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Peng H, Pan M, Zhou Z, Chen C, Xing X, Cheng S, Zhang S, Zheng H, Qian K. The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples. Front Cell Dev Biol 2024; 12:1385041. [PMID: 38784382 PMCID: PMC11111958 DOI: 10.3389/fcell.2024.1385041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Cell-free DNA (cfDNA), a burgeoning class of molecular biomarkers, has been extensively studied across a variety of biomedical fields. As a key component of liquid biopsy, cfDNA testing is gaining prominence in disease detection and management due to the convenience of sample collection and the abundant wealth of genetic information it provides. However, the broader clinical application of cfDNA is currently impeded by a lack of standardization in the preanalytical procedures for cfDNA analysis. A number of fundamental challenges, including the selection of appropriate preanalytical procedures, prevention of short cfDNA fragment loss, and the validation of various cfDNA measurement methods, remain unaddressed. These existing hurdles lead to difficulties in comparing results and ensuring repeatability, thereby undermining the reliability of cfDNA analysis in clinical settings. This review discusses the crucial preanalytical factors that influence cfDNA analysis outcomes, including sample collection, transportation, temporary storage, processing, extraction, quality control, and long-term storage. The review provides clarification on achievable consensus and offers an analysis of the current issues with the goal of standardizing preanalytical procedures for cfDNA analysis.
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Affiliation(s)
- Hongwei Peng
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ming Pan
- Taihe Skills Training Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zongning Zhou
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Congbo Chen
- Department of Urology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xing Xing
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shaoping Cheng
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shanshan Zhang
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hang Zheng
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
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2
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Bronkhorst AJ, Holdenrieder S. The changing face of circulating tumor DNA (ctDNA) profiling: Factors that shape the landscape of methodologies, technologies, and commercialization. MED GENET-BERLIN 2023; 35:201-235. [PMID: 38835739 PMCID: PMC11006350 DOI: 10.1515/medgen-2023-2065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Liquid biopsies, in particular the profiling of circulating tumor DNA (ctDNA), have long held promise as transformative tools in cancer precision medicine. Despite a prolonged incubation phase, ctDNA profiling has recently experienced a strong wave of development and innovation, indicating its imminent integration into the cancer management toolbox. Various advancements in mutation-based ctDNA analysis methodologies and technologies have greatly improved sensitivity and specificity of ctDNA assays, such as optimized preanalytics, size-based pre-enrichment strategies, targeted sequencing, enhanced library preparation methods, sequencing error suppression, integrated bioinformatics and machine learning. Moreover, research breakthroughs have expanded the scope of ctDNA analysis beyond hotspot mutational profiling of plasma-derived apoptotic, mono-nucleosomal ctDNA fragments. This broader perspective considers alternative genetic features of cancer, genome-wide characterization, classical and newly discovered epigenetic modifications, structural variations, diverse cellular and mechanistic ctDNA origins, and alternative biospecimen types. These developments have maximized the utility of ctDNA, facilitating landmark research, clinical trials, and the commercialization of ctDNA assays, technologies, and products. Consequently, ctDNA tests are increasingly recognized as an important part of patient guidance and are being implemented in clinical practice. Although reimbursement for ctDNA tests by healthcare providers still lags behind, it is gaining greater acceptance. In this work, we provide a comprehensive exploration of the extensive landscape of ctDNA profiling methodologies, considering the multitude of factors that influence its development and evolution. By illuminating the broader aspects of ctDNA profiling, the aim is to provide multiple entry points for understanding and navigating the vast and rapidly evolving landscape of ctDNA methodologies, applications, and technologies.
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Affiliation(s)
- Abel J Bronkhorst
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
| | - Stefan Holdenrieder
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
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Fleischhacker M, Arslan E, Reinicke D, Eisenmann S, Theil G, Kollmeier J, Schäper C, Grah C, Klawonn F, Holdenrieder S, Schmidt B. Cell-Free Methylated PTGER4 and SHOX2 Plasma DNA as a Biomarker for Therapy Monitoring and Prognosis in Advanced Stage NSCLC Patients. Diagnostics (Basel) 2023; 13:2131. [PMID: 37443525 DOI: 10.3390/diagnostics13132131] [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: 05/03/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023] Open
Abstract
Notwithstanding some improvement in the earlier detection of patients with lung cancer, most of them still present with a late-stage disease at the time of diagnosis. Next to the most frequently utilized factors affecting the prognosis of lung cancer patients (stage, performance, and age), the recent application of biomarkers obtained by liquid profiling has gained more acceptance. In our study, we aimed to answer these questions: (i) Is the quantification of free-circulating methylated PTGER4 and SHOX2 plasma DNA a useful method for therapy monitoring, and is this also possible for patients treated with different therapy regimens? (ii) Is this approach possible when blood-drawing tubes, which allow for a delayed processing of blood samples, are utilized? Baseline values for mPTGER4 and mSHOX2 do not allow for clear discrimination between different response groups. In contrast, the combination of the methylation values for both genes shows a clear difference between responders vs. non-responders at the time of re-staging. Furthermore, blood drawing into tubes stabilizing the sample allows researchers more flexibility.
