08025 Barcelona, Spain; (I.P.-A.); (A.A.-P.); (V.G.-R.)
- Fundación de Investigación HM Hospitales, HM Hospitales, 28015 Madrid, Spain
- Faculty of Science, Universidad de Alcalá, 28801 Madrid, Spain
| | - Noemí García-Romero
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Madrid, Spain; (N.G.-R.); (J.C.-N.)
- Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043 Madrid, Spain
| | - Adrià Asensi-Puig
- Atrys Health, 08025 Barcelona, Spain; (I.P.-A.); (A.A.-P.); (V.G.-R.)
| | - Josefa Carrión-Navarro
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Madrid, Spain; (N.G.-R.); (J.C.-N.)
- Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043 Madrid, Spain
| | | | - Ángel Ayuso-Sacido
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Madrid, Spain; (N.G.-R.); (J.C.-N.)
- Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043 Madrid, Spain
- Faculty of Medicine, Universidad Francisco de Vitoria, 28223 Madrid, Spain
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25
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Affolter KE, Hellwig S, Nix DA, Bronner MP, Thomas A, Fuertes CL, Hamil CL, Garrido-Laguna I, Scaife CL, Mulvihill SJ, Underhill HR. Detection of circulating tumor DNA without a tumor-informed search using next-generation sequencing is a prognostic biomarker in pancreatic ductal adenocarcinoma. Neoplasia 2021; 23:859-869. [PMID: 34298235 PMCID: PMC8322473 DOI: 10.1016/j.neo.2021.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/08/2021] [Indexed: 01/10/2023] Open
Abstract
The confounding effects of next-generation sequencing (NGS) noise on detection of low frequency circulating tumor DNA (ctDNA) without a priori knowledge of solid tumor mutations has limited the applications of circulating cell-free DNA (ccfDNA) in clinical oncology. Here, we use a 118 gene panel and leverage ccfDNA technical replicates to eliminate NGS-associated errors while also enhancing detection of ctDNA from pancreatic ductal adenocarcinomas (PDACs). Pre-operative ccfDNA and tumor DNA were acquired from 14 patients with PDAC (78.6% stage II-III). Post-operative ccfDNA was also collected from 11 of the patients within 100 days of surgery. ctDNA detection was restricted to variants corresponding to pathogenic mutations in PDAC present in both replicates. PDAC-associated pathogenic mutations were detected in pre-operative ccfDNA in four genes (KRAS, TP53, SMAD4, ALK) from five patients. Of the nine ctDNA variants detected (variant allele frequency: 0.08%-1.59%), five had a corresponding mutation in tumor DNA. Pre-operative detection of ctDNA was associated with shorter survival (312 vs. 826 days; χ2=5.4, P = 0.021). Guiding ctDNA detection in pre-operative ccfDNA based on mutations present in tumor DNA yielded a similar survival analysis. Detection of ctDNA in the post-operative ccfDNA with or without tumor-informed guidance was not associated with outcomes. Therefore, the detection of PDAC-derived ctDNA during a broad and untargeted survey of ccfDNA with NGS may be a valuable, non-invasive, prognostic biomarker to integrate into the clinical assessment and management of patients prior to surgery.
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Affiliation(s)
- Kajsa E Affolter
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | | | - David A Nix
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Mary P Bronner
- Department of Pathology, University of Utah, Salt Lake City, Utah; Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Alun Thomas
- Department of Family and Preventative Medicine, Divisions of Genetic Epidemiology and Public Health, University of Utah, Salt Lake City, Utah
| | - Carrie L Fuertes
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Cindy L Hamil
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | | | | | | | - Hunter R Underhill
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah; Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, Utah; Department of Radiology, University of Utah, Salt Lake City, Utah.
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26
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Cimadamore A, Cheng L, Massari F, Santoni M, Pepi L, Franzese C, Scarpelli M, Lopez-Beltran A, Galosi AB, Montironi R. Circulating Tumor DNA Testing for Homology Recombination Repair Genes in Prostate Cancer: From the Lab to the Clinic. Int J Mol Sci 2021; 22:5522. [PMID: 34073818 PMCID: PMC8197269 DOI: 10.3390/ijms22115522] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/24/2022] Open
Abstract
Approximately 23% of metastatic castration-resistant prostate cancers (mCRPC) harbor deleterious aberrations in DNA repair genes. Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) therapy has shown improvements in overall survival in patients with mCRPC who harbor somatic and/or germline alterations of homology recombination repair (HRR) genes. Peripheral blood samples are typically used for the germline mutation analysis test using the DNA extracted from peripheral blood leucocytes. Somatic alterations can be assessed by extracting DNA from a tumor tissue sample or using circulating tumor DNA (ctDNA) extracted from a plasma sample. Each of these genetic tests has its own benefits and limitations. The main advantages compared to the tissue test are that liquid biopsy is a non-invasive and easily repeatable test with the value of better representing tumor heterogeneity than primary biopsy and of capturing changes and/or resistance mutations in the genetic tumor profile during disease progression. Furthermore, ctDNA can inform about mutation status and guide treatment options in patients with mCRPC. Clinical validation and test implementation into routine clinical practice are currently very limited. In this review, we discuss the state of the art of the ctDNA test in prostate cancer compared to blood and tissue testing. We also illustrate the ctDNA testing workflow, the available techniques for ctDNA extraction, sequencing, and analysis, describing advantages and limits of each techniques.
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Affiliation(s)
- Alessia Cimadamore
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (A.C.); (L.P.); (M.S.)
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, School of Medicine, Indiana University, Indianapolis, IN 46202, USA;
| | - Francesco Massari
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, 40138 Bologna, Italy;
| | - Matteo Santoni
- Oncology Unit, Macerata Hospital, 62100 Macerata, Italy;
| | - Laura Pepi
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (A.C.); (L.P.); (M.S.)
| | - Carmine Franzese
- Department of Specialist Clinical Science and Odontostomatology, Urology Division, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (C.F.); (A.B.G.)
| | - Marina Scarpelli
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (A.C.); (L.P.); (M.S.)
| | - Antonio Lopez-Beltran
- Department of Morphological Sciences, Cordoba University Medical School, 14071 Cordoba, Spain;
| | - Andrea Benedetto Galosi
- Department of Specialist Clinical Science and Odontostomatology, Urology Division, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (C.F.); (A.B.G.)
| | - Rodolfo Montironi
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (A.C.); (L.P.); (M.S.)
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27
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Underhill HR. Leveraging the Fragment Length of Circulating Tumour DNA to Improve Molecular Profiling of Solid Tumour Malignancies with Next-Generation Sequencing: A Pathway to Advanced Non-invasive Diagnostics in Precision Oncology? Mol Diagn Ther 2021; 25:389-408. [PMID: 34018157 PMCID: PMC8249304 DOI: 10.1007/s40291-021-00534-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2021] [Indexed: 12/20/2022]
Abstract
Circulating cell-free DNA (ccfDNA) has emerged as a promising diagnostic tool in oncology. Identification of tumour-derived ccfDNA (i.e. circulating tumour DNA [ctDNA]) provides non-invasive access to a malignancy’s molecular landscape to diagnose, inform therapeutic strategies, and monitor treatment efficacy. Current applications of ccfDNA to detect somatic mutations, however, have been largely constrained to tumour-informed searches and identification of common mutations because of the interaction between ctDNA signal and next-generation sequencing (NGS) noise. Specifically, the low allele frequency of ctDNA associated with non-metastatic and early-stage lesions may be indistinguishable from artifacts that accrue during sample preparation and NGS. Thus, using ccfDNA to achieve non-invasive and personalized molecular profiling to optimize individual patient care is a highly sought goal that remains limited in clinical practice. There is growing evidence, however, that further advances in the field of ccfDNA diagnostics may be achieved by improving detection of somatic mutations through leveraging the inherently shorter fragment lengths of ctDNA compared to non-neoplastic ccfDNA. Here, the origins and rationale for seeking to improve the mutation-based detection of ctDNA by using ccfDNA size profiling are reviewed. Subsequently, in vitro and in silico methods to enrich for a target ccfDNA fragment length are detailed to identify current practices and provide perspective into the potential of using ccfDNA size profiling to impact clinical applications in oncology.
