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Rajandram R, Suren Raj TL, Gobe GC, Kuppusamy S. Liquid biopsy for renal cell carcinoma. Clin Chim Acta 2024; 565:119964. [PMID: 39265757 DOI: 10.1016/j.cca.2024.119964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 09/07/2024] [Accepted: 09/09/2024] [Indexed: 09/14/2024]
Abstract
Liquid biopsies offer a less invasive alternative to tissue biopsies for diagnosis, prognosis, and determining therapeutic potential in renal cell carcinoma (RCC). Unfortunately, clinical studies using liquid biopsy biomarkers in RCC are limited. Accordingly, we examine RCC biomarkers, derived from urine, plasma, serum and feces of potential impact and clinical outcome in these patients. A PRISMA checklist was used to identify valuable liquid biopsy biomarkers for diagnosis (plasma cfDNA, serum- or urine-derived circulating RNAs, exosomes and proteins), prognosis (plasma cfDNA, plasma- or serum-derived RNAs, and proteins), and therapeutic response (plasma- and serum-derived proteins). Although other analytes have been identified, their application for routine clinical use remains unclear. In general, panels appear more effective than single biomarkers. Important considerations included proof of reproducibility. Unfortunately, many of the examined studies were insufficiently large and lacked multi-center rigor. Cost-effectiveness was also not available. Accordingly, it is clear that more standardized protocols need to be developed before liquid biopsies can be successfully integrated into clinical practice in RCC.
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Affiliation(s)
- Retnagowri Rajandram
- Division of Urology, Department of Surgery, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia.
| | - Tulsi Laxmi Suren Raj
- Division of Urology, Department of Surgery, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Glenda Carolyn Gobe
- Kidney Disease Research Collaborative, Translational Research Institute, and School of Biomedical Sciences, University of Queensland, Brisbane, Australia
| | - Shanggar Kuppusamy
- Division of Urology, Department of Surgery, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
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Dong T, Yu C, Mao Q, Han F, Yang Z, Yang Z, Pires N, Wei X, Jing W, Lin Q, Hu F, Hu X, Zhao L, Jiang Z. Advances in biosensors for major depressive disorder diagnostic biomarkers. Biosens Bioelectron 2024; 258:116291. [PMID: 38735080 DOI: 10.1016/j.bios.2024.116291] [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: 12/13/2023] [Revised: 03/25/2024] [Accepted: 04/09/2024] [Indexed: 05/14/2024]
Abstract
Depression is one of the most common mental disorders and is mainly characterized by low mood or lack of interest and pleasure. It can be accompanied by varying degrees of cognitive and behavioral changes and may lead to suicide risk in severe cases. Due to the subjectivity of diagnostic methods and the complexity of patients' conditions, the diagnosis of major depressive disorder (MDD) has always been a difficult problem in psychiatry. With the discovery of more diagnostic biomarkers associated with MDD in recent years, especially emerging non-coding RNAs (ncRNAs), it is possible to quantify the condition of patients with mental illness based on biomarker levels. Point-of-care biosensors have emerged due to their advantages of convenient sampling, rapid detection, miniaturization, and portability. After summarizing the pathogenesis of MDD, representative biomarkers, including proteins, hormones, and RNAs, are discussed. Furthermore, we analyzed recent advances in biosensors for detecting various types of biomarkers of MDD, highlighting representative electrochemical sensors. Future trends in terms of new biomarkers, new sample processing methods, and new detection modalities are expected to provide a complete reference for psychiatrists and biomedical engineers.
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Affiliation(s)
- Tao Dong
- X Multidisciplinary Research Institute, School of Instrument Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; Chongqing Key Laboratory of Micro-Nano Transduction and Intelligent Systems, Collaborative Innovation Center on Micro-Nano Transduction and Intelligent Eco-Internet of Things, Chongqing Key Laboratory of Colleges and Universities on Micro-Nano Systems Technology and Smart Transducing, National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Nan'an District, Chongqing, 400067, China.
| | - Chenghui Yu
- Chongqing Key Laboratory of Micro-Nano Transduction and Intelligent Systems, Collaborative Innovation Center on Micro-Nano Transduction and Intelligent Eco-Internet of Things, Chongqing Key Laboratory of Colleges and Universities on Micro-Nano Systems Technology and Smart Transducing, National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Nan'an District, Chongqing, 400067, China.