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Affiliation(s)
- Michael Fleischhacker
- Klinik für Innere Medizin-Schwerpunkt Pneumologie und Schlafmedizin, DRK Kliniken Berlin/Mitte, 13359 Berlin, Germany
| | - Erkan Arslan
- Lungenarztpraxis Berlin-Reinickendorf, 13403 Berlin, Germany
| | - Dana Reinicke
- Department für Innere Medizin, Universitätsklinikum Halle/Saale, 06120 Halle (Saale), Germany
| | - Stefan Eisenmann
- Department für Innere Medizin, Universitätsklinikum Halle/Saale, 06120 Halle (Saale), Germany
| | - Gerit Theil
- Department für Innere Medizin, Universitätsklinikum Halle/Saale, 06120 Halle (Saale), Germany
| | - Jens Kollmeier
- Lungenklinik Heckeshorn, Helios Klinikum Emil von Behring, 14165 Berlin, Germany
| | - Christoph Schäper
- Klinik und Poliklinik für Innere Medizin B, Universitätsmedizin Greifswald, 17475 Greifswald, Germany
| | - Christian Grah
- Gemeinschaftskrankenhaus Havelhöhe, Pneumologie und Lungenkrebszentrum, 14089 Berlin, Germany
| | - Frank Klawonn
- Department of Computer Science, Ostfalia University, 38302 Wolfenbüttel, Germany
- Biostatistics, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Stefan Holdenrieder
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, 80636 Munich, Germany
| | - Bernd Schmidt
- Klinik für Innere Medizin-Schwerpunkt Pneumologie und Schlafmedizin, DRK Kliniken Berlin/Mitte, 13359 Berlin, Germany
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Diaz IM, Nocon A, Held SAE, Kobilay M, Skowasch D, Bronkhorst AJ, Ungerer V, Fredebohm J, Diehl F, Holdenrieder S, Holtrup F. Pre-Analytical Evaluation of Streck Cell-Free DNA Blood Collection Tubes for Liquid Profiling in Oncology. Diagnostics (Basel) 2023; 13:diagnostics13071288. [PMID: 37046506 PMCID: PMC10093569 DOI: 10.3390/diagnostics13071288] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Excellent pre-analytical stability is an essential precondition for reliable molecular profiling of circulating tumor DNA (ctDNA) in oncological diagnostics. Therefore, in vitro degradation of ctDNA and the additional release of contaminating genomic DNA from lysed blood cells must be prevented. Streck Cell-Free DNA blood collection tubes (cfDNA BCTs) have proposed advantages over standard K2EDTA tubes, but mainly have been tested in healthy individuals. Blood was collected from cancer patients (n = 53) suffering from colorectal (n = 21), pancreatic (n = 11), and non-small-cell lung cancer (n = 21) using cfDNA BCT tubes and K2EDTA tubes that were processed immediately or after 3 days (BCTs) or 6 hours (K2EDTA) at room temperature. The cfDNA isolated from these samples was characterized in terms of yield using LINE-1 qPCR; the level of gDNA contamination; and the mutation status of KRAS, NRAS, and EGFR genes using BEAMing ddPCR. CfDNA yield and gDNA levels were comparable in both tube types and were not affected by prolonged storage of blood samples for at least 3 days in cfDNA BCTs or 6 hours in K2EDTA tubes. In addition, biospecimens collected in K2EDTA tubes and cfDNA BCTs stored for up to 3 days demonstrated highly comparable levels of mutational load across all respective cancer patient cohorts and a wide range of concentrations. Our data support the applicability of clinical oncology specimens collected and stored in cfDNA BCTs for up to 3 days for reliable cfDNA and mutation analyses.
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Chiho M, Ono Y, Hayashi A, Takahashi K, Taniue K, Kakisaka R, Mori M, Ishii T, Sato H, Okada T, Kawabata H, Goto T, Tamamura N, Omori Y, Takahashi K, Katanuma A, Karasaki H, Liss AS, Mizukami Y. Multiplex digital PCR assay to detect multiple KRAS and GNAS mutations associated with pancreatic carcinogenesis from minimal specimen amounts. J Mol Diagn 2023; 25:367-377. [PMID: 36965665 DOI: 10.1016/j.jmoldx.2023.02.007] [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: 03/08/2022] [Revised: 02/14/2023] [Accepted: 02/24/2023] [Indexed: 03/27/2023] Open
Abstract
Digital PCR (dPCR) allows for highly sensitive quantification of low-frequency mutations and facilitates early detection of cancer. However, low throughput targeting of single hotspots in dPCR hinders variant specification when multiple probes are used. Here we developed a dPCR method to simultaneously identify major variants related to pancreatic carcinogenesis. Using a 2-D plot of droplet fluorescence under the optimized concentration of two fluorescent probe pools, we determined the absolute quantification of different KRAS and GNAS variants. Successful detection of the multiple driver mutations was verified in 24 surgically resected tumor samples from 19 patients and 22 FNA samples from patients with pancreatic ductal adenocarcinoma. Precise quantification of the variant allele frequency was optimized using template DNA at a concentration as low as 1-10 ng. Furthermore, amplicons targeting multiple hotspots were successfully enriched with fewer false positives using high-fidelity polymerase, allowing for the detection of various KRAS and GNAS mutations with high probability in small cell/tissue specimens. Using this target enrichment, mutations at a rate of 90% in small residual tissues, such as the FNA needle flush and microscopic lesions in resected specimens, have successfully been identified. The proposed method allows for low-cost and accurate detection of driver mutations to diagnose cancers, even with minimal tissue collection.
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Affiliation(s)
- Maeda Chiho
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan; Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan.
| | - Akihiro Hayashi
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Kenji Takahashi
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Kenzui Taniue
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan; Isotope Science Center, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Rika Kakisaka
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Miyuki Mori
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Takahiro Ishii
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Hiroki Sato
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan; Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Tetsuhiro Okada
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Hidemasa Kawabata
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Takuma Goto
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Nobue Tamamura
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Yuko Omori
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan; Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Kuniyuki Takahashi
- Center for Gastroenterology, Teine Keijinkai Hospital, Sapporo, 006-0811, Japan
| | - Akio Katanuma
- Center for Gastroenterology, Teine Keijinkai Hospital, Sapporo, 006-0811, Japan
| | - Hidenori Karasaki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Andrew Scott Liss
- Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan; Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
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6
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Dameri M, Cirmena G, Ravera F, Ferrando L, Cuccarolo P, Stabile M, Fanelli GN, Nuzzo PV, Calabrese M, Tagliafico A, Ballestrero A, Zoppoli G. Standard Operating Procedures (SOPs) for non-invasive multiple biomarkers detection in an academic setting: a critical review of the literature for the RENOVATE study protocol. Crit Rev Oncol Hematol 2023; 185:103963. [PMID: 36931614 DOI: 10.1016/j.critrevonc.2023.103963] [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: 12/01/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 03/17/2023] Open
Abstract
Liquid biopsy has the potential to drastically change clinical practice, paving the way to a novel non-invasive approach for cancer diagnosis and treatment. One of the limitations for the implementation of liquid biopsy in clinical practice is the lack of shared and reproducible standard operating procedures (SOPs) for sample collection, processing and storage. Here, we present a critical review of the literature focusing on the available SOPs to guide liquid biopsy management in research settings and describe SOPs that our laboratory developed and employed in the context of a prospective clinical-translational trial (RENOVATE, NCT04781062). The main aim of this manuscript is to address common issues, towards the implementation of interlaboratory shared protocols for optimized preanalytical handling of blood and urine samples. To our knowledge, this work is one of the few up-to-date, freely available comprehensive reports on trial-level procedures for the handling of liquid biopsy.
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Affiliation(s)
- Martina Dameri
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy
| | | | - Francesco Ravera
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, 10044, New York, NY, USA
| | | | - Paola Cuccarolo
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy
| | - Mario Stabile
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy
| | - Giuseppe Nicolò Fanelli
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 10021, New York, NY, USA; First Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
| | - Pier Vitale Nuzzo
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, 10044, New York, NY, USA
| | | | - Alberto Tagliafico
- IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy; Department of Health Sciences DISSAL, University of Genoa, 16132, Genoa, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy; IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - Gabriele Zoppoli
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy; IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy.