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Affiliation(s)
- Hunter R Underhill
- Division of Medical Genetics, Department of Pediatrics, University of Utah, 295 Chipeta Way, Salt Lake City, UT, 84108, USA. .,Department of Radiology, University of Utah, Salt Lake City, UT, USA. .,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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28
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Stance of MRD in Non-Hodgkin's Lymphoma and its upsurge in the novel era of cell-free DNA. Clin Transl Oncol 2021; 23:2206-2219. [PMID: 33991328 DOI: 10.1007/s12094-021-02635-4] [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: 02/12/2021] [Accepted: 05/02/2021] [Indexed: 10/21/2022]
Abstract
Cancer genomics has evolved over the years from understanding the pathogenesis of cancer to screening the future possibilities of cancer occurrence. Understanding the genetic profile of tumors holds a prognostic as well as a predictive value in this era of therapeutic surveillance, molecular remission, and precision medicine. Identifying molecular markers in tumors is the current standard of approach, and requires an efficient combination of an accessible sample type and a profoundly sensitive technique. Liquid biopsy or cell-free DNA has evolved as a novel sample type with promising results in recent years. Although cell-free DNA has significant role in various cancer types, this review focuses on its application in Non-Hodgkin's Lymphoma. Beginning with the current concept and clinical relevance of minimal residual disease in Non-Hodgkin's lymphoma, we discuss the literature on circulating DNA and its evolving application in the realm of cutting-edge technology.
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29
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Rodríguez J, Avila J, Rolfo C, Ruíz-Patiño A, Russo A, Ricaurte L, Ordóñez-Reyes C, Arrieta O, Zatarain-Barrón ZL, Recondo G, Cardona AF. When Tissue is an Issue the Liquid Biopsy is Nonissue: A Review. Oncol Ther 2021; 9:89-110. [PMID: 33689160 PMCID: PMC8140006 DOI: 10.1007/s40487-021-00144-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023] Open
Abstract
Precision medicine has impacted the field of medical oncology by introducing personalized therapies, improving all measurable outcomes. This field, in turn, has expanded to obtaining and analyzing a vast and ever-increasing amount of genomic information. One technique currently applied is the liquid biopsy, which consists of detecting and isolating DNA and exosomes in cancer patients. Newly developed techniques have made it possible to use the liquid biopsy in a wide range of settings. However, challenges regarding the validation of its clinical utility exist because of a lack of standardization across different techniques and tumor types, confounder genomic information, lack of appropriate clinical trial designs, and a non-measured, and therefore not estimated, economic impact on population health. Nowadays, liquid biopsy is not routinely used, but ongoing research is increasing its popularity, and a new era in oncology is developing. Therefore, it is essential to have an in-depth understanding of the liquid biopsy technique. In this review, we summarize the leading techniques and liquid biopsy applications in cancer.
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Affiliation(s)
- July Rodríguez
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogota, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G/ONCOLGroup), Universidad El Bosque, Bogota, Colombia
| | - Jenny Avila
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogota, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G/ONCOLGroup), Universidad El Bosque, Bogota, Colombia
| | - Christian Rolfo
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alejandro Ruíz-Patiño
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogota, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G/ONCOLGroup), Universidad El Bosque, Bogota, Colombia
| | - Alessandro Russo
- Medical Oncology Unit A.O. Papardo and Department of Human Pathology, University of Messina, Messina, Italy
| | - Luisa Ricaurte
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogota, Colombia
- Pathology Department, Mayo Clinic, Rochester, MN, USA
| | | | - Oscar Arrieta
- Thoracic Oncology Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | | | - Gonzalo Recondo
- Thoracic Oncology Section, Centro de Educación Médica e Investigaciones Clínicas (CEMIC), Buenos Aires, Argentina
| | - Andrés F Cardona
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogota, Colombia.
- Molecular Oncology and Biology Systems Research Group (Fox-G/ONCOLGroup), Universidad El Bosque, Bogota, Colombia.
- Clinical and Traslational Oncology Group, Clinica del Country, Bogota, Colombia.
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30
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Cheok SK, Narayan A, Arnal-Estape A, Gettinger S, Goldberg SB, Kluger HM, Nguyen D, Patel A, Chiang V. Tumor DNA Mutations From Intraparenchymal Brain Metastases Are Detectable in CSF. JCO Precis Oncol 2021; 5:PO.20.00292. [PMID: 34250381 DOI: 10.1200/po.20.00292] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/29/2020] [Accepted: 12/07/2020] [Indexed: 11/20/2022] Open
Abstract
Discordant responses between brain metastases and extracranial tumors can arise from branched tumor evolution, underscoring the importance of profiling mutations to optimize therapy. However, the morbidity of brain biopsies limits their use. We investigated whether cell-free DNA (cfDNA) in CSF could serve as an effective surrogate marker for genomic profiling of intraparenchymal (IP) brain metastases. METHODS CSF and blood were collected simultaneously from patients with progressive brain metastases undergoing a craniotomy or lumbar puncture. Mutations in both biofluids were measured using an error-suppressed deep sequencing method previously published by our group. Forty-three regions of 24 cancer-associated genes were assayed. RESULTS This study enrolled 14 patients with either IP brain metastases (n = 12) or cytology-positive leptomeningeal disease (LMD, n = 2) and two controls with normal pressure hydrocephalus. Primary cancer types were lung, melanoma, renal cell, and colorectal. cfDNA was measurable in all sixteen samples of CSF. Cancer-associated mutations were found in the CSF of ten patients (eight with IP [67%] and two with LMD [100%]) and plasma of five patients (five with IP [42%] and none with LMD). All patients with plasma cfDNA had extracranial tumors. Among the five patients in the cohort who also had mutation data from time-matched brain metastasis tissue, four patients (80%) had matching mutations detected in CSF and brain, whereas only one patient (20%) had matching mutations detected in plasma and brain. CONCLUSION The detection of mutational DNA in CSF is not restricted to LMD and was found in two thirds of patients with IP brain metastases in our cohort. Analysis of CSF can be a viable alternative to biopsy for detection of somatic mutations in brain metastases.