| | - Qi Mao
- X Multidisciplinary Research Institute, School of Instrument Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Feng Han
- X Multidisciplinary Research Institute, School of Instrument Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Zhenwei Yang
- X Multidisciplinary Research Institute, School of Instrument Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Zhaochu Yang
- Chongqing Key Laboratory of Micro-Nano Transduction and Intelligent Systems, Collaborative Innovation Center on Micro-Nano Transduction and Intelligent Eco-Internet of Things, Chongqing Key Laboratory of Colleges and Universities on Micro-Nano Systems Technology and Smart Transducing, National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Nan'an District, Chongqing, 400067, China
| | - Nuno Pires
- Chongqing Key Laboratory of Micro-Nano Transduction and Intelligent Systems, Collaborative Innovation Center on Micro-Nano Transduction and Intelligent Eco-Internet of Things, Chongqing Key Laboratory of Colleges and Universities on Micro-Nano Systems Technology and Smart Transducing, National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Nan'an District, Chongqing, 400067, China
| | - Xueyong Wei
- X Multidisciplinary Research Institute, School of Instrument Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Weixuan Jing
- X Multidisciplinary Research Institute, School of Instrument Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Qijing Lin
- X Multidisciplinary Research Institute, School of Instrument Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Fei Hu
- X Multidisciplinary Research Institute, School of Instrument Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xiao Hu
- Engineering Research Center of Ministry of Education for Smart Justice, School of Criminal Investigation, Southwest University of Political Science and Law, Chongqing, 401120, China.
| | - Libo Zhao
- X Multidisciplinary Research Institute, School of Instrument Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Zhuangde Jiang
- X Multidisciplinary Research Institute, School of Instrument Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
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Janssen FW, Lak NSM, Janda CY, Kester LA, Meister MT, Merks JHM, van den Heuvel-Eibrink MM, van Noesel MM, Zsiros J, Tytgat GAM, Looijenga LHJ. A comprehensive overview of liquid biopsy applications in pediatric solid tumors. NPJ Precis Oncol 2024; 8:172. [PMID: 39097671 PMCID: PMC11297996 DOI: 10.1038/s41698-024-00657-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/15/2024] [Indexed: 08/05/2024] Open
Abstract
Liquid biopsies are emerging as an alternative source for pediatric cancer biomarkers with potential applications during all stages of patient care, from diagnosis to long-term follow-up. While developments within this field are reported, these mainly focus on dedicated items such as a specific liquid biopsy matrix, analyte, and/or single tumor type. To the best of our knowledge, a comprehensive overview is lacking. Here, we review the current state of liquid biopsy research for the most common non-central nervous system pediatric solid tumors. These include neuroblastoma, renal tumors, germ cell tumors, osteosarcoma, Ewing sarcoma, rhabdomyosarcoma and other soft tissue sarcomas, and liver tumors. Within this selection, we discuss the most important or recent studies involving liquid biopsy-based biomarkers, anticipated clinical applications, and the current challenges for success. Furthermore, we provide an overview of liquid biopsy-based biomarker publication output for each tumor type based on a comprehensive literature search between 1989 and 2023. Per study identified, we list the relevant liquid biopsy-based biomarkers, matrices (e.g., peripheral blood, bone marrow, or cerebrospinal fluid), analytes (e.g., circulating cell-free and tumor DNA, microRNAs, and circulating tumor cells), methods (e.g., digital droplet PCR and next-generation sequencing), the involved pediatric patient cohort, and proposed applications. As such, we identified 344 unique publications. Taken together, while the liquid biopsy field in pediatric oncology is still behind adult oncology, potentially relevant publications have increased over the last decade. Importantly, steps towards clinical implementation are rapidly gaining ground, notably through validation of liquid biopsy-based biomarkers in pediatric clinical trials.
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Affiliation(s)
| | | | | | | | - Michael T Meister
- Princess Máxima Center, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Johannes H M Merks
- Princess Máxima Center, Utrecht, the Netherlands
- Division of Imaging and Oncology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - Marry M van den Heuvel-Eibrink
- Princess Máxima Center, Utrecht, the Netherlands
- Wilhelmina Children's Hospital-Division of CHILDHEALTH, University Medical Center Utrech, University of Utrecht, Utrecht, the Netherlands
| | - Max M van Noesel
- Princess Máxima Center, Utrecht, the Netherlands
- Division of Imaging and Oncology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | | | - Godelieve A M Tytgat
- Princess Máxima Center, Utrecht, the Netherlands
- Department of Genetics, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - Leendert H J Looijenga
- Princess Máxima Center, Utrecht, the Netherlands.
- Department of Pathology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands.
