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Terp SK, Pedersen IS, Stoico MP. Extraction of Cell-Free DNA: Evaluation of Efficiency, Quantity, and Quality. J Mol Diagn 2024; 26:310-319. [PMID: 38336350 DOI: 10.1016/j.jmoldx.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 02/12/2024] Open
Abstract
Cell-free DNA (cfDNA) serves as a valuable biomarker for early disease detection and monitoring. However, the use of cfDNA for analysis faces challenges owing to general low but variable abundance and fragmentation. Preanalytical factors, including cfDNA extraction, impact cfDNA quality and quantity. Efficient and robust cfDNA extraction is essential for reliable results in downstream applications, and various commercial extraction methods exist, each with trade-offs. To aid researchers and clinicians in choosing the proper cfDNA extraction method, manual, semiautomated, and automated methods were evaluated, including the QIAamp Circulating Nucleic Acid Kit (manual and QIAcube), QIAamp MinElute ccfDNA Kit (QIAcube), and QIAsymphony DSP Circulating DNA Kit (QIAsymphony). For each extraction method, cfDNA was extracted on two separate days, using samples obtained from 18 healthy donors. This study assessed extraction efficiency, quantity, and quality using droplet digital PCR and TapeStation. The QIAamp Circulating Nucleic Acid Kit, both manual and semiautomated, outperformed the QIAamp MinElute ccfDNA Kit (QIAcube) and QIAsymphony DSP Circulating DNA Kit (QIAsymphony), showing higher recovery rates and cfDNA quantity. All methods were reproducible, with no day-to-day variability and no contamination by high-molecular-weight DNA. The QIAamp Circulating Nucleic Acid Kit offers high yield without compromising quality. Implementation of the method should consider specific study and clinical needs, taking into account each method's advantages and limitations for optimal outcomes.
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Affiliation(s)
- Simone K Terp
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
| | - Inge S Pedersen
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Malene P Stoico
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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2
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Chang L, Wang D, Han Y, Diao Z, Chen Y, Li J, Zhang R. External quality assessment for detection of colorectal cancer by Septin9 DNA methylation in clinical laboratories. Clin Chim Acta 2024; 552:117663. [PMID: 38008152 DOI: 10.1016/j.cca.2023.117663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/28/2023] [Accepted: 11/15/2023] [Indexed: 11/28/2023]
Abstract
BACKGROUND AND AIMS The incidence and mortality rate of colorectal cancer (CRC) are increasing worldwide. Septin9 methylated (mSEPT9) DNA in circulation can be used as a non-invasive detection method to assist in the early diagnosis of CRC; however, the detection methods and procedures are complicated. This study aimed to evaluate the ability of clinical laboratories to detect Septin9 methylation in plasma cell-free DNA (cfDNA). MATERIALS AND METHODS We prepared a sample panel consisting of positive and negative Septin9 methylation cells and CRC cells. Three positive samples with different methylation levels, one negative sample and one duplicate sample, two samples containing interference, three different CRC cell samples, and a fictitious case report were included. The panel was distributed to 59 laboratories for mSEPT9 analysis, result comparison, and scoring. RESULTS The sample panel, validated by National Medical Products Administration (NMPA)-approved tests and targeted bisulfite sequencing, met expectations and could be used for external quality assessment (EQA). Among the 59 laboratories, 55 (93.22%) correctly reported the mSEPT9 results for all samples, while four (6.79%) reported 15 false negatives and were considered improvable. All false negatives originated from four laboratories using laboratory-developed tests (LDTs), with three failing to detect weakly positive samples, samples containing interference, and samples from different CRC cells, and one reported erroneous results on all positive samples. CONCLUSION Our results illustrated that the detection of mSEPT9 in cfDNA is satisfactory in China. EQA is indispensable because it can help improve the diagnostic capability and quality management of the laboratories, and provide suggestions for the problems existing in mSEPT9 detection.
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Affiliation(s)
- Lu Chang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P.R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Duo Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P.R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Zhenli Diao
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P.R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Yuqing Chen
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P.R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P.R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China.
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P.R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China.
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3
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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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4
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Fairley JA, Badrick T, Denis MG, Dimitrova L, Goodall R, Maas J, Normanno N, Patton SJ, Rouleau E, Russo A, Stockley TL, Deans ZC. Implementation of circulating tumour DNA multi-target mutation testing in plasma: a perspective from an external quality assessment providers' survey. Virchows Arch 2023:10.1007/s00428-023-03558-x. [PMID: 37202567 DOI: 10.1007/s00428-023-03558-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/02/2023] [Accepted: 05/06/2023] [Indexed: 05/20/2023]
Abstract
Demand for large-scale tumour profiling across cancer types has increased in recent years, driven by the emergence of targeted drug therapies. Analysing alternations in plasma circulating tumour DNA (ctDNA) for cancer detection can improve survival; ctDNA testing is recommended when tumour tissue is unavailable. An online survey of molecular pathology testing was circulated by six external quality assessment members of IQN Path to registered laboratories and all IQN Path collaborative corporate members. Data from 275 laboratories across 45 countries were collected; 245 (89%) perform molecular pathology testing, including 177 (64%) which perform plasma ctDNA diagnostic service testing. The most common tests were next-generation sequencing-based (n = 113). Genes with known stratified treatment options, including KRAS (n = 97), NRAS (n = 84), and EGFR (n = 130), were common targets. The uptake of ctDNA plasma testing and plans to implement further testing demonstrates the importance of support from a well-designed EQA scheme.
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Affiliation(s)
- Jennifer A Fairley
- GenQA, Department of Laboratory Medicine, NHS Lothian, Nine Bioquarter, Little France Rd, Edinburgh, EH16 4UX, UK
| | - Tony Badrick
- The Royal College of Pathologists of Australasia, Quality Assurance Programs (RCPAQAP), St. Leonards, Australia
| | - Marc G Denis
- Nantes Université, CHU Nantes, Department of Biochemistry, INSERM, CNRS, Immunology and New Concepts in Immunotherapy, Nantes, France
| | | | - Rebecca Goodall
- EMQN CIC, Unit 4, Enterprise House, Manchester Science Park, Pencroft Way, Manchester, M15 6SE, UK
| | - Joerg Maas
- Deutsche Gesellschaft für Pathologie E.V. (DGP), Berlin, Germany
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - "Fondazione G. Pascale", Via Mariano Semola, 80131, Napoli, Italy
| | - Simon J Patton
- EMQN CIC, Unit 4, Enterprise House, Manchester Science Park, Pencroft Way, Manchester, M15 6SE, UK
| | - Etienne Rouleau
- Department of Medical Biology and Pathology, Gustave Roussy, Cancer Genetics Laboratory, Gustave Roussy, 94800, Villejuif, France
| | - Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Tracy L Stockley
- Laboratory Medicine Program, University Health Network; Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Zandra C Deans
- GenQA, Department of Laboratory Medicine, NHS Lothian, Nine Bioquarter, Little France Rd, Edinburgh, EH16 4UX, UK.
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5
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Caputo V, Ciardiello F, Corte CMD, Martini G, Troiani T, Napolitano S. Diagnostic value of liquid biopsy in the era of precision medicine: 10 years of clinical evidence in cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:102-138. [PMID: 36937316 PMCID: PMC10017193 DOI: 10.37349/etat.2023.00125] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/13/2022] [Indexed: 03/06/2023] Open
Abstract
Liquid biopsy is a diagnostic repeatable test, which in last years has emerged as a powerful tool for profiling cancer genomes in real-time with minimal invasiveness and tailoring oncological decision-making. It analyzes different blood-circulating biomarkers and circulating tumor DNA (ctDNA) is the preferred one. Nevertheless, tissue biopsy remains the gold standard for molecular evaluation of solid tumors whereas liquid biopsy is a complementary tool in many different clinical settings, such as treatment selection, monitoring treatment response, cancer clonal evolution, prognostic evaluation, as well as the detection of early disease and minimal residual disease (MRD). A wide number of technologies have been developed with the aim of increasing their sensitivity and specificity with acceptable costs. Moreover, several preclinical and clinical studies have been conducted to better understand liquid biopsy clinical utility. Anyway, several issues are still a limitation of its use such as false positive and negative results, results interpretation, and standardization of the panel tests. Although there has been rapid development of the research in these fields and recent advances in the clinical setting, many clinical trials and studies are still needed to make liquid biopsy an instrument of clinical routine. This review provides an overview of the current and future clinical applications and opening questions of liquid biopsy in different oncological settings, with particular attention to ctDNA liquid biopsy.