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Affiliation(s)
| | - Azeet Narayan
- Department of Therapeutic Radiology, Yale University, New Haven, CT
| | - Anna Arnal-Estape
- Department of Pathology, Yale University, New Haven, CT.,Yale Cancer Center, New Haven, CT
| | - Scott Gettinger
- Yale Cancer Center, New Haven, CT.,Department of Medicine (Medical Oncology), Yale University, New Haven, CT
| | - Sarah B Goldberg
- Yale Cancer Center, New Haven, CT.,Department of Medicine (Medical Oncology), Yale University, New Haven, CT
| | - Harriet M Kluger
- Yale Cancer Center, New Haven, CT.,Department of Medicine (Medical Oncology), Yale University, New Haven, CT
| | - Don Nguyen
- Department of Pathology, Yale University, New Haven, CT.,Yale Cancer Center, New Haven, CT.,Department of Medicine (Medical Oncology), Yale University, New Haven, CT
| | - Abhijit Patel
- Department of Therapeutic Radiology, Yale University, New Haven, CT.,Yale Cancer Center, New Haven, CT
| | - Veronica Chiang
- Department of Neurosurgery, Yale University, New Haven, CT.,Yale Cancer Center, New Haven, CT
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31
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Tellez-Gabriel M, Knutsen E, Perander M. Current Status of Circulating Tumor Cells, Circulating Tumor DNA, and Exosomes in Breast Cancer Liquid Biopsies. Int J Mol Sci 2020; 21:E9457. [PMID: 33322643 PMCID: PMC7763984 DOI: 10.3390/ijms21249457] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the most common cancer among women worldwide. Although the five-, ten- and fifteen-year survival rates are good for breast cancer patients diagnosed with early-stage disease, some cancers recur many years after completion of primary therapy. Tumor heterogeneity and clonal evolution may lead to distant metastasis and therapy resistance, which are the main causes of breast cancer-associated deaths. In the clinic today, imaging techniques like mammography and tissue biopsies are used to diagnose breast cancer. Even though these methods are important in primary diagnosis, they have limitations when it comes to longitudinal monitoring of residual disease after treatment, disease progression, therapy responses, and disease recurrence. Over the last few years, there has been an increasing interest in the diagnostic, prognostic, and predictive potential of circulating cancer-derived material acquired through liquid biopsies in breast cancer. Thanks to the development of sensitive devices and platforms, a variety of tumor-derived material, including circulating cancer cells (CTCs), circulating DNA (ctDNA), and biomolecules encapsulated in extracellular vesicles, can now be extracted and analyzed from body fluids. Here we will review the most recent studies on breast cancer, demonstrating the clinical potential and utility of CTCs and ctDNA. We will also review literature illustrating the potential of circulating exosomal RNA and proteins as future biomarkers in breast cancer. Finally, we will discuss some of the advantages and limitations of liquid biopsies and the future perspectives of this field in breast cancer management.
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Affiliation(s)
- Marta Tellez-Gabriel
- Department of Medical Biology, Faculty of Health Sciences, UiT—The Arctic University of Norway, 9011 Tromsø, Norway; (E.K.); (M.P.)
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32
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Thakral D, Gupta R, Sahoo RK, Verma P, Kumar I, Vashishtha S. Real-Time Molecular Monitoring in Acute Myeloid Leukemia With Circulating Tumor DNA. Front Cell Dev Biol 2020; 8:604391. [PMID: 33363162 PMCID: PMC7759522 DOI: 10.3389/fcell.2020.604391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023] Open
Abstract
The clonal evolution of acute myeloid leukemia (AML), an oligoclonal hematological malignancy, is driven by a plethora of cytogenetic abnormalities, gene mutations, abnormal epigenetic patterns, and aberrant gene expressions. These alterations in the leukemic blasts promote clinically diverse manifestations with common characteristics of high relapse and drug resistance. Defining and real-time monitoring of a personalized panel of these predictive genetic biomarkers is rapidly being adapted in clinical setting for diagnostic, prognostic, and therapeutic decision-making in AML. A major challenge remains the frequency of invasive biopsy procedures that can be routinely performed for monitoring of AML disease progression. Moreover, a single-site biopsy is not representative of the tumor heterogeneity as it is spatially and temporally constrained and necessitates the understanding of longitudinal and spatial subclonal dynamics in AML. Hematopoietic cells are a major contributor to plasma cell-free DNA, which also contain leukemia-specific aberrations as the circulating tumor-derived DNA (ctDNA) fraction. Plasma cell-free DNA analysis holds immense potential as a minimally invasive tool for genomic profiling at diagnosis as well as clonal evolution during AML disease progression. With the technological advances and increasing sensitivity for detection of ctDNA, both genetic and epigenetic aberrations can be qualitatively and quantitatively evaluated. However, challenges remain in validating the utility of liquid biopsy tools in clinics, and universal recommendations are still awaited towards reliable diagnostics and prognostics. Here, we provide an overview on the scope of ctDNA analyses for prognosis, assessment of response to treatment and measurable residual disease, prediction of disease relapse, development of acquired resistance and beyond in AML.
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Affiliation(s)
- Deepshi Thakral
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Ranjit Kumar Sahoo
- Department of Medical Oncology, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Pramod Verma
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Indresh Kumar
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Sangeeta Vashishtha
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
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33
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Ofori K, Bhagat G, Rai AJ. Exosomes and extracellular vesicles as liquid biopsy biomarkers in diffuse large B-cell lymphoma: Current state of the art and unmet clinical needs. Br J Clin Pharmacol 2020; 87:284-294. [PMID: 33080045 DOI: 10.1111/bcp.14611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 12/15/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin's lymphoma, and it constitutes biologically heterogeneous entities. Standard first-line therapies cure ~60% of patients, the rest being either refractory or experiencing relapse. Currently, there are no robust predictive biomarkers of therapeutic response. Heterogeneity of DLBCL is partly explained by the cell of origin (COO), ie, germinal centre B cell or activated B cell, with the latter exhibiting worse prognosis. While gene expression profiling (GEP) is the gold standard for determining COO, surrogate immunohistochemical algorithms are used clinically, but show significant discordance with GEP. Recently, additional genetic subgroups with different prognoses have been reported. However, the tools/expertise required for analysis prohibit widespread deployment. Liquid biopsy-based assays show promise in providing clinically actionable information, are noninvasive and facilitate serial sampling to assess mechanisms of therapy resistance. Circulating, cell-free DNA analysis has shown enhanced sensitivity for detecting molecular alterations, but this modality cannot determine alterations of the tumor proteome or on signalling pathways. Exosomes are endosomally derived vesicles, are found in high abundance in body fluids and are readily isolated using a variety of methods. Tumour-derived exosomes can yield data regarding genetic, transcriptional, and proteomic changes useful for diagnosis, prognosis, and therapy of DLBCL. At present, standardized techniques for isolating exosomes are lacking and discriminating between exosomes from neoplastic and normal B cells is challenging. Refinements in isolation procedures are required to realize their full potential as precision medicine tools to provide comprehensive information on disease subtypes, identify prognostic factors, allow real-time monitoring of therapy response and delineate novel drug targets.
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Affiliation(s)
- Kenneth Ofori
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 622 West 168th Street, New York, NY, 10032
| | - Govind Bhagat
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 622 West 168th Street, New York, NY, 10032
| | - Alex J Rai
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 622 West 168th Street, New York, NY, 10032
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Vacante M, Ciuni R, Basile F, Biondi A. The Liquid Biopsy in the Management of Colorectal Cancer: An Overview. Biomedicines 2020; 8:E308. [PMID: 32858879 PMCID: PMC7555636 DOI: 10.3390/biomedicines8090308] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023] Open
Abstract
Currently, there is a crucial need for novel diagnostic and prognostic biomarkers with high specificity and sensitivity in patients with colorectal cancer. A "liquid biopsy" is characterized by the isolation of cancer-derived components, such as circulating tumor cells, circulating tumor DNA, microRNAs, long non-coding RNAs, and proteins, from peripheral blood or other body fluids and their genomic or proteomic assessment. The liquid biopsy is a minimally invasive and repeatable technique that could play a significant role in screening and diagnosis, and predict relapse and metastasis, as well as monitoring minimal residual disease and chemotherapy resistance in colorectal cancer patients. However, there are still some practical issues that need to be addressed before liquid biopsy can be widely used in clinical practice. Potential challenges may include low amounts of circulating tumor cells and circulating tumor DNA in samples, lack of pre-analytical and analytical consensus, clinical validation, and regulatory endorsement. The aim of this review was to summarize the current knowledge of the role of liquid biopsy in the management of colorectal cancer.
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Affiliation(s)
- Marco Vacante
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, Via S. Sofia 78, 95123 Catania, Italy; (R.C.); (F.B.); (A.B.)
