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Ho HY, Chung KS(K, Kan CM, Wong SC(C. Liquid Biopsy in the Clinical Management of Cancers. Int J Mol Sci 2024; 25:8594. [PMID: 39201281 PMCID: PMC11354853 DOI: 10.3390/ijms25168594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/02/2024] [Accepted: 08/02/2024] [Indexed: 09/02/2024] Open
Abstract
Liquid biopsy, a noninvasive diagnosis that examines circulating tumor components in body fluids, is increasingly used in cancer management. An overview of relevant literature emphasizes the current state of liquid biopsy applications in cancer care. Biomarkers in liquid biopsy, particularly circulating tumor DNA (ctDNA), circulating tumor RNAs (ctRNA), circulating tumor cells (CTCs), extracellular vesicles (EVs), and other components, offer promising opportunities for early cancer diagnosis, treatment selection, monitoring, and disease assessment. The implementation of liquid biopsy in precision medicine has shown significant potential in various cancer types, including lung cancer, colorectal cancer, breast cancer, and prostate cancer. Advances in genomic and molecular technologies such as next-generation sequencing (NGS) and digital polymerase chain reaction (dPCR) have expanded the utility of liquid biopsy, enabling the detection of somatic variants and actionable genomic alterations in tumors. Liquid biopsy has also demonstrated utility in predicting treatment responses, monitoring minimal residual disease (MRD), and assessing tumor heterogeneity. Nevertheless, standardizing liquid biopsy techniques, interpreting results, and integrating them into the clinical routine remain as challenges. Despite these challenges, liquid biopsy has significant clinical implications in cancer management, offering a dynamic and noninvasive approach to understanding tumor biology and guiding personalized treatment strategies.
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Affiliation(s)
| | | | | | - Sze-Chuen (Cesar) Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China; (H.-Y.H.); (K.-S.C.); (C.-M.K.)
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2
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Stella GM, Lettieri S, Piloni D, Ferrarotti I, Perrotta F, Corsico AG, Bortolotto C. Smart Sensors and Microtechnologies in the Precision Medicine Approach against Lung Cancer. Pharmaceuticals (Basel) 2023; 16:1042. [PMID: 37513953 PMCID: PMC10385174 DOI: 10.3390/ph16071042] [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: 06/08/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND AND RATIONALE The therapeutic interventions against lung cancer are currently based on a fully personalized approach to the disease with considerable improvement of patients' outcome. Alongside continuous scientific progresses and research investments, massive technologic efforts, innovative challenges, and consolidated achievements together with research investments are at the bases of the engineering and manufacturing revolution that allows a significant gain in clinical setting. AIM AND METHODS The scope of this review is thus to focus, rather than on the biologic traits, on the analysis of the precision sensors and novel generation materials, as semiconductors, which are below the clinical development of personalized diagnosis and treatment. In this perspective, a careful revision and analysis of the state of the art of the literature and experimental knowledge is presented. RESULTS Novel materials are being used in the development of personalized diagnosis and treatment for lung cancer. Among them, semiconductors are used to analyze volatile cancer compounds and allow early disease diagnosis. Moreover, they can be used to generate MEMS which have found an application in advanced imaging techniques as well as in drug delivery devices. CONCLUSIONS Overall, these issues represent critical issues only partially known and generally underestimated by the clinical community. These novel micro-technology-based biosensing devices, based on the use of molecules at atomic concentrations, are crucial for clinical innovation since they have allowed the recent significant advances in cancer biology deciphering as well as in disease detection and therapy. There is an urgent need to create a stronger dialogue between technologists, basic researchers, and clinicians to address all scientific and manufacturing efforts towards a real improvement in patients' outcome. Here, great attention is focused on their application against lung cancer, from their exploitations in translational research to their application in diagnosis and treatment development, to ensure early diagnosis and better clinical outcomes.