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Affiliation(s)
- Vincenza Caputo
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Fortunato Ciardiello
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Carminia Maria Della Corte
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Giulia Martini
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Teresa Troiani
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Stefania Napolitano
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
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6
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Kramer A, Schuuring E, Vessies DCL, van der Leest P, Geerlings MJ, Rozendal P, Lanfermeijer M, Linders TC, van Kempen LC, Fijneman RJA, Ligtenberg MJL, Meijer GA, van den Broek D, Retèl VP, Coupé VMH. A Micro-Costing Framework for Circulating Tumor DNA Testing in Dutch Clinical Practice. J Mol Diagn 2023; 25:36-45. [PMID: 36402278 DOI: 10.1016/j.jmoldx.2022.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 07/11/2022] [Accepted: 10/04/2022] [Indexed: 11/18/2022] Open
Abstract
Circulating tumor DNA (ctDNA) is a promising new biomarker with multiple potential applications in cancer care. Estimating total cost of ctDNA testing is necessary for reimbursement and implementation, but challenging because of variations in workflow. We aimed to develop a micro-costing framework for consistent cost calculation of ctDNA testing. First, the foundation of the framework was built, based on the complete step-wise diagnostic workflow of ctDNA testing. Second, the costing method was set up, including costs for personnel, materials, equipment, overhead, and failures. Third, the framework was evaluated by experts and applied to six case studies, including PCR-, mass spectrometry-, and next-generation sequencing-based platforms, from three Dutch hospitals. The developed ctDNA micro-costing framework includes the diagnostic workflow from blood sample collection to diagnostic test result. The framework was developed from a Dutch perspective and takes testing volume into account. An open access tool is provided to allow for laboratory-specific calculations to explore the total costs of ctDNA testing specific workflow parameters matching the setting of interest. It also allows to straightforwardly assess the impact of alternative prices or assumptions on the cost per sample by simply varying the input parameters. The case studies showed a wide range of costs, from €168 to €7638 ($199 to $9124) per sample, and generated information. These costs are sensitive to the (coverage of) platform, setting, and testing volume.
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Affiliation(s)
- Astrid Kramer
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Amsterdam, the Netherlands.
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Daan C L Vessies
- Department of Laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Paul van der Leest
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Pim Rozendal
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mirthe Lanfermeijer
- Department of Laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Theodora C Linders
- Department of Laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Léon C van Kempen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Remond J A Fijneman
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboudumc, Nijmegen, the Netherlands; Department of Pathology, Radboudumc, Nijmegen, the Netherlands
| | - Gerrit A Meijer
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Daan van den Broek
- Department of Laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Valesca P Retèl
- Department of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Health Technology and Services Research, University of Twente, Enschede, the Netherlands
| | - Veerle M H Coupé
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Amsterdam, the Netherlands
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7
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Abstract
Somatic mutations of genes involved in NF-κB, PI3K/AKT, NOTCH, and JAK/STAT signaling pathways play an important role in the pathogenesis of Hodgkin lymphoma (HL). HL tumor cells form only about 5% of the tumor mass; however, it was shown that HL tumor-derived DNA could be detected in the bloodstream. This circulating tumor DNA (ctDNA) reflects the genetic profile of HL tumor cells and can be used for qualitative and quantitative analysis of tumor-specific somatic DNA mutations within the concept of liquid biopsy. Overall, the most frequently mutated gene in HL is STAT6; however, the exact spectrum of mutations differs between individual HL histological subtypes. Importantly, reduction of ctDNA plasma levels after initial treatment is highly correlated with prognosis. Therefore, ctDNA shows great promise as a novel tool for non-invasive tumor genome analysis for biomarker driven therapy as well as for superior minimal residual disease monitoring and treatment resistance detection. Here, we summarize the recent advancements of ctDNA analysis in HL with focus on ctDNA detection methodologies, genetic profiling of HL and its clonal evolution, and the emerging prognostic value of ctDNA.
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8
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Fairley JA, Cheetham MH, Patton SJ, Rouleau E, Denis M, Dequeker EMC, Schuuring E, van Casteren K, Fenizia F, Normanno N, Deans ZC. Results of a worldwide external quality assessment of cfDNA testing in lung Cancer. BMC Cancer 2022; 22:759. [PMID: 35820813 PMCID: PMC9275131 DOI: 10.1186/s12885-022-09849-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Circulating cell free DNA (cfDNA) testing of plasma for EGFR somatic variants in lung cancer patients is being widely implemented and with any new service, external quality assessment (EQA) is required to ensure patient safety. An international consortium, International Quality Network for Pathology (IQNPath), has delivered a second round of assessment to measure the accuracy of cfDNA testing for lung cancer and the interpretation of the results. METHODS A collaboration of five EQA provider organisations, all members of IQNPath, have delivered the assessment during 2018-19 to a total of 264 laboratories from 45 countries. Bespoke plasma reference material containing a range of EGFR mutations at varying allelic frequencies were supplied to laboratories for testing and reporting according to routine procedures. The genotyping accuracy and clinical reporting was reviewed against standardised criteria and feedback was provided to participants. RESULTS The overall genotyping error rate in the EQA was found to be 11.1%. Low allelic frequency samples were the most challenging and were not detected by some testing methods, resulting in critical genotyping errors. This was reflected in higher false negative rates for samples with variant allele frequencies (VAF) rates less than 1.5% compared to higher frequencies. A sample with two different EGFR mutations gave inconsistent detection of both mutations. However, for one sample, where two variants were present at a VAF of less than 1% then both mutations were correctly detected in 145/263 laboratories. Reports often did not address the risk that tumour DNA may have not been tested and limitations of the methodologies provided by participants were insufficient. This was reflected in the average interpretation score for the EQA being 1.49 out of a maximum of 2. CONCLUSIONS The variability in the standard of genotyping and reporting highlighted the need for EQA and educational guidance in this field to ensure the delivery of high-quality clinical services where testing of cfDNA is the only option for clinical management.
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Affiliation(s)
- Jennifer A Fairley
- GenQA, Nine, Edinburgh Bioquarter, 9 Little France Road, Edinburgh, EH16 4SA, UK.
| | - Melanie H Cheetham
- EMQN CIC, Unit 4, Enterprise House, Pencroft Way, Manchester Science Park, Manchester, M15 6SE, UK
| | - Simon J Patton
- EMQN CIC, Unit 4, Enterprise House, Pencroft Way, Manchester Science Park, Manchester, M15 6SE, UK
| | - Etienne Rouleau
- Medical Biology and Pathology Department, Gustave Roussy, Villejuif, France
| | - Marc Denis
- Department of Biochemistry and INSERM U1232, Centre Hospitalier Universitaire de Nantes, 9 quai Moncousu, F-44093, Nantes Cedex, France
| | - Elisabeth M C Dequeker
- Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, KU Leuven, Kapucijnenvoer 35d, 3000, Leuven, Belgium
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Kaat van Casteren
- Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, KU Leuven, Kapucijnenvoer 35d, 3000, Leuven, Belgium
| | | | - Nicola Normanno
- Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131, Napoli, Italy
| | - Zandra C Deans
- GenQA, Nine, Edinburgh Bioquarter, 9 Little France Road, Edinburgh, EH16 4SA, UK
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9
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Heitzer E, van den Broek D, Denis MG, Hofman P, Hubank M, Mouliere F, Paz-Ares L, Schuuring E, Sültmann H, Vainer G, Verstraaten E, de Visser L, Cortinovis D. Recommendations for a practical implementation of circulating tumor DNA mutation testing in metastatic non-small-cell lung cancer. ESMO Open 2022; 7:100399. [PMID: 35202954 PMCID: PMC8867049 DOI: 10.1016/j.esmoop.2022.100399] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/10/2021] [Accepted: 01/19/2022] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Liquid biopsy (LB) is a rapidly evolving diagnostic tool for precision oncology that has recently found its way into routine practice as an adjunct to tissue biopsy (TB). The concept of LB refers to any tumor-derived material, such as circulating tumor DNA (ctDNA) or circulating tumor cells that are detectable in blood. An LB is not limited to the blood and may include other fluids such as cerebrospinal fluid, pleural effusion, and urine, among others. PATIENTS AND METHODS The objective of this paper, devised by international experts from various disciplines, is to review current challenges as well as state-of-the-art applications of ctDNA mutation testing in metastatic non-small-cell lung cancer (NSCLC). We consider pragmatic scenarios for the use of ctDNA from blood plasma to identify actionable targets for therapy selection in NSCLCs. RESULTS Clinical scenarios where ctDNA mutation testing may be implemented in clinical practice include complementary tissue and LB testing to provide the full picture of patients' actual predictive profiles to identify resistance mechanism (i.e. secondary mutations), and ctDNA mutation testing to assist when a patient has a discordant clinical history and is suspected of showing intertumor or intratumor heterogeneity. ctDNA mutation testing may provide interesting insights into possible targets that may have been missed on the TB. Complementary ctDNA LB testing also provides an option if the tumor location is hard to biopsy or if an insufficient sample was taken. These clinical use cases highlight practical scenarios where ctDNA LB may be considered as a complementary tool to TB analysis. CONCLUSIONS Proper implementation of ctDNA LB testing in routine clinical practice is envisioned in the near future. As the clinical evidence of utility expands, the use of LB alongside tissue sample analysis may occur in the patient cases detailed here.