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Manoharan A, Sambandam R, Bhat V. Recent technologies enhancing the clinical utility of circulating tumor DNA. Clin Chim Acta 2020; 510:498-506. [PMID: 32795543 DOI: 10.1016/j.cca.2020.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022]
Abstract
Circulating tumor DNA (ctDNA) is a promising blood based biomarker that is set to revolutionize cancer management. Non-invasive biopsy takes precedence over tissue biopsy for enabling longitudinal monitoring, providing a comprehensive profile of tumor heterogeneity and the ease of repeated sampling. Advanced genomic technologies enable real-time disease monitoring, detect minimal residual disease and recurrence at the earliest stages, the potential time points when treatment significantly reduces morbidity and mortality and enable tailored and personalized therapy. The review highlights evidence from literature that make ctDNA a potential liquid biopsy marker and the clinical utility of the recent techniques that leverage up on ctDNA.
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Affiliation(s)
- Aarthi Manoharan
- Multi-Disciplinary Center for Biomedical Research, Vinayaka Mission's Research Foundation, Aarupadai Veedu Medical College and Hospital (Deemed-to-be-University), Kirumampakkam, Puducherry 607402, India
| | - Ravikumar Sambandam
- Multi-Disciplinary Center for Biomedical Research, Vinayaka Mission's Research Foundation, Aarupadai Veedu Medical College and Hospital (Deemed-to-be-University), Kirumampakkam, Puducherry 607402, India.
| | - Vishnu Bhat
- Multi-Disciplinary Center for Biomedical Research, Vinayaka Mission's Research Foundation, Aarupadai Veedu Medical College and Hospital (Deemed-to-be-University), Kirumampakkam, Puducherry 607402, India
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Kaur P, Campo D, Porras TB, Ring A, Lu J, Chairez Y, Su Y, Kang I, Lang JE. A Pilot Study for the Feasibility of Exome-Sequencing in Circulating Tumor Cells Versus Single Metastatic Biopsies in Breast Cancer. Int J Mol Sci 2020; 21:ijms21144826. [PMID: 32650480 PMCID: PMC7402350 DOI: 10.3390/ijms21144826] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 11/16/2022] Open
Abstract
The comparison of the landscape of somatic alterations in circulating tumor cells (CTCs) versus metastases is challenging. Here, we comprehensively characterized the somatic landscape in bulk (amplified and non-amplified), spike-in breast cancer cells, CTCs, and metastases from breast cancer patients using whole-exome sequencing (WES). We determined the level of genomic concordance for somatic nucleotide variants (SNVs), copy number alterations (CNAs), and structural variants (SVs). The variant allele fractions (VAFs) of somatic variants were remarkably similar between amplified and non-amplified cell line samples as technical replicates. In clinical samples, a significant fraction of somatic variants had low VAFs in CTCs compared to metastases. The most frequently recurrent gene mutations in clinical samples were associated with an elevated C > T mutational signature. We found complex rearrangement patterns including intra- and inter-chromosomal rearrangements, singleton, and recurrent gene fusions, and tandem duplications. We observed high molecular discordance for somatic alterations between paired samples consistent with marked heterogeneity of the somatic landscape. The most prevalent copy number calls were focal deletion events in CTCs and metastases. Our results demonstrate the feasibility of an integrated workflow for the identification of a complete repertoire of somatic alterations and highlight the intrapatient genomic differences that occur between CTCs and metastases.
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Affiliation(s)
- Pushpinder Kaur
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (P.K.); (Y.S.)
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; (J.L.); (I.K.)
| | - Daniel Campo
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA;
| | - Tania B. Porras
- Cancer and Blood Disease Institute, Children Hospital Los Angeles, University of Southern California, Los Angeles, CA 90027, USA;
| | - Alexander Ring
- Department of Oncology and Hematology, UniversitätsSpital Zürich, Rämistrasse 100, 8091 Zürich, Switzerland;
| | - Janice Lu
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; (J.L.); (I.K.)
- Division of Medical Oncology, Department of Medicine and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Yvonne Chairez
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
| | - Yunyun Su
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (P.K.); (Y.S.)
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; (J.L.); (I.K.)
| | - Irene Kang
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; (J.L.); (I.K.)
- Division of Medical Oncology, Department of Medicine and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Julie E. Lang
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (P.K.); (Y.S.)
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; (J.L.); (I.K.)
- Correspondence: ; Tel.: +1-(323)-442-8140
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Brown NA, Elenitoba-Johnson KSJ. Enabling Precision Oncology Through Precision Diagnostics. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2020; 15:97-121. [PMID: 31977297 DOI: 10.1146/annurev-pathmechdis-012418-012735] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genomic testing enables clinical management to be tailored to individual cancer patients based on the molecular alterations present within cancer cells. Genomic sequencing results can be applied to detect and classify cancer, predict prognosis, and target therapies. Next-generation sequencing has revolutionized the field of cancer genomics by enabling rapid and cost-effective sequencing of large portions of the genome. With this technology, precision oncology is quickly becoming a realized paradigm for managing the treatment of cancer patients. However, many challenges must be overcome to efficiently implement the transition of next-generation sequencing from research applications to routine clinical practice, including using specimens commonly available in the clinical setting; determining how to process, store, and manage large amounts of sequencing data; determining how to interpret and prioritize molecular findings; and coordinating health professionals from multiple disciplines.
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Affiliation(s)
- Noah A Brown
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA;
| | - Kojo S J Elenitoba-Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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Rolfo C, Cardona AF, Cristofanilli M, Paz-Ares L, Diaz Mochon JJ, Duran I, Raez LE, Russo A, Lorente JA, Malapelle U, Gil-Bazo I, Jantus-Lewintre E, Pauwels P, Mok T, Serrano MJ. Challenges and opportunities of cfDNA analysis implementation in clinical practice: Perspective of the International Society of Liquid Biopsy (ISLB). Crit Rev Oncol Hematol 2020; 151:102978. [PMID: 32428812 DOI: 10.1016/j.critrevonc.2020.102978] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 04/29/2020] [Indexed: 02/07/2023] Open
Abstract
Precision medicine was born with the development of new diagnostic techniques and targeted drugs, yielding better outcomes in cancer care. With the evolution and increasing sensitivity for detecting oncogenic drivers, liquid biopsies (LBs), specifically cell-free DNA (cfDNA) analysis, have been proposed as a minimally-invasive technique for genomic profiling. Ranging from sequencing techniques to PCR-based methods and other more complex strategies, this approach, currently applicable in some solid tumors with robust evidence, is showing promising opportunities in other cancers. However, difficulties in validating their clinical utility exist within limitation at different levels among several techniques, reporting of the results, lack of appropriate clinical trial designs, and unknown economic impact. One of the aims of the ISLB is to create recommendations to develop reliable and sustainable diagnostic, prognostic and predictive tools using LBs. This paper is addressing these objectives, helping the healthcare providers and scientific community to understand the potential of LB.