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7
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Malapelle U, Pisapia P, Addeo A, Arrieta O, Bellosillo B, Cardona AF, Cristofanilli M, De Miguel-Perez D, Denninghoff V, Durán I, Jantus-Lewintre E, Nuzzo PV, O'Byrne K, Pauwels P, Pickering EM, Raez LE, Russo A, Serrano MJ, Gandara DR, Troncone G, Rolfo C. Liquid biopsy from research to clinical practice: focus on non-small cell lung cancer. Expert Rev Mol Diagn 2021; 21:1165-1178. [PMID: 34570988 DOI: 10.1080/14737159.2021.1985468] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION In the current era of personalized medicine, liquid biopsy has acquired a relevant importance in patient management of advanced stage non-small cell lung cancer (NSCLC). As a matter of fact, liquid biopsy may supplant the problem of inadequate tissue for molecular testing. The term 'liquid biopsy' refers to a number of different biological fluids, but is most clearly associated with plasma-related platforms. It must be taken into account that pre-analytical processing and the selection of the appropriate technology according to the clinical context may condition the results obtained. In addition, novel clinical applications beyond the evaluation of the molecular status of predictive biomarkers are currently under investigation. AREAS COVERED This review summarizes the available evidence on pre-analytical issues and different clinical applications of liquid biopsies in NSCLC patients. EXPERT OPINION Liquid biopsy should be considered not only as a valid alternative but as complementary to tissue-based molecular approaches. Careful attention should be paid to the optimization and standardization of all phases of liquid biopsy samples management in order to determine a significant improvement in either sensitivity or specificity, while significant reducing the number of 'false negative' or 'false positive' molecular results.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico Ii, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico Ii, Naples, Italy
| | - Alfredo Addeo
- Oncology Department, University Hospital Geneva, Geneva, Switzerland
| | - Oscar Arrieta
- Thoracic Oncology Unit, Instituto Nacional de Cancerología (INCan), México City, México
| | - Beatriz Bellosillo
- Department of Pathology, Hospital Del Mar, Barcelona, Spain.,Department of Pathology, Ciberonc, Madrid, Spain
| | - Andres F Cardona
- Department of Oncology, Clinical and Translational Oncology Group, Clínica Del Country, Bogotá, Colombia.,Department of Oncology, Foundation for Clinical and Applied Cancer Research (Ficmac), Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (Fox-g/oncolgroup), Universidad el Bosque, Bogotá, Colombia
| | - Massimo Cristofanilli
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Diego De Miguel-Perez
- GENyO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, Liquid Biopsy and Cancer Interception Group, Granada, Spain.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Valeria Denninghoff
- Department of Pathology, University of Buenos Aires - National Council for Scientific and Technical Research (Conicet), Buenos Aires, Argentina
| | - Ignacio Durán
- Department of Oncology, Hospital Universitario Marques de Valdecilla, IDIVAL, Santander, Spain
| | - Eloísa Jantus-Lewintre
- Department of Pathology, Ciberonc, Madrid, Spain.,Molecular Oncology Laboratory, Fundación Para La Investigación Del Hospital General Universitario De Valencia, Valencia, Spain.,Mixed Unit TRIAL, (Príncipe Felipe Research Centre & Fundación Para La Investigación Del Hospital General Universitario De Valencia), Valencia, Spain.,Department of Biotechnology, Universitat Politècnica De València, Valencia, Spain
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, The Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ken O'Byrne
- Medical Oncology, Princess Alexandra Hospital, Queensland University of Technology, Brisbane City, Australia
| | - Patrick Pauwels
- Center for Oncological Research Antwerp (Core), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp (Uantwerp), Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Edward M Pickering
- Divison of Pulmonary and Critical Care Medicine, Section of Interventional Pulmonology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Luis E Raez
- Thoracic Oncology Program, Memorial Cancer Institute/Memorial Health Care System, Florida International University, Miami, FL, USA
| | - Alessandro Russo
- Department of Oncology, Medical Oncology Unit, A.O. Papardo, Messina, Italy
| | - Maria José Serrano
- GENyO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, Liquid Biopsy and Cancer Interception Group, Granada, Spain
| | - David R Gandara
- Department of Internal Medicine, UC Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico Ii, Naples, Italy
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
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8
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Liquid Biopsy Analysis in Clinical Practice: Focus on Lung Cancer. JOURNAL OF MOLECULAR PATHOLOGY 2021. [DOI: 10.3390/jmp2030021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Lung cancer is the leading cause of cancer death worldwide. Despite the emergence of highly effective targeted therapies, up to 30% of advanced stage non-small cell lung cancer (NSCLC) patients do not undergo tissue molecular testing because of scarce tissue availability. Liquid biopsy, on the other hand, offers these patients a valuable opportunity to receive the best treatment options in a timely manner. Indeed, besides being much faster and less invasive than conventional tissue-based analysis, it can also yield specific information about the genetic make-up and evolution of patients’ tumors. However, several issues, including lack of standardized protocols for sample collection, processing, and interpretation, still need to be addressed before liquid biopsy can be fully incorporated into routine oncology practice. Here, we reviewed the most important challenges hindering the implementation of liquid biopsy in oncology practice, as well as the great advantages of this approach for the treatment of NSCLC patients.
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9
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Assessment of Circulating Nucleic Acids in Cancer: From Current Status to Future Perspectives and Potential Clinical Applications. Cancers (Basel) 2021; 13:cancers13143460. [PMID: 34298675 PMCID: PMC8307284 DOI: 10.3390/cancers13143460] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
Current approaches for cancer detection and characterization are based on radiological procedures coupled with tissue biopsies, despite relevant limitations in terms of overall accuracy and feasibility, including relevant patients' discomfort. Liquid biopsies enable the minimally invasive collection and analysis of circulating biomarkers released from cancer cells and stroma, representing therefore a promising candidate for the substitution or integration in the current standard of care. Despite the potential, the current clinical applications of liquid biopsies are limited to a few specific purposes. The lack of standardized procedures for the pre-analytical management of body fluids samples and the detection of circulating biomarkers is one of the main factors impacting the effective advancement in the applicability of liquid biopsies to clinical practice. The aim of this work, besides depicting current methods for samples collection, storage, quality check and biomarker extraction, is to review the current techniques aimed at analyzing one of the main circulating biomarkers assessed through liquid biopsy, namely cell-free nucleic acids, with particular regard to circulating tumor DNA (ctDNA). ctDNA current and potential applications are reviewed as well.