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Affiliation(s)
- E Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria.
| | - D van den Broek
- Antoni van Leeuwenhoek-Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - M G Denis
- Department of Biochemistry and Molecular Biology, Nantes University Hospital, Nantes, France
| | - P Hofman
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Biobank BB-0033-00025, University Côte d'Azur, Nice, France
| | - M Hubank
- The Royal Marsden NHS Foundation Trust, London, UK
| | - F Mouliere
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - L Paz-Ares
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, H12o-CNIO Lung Cancer Unit, Universidad Complutense & CIBERONC, Madrid, Spain
| | - E Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - H Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Center for Lung Disease (DZL) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - G Vainer
- Department of Pathology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - L de Visser
- Roche Diagnostics International, Rotkreuz, Switzerland
| | - D Cortinovis
- SC Medical Oncology, Azienda Socio Sanitaria Territoriale (ASST) H S Gerardo Monza, Monza, Italy
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10
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Hasenleithner SO, Speicher MR. A clinician’s handbook for using ctDNA throughout the patient journey. Mol Cancer 2022; 21:81. [PMID: 35307037 PMCID: PMC8935823 DOI: 10.1186/s12943-022-01551-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/24/2022] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
The promise of precision cancer medicine presently centers around the genomic sequence of a patient’s tumor being translated into timely, actionable information to inform clinical care. The analysis of cell-free DNA from liquid biopsy, which contains circulating tumor DNA (ctDNA) in patients with cancer, has proven to be amenable to various settings in oncology. However, open questions surrounding the clinical validity and utility of plasma-based analyses have hindered widespread clinical adoption.
Main body
Owing to the rapid evolution of the field, studies supporting the use of ctDNA as a biomarker throughout a patient’s journey with cancer have accumulated in the last few years, warranting a review of the latest status for clinicians who may employ ctDNA in their precision oncology programs. In this work, we take a step back from the intricate coverage of detection approaches described extensively elsewhere and cover basic concepts around the practical implementation of next generation sequencing (NGS)-guided liquid biopsy. We compare relevant targeted and untargeted approaches to plasma DNA analysis, describe the latest evidence for clinical validity and utility, and highlight the value of genome-wide ctDNA analysis, particularly as it relates to early detection strategies and discovery applications harnessing the non-coding genome.
Conclusions
The maturation of liquid biopsy for clinical application will require interdisciplinary efforts to address current challenges. However, patients and clinicians alike may greatly benefit in the future from its incorporation into routine oncology care.
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11
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Lyu X, Tsui YM, Ho DWH, Ng IOL. Liquid Biopsy Using Cell-Free or Circulating Tumor DNA in the Management of Hepatocellular Carcinoma. Cell Mol Gastroenterol Hepatol 2022; 13:1611-1624. [PMID: 35183803 PMCID: PMC9048068 DOI: 10.1016/j.jcmgh.2022.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 12/18/2022]
Abstract
Liver cancer (hepatocellular carcinoma [HCC]) is a fatal cancer worldwide and often is detected at an advanced stage when treatment options are very limited. This drives the development of techniques and platforms for early detection of HCC. In recent years, liquid biopsy has provided a means of noninvasive detection of cancers. By detecting plasma circulating tumor DNA (ctDNA) released from dying cancer cells, the presence of HCC can be detected in a noninvasive manner. In this review, we discuss the molecular characteristics of ctDNA and its various molecular landscapes in HCC. These include the mutational landscape, single-nucleotide variations, copy number variations, methylation landscape, end motif/coordinate preference, hepatitis B virus integration, and mitochondrial DNA mutations. The consistency between the plasma ctDNA and the tumor tissue genomic DNA mutational profile is pivotal for the clinical utility of ctDNA in the clinical management of HCC. With strategic use of genetic information provided from plasma ctDNA profiling and procedure standardization to facilitate implementation in clinical practice, better clinical management would become permissible through more efficient detection and diagnosis of HCC, better prognostication, precision-matched treatment guidance, and more reliable disease monitoring.
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Affiliation(s)
| | | | - Daniel Wai-Hung Ho
- Correspondence Address correspondence to: Daniel Wai-Hung Ho, PhD, Department of Pathology, L704, Laboratory Block, Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong. fax: (852) 2819-5375.
| | - Irene Oi-Lin Ng
- Irene Oi-Lin Ng, MD, PhD, Department of Pathology, Room 7-13, Block T, Queen Mary Hospital, Pokfulam, Hong Kong. fax: 852-28872-5197.
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12
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Bieler J, Pozzorini C, Garcia J, Tuck AC, Macheret M, Willig A, Couraud S, Xing X, Menu P, Steinmetz LM, Payen L, Xu Z. High-Throughput Nucleotide Resolution Predictions of Assay Limitations Increase the Reliability and Concordance of Clinical Tests. JCO Clin Cancer Inform 2021; 5:1085-1095. [PMID: 34731027 DOI: 10.1200/cci.21.00057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
PURPOSE The ability of next-generation sequencing (NGS) assays to interrogate thousands of genomic loci has revolutionized genetic testing. However, translation to the clinic is impeded by false-negative results that pose a risk to patients. In response, regulatory bodies are calling for reliability measures to be reported alongside NGS results. Existing methods to estimate reliability do not account for sample- and position-specific variability, which can be significant. Here, we report an approach that computes reliability metrics for every genomic position and sample interrogated by an NGS assay. METHODS Our approach predicts the limit of detection (LOD), the lowest reliably detectable variant fraction, by taking technical factors into account. We initially explored how LOD is affected by input material amount, library conversion rate, sequencing coverage, and sequencing error rate. This revealed that LOD depends heavily on genomic context and sample properties. Using these insights, we developed a computational approach to predict LOD on the basis of a biophysical model of the NGS workflow. We focused on targeted assays for cell-free DNA, but, in principle, this approach applies to any NGS assay. RESULTS We validated our approach by showing that it accurately predicts LOD and distinguishes reliable from unreliable results when screening 580 lung cancer samples for actionable mutations. Compared with a standard variant calling workflow, our approach avoided most false negatives and improved interassay concordance from 94% to 99%. CONCLUSION Our approach, which we name LAVA (LOD-aware variant analysis), reports the LOD for every position and sample interrogated by an NGS assay. This enables reliable results to be identified and improves the transparency and safety of genetic tests.