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Affiliation(s)
- Christian Rolfo
- Thoracic Oncology Department and Early Phase Clinical Trials Section, School of Medicine, Maryland University, Maryland, USA.
| | - Andrés F Cardona
- Clinical and Translational Oncology Group, Clínica del Country, Bogotá, Colombia; Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia; Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad El Bosque, Bogotá, Colombia
| | - Massimo Cristofanilli
- Department of Medicine, Division of Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, 710 N Fairbanks Court, Suite 8-250A, Chicago, IL, 60611, USA
| | - Luis Paz-Ares
- Hospital Universitario 12 de Octubre, CNIO-H12o Lung Cancer Unit, Universidad Complutense and CIBERONC, Madrid, Spain
| | - Juan Jose Diaz Mochon
- DestiNA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, 18016, Armilla, Granada, Spain; GENYO Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. PTS Granada - Avenida de la Ilustración, 114- 18016, Granada, Spain; Department Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain
| | - Ignacio Duran
- Servicio de Oncologia Medica, Medical Oncology Department, Hospital Universitario Marques de Valdecilla, Edificio Sur, 2 Planta, Despacho 277, 39008, Santander, Spain
| | - Luis E Raez
- Memorial Cancer Institute, Memorial Health Care System, Florida International University, Florida, USA
| | - Alessandro Russo
- Thoracic Oncology Department and Early Phase Clinical Trials Section, School of Medicine, Maryland University, Maryland, USA; Medical Oncology Unit A.O. Papardo & Department of Human Pathology, University of Messina, Italy
| | - Jose A Lorente
- Laboratory of Genetic Identification, Department of Legal Medicine, University of Granada, Av. de la Investigación, 11, 18071, Granada, Spain; Centre for Genomics and Oncological Research - GENYO, Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Umberto Malapelle
- Department of Public Health, University Federico II of Naples, Naples, Italy
| | - Ignacio Gil-Bazo
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Navarra, Spain; University of Navarra, Center for Applied Medical Research, Program of Solid Tumors, Pamplona, Navarra, Spain; Idisna, Navarra Institute for Health Research, Pamplona, Navarra, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Eloisa Jantus-Lewintre
- Molecular Oncology Laboratory, Fundación Investigación, Valencia General University Hospital, Valencia, Spain
| | - Patrick Pauwels
- Center for Oncological Research (CORE), University of Antwerp, & Department of Pathology, Antwerp University Hospital, Edegem, Belgium
| | - Tony Mok
- State Key Laboratory in Oncology in South China, Hong Kong, China
| | - María José Serrano
- Centre for Genomics and Oncological Research - GENYO, Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain; Bio-Health Research Institute (Instituto de Investigación Biosanitaria ibs. GRANADA), Spain; Complejo Hospitalario Universitario Granada (CHUG), Department of Medical Oncology, University of Granada, Granada, Spain.
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McEwen AE, Leary SES, Lockwood CM. Beyond the Blood: CSF-Derived cfDNA for Diagnosis and Characterization of CNS Tumors. Front Cell Dev Biol 2020; 8:45. [PMID: 32133357 PMCID: PMC7039816 DOI: 10.3389/fcell.2020.00045] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/17/2020] [Indexed: 12/15/2022] Open
Abstract
Genetic data are rapidly becoming part of tumor classification and are integral to prognosis and predicting response to therapy. Current molecular tumor profiling relies heavily on tissue resection or biopsy. Tissue profiling has several disadvantages in tumors of the central nervous system, including the challenge associated with invasive biopsy, the heterogeneous nature of many malignancies where a small biopsy can underrepresent the mutational profile, and the frequent lack of obtaining a repeat biopsy, which limits routine monitoring to assess therapy response and/or tumor evolution. Circulating tumor, cell-free DNA (cfDNA), has been proposed as a liquid biopsy to address some limitations of tissue-based genetics. In cancer patients, a portion of cfDNA is tumor-derived and may contain somatic genetic alterations. In central nervous system (CNS) neoplasia, plasma tumor-derived cfDNA is very low or absent, likely due to the blood brain barrier. Interrogating cfDNA in cerebrospinal fluid (CSF) has several advantages. Compared to blood, CSF is paucicellular and therefore predominantly lacks non-tumor cfDNA; however, patients with CNS-limited tumors have significantly enriched tumor-derived cfDNA in CSF. In patients with metastatic CNS disease, mutations in CSF cfDNA are most concordant with the intracranial process. CSF cfDNA can also occasionally uncover additional genetic alterations absent in concurrent biopsy specimens, reflecting tumor heterogeneity. Although CSF is enriched for tumor-derived cfDNA, absolute quantities are low. Highly sensitive, targeted methods including next-generation sequencing and digital PCR are required to detect mutations in CSF cfDNA. Additional technical and bioinformatic approaches also facilitate enhanced ability to detect tumor mutations in CSF cfDNA.
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Affiliation(s)
- Abbye E McEwen
- Department of Pathology, University of Washington, Seattle, WA, United States.,Department of Laboratory Medicine, University of Washington, Seattle, WA, United States.,Brotman Baty Institute for Precision Medicine, Seattle, WA, United States
| | - Sarah E S Leary
- Brotman Baty Institute for Precision Medicine, Seattle, WA, United States.,Seattle Children's Hospital, Cancer and Blood Disorders Center, Seattle, WA, United States.,Department of Pediatrics, University of Washington, Seattle, WA, United States.,Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Christina M Lockwood
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States.,Brotman Baty Institute for Precision Medicine, Seattle, WA, United States
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40
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Yang J, Peng CF, Qi Y, Rao XQ, Guo F, Hou Y, He W, Wu J, Chen YY, Zhao X, Wang YN, Peng H, Wang D, Du L, Luo MY, Huang QF, Liu HL, Yin A. Noninvasive prenatal detection of hemoglobin Bart hydrops fetalis via maternal plasma dispensed with parental haplotyping using the semiconductor sequencing platform. Am J Obstet Gynecol 2020; 222:185.e1-185.e17. [PMID: 31394068 DOI: 10.1016/j.ajog.2019.07.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 07/03/2019] [Accepted: 07/30/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Thalassemia is one of the most common monogenetic diseases in the south of China and Southeast Asia. Hemoglobin Bart's hydrops fetalis syndrome was caused by a homozygous Southeast Asian deletion (-/-) in the HBA gene. Few studies have proved the potential of screen for Bart's hydrops fetalis using fetal cell-free DNA. However, the number of cases is still relatively small. Clinical trials of large samples would be needed. OBJECTIVE In this study, we aimed to develop a noninvasive method of target-captured sequencing and genotyping by the Bayesian method using cell-free fetal DNA to identify the fetal genotype in pregnant women who are at risk of having hemoglobin Bart hydrops fetalis in a large-scale study. STUDY DESIGN In total, 192,173 couples from 30 hospitals were enrolled in our study and 878 couples were recruited, among whom both the pregnant women and their husbands were detected to be carriers of Southeast Asian type (-/αα) of α-thalassemia. Prenatal diagnosis was performed by chorionic villus sampling, amniocentesis, or cordocentesis using gap-polymerase chain reaction considered as the golden standard. RESULTS As a result, we found that the sensitivity and specificity of our noninvasive method were 98.81% and 94.72%, respectively, in the training set as well as 100% and 99.31%, respectively, in the testing set. Moreover, our method could identify all of 885 maternal samples with the Southeast Asian carrier and 36 trisomy samples with 100% of sensitivity in T13, T18, and T21 and 99.89% (1 of 917) and 99.88% (1 of 888) of specificity in T18 and T21, respectively. CONCLUSION Our method opens the possibility of early screening for maternal genotyping of α-thalassemia, fetal aneuploidies in chromosomes 13/18/21, and hemoglobin Bart hydrops fetalis detection in 1 tube of maternal plasma.
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Affiliation(s)
- Jiexia Yang
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Chun-Fang Peng
- CapitalBio Genomics Co, Ltd, Dongguan, and CapitalBio Technology Inc, Beijing, China
| | - Yiming Qi
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Xing-Qiang Rao
- CapitalBio Genomics Co, Ltd, Dongguan, and CapitalBio Technology Inc, Beijing, China
| | - Fangfang Guo
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Yaping Hou
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Wei He
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Jing Wu
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Yang-Yi Chen
- CapitalBio Genomics Co, Ltd, Dongguan, and CapitalBio Technology Inc, Beijing, China
| | - Xin Zhao
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Yu-Nan Wang
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Haishan Peng
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Dongmei Wang
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Li Du
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Ming-Yong Luo
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Quan-Fei Huang
- CapitalBio Genomics Co, Ltd, Dongguan, and CapitalBio Technology Inc, Beijing, China
| | - Hai-Liang Liu
- CapitalBio Genomics Co, Ltd, Dongguan, and CapitalBio Technology Inc, Beijing, China.
| | - Aihua Yin
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China.