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10
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Voss T, Ullius A, Schönborn M, Oelmüller U. Sensitivity assessment of workflows detecting rare circulating cell-free DNA targets: A study design proposal. PLoS One 2021; 16:e0253401. [PMID: 34228726 PMCID: PMC8260181 DOI: 10.1371/journal.pone.0253401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/03/2021] [Indexed: 11/18/2022] Open
Abstract
The field of liquid biopsy has seen extensive growth in recent decades, making it one of the most promising areas in molecular diagnostics. Circulating cell-free DNA (ccfDNA) especially is used as an analyte in a growing number of diagnostic assays. These assays require specified preanalytical workflows delivering ccfDNA in qualities and quantities that facilitate correct and reliable results. As each step and component used in the preanalytical process has the potential to influence the assay sensitivity and other performance characteristics, it is key to find an unbiased experimental setup to test these factors in diagnostic or research laboratories. We defined one such setup by using blood from healthy subjects and commercially available products for blood collection, spike-in material, ccfDNA isolation, and qPCR assays. As the primary read-out, we calculated the probit model-based LOD95 (limit of detection of the 95th percentile) from the qPCR assay results. In a proof of principle study we tested two different but widely used blood ccfDNA profile stabilization technologies in blood collection tubes, the Cell-Free DNA BCT and the PAXgene Blood ccfDNA Tube. We tested assays for three different EGFR gene mutations and one BRAF gene mutation. The study design revealed differences in performance between the two tested technologies for all four mutations. In conclusion, we successfully established a blueprint for a test procedure capable of verifying and validating a liquid biopsy workflow from blood collection to the analytical result.
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Affiliation(s)
- Thorsten Voss
- R&D Department, QIAGEN GmbH, Hilden, Germany
- * E-mail:
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11
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Pisapia P, Costa JL, Pepe F, Russo G, Gragnano G, Russo A, Iaccarino A, de Miguel-Perez D, Serrano MJ, Denninghoff V, Quagliata L, Rolfo C, Malapelle U. Next generation sequencing for liquid biopsy based testing in non-small cell lung cancer in 2021. Crit Rev Oncol Hematol 2021; 161:103311. [PMID: 33781866 DOI: 10.1016/j.critrevonc.2021.103311] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/15/2022] Open
Abstract
Lung cancer is the leading cause of cancer death worldwide, with non-small cell lung cancer (NSCLC) representing its most commonly diagnosed sub-type. Despite the significant improvements in lung cancer biomarkers knowledge, accompanied by substantial technological advances in molecular tumor profiling, a considerable fraction (up to 30 %) of advanced NSCLC patient presents with major testing challenges or tissue unavailability for molecular analysis. In this context, liquid biopsy is on the rise, currently gaining considerable interest within the molecular pathology and oncology community. Molecular profiling of liquid biopsy specimens using next generation molecular biology methodologies is a rapidly evolving field with promising applications not exclusively limited to advanced stages but also more recently expanding to early stages cancer patients. Here, we offer an overview of some of the most consolidated and emerging applications of next generation sequencing technologies for liquid biopsy testing in NSCLC.
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Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - José Luis Costa
- Medical Affairs Clinical NGS and Oncology Division Life Sciences Solutions, Thermo Fisher Scientific, Zug, Switzerland
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Diego de Miguel-Perez
- Liquid Biopsy and Metastasis Research Group, GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government PTS, Granada, Spain; Thoracic Medical Oncology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland, Baltimore, MD, USA
| | - Maria Josè Serrano
- Liquid Biopsy and Metastasis Research Group, GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government PTS, Granada, Spain
| | - Valeria Denninghoff
- University of Buenos Aires - National Council for Scientific and Technical Research (CONICET), Buenos Aires, Argentina
| | - Luca Quagliata
- Medical Affairs Clinical NGS and Oncology Division Life Sciences Solutions, Thermo Fisher Scientific, Zug, Switzerland
| | - Christian Rolfo
- Thoracic Medical Oncology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland, Baltimore, MD, USA
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy.
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12
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Andersson D, Kristiansson H, Kubista M, Ståhlberg A. Ultrasensitive circulating tumor DNA analysis enables precision medicine: experimental workflow considerations. Expert Rev Mol Diagn 2021; 21:299-310. [PMID: 33683971 DOI: 10.1080/14737159.2021.1889371] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Circulating tumor DNA (ctDNA) has become a relevant biomarker in cancer management, allowing tumor assessment through analysis of minimally invasive liquid biopsies. Applications include screening, diagnostics, monitoring of treatment efficacy and detection of minimal residual disease as well as relapse. The potential of ctDNA analysis is significant, but several biological and technical challenges need to be addressed before widespread clinical implementation.Areas covered: Several clinical applications where ctDNA analysis may be beneficial require detection of individual DNA molecules. Consequently, to acquire accurate and informative data the entire workflow from sampling to final data interpretation needs to be optimized. In this review, we discuss the biological and technical challenges of ctDNA analysis and how preanalytical and analytical approaches affect different cancer applications.Expert opinion: While numerous studies have demonstrated the potential of using ctDNA in cancer applications, yet few reports about true clinical utility exist. Despite encouraging data, the sensitivity of ctDNA analyses, i.e. the probability to detect presence of cancer in liquid biopsies, is still an issue. Analysis of multiple mutations in combination with simultaneous assessment of other analytes is one solution. Improved standardization and guidelines will also facilitate the introduction of ctDNA analysis into clinical routine.
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Affiliation(s)
- Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Helena Kristiansson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Kubista
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic.,TATAA Biocenter, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
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13
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Sorber L, Zwaenepoel K, Jacobs J, De Winne K, Van Casteren K, Augustus E, Lardon F, Prenen H, Peeters M, Van Meerbeeck J, Roeyen G, Rolfo C, Pauwels P. Specialized Blood Collection Tubes for Liquid Biopsy: Improving the Pre-analytical Conditions. Mol Diagn Ther 2021; 24:113-124. [PMID: 31838654 DOI: 10.1007/s40291-019-00442-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION The potential of circulating cell-free DNA (cfDNA) analysis as a liquid biopsy has led to the development of several specialized measuring tools. Interest in the (pre-)analytical conditions of the liquid biopsy workflow has increased over the past few years. METHODS In this study, we performed a systematic review of the cfDNA stabilizing efficacy in standard EDTA and specialized blood collection tubes (BCTs), namely CellSave, Norgen, PAXgene, Roche, and Streck tubes, and compared the efficacy of the latter three BCTs in a situation resembling the clinical setting. Blood samples were collected from ten KRAS-mutated metastatic cancer patients and stored for 72 h. During this time, samples were shaken and kept at either 6 °C or at room temperature for 24 h to mimic transport. RESULTS We demonstrated that while cfDNA levels in EDTA tubes are only stable for a couple of (≤ 6) hours, they could be sustained for at least 48-72 h in all three specialized BCTs, irrespective of temperature. This timespan enables a fast turnaround time, which is one of the advantages of liquid biopsy. CONCLUSIONS The choice between these specialized BCTs is less vital when they are processed correctly within a few days.