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Affiliation(s)
| | | | - Jessica Garcia
- Laboratoire de Biochimie et Biologie Moléculaire, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France.,Institut de Cancérologie des Hospices Civils de Lyon, CIRculating CANcer Program (CIRCAN), Lyon, France
| | - Alex C Tuck
- SOPHiA GENETICS SA, Saint Sulpice, Switzerland
| | | | | | - Sébastien Couraud
- Institut de Cancérologie des Hospices Civils de Lyon, CIRculating CANcer Program (CIRCAN), Lyon, France.,Service de Pneumologie aigue spécialisée et cancérologie thoracique, Groupement hospitalier sud, Institut de Cancérologie des Hospices Civils de Lyon, Pierre Bénite, France
| | | | | | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA.,Department of Genetics, School of Medicine, Stanford University, Stanford, CA
| | - Léa Payen
- Laboratoire de Biochimie et Biologie Moléculaire, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France.,Institut de Cancérologie des Hospices Civils de Lyon, CIRculating CANcer Program (CIRCAN), Lyon, France
| | - Zhenyu Xu
- SOPHiA GENETICS SA, Saint Sulpice, Switzerland
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13
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Therapy Monitoring of EGFR-Positive Non–Small-Cell Lung Cancer Patients Using ddPCR Multiplex Assays. J Mol Diagn 2021; 23:495-505. [DOI: 10.1016/j.jmoldx.2021.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/30/2020] [Accepted: 01/12/2021] [Indexed: 12/18/2022] Open
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14
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Abstract
Response evaluation for cancer treatment consists primarily of clinical and radiological assessments. In addition, a limited number of serum biomarkers that assess treatment response are available for a small subset of malignancies. Through recent technological innovations, new methods for measuring tumor burden and treatment response are becoming available. By utilization of highly sensitive techniques, tumor-specific mutations in circulating DNA can be detected and circulating tumor DNA (ctDNA) can be quantified. These so-called liquid biopsies provide both molecular information about the genomic composition of the tumor and opportunities to evaluate tumor response during therapy. Quantification of tumor-specific mutations in plasma correlates well with tumor burden. Moreover, with liquid biopsies, it is also possible to detect mutations causing secondary resistance during treatment. This review focuses on the clinical utility of ctDNA as a response and follow-up marker in patients with non-small cell lung cancer, melanoma, colorectal cancer, and breast cancer. Relevant studies were retrieved from a literature search using PubMed database. An overview of the available literature is provided and the relevance of ctDNA as a response marker in anti-cancer therapy for clinical practice is discussed. We conclude that the use of plasma-derived ctDNA is a promising tool for treatment decision-making based on predictive testing, detection of resistance mechanisms, and monitoring tumor response. Necessary steps for translation to daily practice and future perspectives are discussed.
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15
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IJzerman MJ, de Boer J, Azad A, Degeling K, Geoghegan J, Hewitt C, Hollande F, Lee B, To YH, Tothill RW, Wright G, Tie J, Dawson SJ. Towards Routine Implementation of Liquid Biopsies in Cancer Management: It Is Always Too Early, until Suddenly It Is Too Late. Diagnostics (Basel) 2021; 11:103. [PMID: 33440749 PMCID: PMC7826562 DOI: 10.3390/diagnostics11010103] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
Blood-based liquid biopsies are considered a new and promising diagnostic and monitoring tool for cancer. As liquid biopsies only require a blood draw, they are non-invasive, potentially more rapid and assumed to be a less costly alternative to genomic analysis of tissue biopsies. A multi-disciplinary workshop (n = 98 registrations) was organized to discuss routine implementation of liquid biopsies in cancer management. Real-time polls were used to engage with experts' about the current evidence of clinical utility and the barriers to implementation of liquid biopsies. Clinical, laboratory and health economics presentations were given to illustrate the opportunities and current levels of evidence, followed by three moderated break-out sessions to discuss applications. The workshop concluded that tumor-informed assays using next-generation sequencing (NGS) or PCR-based genotyping assays will most likely provide better clinical utility than tumor-agnostic assays, yet at a higher cost. For routine application, it will be essential to determine clinical utility, to define the minimum quality standards and performance of testing platforms and to ensure their use is integrated into current clinical workflows including how they complement tissue biopsies and imaging. Early health economic models may help identifying the most viable application of liquid biopsies. Alternative funding models for the translation of complex molecular diagnostics, such as liquid biopsies, may also be explored if clinical utility has been demonstrated and when their use is recommended in multi-disciplinary consensus guidelines.
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Affiliation(s)
- Maarten J. IJzerman
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne Centre for Cancer Research, Parkville, VIC 3000, Australia; (K.D.); (F.H.); (R.W.T.); (S.-J.D.)
- Centre for Health Policy, Faculty of Medicine, Dentistry and Health Sciences, Melbourne School of Population and Global Health, Parkville, VIC 3053, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia; (A.A.); (B.L.); (Y.H.T.); (J.T.)
| | - Jasper de Boer
- Victorian Comprehensive Cancer Centre, Parkville, VIC 3050, Australia;
| | - Arun Azad
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia; (A.A.); (B.L.); (Y.H.T.); (J.T.)
| | - Koen Degeling
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne Centre for Cancer Research, Parkville, VIC 3000, Australia; (K.D.); (F.H.); (R.W.T.); (S.-J.D.)
- Centre for Health Policy, Faculty of Medicine, Dentistry and Health Sciences, Melbourne School of Population and Global Health, Parkville, VIC 3053, Australia
| | | | - Chelsee Hewitt
- Department of Pathology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia;
| | - Frédéric Hollande
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne Centre for Cancer Research, Parkville, VIC 3000, Australia; (K.D.); (F.H.); (R.W.T.); (S.-J.D.)
| | - Belinda Lee
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia; (A.A.); (B.L.); (Y.H.T.); (J.T.)
- Division of Personalised Oncology, Walter and Eliza Hall Research Institute, Melbourne, VIC 3052, Australia
- Department of Medical Oncology, Northern Health, Epping, VIC 3076, Australia
| | - Yat Ho To
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia; (A.A.); (B.L.); (Y.H.T.); (J.T.)
- Division of Personalised Oncology, Walter and Eliza Hall Research Institute, Melbourne, VIC 3052, Australia
| | - Richard W. Tothill
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne Centre for Cancer Research, Parkville, VIC 3000, Australia; (K.D.); (F.H.); (R.W.T.); (S.-J.D.)
| | - Gavin Wright
- Department of Surgery, St. Vincents Hospital, Melbourne, VIC 3065, Australia;
| | - Jeanne Tie
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia; (A.A.); (B.L.); (Y.H.T.); (J.T.)
- Division of Personalised Oncology, Walter and Eliza Hall Research Institute, Melbourne, VIC 3052, Australia
- Department of Medical Oncology, Western Health, St. Albans, VIC 3021, Australia
| | - Sarah-Jane Dawson
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne Centre for Cancer Research, Parkville, VIC 3000, Australia; (K.D.); (F.H.); (R.W.T.); (S.-J.D.)
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia; (A.A.); (B.L.); (Y.H.T.); (J.T.)
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16
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Keppens C, Van Royen Y, Brysse A, Cotteret S, Høgdall E, Kuhlmann TP, O'Sullivan B, Pauwels P, Pauwels S, Rot M, Vanderheyden N, Van Hee I, Dequeker EM. Incidents in Molecular Pathology: Frequency and Causes During Routine Testing. Arch Pathol Lab Med 2021; 145:1270-1279. [PMID: 33406246 DOI: 10.5858/arpa.2020-0152-oa] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2020] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Errors in laboratory medicine could compromise patient safety. Good laboratory practice includes identifying and managing nonconformities in the total test process. Varying error percentages have been described in other fields but are lacking for molecular oncology. OBJECTIVES.— To gain insight into incident causes and frequency in the total test process from 8 European institutes routinely performing biomarker tests in non-small cell lung cancer and colorectal cancer. DESIGN.— All incidents documented in 2018 were collected from all hospital services for pre-preanalytical entries before the biomarker test, as well as specific incidents for biomarker tests. RESULTS.— There were 5185 incidents collected, of which 4363 (84.1%) occurred in the pre-preanalytical phase (all hospital services), 2796 of 4363 (64.1%) related to missing or incorrect request form information. From the other 822 specific incidents, 166 (20.2%) were recorded in the preanalytical phase, 275 (33.5%) in the analytical phase, and 194 (23.6%) in the postanalytical phase, mainly due to incorrect report content. Only 47 of 822 (5.7%) incidents were recorded in the post-postanalytical phase, and 123 (15.0%) in the complete total test process. For 17 of 822 (2.1%) incidents the time point was unknown. Pre-preanalytical incidents were resolved sooner than incidents on the complete process (mean 6 versus 60 days). For 1215 of 5168 (23.5%) incidents with known causes a specific action was undertaken besides documenting them, not limited to accredited institutes. CONCLUSIONS.— There was a large variety in the number and extent of documented incidents. Correct and complete information on the request forms and final reports are highly error prone and require additional focus.