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Noguchi T, Sakai K, Iwahashi N, Matsuda K, Matsukawa H, Yahata T, Toujima S, Nishio K, Ino K. Changes in the gene mutation profiles of circulating tumor DNA detected using CAPP-Seq in neoadjuvant chemotherapy-treated advanced ovarian cancer. Oncol Lett 2020; 19:2713-2720. [PMID: 32218822 PMCID: PMC7068231 DOI: 10.3892/ol.2020.11356] [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: 10/31/2019] [Accepted: 12/03/2019] [Indexed: 01/09/2023] Open
Abstract
Cancer Personalized Profiling by deep Sequencing (CAPP-Seq) is a novel ultrasensitive next-generation sequencing-based approach that is used to detect circulating tumor DNA (ctDNA). The aim of the present study was to compare the gene mutation profiles and blood tumor mutation burden (bTMB) measured between pre- and post-neoadjuvant chemotherapy (NAC), utilizing CAPP-seq for plasma ctDNA in patients with advanced ovarian cancer. The current study included 10 patients (6 NAC-sensitive and 4 NAC-resistant) clinically diagnosed as having stage III or IV ovarian cancer and were administered NAC between May 2017 and February 2019. The plasma ctDNA samples were collected at pre- and post-NAC, and comprehensive gene mutation analysis was performed using CAPP-seq. In 5 out of 6 NAC-sensitive cases, the variant allele frequency (VAF) of non-synonymous somatic mutations decreased following NAC. In 2 out of the 4 NAC-resistant cases, the VAF of non-synonymous somatic mutations increased, and new somatic mutations emerged following NAC. In regard to TP53 mutation, the rate of TP53 mutation in the NAC-resistant cases was significantly higher compared with NAC-sensitive cases. Finally, the bTMB decreased significantly after NAC treatment in the NAC-sensitive cases, even though there were no significant differences in the pretreatment bTMB levels between the NAC-sensitive and NAC-resistant cases. These results indicated that gene mutation can be profiled and monitored using liquid biopsy-based CAPP-Seq in patients with advanced ovarian cancer with NAC treatment, and TP53 mutation in the ctDNA and bTMB may be novel biomarkers that can be used for patient monitoring during NAC treatment.
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Affiliation(s)
- Tomoko Noguchi
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka 589-8511, Japan
| | - Naoyuki Iwahashi
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Kaho Matsuda
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Hitomi Matsukawa
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Tamaki Yahata
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Saori Toujima
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka 589-8511, Japan
| | - Kazuhiko Ino
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
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Yan W, Xu T, Zhu H, Yu J. Clinical Applications of Cerebrospinal Fluid Circulating Tumor DNA as a Liquid Biopsy for Central Nervous System Tumors. Onco Targets Ther 2020; 13:719-731. [PMID: 32158224 PMCID: PMC6986252 DOI: 10.2147/ott.s229562] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/11/2020] [Indexed: 12/19/2022] Open
Abstract
Central nervous system (CNS) malignancies are associated with poor prognosis, as well as exceptional morbidity and mortality, likely as a result of low rates of early diagnosis and limited knowledge of the tumor growth and resistance mechanisms, dissemination, and evolution in the CNS. Monitoring patients with CNS malignancies for treatment response and tumor recurrence can be challenging because of the difficulty and risks of brain biopsies and the low specificity and sensitivity of the less invasive methodologies that are currently available. Therefore, there is an urgent need to detect and validate reliable and minimally invasive biomarkers for CNS tumors that can be used separately or in combination with current clinical practices. The circulating tumor DNA (ctDNA) of cerebrospinal fluid (CSF) samples can outline the genetic landscape of entire CNS tumors effectively and is a promising, suitable biomarker, though its role in managing CNS malignancies has not been studied extensively. This review summarizes recent studies that explore the diagnostic, prognostic, and predictive roles of CSF-ctDNA as a liquid biopsy with primary and metastatic CNS malignancies.
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Affiliation(s)
- Weiwei Yan
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China.,Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, People's Republic of China
| | - Tingting Xu
- Department of Respiratory Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, People's Republic of China
| | - Hui Zhu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, People's Republic of China
| | - Jinming Yu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, People's Republic of China
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Scherer F. Capturing Tumor Heterogeneity and Clonal Evolution by Circulating Tumor DNA Profiling. Recent Results Cancer Res 2020; 215:213-230. [PMID: 31605231 DOI: 10.1007/978-3-030-26439-0_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Most malignancies are characterized by remarkable molecular heterogeneity. The understanding of genetic and epigenetic processes underlying tumor heterogeneity has become increasingly important for the clinical management of cancer patients. This includes the identification of patients who likely benefit from conventional or targeted therapies, classification of patients into risk groups based on their mutational landscape, and the detection of molecular mechanisms that drive treatment resistance and cancer progression. Detection of tumor heterogeneity by tumor tissue genotyping is hampered by the fact that tissue sampling is often insufficient for comprehensive genetic assessment and is associated with a higher risk of surgical complications. Detection and profiling of circulating tumor DNA (ctDNA) have emerged as a promising alternative to direct tumor genotyping. It potentially enables noninvasive and quantitative characterization of the full genetic landscape and identification of clonal evolution during treatment and towards disease progression in cancer patients. In the present chapter, we explore the role of noninvasive genotyping and ctDNA profiling for accurate and robust characterization of various types of tumor heterogeneity and its relevance for management of patients with hematologic and solid cancers.
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Affiliation(s)
- Florian Scherer
- Department of Hematology, Oncology, and Stem Cell Transplantation, University Medical Center Freiburg, Albert-Ludwigs-University, Hugstetter Straße 55, 79106, Freiburg, Germany.
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Ziada AS, Lu MY, Ignas‐Menzies J, Paintsil E, Li M, Ogbuagu O, Saberi S, Hsieh AYY, Sattha B, Harrigan PR, Kalloger S, Côté HCF. Mitochondrial DNA somatic mutation burden and heteroplasmy are associated with chronological age, smoking, and HIV infection. Aging Cell 2019; 18:e13018. [PMID: 31407474 PMCID: PMC6826146 DOI: 10.1111/acel.13018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/28/2019] [Accepted: 07/14/2019] [Indexed: 12/03/2022] Open
Abstract
The gradual accumulation of mitochondrial DNA (mtDNA) mutations is implicated in aging and may contribute to the accelerated aging phenotype seen with tobacco smoking and HIV infection. mtDNA mutations are thought to arise from oxidative damage; however, recent reports implicate polymerase γ errors during mtDNA replication. Investigations of somatic mtDNA mutations have been hampered by technical challenges in measuring low-frequency mutations. We use primer ID-based next-generation sequencing to quantify both somatic and heteroplasmic blood mtDNA point mutations within the D-loop, in 164 women and girls aged 2-72 years, of whom 35% were smokers and 56% were HIV-positive. Somatic mutations and the occurrence of heteroplasmic mutations increased with age. While transitions are theorized to result from polymerase γ errors, transversions are believed to arise from DNA oxidative damage. In our study, both transition and transversion mutations were associated with age. However, transition somatic mutations were more prevalent than transversions, and no heteroplasmic transversions were observed. We also measured elevated somatic mutations, but not heteroplasmy, in association with high peak HIV viremia. Conversely, heteroplasmy was higher among smokers, but somatic mutations were not, suggesting that smoking promotes the expansion of preexisting mutations rather than de novo mutations. Taken together, our results are consistent with blood mtDNA mutations increasing with age, inferring a greater contribution of polymerase γ errors in mtDNA mutagenesis. We further suggest that smoking and HIV infection both contribute to the accumulation of mtDNA mutations, though in different ways.