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Affiliation(s)
- Laure Sorber
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium. .,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650, Edegem, Belgium.
| | - Karen Zwaenepoel
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650, Edegem, Belgium
| | - Julie Jacobs
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650, Edegem, Belgium
| | - Koen De Winne
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650, Edegem, Belgium
| | - Kaat Van Casteren
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650, Edegem, Belgium.,Biomedical Quality Assurance Research Unit, KU Leuven (KUL), 3000, Louvain, Belgium
| | - Elien Augustus
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650, Edegem, Belgium
| | - Filip Lardon
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Hans Prenen
- Clinical Trials Unit, Department of Oncology and Phase 1, Antwerp University Hospital (UZA), 2650, Edegem, Belgium
| | - Marc Peeters
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium.,Department of Oncology, Multidisciplinary Oncological Center Antwerp (MOCA), Antwerp University Hospital (UZA), 2650, Edegem, Belgium
| | - Jan Van Meerbeeck
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium.,Department of Pulmonology and Thoracic Oncology, Antwerp University Hospital (UZA), 2650, Edegem, Belgium
| | - Geert Roeyen
- Hepatobiliary Transplantation and Endocrine Surgery, Antwerp University Hospital (UZA), 2650, Edegem, Belgium
| | - Christian Rolfo
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium.,Thoracic Medical Oncology and Early Clinical Trials, Marlene and Steward Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, 21201, Baltimore, MD, USA
| | - Patrick Pauwels
- Center for Oncological Research (CORE) Antwerp, University of Antwerp (UAntwerp), Universiteitsplein 1, 2610, Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650, Edegem, Belgium.,Biobank UZA/UAntwerpen, Antwerp University Hospital (UZA), 2650, Edegem, Belgium
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14
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Okada T, Mizukami Y, Ono Y, Sato H, Hayashi A, Kawabata H, Koizumi K, Masuda S, Teshima S, Takahashi K, Katanuma A, Omori Y, Iwano H, Yamada M, Yokochi T, Asahara S, Kawakubo K, Kuwatani M, Sakamoto N, Enomoto K, Goto T, Sasajima J, Fujiya M, Ueda J, Matsumoto S, Taniue K, Sugitani A, Karasaki H, Okumura T. Digital PCR-based plasma cell-free DNA mutation analysis for early-stage pancreatic tumor diagnosis and surveillance. J Gastroenterol 2020; 55:1183-1193. [PMID: 32939577 DOI: 10.1007/s00535-020-01724-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/17/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Cell-free DNA (cfDNA) shed from tumors into the circulation offers a tool for cancer detection. Here, we evaluated the feasibility of cfDNA measurement and utility of digital PCR (dPCR)-based assays, which reduce subsampling error, for diagnosing pancreatic ductal adenocarcinoma (PDA) and surveillance of intraductal papillary mucinous neoplasm (IPMN). METHODS We collected plasma from seven institutions for cfDNA measurements. Hot-spot mutations in KRAS and GNAS in the cfDNA from patients with PDA (n = 96), undergoing surveillance for IPMN (n = 112), and normal controls (n = 76) were evaluated using pre-amplification dPCR. RESULTS Upon Qubit measurement and copy number assessment of hemoglobin-subunit (HBB) and mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 (MT-ND1) in plasma cfDNA, HBB offered the best resolution between patients with PDA relative to healthy subjects [area under the curve (AUC) 0.862], whereas MT-ND1 revealed significant differences between IPMN and controls (AUC 0.851). DPCR utilizing pre-amplification cfDNA afforded accurate tumor-derived mutant KRAS detection in plasma in resectable PDA (AUC 0.861-0.876) and improved post-resection recurrence prediction [hazard ratio (HR) 3.179, 95% confidence interval (CI) 1.025-9.859] over that for the marker CA19-9 (HR 1.464; 95% CI 0.674-3.181). Capturing KRAS and GNAS could also provide genetic evidence in patients with IPMN-associated PDA and undergoing pancreatic surveillance. CONCLUSIONS Plasma cfDNA quantification by distinct measurements is useful to predict tumor burden. Through appropriate methods, dPCR-mediated mutation detection in patients with localized PDA and IPMN likely to progress to invasive carcinoma is feasible and complements conventional biomarkers.
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Affiliation(s)
- Tetsuhiro Okada
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan.
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan.
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Hiroki Sato
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Akihiro Hayashi
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Hidemasa Kawabata
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Kazuya Koizumi
- Center for Gastroenterology, Shonan Kamakura General Hospital, Kamakura, Japan
| | - Sakue Masuda
- Center for Gastroenterology, Shonan Kamakura General Hospital, Kamakura, Japan
| | - Shinichi Teshima
- Department of Pathology, Shonan Kamakura General Hospital, Kamakura, Japan
| | | | - Akio Katanuma
- Center for Gastroenterology, Teine-Keijinkai Hospital, Sapporo, Japan
| | - Yuko Omori
- Department of Pathology, Teine-Keijinkai Hospital, Sapporo, Japan
| | - Hirotoshi Iwano
- Department of Gastroenterology and Endoscopic Unit, Shibetsu City Hospital, Shibetsu, Japan
| | - Masataka Yamada
- Department of Gastroenterology and Endoscopic Unit, Shibetsu City Hospital, Shibetsu, Japan
| | - Tomoki Yokochi
- Department of Clinical Research, Chiba Tokushukai Hospital, Funabashi, Japan
| | - Shingo Asahara
- Department of Clinical Research, Chiba Tokushukai Hospital, Funabashi, Japan
| | - Kazumichi Kawakubo
- Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Masaki Kuwatani
- Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Naoya Sakamoto
- Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Katsuro Enomoto
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Takuma Goto
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Junpei Sasajima
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Mikihiro Fujiya
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
| | - Jun Ueda
- Center for Advanced Research and Education, Asahikawa Medical University, Asahikawa, Japan
| | - Seiji Matsumoto
- Center for Advanced Research and Education, Asahikawa Medical University, Asahikawa, Japan
| | - Kenzui Taniue
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | - Ayumu Sugitani
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | - Hidenori Karasaki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | - Toshikatsu Okumura
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
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15
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Pös Z, Pös O, Styk J, Mocova A, Strieskova L, Budis J, Kadasi L, Radvanszky J, Szemes T. Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes. Int J Mol Sci 2020; 21:ijms21228634. [PMID: 33207777 PMCID: PMC7697251 DOI: 10.3390/ijms21228634] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
Analyzes of cell-free nucleic acids (cfNAs) have shown huge potential in many biomedical applications, gradually entering several fields of research and everyday clinical care. Many biological properties of cfNAs can be informative to gain deeper insights into the function of the organism, such as their different types (DNA, RNAs) and subtypes (gDNA, mtDNA, bacterial DNA, miRNAs, etc.), forms (naked or vesicle bound NAs), fragmentation profiles, sequence composition, epigenetic modifications, and many others. On the other hand, the workflows of their analyzes comprise many important steps, from sample collection, storage and transportation, through extraction and laboratory analysis, up to bioinformatic analyzes and statistical evaluations, where each of these steps has the potential to affect the outcome and informational value of the performed analyzes. There are, however, no universal or standard protocols on how to exactly proceed when analyzing different cfNAs for different applications, at least according to our best knowledge. We decided therefore to prepare an overview of the available literature and products commercialized for cfNAs processing, in an attempt to summarize the benefits and limitations of the currently available approaches, devices, consumables, and protocols, together with various factors influencing the workflow, its processes, and outcomes.