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Affiliation(s)
- Giulia Maria Stella
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Sara Lettieri
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Davide Piloni
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Ilaria Ferrarotti
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Fabio Perrotta
- Department of Translational Medical Sciences, University of Campania "L. Vanvitelli", 80131 Napoli, Italy
- U.O.C. Clinica Pneumologica "L. Vanvitelli", A.O. dei Colli, Ospedale Monaldi, 80131 Napoli, Italy
| | - Angelo Guido Corsico
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Chandra Bortolotto
- Department of Clinical-Surgical, Diagnostic and Paediatric Sciences, University of Pavia Medical School, 27100 Pavia, Italy
- Department of Diagnostic Services and Imaging, Unit of Radiology, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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3
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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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4
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Pham TMQ, Phan TH, Jasmine TX, Tran TTT, Huynh LAK, Vo TL, Nai THT, Tran TT, Truong MH, Tran NC, Nguyen VTC, Nguyen TH, Nguyen THH, Le NDK, Nguyen TD, Nguyen DS, Truong DK, Do TTT, Phan MD, Giang H, Nguyen HN, Tran LS. Multimodal analysis of genome-wide methylation, copy number aberrations, and end motif signatures enhances detection of early-stage breast cancer. Front Oncol 2023; 13:1127086. [PMID: 37223690 PMCID: PMC10200909 DOI: 10.3389/fonc.2023.1127086] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/24/2023] [Indexed: 05/25/2023] Open
Abstract
Introduction Breast cancer causes the most cancer-related death in women and is the costliest cancer in the US regarding medical service and prescription drug expenses. Breast cancer screening is recommended by health authorities in the US, but current screening efforts are often compromised by high false positive rates. Liquid biopsy based on circulating tumor DNA (ctDNA) has emerged as a potential approach to screen for cancer. However, the detection of breast cancer, particularly in early stages, is challenging due to the low amount of ctDNA and heterogeneity of molecular subtypes. Methods Here, we employed a multimodal approach, namely Screen for the Presence of Tumor by DNA Methylation and Size (SPOT-MAS), to simultaneously analyze multiple signatures of cell free DNA (cfDNA) in plasma samples of 239 nonmetastatic breast cancer patients and 278 healthy subjects. Results We identified distinct profiles of genome-wide methylation changes (GWM), copy number alterations (CNA), and 4-nucleotide oligomer (4-mer) end motifs (EM) in cfDNA of breast cancer patients. We further used all three signatures to construct a multi-featured machine learning model and showed that the combination model outperformed base models built from individual features, achieving an AUC of 0.91 (95% CI: 0.87-0.95), a sensitivity of 65% at 96% specificity. Discussion Our findings showed that a multimodal liquid biopsy assay based on analysis of cfDNA methylation, CNA and EM could enhance the accuracy for the detection of early- stage breast cancer.
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Affiliation(s)
- Thi Mong Quynh Pham
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Thanh Hai Phan
- Ultrasound Department Medic Medical Center, Ho Chi Minh, Vietnam
| | | | - Thuy Thi Thu Tran
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Le Anh Khoa Huynh
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Department of Biostatistics, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Thi Loan Vo
- Ultrasound Department Medic Medical Center, Ho Chi Minh, Vietnam
| | | | - Thuy Trang Tran
- Ultrasound Department Medic Medical Center, Ho Chi Minh, Vietnam
| | - My Hoang Truong
- Ultrasound Department Medic Medical Center, Ho Chi Minh, Vietnam
| | - Ngan Chau Tran
- Ultrasound Department Medic Medical Center, Ho Chi Minh, Vietnam
| | - Van Thien Chi Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Trong Hieu Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Thi Hue Hanh Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Nguyen Duy Khang Le
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Thanh Dat Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Duy Sinh Nguyen
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
- Faculty of Medicine Nguyen Tat Thanh University, Ho Chi Minh, Vietnam
| | | | | | - Minh-Duy Phan
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Hoai-Nghia Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Le Son Tran
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
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McCarthy A, Rajabi H, McClenaghan B, Fahner NA, Porter E, Singer GAC, Hajibabaei M. Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence-based metabarcoding. Mol Ecol Resour 2023; 23:581-591. [PMID: 36366953 DOI: 10.1111/1755-0998.13732] [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: 02/08/2021] [Revised: 09/15/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
Environmental DNA (eDNA)-based methods of species detection are enabling various applications in ecology and conservation including large-scale biomonitoring efforts. qPCR is widely used as the standard approach for species-specific detection, often targeting a fish species of interest from aquatic eDNA. However, DNA metabarcoding has the potential to displace qPCR in certain eDNA applications. In this study, we compare the sensitivity of the latest Illumina NovaSeq 6000 NGS platform to qPCR TaqMan assays by measuring limits of detection and by analysing eDNA from water samples collected from Churchill River and Lake Melville, NL, Canada. Species-specific, targeted next generation sequencing (NGS) assays had significantly higher sensitivity than qPCR, with limits of detection 14- to 29-fold lower. For example, when analysing eDNA, qPCR detected Gadus ogac (Greenland cod) in 21% of samples, but targeted NGS detected this species in 29% of samples. General NGS assays were as sensitive as qPCR, while simultaneously detecting 15 fish species from eDNA samples. With over 34,000 fish species on the planet, parallel and sensitive methods such as NGS will be required to support effective biomonitoring at both regional and global scales.