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Hosoi H, Hori Y, Fukutsuka K, Osuga M, Koh Y, Mushino T, Hanaoka N, Yamamoto N, Ohno H, Sonoki T. Detection of the JAK2 V617F Mutation in Urinary Cell-free DNA in Patients with Myeloproliferative Neoplasms. Intern Med 2024; 63:1987-1993. [PMID: 38008450 PMCID: PMC11309855 DOI: 10.2169/internalmedicine.2837-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/15/2023] [Indexed: 11/28/2023] Open
Abstract
Objective Testing for the Janus activating kinase 2 (JAK2) V617F mutation is important for diagnosing and treating myeloproliferative neoplasms (MPNs). Recently, urine cell-free DNA (ucfDNA) was reported to be useful for detecting tumor-specific gene mutations in several solid tumors. However, its utility in detecting such mutations in hematological malignancies has not yet been assessed. In this study, we assessed whether or not the JAK2 V617F mutation could be detected in ucfDNA and whether or not its positivity rate in ucfDNA was associated with the JAK2 V617F allele ratio of peripheral blood cells in patients with MPN. Methods The JAK2 V617F allele ratio of genomic DNA from peripheral blood cells was determined using quantitative polymerase chain reaction (qPCR) or droplet digital PCR (ddPCR). ucfDNA was subjected to ddPCR. The correlation between the JAK2 V617F mutation positivity rates of blood-derived DNA and those of ucfDNA was assessed. Materials Twelve patients with polycythemia vera and 12 patients with essential thrombocythemia were enrolled. Ethylenediaminetetraacetic acid-treated peripheral blood (100 mL) and 15-30 mL of fresh urine were used. Results The JAK2 V617F mutation was detected in the ucfDNA from all 20 JAK2 V617F mutation-positive patients. In addition, the JAK2 V617F mutation positivity rate of ucfDNA was correlated with the JAK2 V617F allele ratio of blood-derived DNA, including in both estimated glomerular filtration rate (eGFR) groups (patients with an eGFR ≥50 or <50 mL/min/1.73 m2). Conclusion Our results indicate that ucfDNA is a valuable tool for diagnosing and monitoring MPN. Given these findings, other disease-specific gene mutations in hematological malignancies may also be detectable in ucfDNA.
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Affiliation(s)
- Hiroki Hosoi
- Department of Hematology/Oncology, Wakayama Medical University, Japan
| | - Yoshikazu Hori
- Department of Hematology/Oncology, Wakayama Medical University, Japan
| | | | - Mitsuo Osuga
- Center for Biomedical Sciences, Wakayama Medical University, Japan
| | - Yasuhiro Koh
- Center for Biomedical Sciences, Wakayama Medical University, Japan
- Internal Medicine III, Wakayama Medical University, Japan
| | - Toshiki Mushino
- Department of Hematology/Oncology, Wakayama Medical University, Japan
| | - Nobuyoshi Hanaoka
- Department of Hematology/Oncology, Wakayama Medical University, Japan
- Department of General Medicine, National Hospital Organization Kumamotominami National Hospital, Japan
| | - Nobuyuki Yamamoto
- Center for Biomedical Sciences, Wakayama Medical University, Japan
- Internal Medicine III, Wakayama Medical University, Japan
| | - Hitoshi Ohno
- Tenri Institute of Medical Research, Tenri Hospital, Japan
| | - Takashi Sonoki
- Department of Hematology/Oncology, Wakayama Medical University, Japan
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Chen L, Ma R, Luo C, Xie Q, Ning X, Sun K, Meng F, Zhou M, Sun J. Noninvasive early differential diagnosis and progression monitoring of ovarian cancer using the copy number alterations of plasma cell-free DNA. Transl Res 2023; 262:12-24. [PMID: 37499745 DOI: 10.1016/j.trsl.2023.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/20/2023] [Accepted: 07/23/2023] [Indexed: 07/29/2023]
Abstract
Ovarian cancer (OV) is the most lethal gynecological malignancy and requires improved early detection methods and more effective intervention to achieve a better prognosis. The lack of sensitive and noninvasive biomarkers with clinical utility remains a challenge. Here, we conducted a genome-wide copy number variation (CNV) profiling analysis using low-coverage whole genome sequencing (LC-WGS) of plasma cfDNA in patients with nonmalignant and malignant ovarian tumors and identified 10 malignancy-specific and 12 late-stage-specific CNV markers from plasma cfDNA LC-WGS data. Concordance analysis indicated a significant correlation of identified CNV markers between CNV profiles of plasma cfDNA and tissue DNA (Pearson's r = 0.64, P = 0.006 for the TCGA cohort and r = 0.51, P = 0.04 for the Dariush cohort). By leveraging these specific CNV markers and machine learning algorithms, we developed robust predictive models showing excellent performance in distinguishing between malignant and nonmalignant ovarian tumors with F1-scores of 0.90 and ranging from 0.75 to 0.99, and prediction accuracy of 0.89 and ranging from 0.66 to 0.98, respectively, as well as between early- and late-stage ovarian tumors with F1-scores of 0.84 and ranging from 0.61 to 1.00, and prediction accuracy of 0.82 and ranging from 0.63 to 0.96 in our institute cohort and other external validation cohorts. Furthermore, we also discovered and validated certain CNV features associated with survival outcomes and platinum-based chemotherapy response in multicenter cohorts. In conclusion, our study demonstrated the clinical utility of CNV profiling in plasma cfDNA using LC-WGS as a cost-effective and accessible liquid biopsy for OV.