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Affiliation(s)
- Cleo Keppens
- From the Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, University of Leuven, Leuven, Belgium (Keppens, Van Royen, Dequeker)
| | - Yann Van Royen
- From the Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, University of Leuven, Leuven, Belgium (Keppens, Van Royen, Dequeker)
| | - Anne Brysse
- Unilab, Service de Génétique Humaine, CHU de Liège, Liège, Belgium (Brysse)
| | - Sophie Cotteret
- Pathologie Moléculaire, Laboratoire de Cytogénétique, Institut Gustave Roussy, Villejuif Cedex, France (Cotteret)
| | - Estrid Høgdall
- Department of Pathology, Herlev Hospital, Herlev, Denmark (Høgdall, Kuhlmann)
| | - Tine Plato Kuhlmann
- Department of Pathology, Herlev Hospital, Herlev, Denmark (Høgdall, Kuhlmann)
| | - Brendan O'Sullivan
- Histopathology, Cellular Pathology, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom (O'Sullivan)
| | - Patrick Pauwels
- Centre for Oncological Research (CORE), University of Antwerp, Edegem, Belgium (P. Pauwels).,Pathologische Anatomie, University Hospital Antwerp, Edegem, Belgium (P. Pauwels, S. Pauwels)
| | - Siegrid Pauwels
- Pathologische Anatomie, University Hospital Antwerp, Edegem, Belgium (P. Pauwels, S. Pauwels)
| | - Mitja Rot
- Laboratory for Cytology and Pathology, University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia (Rot)
| | - Nancy Vanderheyden
- Pathologische Ontleedkunde, University Hospital Leuven, Leuven, Belgium (Vanderheyden)
| | - Ilse Van Hee
- Anatomo Pathologie, Imelda Ziekenhuis, Bonheiden, Belgium (Van Hee)
| | - Elisabeth Mc Dequeker
- From the Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, University of Leuven, Leuven, Belgium (Keppens, Van Royen, Dequeker)
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17
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Geerlings MJ, Hofste LSM, Kamping EJ, Abdi Z, Tolmeijer SH, Garms LM, Klarenbeek BR, Ligtenberg MJL. Effect of Pneumatic Tube System Transport on Cell-Free DNA. Clin Chem 2020; 67:434-435. [PMID: 33280007 DOI: 10.1093/clinchem/hvaa285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Maartje J Geerlings
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lisa S M Hofste
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Zumaya Abdi
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sofie H Tolmeijer
- Department of Medical Oncology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Linda M Garms
- Department of Surgery, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
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18
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Lamy PJ, van der Leest P, Lozano N, Becht C, Duboeuf F, Groen HJM, Hilgers W, Pourel N, Rifaela N, Schuuring E, Alix-Panabières C. Mass Spectrometry as a Highly Sensitive Method for Specific Circulating Tumor DNA Analysis in NSCLC: A Comparison Study. Cancers (Basel) 2020; 12:cancers12103002. [PMID: 33081150 PMCID: PMC7602843 DOI: 10.3390/cancers12103002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary We compared the UltraSEEK™ Lung Panel on the MassARRAY® System (Agena Bioscience) with the FDA-approved Cobas® EGFR Mutation Test v2 for the detection of EGFR mutations in liquid biopsies of NSCLC patients, accompanied with preanalytical sample assessment using the novel Liquid IQ® Panel. For the detection of relevant predictive mutations using the UltraSEEK™ Lung Panel, an input of over 10 ng showed 100% concordance with Cobas® EGFR Mutation Test v2 and detection of all tissue confirmed mutations. In case of lower ccfDNA input, the risk of missing clinically relevant mutations should be considered. The use of a preanalytical ccfDNA quality control assay such as the Liquid IQ® Panel is recommended to confidently interpret results, avoiding bias induced by non-specific genomic DNA and low input of specific tumoral ccfDNA fragments. Abstract Plasma-based tumor mutational profiling is arising as a reliable approach to detect primary and therapy-induced resistance mutations required for accurate treatment decision making. Here, we compared the FDA-approved Cobas® EGFR Mutation Test v2 with the UltraSEEK™ Lung Panel on the MassARRAY® System on detection of EGFR mutations, accompanied with preanalytical sample assessment using the novel Liquid IQ® Panel. 137 cancer patient-derived cell-free plasma samples were analyzed with the Cobas® and UltraSEEK™ tests. Liquid IQ® analysis was initially validated (n = 84) and used to determine ccfDNA input for all samples. Subsequently, Liquid IQ® results were applied to harmonize ccfDNA input for the Cobas® and UltraSEEK™ tests for 63 NSCLC patients. The overall concordance between the Cobas® and UltraSEEK™ tests was 86%. The Cobas® test detected more EGFR exon19 deletions and L858R mutations, while the UltraSEEK™ test detected more T790M mutations. A 100% concordance in both the clinical (n = 137) and harmonized (n = 63) cohorts was observed when >10 ng of ccfDNA was used as determined by the Liquid IQ® Panel. The Cobas® and UltraSEEK™ tests showed similar sensitivity in EGFR mutation detection, particularly when ccfDNA input was sufficient. It is recommended to preanalytically determine the ccfDNA concentration accurately to ensure sufficient input for reliable interpretation and treatment decision making.
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Affiliation(s)
- Pierre-Jean Lamy
- Biopathologie et Génétique des Cancers, Institute d’Analyse Médicale Imagenome, Inovie, 6 Rue Fontenille, 34000 Montpellier, France;
- Correspondence: ; Tel.: +33-430-053-100
| | - Paul van der Leest
- Department of Pathology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (N.R.); (E.S.)
| | - Nicolas Lozano
- Biopathologie et Génétique des Cancers, Institute d’Analyse Médicale Imagenome, Inovie, 6 Rue Fontenille, 34000 Montpellier, France;
| | - Catherine Becht
- Oncologie Médicale, Clinique Clémenville, 25 rue Clémenville, 34000 Montpellier, France; (C.B.); (F.D.)
| | - Frédérique Duboeuf
- Oncologie Médicale, Clinique Clémenville, 25 rue Clémenville, 34000 Montpellier, France; (C.B.); (F.D.)
| | - Harry J. M. Groen
- Department of Pulmonary Medicine, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands;
| | - Werner Hilgers
- Oncologie Médicale, Institute Sainte Catherine, 250 Chemin de Baigne Pieds, 84918 Avignon, France; (W.H.); (N.P.)
| | - Nicolas Pourel
- Oncologie Médicale, Institute Sainte Catherine, 250 Chemin de Baigne Pieds, 84918 Avignon, France; (W.H.); (N.P.)
| | - Naomi Rifaela
- Department of Pathology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (N.R.); (E.S.)
| | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (N.R.); (E.S.)
| | - Catherine Alix-Panabières
- Laboratoire de Cellules Rares Circulantes, University Medical Center of Montpellier, 641, Avenue du Doyen Gaston GIRAUD, 34093 Montpellier, France;
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19
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Pessoa LS, Heringer M, Ferrer VP. ctDNA as a cancer biomarker: A broad overview. Crit Rev Oncol Hematol 2020; 155:103109. [PMID: 33049662 DOI: 10.1016/j.critrevonc.2020.103109] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/17/2020] [Accepted: 09/07/2020] [Indexed: 02/07/2023] Open
Abstract
Circulating tumor DNA (ctDNA) in fluids has gained attention because ctDNA seems to identify tumor-specific abnormalities, which could be used for diagnosis, follow-up of treatment, and prognosis: the so-called liquid biopsy. Liquid biopsy is a minimally invasive approach and presents the sum of ctDNA from primary and secondary tumor sites. It has been possible not only to quantify the amount of ctDNA but also to identify (epi)genetic changes. Specific mutations in genes have been identified in the plasma of patients with several types of cancer, which highlights ctDNA as a possible cancer biomarker. However, achieving detectable concentrations of ctDNA in body fluids is not an easy task. ctDNA fragments present a short half-life, and there are no cut-off values to discriminate high and low ctDNA concentrations. Here, we discuss the use of ctDNA as a cancer biomarker, the main methodologies, the inherent difficulties, and the clinical predictive value of ctDNA.