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Affiliation(s)
- Adam S. Ziada
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverBCCanada
- Centre for Blood ResearchUniversity of British ColumbiaVancouverBCCanada
| | - Meng Ying Lu
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverBCCanada
- Centre for Blood ResearchUniversity of British ColumbiaVancouverBCCanada
| | - Jarek Ignas‐Menzies
- Department of Mechanical EngineeringUniversity of British ColumbiaVancouverBCCanada
| | - Elijah Paintsil
- Department of PediatricsYale School of MedicineNew HavenCTUSA
- School of Public HealthYale UniversityNew HavenCTUSA
- Department of Pharmacology, Yale School of MedicineNew HavenCTUSA
| | - Min Li
- Department of PediatricsYale School of MedicineNew HavenCTUSA
| | - Onyema Ogbuagu
- Department of MedicineYale School of MedicineNew HavenCTUSA
| | - Sara Saberi
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverBCCanada
- Centre for Blood ResearchUniversity of British ColumbiaVancouverBCCanada
| | - Anthony Y. Y. Hsieh
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverBCCanada
- Centre for Blood ResearchUniversity of British ColumbiaVancouverBCCanada
| | - Beheroze Sattha
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverBCCanada
- Centre for Blood ResearchUniversity of British ColumbiaVancouverBCCanada
| | | | - Steve Kalloger
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverBCCanada
| | - Hélène C. F. Côté
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverBCCanada
- Centre for Blood ResearchUniversity of British ColumbiaVancouverBCCanada
- Women’s Health Research InstituteVancouverBCCanada
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45
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Canale M, Pasini L, Bronte G, Delmonte A, Cravero P, Crinò L, Ulivi P. Role of liquid biopsy in oncogene-addicted non-small cell lung cancer. Transl Lung Cancer Res 2019; 8:S265-S279. [PMID: 31857950 DOI: 10.21037/tlcr.2019.09.15] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The discovery of actionable oncogene in non-small cell lung cancer (NSCLC) allowed the identification of a subgroup of patients who benefit from targeted tyrosine kinase inhibitors more than others. Mutations in the epidermal growth factor receptor (EGFR), translocations in the anaplastic lymphoma kinase (ALK) and rearrangements in the ROS proto-oncogene 1 (ROS1) must be identified in tumor tissue to guide the proper treatment choice. Liquid biopsy is based on the analysis of tumor materials released in the circulation. Liquid biopsy can be complementary to tissue biopsy, both at baseline and at progression, especially in the detection of somatic gene alterations emerging during the treatment with tyrosine kinase inhibitors (TKIs). Particularly, circulating DNA is used to find mutations in driver oncogenes, while circulating tumor cells, extracellular vesicles (EVs) and cell-free microRNAs (cfmiRNAs) are still under investigation. To help the unbiased use of liquid biopsy in the choice of the appropriate therapy, some recommendations were delivered by expert panels. Currently, analysis of EGFR mutations in cell-free DNA (cfDNA) is recommended at baseline when tissue biopsy harbors scarce tumor cells, and at progression before performing tissue biopsy; liquid biopsy analysis for other oncogenic drivers is not indicated in the clinical practice.
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Affiliation(s)
- Matteo Canale
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Luigi Pasini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Giuseppe Bronte
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Angelo Delmonte
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Paola Cravero
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Lucio Crinò
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Paola Ulivi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
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Soda N, Rehm BHA, Sonar P, Nguyen NT, Shiddiky MJA. Advanced liquid biopsy technologies for circulating biomarker detection. J Mater Chem B 2019; 7:6670-6704. [PMID: 31646316 DOI: 10.1039/c9tb01490j] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Liquid biopsy is a new diagnostic concept that provides important information for monitoring and identifying tumor genomes in body fluid samples. Detection of tumor origin biomolecules like circulating tumor cells (CTCs), circulating tumor specific nucleic acids (circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), microRNAs (miRNAs), long non-coding RNAs (lnRNAs)), exosomes, autoantibodies in blood, saliva, stool, urine, etc. enables cancer screening, early stage diagnosis and evaluation of therapy response through minimally invasive means. From reliance on painful and hazardous tissue biopsies or imaging depending on sophisticated equipment, cancer management schemes are witnessing a rapid evolution towards minimally invasive yet highly sensitive liquid biopsy-based tools. Clinical application of liquid biopsy is already paving the way for precision theranostics and personalized medicine. This is achieved especially by enabling repeated sampling, which in turn provides a more comprehensive molecular profile of tumors. On the other hand, integration with novel miniaturized platforms, engineered nanomaterials, as well as electrochemical detection has led to the development of low-cost and simple platforms suited for point-of-care applications. Herein, we provide a comprehensive overview of the biogenesis, significance and potential role of four widely known biomarkers (CTCs, ctDNA, miRNA and exosomes) in cancer diagnostics and therapeutics. Furthermore, we provide a detailed discussion of the inherent biological and technical challenges associated with currently available methods and the possible pathways to overcome these challenges. The recent advances in the application of a wide range of nanomaterials in detecting these biomarkers are also highlighted.
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Affiliation(s)
- Narshone Soda
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery (GRIDD), Griffith University, Nathan, QLD 4111, Australia
| | - Prashant Sonar
- School of Chemistry, Physics and Mechanical Engineering, Molecular Design and Synthesis, Queensland University of Technology (QUT), Brisbane, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia
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van der Pol Y, Mouliere F. Toward the Early Detection of Cancer by Decoding the Epigenetic and Environmental Fingerprints of Cell-Free DNA. Cancer Cell 2019; 36:350-368. [PMID: 31614115 DOI: 10.1016/j.ccell.2019.09.003] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/18/2019] [Accepted: 09/06/2019] [Indexed: 12/15/2022]
Abstract
Widespread adaptation of liquid biopsy for the early detection of cancer has yet to reach clinical utility. Circulating tumor DNA is commonly detected though the presence of genetic alterations, but only a minor fraction of tumor-derived cell-free DNA (cfDNA) fragments exhibit mutations. The cellular processes occurring in cancer development mark the chromatin. These epigenetic marks are reflected by modifications in the cfDNA methylation, fragment size, and structure. In this review, we describe how going beyond DNA sequence information alone, by analyzing cfDNA epigenetic and immune signatures, boosts the potential of liquid biopsy for the early detection of cancer.