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Affiliation(s)
- Lu Chen
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, P. R. China; School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou P. R. China
| | - Rong Ma
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, P. R. China
| | - Chang Luo
- Department of Birth Control, Red Cross Central Hospital of Harbin, Harbin, P. R. China
| | - Qin Xie
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, P. R. China
| | - Xin Ning
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, P. R. China
| | - Kaidi Sun
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, P. R. China
| | - Fanling Meng
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, P. R. China.
| | - Meng Zhou
- School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou P. R. China.
| | - Jie Sun
- School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou P. R. China.
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Adhit KK, Wanjari A, Menon S, K S. Liquid Biopsy: An Evolving Paradigm for Non-invasive Disease Diagnosis and Monitoring in Medicine. Cureus 2023; 15:e50176. [PMID: 38192931 PMCID: PMC10772356 DOI: 10.7759/cureus.50176] [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: 08/23/2023] [Accepted: 12/08/2023] [Indexed: 01/10/2024] Open
Abstract
Liquid biopsy stands as an innovative instrument in the realm of precision medicine, enabling non-invasive disease diagnosis and the early detection of cancer. Liquid biopsy helps in the extraction of circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and cell-free DNA (cfDNA) from blood samples and other body fluids, thereby facilitating disease diagnosis and prediction of high-risk patients. Various techniques such as advanced sequencing methods and biomarker-based cell capture have led to the isolation and study of the different biomarkers such as ctDNA, cfDNA, and CTCs. These biopsies also have immense potential in the early detection and diagnosis of various diseases across all medical specialties, prediction and screening of high-risk cases, and detection of different immune response patterns in response to infectious diseases, and also help in predicting treatment outcomes. Although liquid biopsy has the potential to disrupt the field of medical diagnosis, it is met by various challenges such as limited tumor-derived components, less specificity, and inadequate advancement in methods to isolate biomarkers. Despite all these challenges, liquid biopsies provide the potential to become a minimally invasive method of diagnosis that would facilitate real-time monitoring of patients, which differentiates them from traditional tissue biopsies. This article aims to provide a complete overview of the current technologies, different biomarkers, and body fluids that can be used in liquid biopsy and its clinical applications and the potential impact that liquid biopsy holds in the field of precision medicine, facilitating early diagnosis and prompt management of various diseases and cancers.
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Affiliation(s)
- Kanishk K Adhit
- Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Anil Wanjari
- Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Sharanya Menon
- Pathology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Siddhaarth K
- Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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Ntzifa A, Lianidou E. Pre-analytical conditions and implementation of quality control steps in liquid biopsy analysis. Crit Rev Clin Lab Sci 2023; 60:573-594. [PMID: 37518938 DOI: 10.1080/10408363.2023.2230290] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023]
Abstract
Over the last decade, great advancements have been made in the field of liquid biopsy through extensive research and the development of new technologies that facilitate the use of liquid biopsy for cancer patients. This is shown by the numerous liquid biopsy tests that gained clearance by the US Food and Drug Administration (FDA) in recent years. Liquid biopsy has significantly altered cancer treatment by providing clinicians with powerful and immediate information about therapeutic decisions. However, the clinical integration of liquid biopsy is still challenging and there are many critical factors to consider prior to its implementation into routine clinical practice. Lack of standardization due to technical challenges and the definition of the clinical utility of specific assays further complicates the establishment of Standard Operating Procedures (SOPs) in liquid biopsy. Harmonization of laboratories to established guidelines is of major importance to overcome inter-lab variabilities observed. Quality control assessment in diagnostic laboratories that offer liquid biopsy testing will ensure that clinicians can base their therapeutic decisions on robust results. The regular participation of laboratories in external quality assessment schemes for liquid biopsy testing aims to promptly pinpoint deficiencies and efficiently educate laboratories to improve their quality of services. Accreditation of liquid biopsy diagnostic laboratories based on the ISO15189 standard in Europe or by CLIA/CAP accreditation procedures in the US is the best way to achieve the adaptation of liquid biopsy into the clinical setting by assuring reliable results for the clinicians and their cancer patients. Nowadays, various organizations from academia, industry, and regulatory agencies collaborate to set a framework that will include all procedures from the pre-analytical phase and the analytical process to the final interpretation of results. In this review, we underline several challenges in the analysis of circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) concerning standardization of protocols, quality control assessment, harmonization of laboratories, and compliance to specific guidelines that need to be thoroughly considered before liquid biopsy enters the clinic.
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Affiliation(s)
- Aliki Ntzifa
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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