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Affiliation(s)
- Zuzana Pös
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
| | - Ondrej Pös
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
| | - Jakub Styk
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Faculty of Medicine, Institute of Medical Biology, Genetics and Clinical Genetics, 811 08 Bratislava, Slovakia
| | - Angelika Mocova
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | | | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Slovak Center of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Ludevit Kadasi
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | - Jan Radvanszky
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (J.R.); (T.S.); Tel.: +421-2-60296637 (J.R.); +421-2-9026-8807 (T.S.)
| | - Tomas Szemes
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (J.R.); (T.S.); Tel.: +421-2-60296637 (J.R.); +421-2-9026-8807 (T.S.)
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16
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Ono Y, Hayashi A, Maeda C, Suzuki M, Wada R, Sato H, Kawabata H, Okada T, Goto T, Karasaki H, Mizukami Y, Okumura T. Time-saving method for directly amplifying and capturing a minimal amount of pancreatic tumor-derived mutations from fine-needle aspirates using digital PCR. Sci Rep 2020; 10:12332. [PMID: 32704002 PMCID: PMC7378187 DOI: 10.1038/s41598-020-69221-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/23/2020] [Indexed: 02/08/2023] Open
Abstract
It is challenging to secure a cytopathologic diagnosis using minute amounts of tumor fluids and tissue fragments. Hence, we developed a rapid, accurate, low-cost method for detecting tumor cell-derived DNA from limited amounts of specimens and samples with a low tumor cellularity, to detect KRAS mutations in pancreatic ductal carcinomas (PDA) using digital PCR (dPCR). The core invention is based on the suspension of tumor samples in pure water, which causes an osmotic burst; the crude suspension could be directly subjected to emulsion PCR in the platform. We examined the feasibility of this process using needle aspirates from surgically resected pancreatic tumor specimens (n = 12). We successfully amplified and detected mutant KRAS in 11 of 12 tumor samples harboring the mutation; the positive mutation frequency was as low as 0.8%. We used residual specimens from fine-needle aspiration/biopsy and needle flush processes (n = 10) for method validation. In 9 of 10 oncogenic KRAS pancreatic tumor samples, the "water-burst" method resulted in a positive mutation call. We describe a dPCR-based, super-sensitive screening protocol for determining KRAS mutation availability using tiny needle aspirates from PDAs processed using simple steps. This method might enable pathologists to secure a more accurate, minimally invasive diagnosis using minute tissue fragments.
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Affiliation(s)
- Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Akihiro Hayashi
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Chiho Maeda
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
| | - Mayumi Suzuki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
| | - Reona Wada
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
| | - Hiroki Sato
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Hidemasa Kawabata
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Tetsuhiro Okada
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Takuma Goto
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
| | - Hidenori Karasaki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan
| | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, 065-0033, Japan.
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan.
| | - Toshikatsu Okumura
- Division of Gastroenterology and Hepatology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, 078-8510, Japan
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17
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Ungerer V, Bronkhorst AJ, Holdenrieder S. Preanalytical variables that affect the outcome of cell-free DNA measurements. Crit Rev Clin Lab Sci 2020; 57:484-507. [DOI: 10.1080/10408363.2020.1750558] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Abel J. Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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18
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Abstract
Abstract
It is well documented that in the chain from sample to the result in a clinical laboratory, the pre-analytical phase is the weakest and most vulnerable link. This also holds for the use and analysis of extracellular nucleic acids. In this short review, we will summarize and critically evaluate the most important steps of the pre-analytical phase, i.e. the choice of the best control population for the patients to be analyzed, the actual blood draw, the choice of tubes for blood drawing, the impact of delayed processing of blood samples, the best method for getting rid of cells and debris, the choice of matrix, i.e. plasma vs. serum vs. other body fluids, and the impact of long-term storage of cell-free liquids on the outcome. Even if the analysis of cell-free nucleic acids has already become a routine application in the area of non-invasive prenatal screening (NIPS) and in the care of cancer patients (search for resistance mutations in the EGFR gene), there are still many unresolved issues of the pre-analytical phase which need to be urgently tackled.
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Affiliation(s)
- Michael Fleischhacker
- DRK Kliniken Berlin Mitte , Klinik für Innere Medizin – Pneumologie und Schlafmedizin , Drontheimer Str. 39 – 40 , 13359 Berlin , Germany
| | - Bernd Schmidt
- DRK Kliniken Berlin Mitte , Klinik für Innere Medizin – Pneumologie und Schlafmedizin , Berlin , Germany
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Otandault A, Anker P, Al Amir Dache Z, Guillaumon V, Meddeb R, Pastor B, Pisareva E, Sanchez C, Tanos R, Tousch G, Schwarzenbach H, Thierry AR. Recent advances in circulating nucleic acids in oncology. Ann Oncol 2020; 30:374-384. [PMID: 30753271 DOI: 10.1093/annonc/mdz031] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) is one of the fastest growing and most exciting areas in oncology in recent years. Its potential clinical uses cover now each phase of cancer patient management care (predictive information, detection of the minimal residual disease, early detection of resistance, treatment monitoring, recurrence surveillance, and cancer early detection/screening). This review relates the recent advances in the application of circulating DNA or RNA in oncology building on unpublished or initial findings/work presented at the 10th international symposium on circulating nucleic acids in plasma and serum held in Montpellier from the 20th to the 22nd of September 2017. This year, presenters revealed their latest data and crucial observations notably in relation to (i) the circulating cell-free (cfDNA) structure and implications regarding their optimal detection; (ii) their role in the metastatic or immunological processes; (iii) evaluation of miRNA panels for cancer patient follow up; (iv) the detection of the minimal residual disease; (v) the evaluation of a screening tests for cancer using cfDNA analysis; and (vi) elements of preanalytical guidelines. This work reviews the recent progresses in the field brought to light in the meeting, as well as in the most important reports from the literature, past and present. It proposes a broader picture of the basic research and its potential, and of the implementation and current challenges in the use of circulating nucleic acids in oncology.
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Affiliation(s)
- A Otandault
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - P Anker
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - Z Al Amir Dache
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - V Guillaumon
- Regional Institute of Cancer of Montpellier, Montpellier; SIRIC, Integrated Cancer Research Site, Montpellier, France
| | - R Meddeb
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - B Pastor
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - E Pisareva
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - C Sanchez
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - R Tanos
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - G Tousch
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - H Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - A R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier.