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Affiliation(s)
- Avery McCarthy
- Centre for Environmental Genomics Applications, eDNAtec Inc., Newfoundland and Labrador, St. John's, Canada
| | - Hoda Rajabi
- Centre for Environmental Genomics Applications, eDNAtec Inc., Newfoundland and Labrador, St. John's, Canada
| | - Beverly McClenaghan
- Centre for Environmental Genomics Applications, eDNAtec Inc., Newfoundland and Labrador, St. John's, Canada
| | - Nicole A Fahner
- Centre for Environmental Genomics Applications, eDNAtec Inc., Newfoundland and Labrador, St. John's, Canada
| | - Emily Porter
- Centre for Environmental Genomics Applications, eDNAtec Inc., Newfoundland and Labrador, St. John's, Canada
| | - Gregory A C Singer
- Centre for Environmental Genomics Applications, eDNAtec Inc., Newfoundland and Labrador, St. John's, Canada
| | - Mehrdad Hajibabaei
- Centre for Environmental Genomics Applications, eDNAtec Inc., Newfoundland and Labrador, St. John's, Canada.,Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Ontario, Guelph, Canada
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6
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Wu NJW, Aquilina M, Qian BZ, Loos R, Gonzalez-Garcia I, Santini CC, Dunn KE. The Application of Nanotechnology for Quantification of Circulating Tumour DNA in Liquid Biopsies: A Systematic Review. IEEE Rev Biomed Eng 2023; 16:499-513. [PMID: 35302938 DOI: 10.1109/rbme.2022.3159389] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Technologies for quantifying circulating tumour DNA (ctDNA) in liquid biopsies could enable real-time measurements of cancer progression, profoundly impacting patient care. Sequencing methods can be too complex and time-consuming for regular point-of-care monitoring, but nanotechnology offers an alternative, harnessing the unique properties of objects tens to hundreds of nanometres in size. This systematic review was performed to identify all examples of nanotechnology-based ctDNA detection and assess their potential for clinical use. Google Scholar, PubMed, Web of Science, Google Patents, Espacenet and Embase/MEDLINE were searched up to 23rd March 2021. The review identified nanotechnology-based methods for ctDNA detection for which quantitative measures (e.g., limit of detection, LOD) were reported and biologically relevant samples were used. The pre-defined inclusion criteria were met by 66 records. LODs ranged from 10 zM to 50nM. 25 records presented an LOD of 10fM or below. Nanotechnology-based approaches could provide the basis for the next wave of advances in ctDNA diagnostics, enabling analysis at the point-of-care, but none are currently used clinically. Further work is needed in development and validation; trade-offs are expected between different performance measures e.g., number of sequences detected and time to result.