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Affiliation(s)
- Luciana Santos Pessoa
- Brain's Biomedicine Laboratory, Paulo Niemeyer State Brain Institute, Rio de Janeiro, Rio de Janeiro, Brazil; Center for Experimental Surgery, Graduate Program in Surgical Sciences, Department of Surgery, Faculty of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Manoela Heringer
- Brain's Biomedicine Laboratory, Paulo Niemeyer State Brain Institute, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Valéria Pereira Ferrer
- Department of Cellular and Molecular Biology, Institute of Biology, Fluminense Federal University, Niteroi, Rio de Janeiro, Brazil.
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20
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Lopez EM, Tanner AM, Du E, Patel SN, Weiss J, Weissler MC, Hackman T, Gupta GP, Zevallos J, Elmore S, Betancourt R, Thorne L, Sheth S, Gulley ML. Decline in circulating viral and human tumor markers after resection of head and neck carcinoma. Head Neck 2020; 43:27-34. [PMID: 32860343 DOI: 10.1002/hed.26444] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/12/2020] [Accepted: 08/14/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND DNA sequencing panels can simultaneously quantify human and viral tumor markers in blood. We explored changes in levels of plasma tumor markers following surgical resection of head and neck carcinoma. METHODS In preresection and postresection plasmas, targeted DNA sequencing quantified variants in 28 human cancer genes and levels of oncogenic pathogens (human papillomavirus [HPV], Epstein-Barr virus [EBV], Helicobacter pylori) from 21 patients with head and neck squamous cell carcinoma. RESULTS Preresection, 11 of 21 patients (52%) had detectable tumor markers in plasma, most commonly TP53 mutation or HPV genome. Several days postresection, levels fell to undetectable in 8 of 10 evaluable patients, while two high-stage patients retained circulating tumor markers. CONCLUSIONS Modern sequencing technology can simultaneously quantify human gene variants and oncogenic viral genomes in plasma. Falling levels of cancer-specific markers upon resection can help identify viral and human markers to track at subsequent timepoints as a means to evaluate efficacy of interventions.
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Affiliation(s)
- Erin M Lopez
- Department of Otolaryngology-Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - April Michelle Tanner
- Department of Otolaryngology-Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Eugenie Du
- Department of Otolaryngology-Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Samip N Patel
- Department of Otolaryngology-Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jared Weiss
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Medicine, Oncology Division, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark C Weissler
- Department of Otolaryngology-Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Trevor Hackman
- Department of Otolaryngology-Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jose Zevallos
- Department of Otolaryngology-Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sandra Elmore
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Renee Betancourt
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Leigh Thorne
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Siddharth Sheth
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Medicine, Oncology Division, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Margaret L Gulley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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21
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Weber S, Spiegl B, Perakis SO, Ulz CM, Abuja PM, Kashofer K, van der Leest P, Azpurua MA, Tamminga M, Brudzewsky D, Rothwell DG, Mohan S, Sartori A, Lampignano R, Konigshofer Y, Sprenger-Haussels M, Wikman H, Bergheim IR, Kloten V, Schuuring E, Speicher MR, Heitzer E. Technical Evaluation of Commercial Mutation Analysis Platforms and Reference Materials for Liquid Biopsy Profiling. Cancers (Basel) 2020; 12:E1588. [PMID: 32560092 PMCID: PMC7352370 DOI: 10.3390/cancers12061588] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/15/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023] Open
Abstract
Molecular profiling from liquid biopsy, in particular cell-free DNA (cfDNA), represents an attractive alternative to tissue biopsies for the detection of actionable targets and tumor monitoring. In addition to PCR-based assays, Next Generation Sequencing (NGS)-based cfDNA assays are now commercially available and are being increasingly adopted in clinical practice. However, the validity of these products as well as the clinical utility of cfDNA in the management of patients with cancer has yet to be proven. Within framework of the Innovative Medicines Initiative (IMI) program CANCER-ID we evaluated the use of commercially available reference materials designed for ctDNA testing and cfDNA derived from Diagnostic Leukaphereses (DLA) for inter- and intra-assay as well as intra- and inter-laboratory comparisons. In three experimental setups, a broad range of assays including ddPCR, MassARRAY and various NGS-based assays were tested. We demonstrate that both reference materials with predetermined VAFs and DLA samples are extremely useful for the performance assessment of mutation analysis platforms. Moreover, our data indicate a substantial variability of NGS assays with respect to sensitivity and specificity highlighting the importance of extensive validation of the test performance before offering these tests in clinical routine practice.
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Affiliation(s)
- Sabrina Weber
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (S.W.); (B.S.); (S.O.P.); (M.R.S.)
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, 8010 Graz, Austria;
| | - Benjamin Spiegl
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (S.W.); (B.S.); (S.O.P.); (M.R.S.)
| | - Samantha O. Perakis
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (S.W.); (B.S.); (S.O.P.); (M.R.S.)
| | - Christine M. Ulz
- Institute of Pathology, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (C.M.U.); (K.K.); (P.v.d.L.)
| | - Peter M. Abuja
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, 8010 Graz, Austria;
- Institute of Pathology, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (C.M.U.); (K.K.); (P.v.d.L.)
| | - Karl Kashofer
- Institute of Pathology, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (C.M.U.); (K.K.); (P.v.d.L.)
| | - Paul van der Leest
- Institute of Pathology, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (C.M.U.); (K.K.); (P.v.d.L.)
| | - Maria Aguirre Azpurua
- University of Groningen, University Medical Center of Groningen, 9713 GZ Groningen, The Netherlands; (M.A.A.); (M.T.); (E.S.)
| | - Menno Tamminga
- University of Groningen, University Medical Center of Groningen, 9713 GZ Groningen, The Netherlands; (M.A.A.); (M.T.); (E.S.)
| | - Dan Brudzewsky
- LGC SeraCare Life Sciences, Milford, MA 01757, USA; (D.B.); (Y.K.)
| | - Dominic G. Rothwell
- Cancer Research UK MI, University of Manchester, Manchester SK10 4TG, UK; (D.G.R.); (S.M.)
| | - Sumitra Mohan
- Cancer Research UK MI, University of Manchester, Manchester SK10 4TG, UK; (D.G.R.); (S.M.)
| | | | - Rita Lampignano
- Bayer AG, Biomarker Research, 42113 Wuppertal, Germany; (R.L.); (V.K.)
| | - Yves Konigshofer
- LGC SeraCare Life Sciences, Milford, MA 01757, USA; (D.B.); (Y.K.)
| | | | - Harriet Wikman
- University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany;
| | - Inger R. Bergheim
- Department of Cancer Genetics, Institute of Cancer Research, Oslo University Hospital, N-0310 Oslo, Norway;
| | - Vera Kloten
- Bayer AG, Biomarker Research, 42113 Wuppertal, Germany; (R.L.); (V.K.)
| | - Ed Schuuring
- University of Groningen, University Medical Center of Groningen, 9713 GZ Groningen, The Netherlands; (M.A.A.); (M.T.); (E.S.)
| | - Michael R. Speicher
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (S.W.); (B.S.); (S.O.P.); (M.R.S.)
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (S.W.); (B.S.); (S.O.P.); (M.R.S.)
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, 8010 Graz, Austria;
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22
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van der Leest P, Boonstra PA, ter Elst A, van Kempen LC, Tibbesma M, Koopmans J, Miedema A, Tamminga M, Groen HJM, Reyners AKL, Schuuring E. Comparison of Circulating Cell-Free DNA Extraction Methods for Downstream Analysis in Cancer Patients. Cancers (Basel) 2020; 12:E1222. [PMID: 32414097 PMCID: PMC7281769 DOI: 10.3390/cancers12051222] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/05/2020] [Accepted: 05/08/2020] [Indexed: 12/28/2022] Open
Abstract
Circulating cell-free DNA (ccfDNA) may contain DNA originating from the tumor in plasma of cancer patients (ctDNA) and enables noninvasive cancer diagnosis, treatment predictive testing, and response monitoring. A recent multicenter evaluation of workflows by the CANCER-ID consortium using artificial spiked-in plasma showed significant differences and consequently the importance of carefully selecting ccfDNA extraction methods. Here, the quantity and integrity of extracted ccfDNA from the plasma of cancer patients were assessed. Twenty-one cancer patient-derived cell-free plasma samples were selected to compare the Qiagen CNA, Maxwell RSC ccfDNA plasma, and Zymo manual quick ccfDNA kit. High-volume citrate plasma samples collected by diagnostic leukapheresis from six cancer patients were used to compare the Qiagen CNA (2 mL) and QIAamp MinElute ccfDNA kit (8 mL). This study revealed similar integrity and similar levels of amplified short-sized fragments and tumor-specific mutants comparing the CNA and RSC kits. However, the CNA kit consistently showed the highest yield of ccfDNA and short-sized fragments, while the RSC and ME kits showed higher variant allelic frequencies (VAFs). Our study pinpoints the importance of standardizing preanalytical conditions as well as consensus on defining the input of ccfDNA to accurately detect ctDNA and be able to compare results in a clinical routine practice, within and between clinical studies.