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Affiliation(s)
- Ymke van der Pol
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Florent Mouliere
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
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Carrasco P, Inostroza C, Didier M, Godoy M, Holt CL, Tabak J, Loftus A. Optimizing DNA recovery and forensic typing of degraded blood and dental remains using a specialized extraction method, comprehensive qPCR sample characterization, and massively parallel sequencing. Int J Legal Med 2019; 134:79-91. [PMID: 31414202 PMCID: PMC6949324 DOI: 10.1007/s00414-019-02124-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/10/2019] [Indexed: 12/30/2022]
Abstract
Human dental remains encountered in criminal casework evidence, missing person cases, or mass disaster tragedies provide a valuable sample source for DNA typing when suitable soft tissue is unavailable. Using traditional methods, teeth samples can be challenging to process, resulting in low-quantity and/or quality nuclear DNA and insufficient profiles for comparisons. This study examines the performance of a three-part nuclear DNA analysis workflow for teeth samples based on (1) improved dental tissue recovery using the Dental Forensic Kit (DFKMR) (Universidad de los Andes) and DNA extraction with QuickExtract™ FFPE DNA Extraction Kit (Lucigen®), (2) quantification with InnoQuant® HY (InnoGenomics Technologies) for sensitive assessment of total human and male DNA quantity/quality, and (3) massively parallel sequencing for simultaneous genotyping of 231 short tandem repeat (STR) and single-nucleotide polymorphism (SNP) markers with the ForenSeq® DNA Signature Prep Kit (Verogen, Inc.). Initial evaluation of artificially degraded blood samples (n = 10) achieved highly sensitive and informative quantification results with InnoQuant® HY, enabling successful first pass genotyping with the MiSeq FGx® System. Twenty-three STR alleles (out of 85) and 70 identity informative SNP loci (out of 94) were recovered from two pg total long target DNA input (0.86 ng total short target input) and an InnoQuant degradation index (DI) of 460 (severely degraded). The three-part workflow was subsequently applied to teeth samples (dental pulp, root cement tissues; n = 13) with postmortem intervals (PMI) of the teeth ranging from 8 days to approximately 6 months. Informative SNP and STR DNA profiles were obtained, to include 78 STR alleles and 85 identity informative SNP loci typed (of 94 total SNP targets) in a 1 month, four-day PMI root cement sample with one pg total long target DNA input and a DI of 76. These data indicate successful performance of the proposed workflow from degraded DNA from teeth samples.
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Affiliation(s)
- Patricio Carrasco
- Universidad de los Andes, Mons. Álvaro del Portillo 12.455, Las Condes, Santiago Chile
| | - Carolina Inostroza
- Universidad de los Andes, Mons. Álvaro del Portillo 12.455, Las Condes, Santiago Chile
| | - Meghan Didier
- Verogen, Inc., 11111 Flintkote Avenue, San Diego, CA 92121 USA
| | - Marianela Godoy
- Universidad de los Andes, Mons. Álvaro del Portillo 12.455, Las Condes, Santiago Chile
| | - Cydne L. Holt
- Verogen, Inc., 11111 Flintkote Avenue, San Diego, CA 92121 USA
| | - Jonathan Tabak
- Verogen, Inc., 11111 Flintkote Avenue, San Diego, CA 92121 USA
| | - Andrew Loftus
- InnoGenomics Technologies, LLC, 1441 Canal Street, New Orleans, LA 70112 USA
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McDonald BR, Contente-Cuomo T, Sammut SJ, Odenheimer-Bergman A, Ernst B, Perdigones N, Chin SF, Farooq M, Mejia R, Cronin PA, Anderson KS, Kosiorek HE, Northfelt DW, McCullough AE, Patel BK, Weitzel JN, Slavin TP, Caldas C, Pockaj BA, Murtaza M. Personalized circulating tumor DNA analysis to detect residual disease after neoadjuvant therapy in breast cancer. Sci Transl Med 2019; 11:eaax7392. [PMID: 31391323 PMCID: PMC7236617 DOI: 10.1126/scitranslmed.aax7392] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 04/17/2019] [Accepted: 07/03/2019] [Indexed: 12/17/2022]
Abstract
Longitudinal analysis of circulating tumor DNA (ctDNA) has shown promise for monitoring treatment response. However, most current methods lack adequate sensitivity for residual disease detection during or after completion of treatment in patients with nonmetastatic cancer. To address this gap and to improve sensitivity for minute quantities of residual tumor DNA in plasma, we have developed targeted digital sequencing (TARDIS) for multiplexed analysis of patient-specific cancer mutations. In reference samples, by simultaneously analyzing 8 to 16 known mutations, TARDIS achieved 91 and 53% sensitivity at mutant allele fractions (AFs) of 3 in 104 and 3 in 105, respectively, with 96% specificity, using input DNA equivalent to a single tube of blood. We successfully analyzed up to 115 mutations per patient in 80 plasma samples from 33 women with stage I to III breast cancer. Before treatment, TARDIS detected ctDNA in all patients with 0.11% median AF. After completion of neoadjuvant therapy, ctDNA concentrations were lower in patients who achieved pathological complete response (pathCR) compared to patients with residual disease (median AFs, 0.003 and 0.017%, respectively, P = 0.0057, AUC = 0.83). In addition, patients with pathCR showed a larger decrease in ctDNA concentrations during neoadjuvant therapy. These results demonstrate high accuracy for assessment of molecular response and residual disease during neoadjuvant therapy using ctDNA analysis. TARDIS has achieved up to 100-fold improvement beyond the current limit of ctDNA detection using clinically relevant blood volumes, demonstrating that personalized ctDNA tracking could enable individualized clinical management of patients with cancer treated with curative intent.
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Affiliation(s)
- Bradon R McDonald
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Tania Contente-Cuomo
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Stephen-John Sammut
- Department of Oncology and Cancer Research UK Cambridge Institute and Cancer Centre, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Ahuva Odenheimer-Bergman
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | | | - Nieves Perdigones
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Suet-Feung Chin
- Department of Oncology and Cancer Research UK Cambridge Institute and Cancer Centre, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Maria Farooq
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | | | | | - Karen S Anderson
- Mayo Clinic, Scottsdale, AZ 85259, USA
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | | | | | | | | | | | | | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute and Cancer Centre, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Muhammed Murtaza
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA.
- Mayo Clinic, Scottsdale, AZ 85259, USA
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50
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Ahmed KI, Govardhan HB, Roy M, Naveen T, Siddanna P, Sridhar P, Suma MN, Nelson N. Cell-free circulating tumor DNA in patients with high-grade glioma as diagnostic biomarker - A guide to future directive. Indian J Cancer 2019; 56:65-69. [PMID: 30950448 DOI: 10.4103/ijc.ijc_551_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Owing to the aggressive nature of high-grade gliomas (HGGs), its early diagnosis holds the key to a favorable prognosis. Currently, tissue biopsy is the gold standard to verify HGG's initial diagnosis and can be challenging due to its invasive nature. In this study, our objective was a noninvasive panel for timely detection of HGG and its progression using cell-free circulating tumor DNA (cfTDNA). MATERIALS AND METHODS Twenty-seven patients with HGG were tested with a 50-gene tumor panel. cfTDNA isolated from serum was checked for single-nucleotide variations (SNVs) or copy number alterations using targeted next-generation sequencing, with further validation of results by checking respective formalin-fixed paraffin-embedded tumor tissues for the same genetic alterations. RESULTS About 88.8% of the patients were detected with HGG-associated cfTDNA. Around 25% patients were detected with one, 25% patients had three, 25% patients had four, and 12.5% patients each had five and six genetic alterations. About 12 of 50 genes were detected in the serum samples. The SNVs detected included TP53 in 87.5% of patients; PIK3CA and EGFR in 50% of patients; PTEN in 37.5%; KIT and VHL in each 25% of patients; and RB1, NF2, MET, ATRX, CDK2A, and CTNNB1 each in 8.3%-16.6%. On combining EGFR, KIT, PTEN, PIK3CA, TP53, and VHL genes (Govardhan Diagnostic Genetic Module for high-grade glioma), at least one of the genetic alterations was found in 100% of patients. Conclusion These findings illustrate that cfTDNA is easily demonstrable and can be used as a surrogate to tissue biopsy in brain tumor.
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Affiliation(s)
- Khaleel Ibrahim Ahmed
- Department of Radiation Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - H B Govardhan
- Department of Radiation Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - Manisha Roy
- Department of Radiation Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - T Naveen
- Department of Radiation Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - P Siddanna
- Department of Radiation Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - P Sridhar
- Department of Radiation Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - M N Suma
- Department of Radiation Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - Noopur Nelson
- Department of Radiation Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
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