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Eyck BM, Jansen MP, Noordman BJ, Atmodimedjo PN, van der Wilk BJ, Martens JW, Helmijr JA, Beaufort CM, Mostert B, Doukas M, Wijnhoven BP, Lagarde SM, van Lanschot JJB, Dinjens WN. Detection of circulating tumour DNA after neoadjuvant chemoradiotherapy in patients with locally advanced oesophageal cancer. J Pathol 2023; 259:35-45. [PMID: 36196486 PMCID: PMC10092085 DOI: 10.1002/path.6016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/05/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022]
Abstract
Active surveillance instead of standard surgery after neoadjuvant chemoradiotherapy (nCRT) has been proposed for patients with oesophageal cancer. Circulating tumour DNA (ctDNA) may be used to facilitate selection of patients for surgery. We show that detection of ctDNA after nCRT seems highly suggestive of major residual disease. Tumour biopsies and blood samples were taken before, and 6 and 12 weeks after, nCRT. Biopsies were analysed with regular targeted next-generation sequencing (NGS). Circulating cell-free DNA (cfDNA) was analysed using targeted NGS with unique molecular identifiers and digital polymerase chain reaction. cfDNA mutations matching pre-treatment biopsy mutations confirmed the presence of ctDNA. In total, 31 patients were included, of whom 24 had a biopsy mutation that was potentially detectable in cfDNA (77%). Pre-treatment ctDNA was detected in nine of 24 patients (38%), four of whom had incurable disease progression before surgery. Pre-treatment ctDNA detection had a sensitivity of 47% (95% CI 24-71) (8/17), specificity of 85% (95% CI 42-99) (6/7), positive predictive value (PPV) of 89% (95% CI 51-99) (8/9), and negative predictive value (NPV) of 40% (95% CI 17-67) (6/15) for detecting major residual disease (>10% residue in the resection specimen or progression before surgery). After nCRT, ctDNA was detected in three patients, two of whom had disease progression. Post-nCRT ctDNA detection had a sensitivity of 21% (95% CI 6-51) (3/14), specificity of 100% (95% CI 56-100) (7/7), PPV of 100% (95% CI 31-100) (3/3), and NPV of 39% (95% CI 18-64) (7/18) for detecting major residual disease. The addition of ctDNA to the current set of diagnostics did not lead to more patients being clinically identified with residual disease. These results indicate that pre-treatment and post-nCRT ctDNA detection may be useful in identifying patients at high risk of disease progression. The addition of ctDNA analysis to the current set of diagnostic modalities may not improve detection of residual disease after nCRT. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Ben M Eyck
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Maurice Phm Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Bo Jan Noordman
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Berend J van der Wilk
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - John Wm Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Jean A Helmijr
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Corine M Beaufort
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Bianca Mostert
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Michail Doukas
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Bas Pl Wijnhoven
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Sjoerd M Lagarde
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - J Jan B van Lanschot
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Winand Nm Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, Rotterdam, The Netherlands
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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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9
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Pisapia P, Pepe F, Gristina V, La Mantia M, Francomano V, Russo G, Iaccarino A, Galvano A. A narrative review on the implementation of liquid biopsy as a diagnostic tool in thoracic tumors during the COVID-19 pandemic. MEDIASTINUM (HONG KONG, CHINA) 2022; 5:27. [PMID: 35118332 PMCID: PMC8794438 DOI: 10.21037/med-21-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/13/2021] [Indexed: 12/11/2022]
Abstract
Objective In this review, we evaluate the role of liquid biopsy in managing lung cancer patients during the still ongoing coronavirus disease 2019 (COVID-19) healthcare emergency. Background The novel influenza coronavirus (severe acute respiratory syndrome coronavirus or SARS-CoV-2) has upended several aspects of our lives, including medical activities. In this setting, many routine cancer diagnostic and therapeutic procedures have been suspended, leading to delays in diagnosis, treatments, and, ultimately, increases in cancer mortality rates. Equally drastic has been the impact of COVID-19 on clinical trials, many of which have been stalled or have never begun. This has left many patients who were hoping to receive innovative treatments in a limbo. Although, as of today, the introduction of drastic security measures has been crucially important to contain the pandemic, one cannot ignore the need to continue providing chronically ill patients all the health care they need, in terms of detection, prevention, and treatment. In these unprecedented times, liquid biopsy, more than ever before, may play a relevant role in the adequate management of these frail patients. Methods we performed a deep analysis of the recent international literature published in English on PUBMED in the last six months focused on the impact of SARS-CoV-2 on the management of lung cancer patients, focusing the attention on the role of liquid biopsy. Conclusions COVID-19 pandemic has significantly modified our lives and overall medical practice. In these unprecedented times, liquid biopsy may represent a valid and less time-consuming diagnostic approach than conventional tissue and cytological specimens.