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20
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Southwood M, Krenz T, Cant N, Maurya M, Gazdova J, Maxwell P, McGready C, Moseley E, Hughes S, Stewart P, Salto-Tellez M, Groelz D, Rassl D. Systematic evaluation of PAXgene® tissue fixation for the histopathological and molecular study of lung cancer. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2019; 6:40-54. [PMID: 31571426 PMCID: PMC6966705 DOI: 10.1002/cjp2.145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/04/2019] [Accepted: 09/13/2019] [Indexed: 12/25/2022]
Abstract
Whilst adequate for most existing pathological tests, formalin is generally considered a poor DNA preservative and use of alternative fixatives may prove advantageous for molecular testing of tumour material; an increasingly common approach to identify targetable driver mutations in lung cancer patients. We collected paired PAXgene® tissue-fixed and formalin-fixed samples of block-sized tumour and lung parenchyma, Temno-needle core tumour biopsies and fine needle tumour aspirates (FNAs) from non-small cell lung cancer resection specimens. Traditionally processed formalin fixed paraffin wax embedded (FFPE) samples were compared to paired PAXgene® tissue fixed paraffin-embedded (PFPE) samples. We evaluated suitability for common laboratory tests (H&E staining and immunohistochemistry) and performance for downstream molecular investigations relevant to lung cancer, including RT-PCR and next generation DNA sequencing (NGS). Adequate and comparable H&E staining was seen in all sample types and nuclear staining was preferable in PAXgene® fixed Temno tumour biopsies and tumour FNA samples. Immunohistochemical staining was broadly comparable. PFPE samples enabled greater yields of less-fragmented DNA than FFPE comparators. PFPE samples were also superior for PCR and NGS performance, both in terms of quality control metrics and for variant calling. Critically we identified a greater number of genetic variants in the epidermal growth factor receptor gene when using PFPE samples and the Ingenuity® Variant Analysis pipeline. In summary, PFPE samples are adequate for histopathological diagnosis and suitable for the majority of existing laboratory tests. PAXgene® fixation is superior for DNA and RNA integrity, particularly in low-yield samples and facilitates improved NGS performance, including the detection of actionable lung cancer mutations for precision medicine in lung cancer samples.
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Affiliation(s)
- Mark Southwood
- Pathology Research, Royal Papworth Hospital NHS Foundation Trust, University of Cambridge Clinical School of Medicine, Cambridge, UK
| | - Tomasz Krenz
- Sample Technologies Department, QIAGEN GmbH, Hilden, Germany
| | - Natasha Cant
- Sample Technologies Department, QIAGEN Ltd., Manchester, UK
| | - Manisha Maurya
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Jana Gazdova
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Perry Maxwell
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Claire McGready
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Ellen Moseley
- Pathology Research, Royal Papworth Hospital NHS Foundation Trust, University of Cambridge Clinical School of Medicine, Cambridge, UK
| | - Susan Hughes
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Peter Stewart
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Manuel Salto-Tellez
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Daniel Groelz
- Sample Technologies Department, QIAGEN GmbH, Hilden, Germany
| | - Doris Rassl
- Pathology Research, Royal Papworth Hospital NHS Foundation Trust, University of Cambridge Clinical School of Medicine, Cambridge, UK
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Salvianti F, Gelmini S, Costanza F, Mancini I, Sonnati G, Simi L, Pazzagli M, Pinzani P. The pre-analytical phase of the liquid biopsy. N Biotechnol 2019; 55:19-29. [PMID: 31580920 DOI: 10.1016/j.nbt.2019.09.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 09/11/2019] [Accepted: 09/26/2019] [Indexed: 02/07/2023]
Abstract
The term 'liquid biopsy', introduced in 2013 in reference to the analysis of circulating tumour cells (CTCs) in cancer patients, was extended to cell-free nucleic acids (cfNAs) circulating in blood and other body fluids. CTCs and cfNAs are now considered diagnostic and prognostic markers, used as surrogate materials for the molecular characterisation of solid tumours, in particular for research on tumour-specific or actionable somatic mutations. Molecular characterisation of cfNAs and CTCs (especially at the single cell level) is technically challenging, requiring highly sensitive and specific methods and/or multi-step processes. The analysis of the liquid biopsy relies on a plethora of methods whose standardisation cannot be accomplished without disclosing criticisms related to the pre-analytical phase. Thus, pre-analytical factors potentially influencing downstream cellular and molecular analyses must be considered in order to translate the liquid biopsy approach into clinical practice. The present review summarises the most recent reports in this field, discussing the main pre-analytical aspects related to CTCs, cfNAs and exosomes in blood samples for liquid biopsy analysis. A short discussion on non-blood liquid biopsy samples is also included.
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Affiliation(s)
- Francesca Salvianti
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
| | - Stefania Gelmini
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy.
| | - Filomena Costanza
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
| | - Irene Mancini
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
| | - Gemma Sonnati
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
| | - Lisa Simi
- Molecular and Clinical Biochemistry Laboratory, Careggi University Hospital, Viale Pieraccini,6, 50139 Florence, Italy
| | - Mario Pazzagli
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
| | - Pamela Pinzani
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
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Enko D, Halwachs-Baumann G, Kriegshäuser G. Plasma free DNA: Evaluation of temperature-associated storage effects observed for Roche Cell-Free DNA collection tubes. Biochem Med (Zagreb) 2019; 29:010904. [PMID: 30799979 PMCID: PMC6366949 DOI: 10.11613/bm.2019.010904] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/31/2018] [Indexed: 12/13/2022] Open
Abstract
Introduction Standardized pre-analytical blood sample procedures for the analysis of circulating cell-free DNA (ccfDNA) are still not available. Therefore, the present study aimed at evaluating the impact of storage conditions related to different times (24 and 48 h) and temperatures (room temperature (RT) and 4 - 8 °C) on the plasma ccfDNA concentration of blood samples drawn into Cell-Free DNA collection tubes (Roche Diagnostics GmbH, Mannheim, Germany). Materials and methods Venous blood from 30 healthy individuals was collected into five 8.5 mL Cell-Free DNA Collection Tubes (Roche Diagnostics GmbH) each. Plasma samples were processed at time point of blood collection (tube 1), and after storage under the following conditions: 24 h at RT (tube 2) or 4-8 °C (tube 3), and 48 h at RT (tube 4) or 4 - 8 °C (tube 5). Circulating cell-free DNA concentrations were determined by EvaGreen chemistry-based droplet digital PCR (ddPCR). Results No statistically significant differences between median (interquartile range) plasma ccfDNA concentrations (ng/mL) at time point of blood collection (3.17 (2.13 – 3.76)) and after storage for 24 h (RT: 3.02 (2.41 – 3.68); 4-8 °C: 3.21 (2.19 – 3.46)) and 48 h (RT: 3.13 (2.10 – 3.76); 4-8 °C: 3.09 (2.19 – 3.50)) were observed (P values from 0.102 – 0.975). Conclusions No unwanted release of genomic DNA from white blood cells could be detected in plasma samples after tube storage for 24 and 48 h regardless of storage temperature.