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Affiliation(s)
- Paul van der Leest
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Pieter A. Boonstra
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.A.B.); (A.K.L.R.)
| | - Arja ter Elst
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Léon C. van Kempen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Marco Tibbesma
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Jill Koopmans
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Anneke Miedema
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Menno Tamminga
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (M.T.); (H.J.M.G.)
| | - Harry J. M. Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (M.T.); (H.J.M.G.)
| | - Anna K. L. Reyners
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.A.B.); (A.K.L.R.)
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
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23
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Rolfo C, Cardona AF, Cristofanilli M, Paz-Ares L, Diaz Mochon JJ, Duran I, Raez LE, Russo A, Lorente JA, Malapelle U, Gil-Bazo I, Jantus-Lewintre E, Pauwels P, Mok T, Serrano MJ. Challenges and opportunities of cfDNA analysis implementation in clinical practice: Perspective of the International Society of Liquid Biopsy (ISLB). Crit Rev Oncol Hematol 2020; 151:102978. [PMID: 32428812 DOI: 10.1016/j.critrevonc.2020.102978] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 04/29/2020] [Indexed: 02/07/2023] Open
Abstract
Precision medicine was born with the development of new diagnostic techniques and targeted drugs, yielding better outcomes in cancer care. With the evolution and increasing sensitivity for detecting oncogenic drivers, liquid biopsies (LBs), specifically cell-free DNA (cfDNA) analysis, have been proposed as a minimally-invasive technique for genomic profiling. Ranging from sequencing techniques to PCR-based methods and other more complex strategies, this approach, currently applicable in some solid tumors with robust evidence, is showing promising opportunities in other cancers. However, difficulties in validating their clinical utility exist within limitation at different levels among several techniques, reporting of the results, lack of appropriate clinical trial designs, and unknown economic impact. One of the aims of the ISLB is to create recommendations to develop reliable and sustainable diagnostic, prognostic and predictive tools using LBs. This paper is addressing these objectives, helping the healthcare providers and scientific community to understand the potential of LB.
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Affiliation(s)
- Christian Rolfo
- Thoracic Oncology Department and Early Phase Clinical Trials Section, School of Medicine, Maryland University, Maryland, USA.
| | - Andrés F Cardona
- Clinical and Translational Oncology Group, Clínica del Country, Bogotá, Colombia; Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia; Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad El Bosque, Bogotá, Colombia
| | - Massimo Cristofanilli
- Department of Medicine, Division of Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, 710 N Fairbanks Court, Suite 8-250A, Chicago, IL, 60611, USA
| | - Luis Paz-Ares
- Hospital Universitario 12 de Octubre, CNIO-H12o Lung Cancer Unit, Universidad Complutense and CIBERONC, Madrid, Spain
| | - Juan Jose Diaz Mochon
- DestiNA Genomica S.L. Parque Tecnológico Ciencias de la Salud (PTS), Avenida de la Innovación 1, Edificio BIC, 18016, Armilla, Granada, Spain; GENYO Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government. PTS Granada - Avenida de la Ilustración, 114- 18016, Granada, Spain; Department Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain
| | - Ignacio Duran
- Servicio de Oncologia Medica, Medical Oncology Department, Hospital Universitario Marques de Valdecilla, Edificio Sur, 2 Planta, Despacho 277, 39008, Santander, Spain
| | - Luis E Raez
- Memorial Cancer Institute, Memorial Health Care System, Florida International University, Florida, USA
| | - Alessandro Russo
- Thoracic Oncology Department and Early Phase Clinical Trials Section, School of Medicine, Maryland University, Maryland, USA; Medical Oncology Unit A.O. Papardo & Department of Human Pathology, University of Messina, Italy
| | - Jose A Lorente
- Laboratory of Genetic Identification, Department of Legal Medicine, University of Granada, Av. de la Investigación, 11, 18071, Granada, Spain; Centre for Genomics and Oncological Research - GENYO, Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Umberto Malapelle
- Department of Public Health, University Federico II of Naples, Naples, Italy
| | - Ignacio Gil-Bazo
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Navarra, Spain; University of Navarra, Center for Applied Medical Research, Program of Solid Tumors, Pamplona, Navarra, Spain; Idisna, Navarra Institute for Health Research, Pamplona, Navarra, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Eloisa Jantus-Lewintre
- Molecular Oncology Laboratory, Fundación Investigación, Valencia General University Hospital, Valencia, Spain
| | - Patrick Pauwels
- Center for Oncological Research (CORE), University of Antwerp, & Department of Pathology, Antwerp University Hospital, Edegem, Belgium
| | - Tony Mok
- State Key Laboratory in Oncology in South China, Hong Kong, China
| | - María José Serrano
- Centre for Genomics and Oncological Research - GENYO, Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain; Bio-Health Research Institute (Instituto de Investigación Biosanitaria ibs. GRANADA), Spain; Complejo Hospitalario Universitario Granada (CHUG), Department of Medical Oncology, University of Granada, Granada, Spain.
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24
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External Quality Assessment Schemes for Biomarker Testing in Oncology: Comparison of Performance between Formalin-Fixed, Paraffin-Embedded-Tissue and Cell-Free Tumor DNA in Plasma. J Mol Diagn 2020; 22:736-747. [PMID: 32205291 DOI: 10.1016/j.jmoldx.2020.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 02/08/2020] [Accepted: 02/20/2020] [Indexed: 01/06/2023] Open
Abstract
Liquid biopsies have emerged as a useful addition to tissue biopsies in molecular pathology. Literature has shown lower laboratory performances when a new method of variant analysis is introduced. This study evaluated the differences in variant analysis between tissue and plasma samples after the introduction of liquid biopsy in molecular analysis. Data from a pilot external quality assessment scheme for the detection of molecular variants in plasma samples and from external quality assessment schemes for the detection of molecular variants in tissue samples were collected. Laboratory performance and error rates by sample were compared between matrices for variants present in both scheme types. Results showed lower overall performance [65.6% (n = 276) versus 89.2% (n = 1607)] and higher error rates [21.0% to 43.5% (n = 138) versus 8.7% to 16.7% (n = 234 to 689)] for the detection of variants in plasma compared to tissue, respectively. In the plasma samples, performance was decreased for variants with an allele frequency of 1% compared to 5% [56.5% (n = 138) versus 74.6% (n = 138)]. The implementation of liquid biopsy in the detection of circulating tumor DNA in plasma was associated with poor laboratory performance. It is important both to apply optimal detection methods and to extensively validate new methods for testing circulating tumor DNA before treatment decisions are made.