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Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Valerio Gristina
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Maria La Mantia
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | | | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Antonio Galvano
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
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Rapid Multiplex Strip Test for the Detection of Circulating Tumor DNA Mutations for Liquid Biopsy Applications. BIOSENSORS 2022; 12:bios12020097. [PMID: 35200357 PMCID: PMC8869478 DOI: 10.3390/bios12020097] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/26/2022] [Accepted: 02/01/2022] [Indexed: 01/16/2023]
Abstract
In the era of personalized medicine, molecular profiling of patient tumors has become the standard practice, especially for patients with advanced disease. Activating point mutations of the KRAS proto-oncogene are clinically relevant for many types of cancer, including colorectal cancer (CRC). While several approaches have been developed for tumor genotyping, liquid biopsy has been gaining much attention in the clinical setting. Analysis of circulating tumor DNA for genetic alterations has been challenging, and many methodologies with both advantages and disadvantages have been developed. We here developed a gold nanoparticle-based rapid strip test that has been applied for the first time for the multiplex detection of KRAS mutations in circulating tumor DNA (ctDNA) of CRC patients. The method involved ctDNA isolation, PCR-amplification of the KRAS gene, multiplex primer extension (PEXT) reaction, and detection with a multiplex strip test. We have optimized the efficiency and specificity of the multiplex strip test in synthetic DNA targets, in colorectal cancer cell lines, in tissue samples, and in blood-derived ctDNA from patients with advanced colorectal cancer. The proposed strip test achieved rapid and easy multiplex detection (normal allele and three major single-point mutations) of the clinically relevant KRAS mutations in ctDNA in blood samples of CRC patients with high specificity and repeatability. This multiplex strip test represents a minimally invasive, rapid, low-cost, and promising diagnostic tool for the detection of clinically relevant mutations in cancer patients.
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11
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Nguyen HT, Luong BA, Tran DH, Nguyen TH, Ngo QD, Le LGH, Ho QC, Nguyen HHT, Nguyen CM, Tran VU, Pham TVN, Le MT, Le NAT, Le TK, Nguyen TL, Pham HAT, Le HT, Duong HDT, Hoang AV, Nguyen HB, Truong Dinh K, Phan MD, Nguyen HN, Do TTT, Giang H, Tran LS, Tran DT. Ultra-Deep Sequencing of Plasma-Circulating DNA for the Detection of Tumor- Derived Mutations in Patients with Nonmetastatic Colorectal Cancer. Cancer Invest 2021; 40:354-365. [PMID: 34894952 DOI: 10.1080/07357907.2021.2017951] [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: 10/19/2022]
Abstract
Identification of tumor-derived mutation (TDM) in liquid biopsies (LB), especially in early-stage patients, faces several challenges, including low variant-allele frequencies, interference by white blood cell (WBC)-derived mutations (WDM), benign somatic mutations and tumor heterogeneity. Here, we addressed the above-mentioned challenges in a cohort of 50 nonmetastatic colorectal cancer patients, via a workflow involving parallel sequencing of paired WBC- and tumor-gDNA. After excluding potential false positive mutations, we detected at least one TDM in LB of 56% (28/50) of patients, with the majority showing low-patient coverage, except for one TDM mapped to KMT2D that recurred in 30% (15/30) of patients.