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Affiliation(s)
- Dietmar Enko
- Institute of Clinical Chemistry and Laboratory Medicine, General Hospital Steyr, Steyr, Austria.,Clinical Institute of Medical and Laboratory Diagnostics, Medical University Graz, Graz, Austria
| | | | - Gernot Kriegshäuser
- Institute of Clinical Chemistry and Laboratory Medicine, General Hospital Steyr, Steyr, Austria.,Clinical Institute of Medical and Laboratory Diagnostics, Medical University Graz, Graz, Austria
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Preanalytical challenges – time for solutions. ACTA ACUST UNITED AC 2019; 57:974-981. [DOI: 10.1515/cclm-2018-1334] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/08/2019] [Indexed: 11/15/2022]
Abstract
Abstract
The European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) Working Group for the Preanalytical Phase (WG-PRE) was originally established in 2013, with the main aims of (i) promoting the importance of quality in the preanalytical phase of the testing process, (ii) establishing best practices and providing guidance for critical activities in the preanalytical phase, (iii) developing and disseminating European surveys for exploring practices concerning preanalytical issues, (iv) organizing meetings, workshops, webinars or specific training courses on preanalytical issues. As education is a core activity of the WG-PRE, a series of European conferences have been organized every second year across Europe. This collective article summarizes the leading concepts expressed during the lectures of the fifth EFLM Preanalytical Conference “Preanalytical Challenges – Time for solutions”, held in Zagreb, 22–23 March, 2019. The topics covered include sample stability, preanalytical challenges in hematology testing, feces analysis, bio-banking, liquid profiling, mass spectrometry, next generation sequencing, laboratory automation, the importance of knowing and measuring the exact sampling time, technology aids in managing inappropriate utilization of laboratory resources, management of hemolyzed samples and preanalytical quality indicators.
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Pisapia P, Malapelle U, Troncone G. Liquid Biopsy and Lung Cancer. Acta Cytol 2018; 63:489-496. [PMID: 30566947 DOI: 10.1159/000492710] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/07/2018] [Indexed: 12/11/2022]
Abstract
The identification of non-small cell lung cancer (NSCLC) patients potentially responsive to targeted therapies relies on a number of relevant biomarkers, including EGFR, ALK, ROS-1, and PD-L1. Biomarker identification is most commonly based on surgical sample collection. However, when tissues are difficult to reach or when multiple analyses are necessary to monitor tumor progression and treatment response, liquid biopsy is a valid noninvasive alternative. This analysis, which is preferentially performed on circulating tumor DNA (ctDNA) extracted from plasma samples, has the major advantage of reducing the inherent risks and discomfort of tissue biopsy. However, a major disadvantage is that it yields only a low number of ctDNA targets. Thus, to avoid false-positive and false-negative results, it is important to adopt and validate technologies with high sensitivity and specificity in the pre-analytical phase of sampling. This review succinctly addresses the principal methodologies for analyzing plasma-derived ctDNA in NSCLC patients.
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Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy,
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Grölz D, Hauch S, Schlumpberger M, Guenther K, Voss T, Sprenger-Haussels M, Oelmüller U. Liquid Biopsy Preservation Solutions for Standardized Pre-Analytical Workflows-Venous Whole Blood and Plasma. CURRENT PATHOBIOLOGY REPORTS 2018; 6:275-286. [PMID: 30595972 PMCID: PMC6290703 DOI: 10.1007/s40139-018-0180-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW Liquid biopsy analyses based on circulating cell-free nucleic acids, circulating tumor cells or other diseased cells from organs, and exosomes or other microvesicles in blood offer new means for non-invasive diagnostic applications. The main goal of this review is to explain the importance of preserving whole blood specimens after blood draw for use as liquid biopsies, and to summarize preservation solutions that are currently available. RECENT FINDINGS Despite the great potential of liquid biopsies for diagnostics and disease management, besides non-invasive prenatal testing (NIPT), only a few liquid biopsy applications are fully implemented for routine in vitro diagnostic testing. One major barrier is the lack of standardized pre-analytical workflows, including the collection of consistent quality blood specimens and the generation of good-quality plasma samples therefrom. Broader use of liquid biopsies in clinical routine applications therefore requires improved pre-analytical procedures to enable high-quality specimens to obtain unbiased analyte profiles (DNA, RNA, proteins, etc.) as they are in the patient's body. SUMMARY A growing number of stabilizing reagents and dedicated blood collection tubes are available for the post-collection preservation of circulating cell-free DNA (ccfDNA) profiles in whole blood. In contrast, solutions for the preservation of circulating tumor cells (CTC) that enable both, enumeration and molecular analyses are rare. Solutions for extracellular vesicle (EV) populations, including exosomes, do not yet exist.
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Affiliation(s)
- Daniel Grölz
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | - Siegfried Hauch
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | | | - Kalle Guenther
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | - Thorsten Voss
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | | | - Uwe Oelmüller
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
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Castro-Giner F, Gkountela S, Donato C, Alborelli I, Quagliata L, Ng CKY, Piscuoglio S, Aceto N. Cancer Diagnosis Using a Liquid Biopsy: Challenges and Expectations. Diagnostics (Basel) 2018; 8:diagnostics8020031. [PMID: 29747380 PMCID: PMC6023445 DOI: 10.3390/diagnostics8020031] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 01/05/2023] Open
Abstract
The field of cancer diagnostics has recently been impacted by new and exciting developments in the area of liquid biopsy. A liquid biopsy is a minimally invasive alternative to surgical biopsies of solid tissues, typically achieved through the withdrawal of a blood sample or other body fluids, allowing the interrogation of tumor-derived material including circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) fragments that are present at a given time point. In this short review, we discuss a few studies that summarize the state-of-the-art in the liquid biopsy field from a diagnostic perspective, and speculate on current challenges and expectations of implementing liquid biopsy testing for cancer diagnosis and monitoring in the clinical setting.
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Affiliation(s)
- Francesc Castro-Giner
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland.
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Sofia Gkountela
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland.
| | - Cinzia Donato
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland.
| | - Ilaria Alborelli
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland.
| | - Luca Quagliata
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland.
| | - Charlotte K Y Ng
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland.
- Hepatology Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4031 Basel, Switzerland.
| | | | - Nicola Aceto
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland.
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Evaluation of Streck BCT and PAXgene Stabilised Blood Collection Tubes for Cell-Free Circulating DNA Studies in Plasma. Mol Diagn Ther 2017. [DOI: 10.1007/s40291-017-0284-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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