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25
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Koo KM, Mainwaring PN. The role of circulating tumor DNA testing in breast cancer liquid biopsies: getting ready for prime time. BREAST CANCER MANAGEMENT 2020. [DOI: 10.2217/bmt-2020-0003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Kevin M Koo
- XING Technologies Pty Ltd, 4073, Brisbane, QLD, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), 4072, Brisbane, QLD, Australia
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26
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van den Broek D, Hiltermann TJN, Biesma B, Dinjens WNM, 't Hart NA, Hinrichs JWJ, Leers MPG, Monkhorst K, van Oosterhout M, Scharnhorst V, Schuuring E, Speel EJM, van den Heuvel MM, van Schaik RHN, von der Thüsen J, Willems SM, de Visser L, Ligtenberg MJL. Implementation of Novel Molecular Biomarkers for Non-small Cell Lung Cancer in the Netherlands: How to Deal With Increasing Complexity. Front Oncol 2020; 9:1521. [PMID: 32039011 PMCID: PMC6987414 DOI: 10.3389/fonc.2019.01521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/17/2019] [Indexed: 12/30/2022] Open
Abstract
The diagnostic landscape of non-small cell lung cancer (NSCLC) is changing rapidly with the availability of novel treatments. Despite high-level healthcare in the Netherlands, not all patients with NSCLC are tested with the currently relevant predictive tumor markers that are necessary for optimal decision-making for today's available targeted or immunotherapy. An expert workshop on the molecular diagnosis of NSCLC involving pulmonary oncologists, clinical chemists, pathologists, and clinical scientists in molecular pathology was held in the Netherlands on December 10, 2018. The aims of the workshop were to facilitate cross-disciplinary discussions regarding standards of practice, and address recent developments and associated challenges that impact future practice. This paper presents a summary of the discussions and consensus opinions of the workshop participants on the initial challenges of harmonization of the detection and clinical use of predictive markers of NSCLC. A key theme identified was the need for broader and active participation of all stakeholders involved in molecular diagnostic services for NSCLC, including healthcare professionals across all disciplines, the hospitals and clinics involved in service delivery, healthcare insurers, and industry groups involved in diagnostic and treatment innovations. Such collaboration is essential to integrate different technologies into molecular diagnostics practice, to increase nationwide patient access to novel technologies, and to ensure consensus-preferred biomarkers are tested.
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Affiliation(s)
- Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - T. Jeroen N. Hiltermann
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Bonne Biesma
- Department of Pulmonary Diseases, Jeroen Bosch Hospital, 's-Hertogenbosch, Netherlands
| | - Winand N. M. Dinjens
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Nils A. 't Hart
- Department of Pathology, Isala Klinieken, Zwolle, Netherlands
| | - John W. J. Hinrichs
- Symbiant Pathology Expert Centre, Alkmaar, Netherlands
- Department of Pathology, University Medical Center, Utrecht, Netherlands
| | - Mathie P. G. Leers
- Department of Clinical Chemistry, Zuyderland Medical Center, Sittard-Geleen, Netherlands
| | - Kim Monkhorst
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Ernst-Jan M. Speel
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | | | - Ron H. N. van Schaik
- Department of Clinical Chemistry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jan von der Thüsen
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Stefan M. Willems
- Department of Pathology, University Medical Center, Utrecht, Netherlands
| | | | - Marjolijn J. L. Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands
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27
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Andrikovics H, Őrfi Z, Meggyesi N, Bors A, Varga L, Kövy P, Vilimszky Z, Kolics F, Gopcsa L, Reményi P, Tordai A. Current Trends in Applications of Circulatory Microchimerism Detection in Transplantation. Int J Mol Sci 2019; 20:E4450. [PMID: 31509957 PMCID: PMC6769866 DOI: 10.3390/ijms20184450] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/05/2019] [Accepted: 09/05/2019] [Indexed: 02/07/2023] Open
Abstract
Primarily due to recent advances of detection techniques, microchimerism (the proportion of minor variant population is below 1%) has recently gained increasing attention in the field of transplantation. Availability of polymorphic markers, such as deletion insertion or single nucleotide polymorphisms along with a vast array of high sensitivity detection techniques, allow the accurate detection of small quantities of donor- or recipient-related materials. This diagnostic information can improve monitoring of allograft injuries in solid organ transplantations (SOT) as well as facilitate early detection of relapse in allogeneic hematopoietic stem cell transplantation (allo-HSCT). In the present review, genetic marker and detection platform options applicable for microchimerism detection are discussed. Furthermore, current results of relevant clinical studies in the context of microchimerism and SOT or allo-HSCT respectively are also summarized.
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Affiliation(s)
- Hajnalka Andrikovics
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
- Department of Pathophysiology, Semmelweis University, 1089 Budapest, Hungary
| | - Zoltán Őrfi
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - Nóra Meggyesi
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - András Bors
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - Lívia Varga
- School of PhD Studies, Semmelweis University, 1085 Budapest, Hungary
- Hungarian National Blood Transfusion Service, 1113 Budapest, Hungary
| | - Petra Kövy
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
- School of PhD Studies, Semmelweis University, 1085 Budapest, Hungary
| | - Zsófia Vilimszky
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - Fanni Kolics
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - László Gopcsa
- Department of Hematology and Stem Cell Transplantation, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - Péter Reményi
- Department of Hematology and Stem Cell Transplantation, Central Hospital of Southern Pest National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary
| | - Attila Tordai
- Department of Pathophysiology, Semmelweis University, 1089 Budapest, Hungary.
- Department of Transfusion Medicine, Semmelweis University, 1089 Budapest, Hungary.
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28
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Chai SY, Peng R, Zhang R, Zhou L, Pillay N, Tay KH, Badrick T, Li J, Horan MP. External Quality Assurance of Current Technology for the Testing of Cancer-Associated Circulating Free DNA Variants. Pathol Oncol Res 2019; 26:1595-1603. [PMID: 31487000 DOI: 10.1007/s12253-019-00744-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023]
Abstract
Liquid biopsy testing is rapidly emerging as a diagnostic means of identifying circulating free DNA (cfDNA) disease-associated variants. However, the reporting of cfDNA variants remains inconsistent due in part to the application of multiple testing pipelines which raise uncertainty about current cfDNA detection efficiency. External quality assurance (EQA) programs are required to monitor, evaluate and help improve laboratory performance for cfDNA variant detection and in clinical interpretation. This study therefore evaluated the performance of diagnostic laboratories currently performing cfDNA testing in China, Australia and New Zealand. A total of 89 laboratories participated in this EQA program. Reference testing material comprised of cfDNA manufactured to contain six different genotypes in four different genes (EGFR, KRAS, BRAF, NRAS). The predicted genotypic variant allelic frequencies ranged between 0.5% - 2.5%. Proficiency testing used a z-score on the laboratory consensus allelic frequency data to compare laboratory performance for the detection of the different genotypes. Allelic frequency genotyping data were received from 88 of the 89 laboratories. Next generation sequencing and digital PCR testing platforms were primarily used by participants in this pilot EQA. The average consensus data for each cfDNA genotype identified allelic frequencies ranging between 0.39% - 4.4%. Z-score proficiency testing found that >92% of clinical laboratories were concordant for detecting the cfDNA variants. The data from this pilot study suggest that current cfDNA testing platforms can detect cfDNA allelic frequency variants from 0.39% and above with high levels of confidence. In addition, these data highlight the importance of laboratories enrolling on EQA programs so that proficiency in cfDNA diagnostic testing can be determined and potential sources of error identified and addressed.
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Affiliation(s)
- Sze Yee Chai
- RCPAQAP Molecular Genetics, St Leonard's, Sydney, Australia
| | - Rongxue Peng
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, P R China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P R China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, P R China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P R China
| | - Li Zhou
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, P R China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P R China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P R China
| | | | - Kwang Hong Tay
- RCPAQAP Molecular Genetics, St Leonard's, Sydney, Australia
| | - Tony Badrick
- RCPAQAP Molecular Genetics, St Leonard's, Sydney, Australia
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, P R China. .,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P R China. .,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P R China.
| | - Martin P Horan
- RCPAQAP Molecular Genetics, St Leonard's, Sydney, Australia.
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O’Connor DJ, Buckland J, Almond N, Boyle J, Coxon C, Gaki E, Martin J, Mattiuzzo G, Metcalfe C, Page M, Rose N, Valdazo-Gonzalez B, Zhao Y, Schneider CK. Commonly setting biological standards in rare diseases. Expert Opin Orphan Drugs 2019. [DOI: 10.1080/21678707.2019.1652598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - Jenny Buckland
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Neil Almond
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Jennifer Boyle
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Carmen Coxon
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Eleni Gaki
- Medicines & Healthcare products Regulatory Agency (MHRA), London, UK
| | - Javier Martin
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Giada Mattiuzzo
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Clive Metcalfe
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Mark Page
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Nicola Rose
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Begona Valdazo-Gonzalez
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Yuan Zhao
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
| | - Christian K. Schneider
- National Institute for Biological Standards and Control (NIBSC), Blanche Ln, South Mimms, Potters Bar, UK
- Twincore Centre for Experimental and Clinical Infection Research GmbH, Hannover, Germany
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