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Affiliation(s)
| | - Bac An Luong
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Duc-Huy Tran
- University Medical Center, Ho Chi Minh City, Vietnam
| | | | - Quoc Dat Ngo
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | | | - Quoc Chuong Ho
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | | | | | - Vu Uyen Tran
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | | | - Minh Triet Le
- University Medical Center, Ho Chi Minh City, Vietnam
| | | | - Trung Kien Le
- University Medical Center, Ho Chi Minh City, Vietnam
| | | | | | - Hong Thuy Le
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | | | - Anh Vu Hoang
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | | | | | - Minh-Duy Phan
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | | | | | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Le Son Tran
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Diep Tuan Tran
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
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12
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Nguyen HN, Cao NPT, Van Nguyen TC, Le KND, Nguyen DT, Nguyen QTT, Nguyen THT, Van Nguyen C, Le HT, Nguyen MLT, Nguyen TV, Tran VU, Luong BA, Le LGH, Ho QC, Pham HAT, Vo BT, Nguyen LT, Dang ATH, Nguyen SD, Do DM, Do TTT, Hoang AV, Dinh KT, Phan MD, Giang H, Tran LS. Liquid biopsy uncovers distinct patterns of DNA methylation and copy number changes in NSCLC patients with different EGFR-TKI resistant mutations. Sci Rep 2021; 11:16436. [PMID: 34385540 PMCID: PMC8361064 DOI: 10.1038/s41598-021-95985-6] [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] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/31/2021] [Indexed: 01/19/2023] Open
Abstract
Targeted therapy with tyrosine kinase inhibitors (TKI) provides survival benefits to a majority of patients with non-small cell lung cancer (NSCLC). However, resistance to TKI almost always develops after treatment. Although genetic and epigenetic alterations have each been shown to drive resistance to TKI in cell line models, clinical evidence for their contribution in the acquisition of resistance remains limited. Here, we employed liquid biopsy for simultaneous analysis of genetic and epigenetic changes in 122 Vietnamese NSCLC patients undergoing TKI therapy and displaying acquired resistance. We detected multiple profiles of resistance mutations in 51 patients (41.8%). Of those, genetic alterations in EGFR, particularly EGFR amplification (n = 6), showed pronounced genome instability and genome-wide hypomethylation. Interestingly, the level of hypomethylation was associated with the duration of response to TKI treatment. We also detected hypermethylation in regulatory regions of Homeobox genes which are known to be involved in tumor differentiation. In contrast, such changes were not observed in cases with MET (n = 4) and HER2 (n = 4) amplification. Thus, our study showed that liquid biopsy could provide important insights into the heterogeneity of TKI resistance mechanisms in NSCLC patients, providing essential information for prediction of resistance and selection of subsequent treatment.
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Affiliation(s)
- Hoai-Nghia Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam.
| | | | | | | | | | | | | | | | - Ha Thu Le
- Ha Noi Oncology Hospital, Ha Noi, Vietnam
| | | | | | - Vu Uyen Tran
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Bac An Luong
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Linh Gia Hoang Le
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Quoc Chuong Ho
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | - Binh Thanh Vo
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | | | - Anh-Thu Huynh Dang
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | - Duc Minh Do
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | - Anh Vu Hoang
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | - Minh-Duy Phan
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.
| | - Le Son Tran
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.
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13
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Woerner AE, Mandape S, King JL, Muenzler M, Crysup B, Budowle B. Reducing noise and stutter in short tandem repeat loci with unique molecular identifiers. Forensic Sci Int Genet 2020; 51:102459. [PMID: 33429137 DOI: 10.1016/j.fsigen.2020.102459] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/28/2020] [Accepted: 12/21/2020] [Indexed: 12/24/2022]
Abstract
Unique molecular identifiers (UMIs) are a promising approach to contend with errors generated during PCR and massively parallel sequencing (MPS). With UMI technology, random molecular barcodes are ligated to template DNA molecules prior to PCR, allowing PCR and sequencing error to be tracked and corrected bioinformatically. UMIs have the potential to be particularly informative for the interpretation of short tandem repeats (STRs). Traditional MPS approaches may simply lead to the observation of alleles that are consistent with the hypotheses of stutter, while with UMIs stutter products bioinformatically may be re-associated with their parental alleles and subsequently removed. Herein, a bioinformatics pipeline named strumi is described that is designed for the analysis of STRs that are tagged with UMIs. Unlike other tools, strumi is an alignment-free machine learning driven algorithm that clusters individual MPS reads into UMI families, infers consensus super-reads that represent each family and provides an estimate the resulting haplotype's accuracy. Super-reads, in turn, approximate independent measurements not of the PCR products, but of the original template molecules, both in terms of quantity and sequence identity. Provisional assessments show that naïve threshold-based approaches generate super-reads that are accurate (∼97 % haplotype accuracy, compared to ∼78 % when UMIs are not used), and the application of a more nuanced machine learning approach increases the accuracy to ∼99.5 % depending on the level of certainty desired. With these features, UMIs may greatly simplify probabilistic genotyping systems and reduce uncertainty. However, the ability to interpret alleles at trace levels also permits the interpretation, characterization and quantification of contamination as well as somatic variation (including somatic stutter), which may present newfound challenges.
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Affiliation(s)
- August E Woerner
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.
| | - Sammed Mandape
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Melissa Muenzler
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Benjamin Crysup
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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14
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Pritchard JJG, Hamilton G, Hurst CD, Fraser S, Orange C, Knowles MA, Jones RJ, Leung HY, Iwata T. Monitoring of urothelial cancer disease status after treatment by digital droplet PCR liquid biopsy assays. Urol Oncol 2020; 38:737.e1-737.e10. [PMID: 32532529 DOI: 10.1016/j.urolonc.2020.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/12/2020] [Accepted: 05/10/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Real-time monitoring of disease status would be beneficial for timely decision making in the treatment of urothelial cancer (UC), and may accelerate the evaluation of clinical trials. Use of cell free tumor DNA (cftDNA) as a biomarker in liquid biopsy is minimally invasive and its successful use has been reported in various cancer types, including UC. The objective of this study was to evaluate the use of digital droplet PCR (ddPCR)-based assays to monitor UC after treatment. METHOD AND MATERIALS Blood, urine and matching formalin fixed, paraffin embedded diagnostic specimens were collected from 20 patients diagnosed with stage T1 (n = 2) and T2/T3 (n = 18) disease. SNaPshot assays, Sanger sequencing and whole exome sequencing were used to identify tumor-specific mutations, and somatic mutation status was confirmed using patient-matched DNAs extracted from buffy coats and peripheral blood mononucleocytes. The ddPCR assays of the tumor-specific mutations were used to detect the fractional abundance of cftDNA in plasma and urine. RESULTS SNaPshot and Sanger sequencing identified point mutations in 70% of the patients that were assayable by ddPCR. Cases of remission and relapse monitored by assays for PIK3CA E542K and TP53 Y163C mutations in plasma and urine concurred with clinical observations up to 48 months from the start of chemotherapy. A new ddPCR assay for the telomerase reverse transcriptase (TERT) promoter (-124) mutation was developed. The TERT assay was able to detect mutations in cases below the limit of detection by SNaPshot. Whole exome sequencing identified a novel mutation, CNTNAP4 G727*. A ddPCR assay designed to detect this mutation was able to distinguish mutant from wild-type alleles. CONCLUSIONS The study demonstrated that ddPCR assays could be used to detect cftDNA in liquid biopsy monitoring of the post-therapy disease status in patients with UC. Overall, 70% of the patients in our study harbored mutations that were assayable by ddPCR.
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Affiliation(s)
- John J G Pritchard
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Graham Hamilton
- Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom
| | - Carolyn D Hurst
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Sioban Fraser
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Clare Orange
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Margaret A Knowles
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Robert J Jones
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom; Cancer Research UK Beatson Institute, Glasgow, United Kingdom; Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Hing Y Leung
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom; Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Tomoko Iwata
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
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15
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Tran LS, Nguyen QTT, Nguyen CV, Tran VU, Nguyen THT, Le HT, Nguyen MLT, Le VT, Pham LS, Vo BT, Dang ATH, Nguyen LT, Nguyen TCV, Pham HAT, Tran TT, Nguyen LH, Nguyen TTT, Nguyen KHT, Vu YV, Nguyen NH, Bui VQ, Bui HH, Do TTT, Lam NV, Truong Dinh K, Phan MD, Nguyen HN, Giang H. Ultra-Deep Massive Parallel Sequencing of Plasma Cell-Free DNA Enables Large-Scale Profiling of Driver Mutations in Vietnamese Patients With Advanced Non-Small Cell Lung Cancer. Front Oncol 2020; 10:1351. [PMID: 32850431 PMCID: PMC7418519 DOI: 10.3389/fonc.2020.01351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/26/2020] [Indexed: 01/15/2023] Open
Abstract
Population-specific profiling of mutations in cancer genes is of critical importance for the understanding of cancer biology in general as well as the establishment of optimal diagnostics and treatment guidelines for that particular population. Although genetic analysis of tumor tissue is often used to detect mutations in cancer genes, the invasiveness and limited accessibility hinders its application in large-scale population studies. Here, we used ultra-deep massive parallel sequencing of plasma cell free DNA (cfDNA) to identify the mutation profiles of 265 Vietnamese patients with advanced non-small cell lung cancer (NSCLC). Compared to a cohort of advanced NSCLC patients characterized by sequencing of tissue samples, cfDNA genomic testing, despite lower mutation detection rates, was able to detect major mutations in tested driver genes that reflected similar mutation composition and distribution pattern, as well as major associations between mutation prevalence and clinical features. In conclusion, ultra-deep sequencing of plasma cfDNA represents an alternative approach for population-wide genetic profiling of cancer genes where recruitment of patients is limited to the accessibility of tumor tissue site.
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Affiliation(s)
| | | | | | | | | | - Ha Thu Le
- Ha Noi Oncology Hospital, Hanoi, Vietnam
| | | | | | - Lam-Son Pham
- Vietnam National Cancer Hospital, Hanoi, Vietnam
| | | | - Anh-Thu Huynh Dang
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | | | | | | | | | | | - Yen-Vi Vu
- Gene Solutions, Ho Chi Minh City, Vietnam
| | | | | | | | | | - Nien Vinh Lam
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | - Hoai-Nghia Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hoa Giang
- Gene Solutions, Ho Chi Minh City, Vietnam
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16
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Esagian SM, Grigoriadou GΙ, Nikas IP, Boikou V, Sadow PM, Won JK, Economopoulos KP. Comparison of liquid-based to tissue-based biopsy analysis by targeted next generation sequencing in advanced non-small cell lung cancer: a comprehensive systematic review. J Cancer Res Clin Oncol 2020; 146:2051-2066. [PMID: 32462295 PMCID: PMC7456570 DOI: 10.1007/s00432-020-03267-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
Abstract
PURPOSE To explore whether targeted next generation sequencing (NGS) of liquid biopsy in advanced non-small cell lung cancer (NSCLC) could potentially overcome the innate problems that arise with standard tissue biopsy, like intratumoral heterogeneity and the inability to obtain adequate samples for analysis. METHODS The Scopus, Cochrane Library, and MEDLINE (via PubMed) databases were searched for studies with matched tissue and liquid biopsies from advanced NSCLC patients, analyzed with targeted NGS. The number of mutations detected in tissue biopsy only, liquid biopsy only, or both was assessed and the positive percent agreement (PPA) of the two methods was calculated for every clinically relevant gene. RESULTS A total of 644 unique relevant articles were retrieved and data were extracted from 38 studies fulfilling the inclusion criteria. The sample size was composed of 2000 mutations tested in matched tissue and liquid biopsies derived from 1141 patients. No studies analyzed circulating tumor cells. The calculated PPA rates were 53.6% (45/84) for ALK, 53.9% (14/26) for BRAF, 56.5% (13/23) for ERBB2, 67.8% (428/631) for EGFR, 64.2% (122/190) for KRAS, 58.6% (17/29) for MET, 54.6% (12/22) for RET, and 53.3% (8/15) for ROS1. We additionally recorded data for 65 genes that are not recommended by current guidelines for mutational testing. An extra category containing results of unspecified genes was added, with a PPA rate of 55.7% (122/219). CONCLUSION Despite many advantages, liquid biopsy might be unable to fully substitute its tissue counterpart in detecting clinically relevant mutations in advanced NSCLC patients. However, it may serve as a helpful tool when making therapeutic decisions. More studies are needed to evaluate its role in everyday clinical practice.
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Affiliation(s)
- Stepan M Esagian
- Oncology Working Group, Society of Junior Doctors, Athens, Greece
| | - Georgia Ι Grigoriadou
- Oncology Working Group, Society of Junior Doctors, Athens, Greece
- 1st Department of Medical Oncology, Theageneio Anticancer Hospital, Thessaloníki, Greece
| | - Ilias P Nikas
- School of Medicine, European University of Cyprus, Nicosia, Cyprus
| | - Vasileios Boikou
- Oncology Working Group, Society of Junior Doctors, Athens, Greece
- Athens University of Economics and Business, Athens, Greece
| | - Peter M Sadow
- Department of Pathology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Jae-Kyung Won
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Konstantinos P Economopoulos
- Oncology Working Group, Society of Junior Doctors, Athens, Greece.
- Department of Surgery, Duke University Medical Center, 2301 Erwin Rd, Durham, NC, 27710, USA.
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