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Edsjö A, Russnes HG, Lehtiö J, Tamborero D, Hovig E, Stenzinger A, Rosenquist R. High-throughput molecular assays for inclusion in personalised oncology trials - State-of-the-art and beyond. J Intern Med 2024; 295:785-803. [PMID: 38698538 DOI: 10.1111/joim.13785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
In the last decades, the development of high-throughput molecular assays has revolutionised cancer diagnostics, paving the way for the concept of personalised cancer medicine. This progress has been driven by the introduction of such technologies through biomarker-driven oncology trials. In this review, strengths and limitations of various state-of-the-art sequencing technologies, including gene panel sequencing (DNA and RNA), whole-exome/whole-genome sequencing and whole-transcriptome sequencing, are explored, focusing on their ability to identify clinically relevant biomarkers with diagnostic, prognostic and/or predictive impact. This includes the need to assess complex biomarkers, for example microsatellite instability, tumour mutation burden and homologous recombination deficiency, to identify patients suitable for specific therapies, including immunotherapy. Furthermore, the crucial role of biomarker analysis and multidisciplinary molecular tumour boards in selecting patients for trial inclusion is discussed in relation to various trial concepts, including drug repurposing. Recognising that today's exploratory techniques will evolve into tomorrow's routine diagnostics and clinical study inclusion assays, the importance of emerging technologies for multimodal diagnostics, such as proteomics and in vivo drug sensitivity testing, is also discussed. In addition, key regulatory aspects and the importance of patient engagement in all phases of a clinical trial are described. Finally, we propose a set of recommendations for consideration when planning a new precision cancer medicine trial.
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Affiliation(s)
- Anders Edsjö
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Hege G Russnes
- Department of Pathology, Oslo University Hospital, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Janne Lehtiö
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Stockholm, Sweden
- Cancer genomics and proteomics, Karolinska University Hospital, Solna, Sweden
| | - David Tamborero
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Stockholm, Sweden
| | - Eivind Hovig
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Albrecht Stenzinger
- Institute of Pathology, Division of Molecular Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
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2
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van der Leest P, Rozendal P, Hinrichs J, van Noesel CJM, Zwaenepoel K, Deiman B, Huijsmans CJJ, van Eijk R, Speel EJM, van Haastert RJ, Ligtenberg MJL, van Schaik RHN, Jansen MPHM, Dubbink HJ, de Leng WW, Leers MPG, Tamminga M, van den Broek D, van Kempen LC, Schuuring E. External Quality Assessment on Molecular Tumor Profiling with Circulating Tumor DNA-Based Methodologies Routinely Used in Clinical Pathology within the COIN Consortium. Clin Chem 2024; 70:759-767. [PMID: 38484302 DOI: 10.1093/clinchem/hvae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/21/2023] [Indexed: 05/03/2024]
Abstract
BACKGROUND Identification of tumor-derived variants in circulating tumor DNA (ctDNA) has potential as a sensitive and reliable surrogate for tumor tissue-based routine diagnostic testing. However, variations in pre(analytical) procedures affect the efficiency of ctDNA recovery. Here, an external quality assessment (EQA) was performed to determine the performance of ctDNA mutation detection work flows that are used in current diagnostic settings across laboratories within the Dutch COIN consortium (ctDNA on the road to implementation in The Netherlands). METHODS Aliquots of 3 high-volume diagnostic leukapheresis (DLA) plasma samples and 3 artificial reference plasma samples with predetermined mutations were distributed among 16 Dutch laboratories. Participating laboratories were requested to perform ctDNA analysis for BRAF exon 15, EGFR exon 18-21, and KRAS exon 2-3 using their regular circulating cell-free DNA (ccfDNA) analysis work flow. Laboratories were assessed based on adherence to the study protocol, overall detection rate, and overall genotyping performance. RESULTS A broad range of preanalytical conditions (e.g., plasma volume, elution volume, and extraction methods) and analytical methodologies (e.g., droplet digital PCR [ddPCR], small-panel PCR assays, and next-generation sequencing [NGS]) were used. Six laboratories (38%) had a performance score of >0.90; all other laboratories scored between 0.26 and 0.80. Although 13 laboratories (81%) reached a 100% overall detection rate, the therapeutically relevant EGFR p.(S752_I759del) (69%), EGFR p.(N771_H773dup) (50%), and KRAS p.(G12C) (48%) mutations were frequently not genotyped accurately. CONCLUSIONS Divergent (pre)analytical protocols could lead to discrepant clinical outcomes when using the same plasma samples. Standardization of (pre)analytical work flows can facilitate the implementation of reproducible liquid biopsy testing in the clinical routine.
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Affiliation(s)
- Paul van der Leest
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Pim Rozendal
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - John Hinrichs
- Department of Pathology, Symbiant B.V., Alkmaar, the Netherlands
| | - Carel J M van Noesel
- Department of Pathology, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Karen Zwaenepoel
- Department of Pathology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Birgit Deiman
- Clinical Laboratory, Catharina Hospital Eindhoven, Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Eindhoven University of Technology, Eindhoven, the Netherlands
- Department of Biomedical Engineering, Laboratory of Chemical Biology, Eindhoven University of Technology, Eindhoven, the Netherlands
- Expert Center Clinical Chemistry Eindhoven, Eindhoven, the Netherlands
| | - Cornelis J J Huijsmans
- Pathologie-DNA, Laboratory for Molecular Diagnostics, Location Jeroen Bosch Hospital, 's-Hertogenbosch, the Netherlands
| | - Ronald van Eijk
- Department of Pathology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Ernst Jan M Speel
- Department of Pathology, GROW-School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Rick J van Haastert
- Department of Clinical Chemistry, St. Antonius Hospital, Nieuwegein, the Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Pathology, Radboud Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ron H N van Schaik
- Department of Clinical Chemistry, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Maurice P H M Jansen
- Department of Medical Oncology, Laboratory of Translational Genomics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Wendy W de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mathie P G Leers
- Department of Clinical Chemistry & Hematology, Zuyderland Medical Center, Heerlen, the Netherlands
| | - Menno Tamminga
- Department of Pulmonary Medicine, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Léon C van Kempen
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Cheng JC, Swarup N, Wong DTW, Chia D. A review on the impact of single-stranded library preparation on plasma cell-free diversity for cancer detection. Front Oncol 2024; 14:1332004. [PMID: 38511142 PMCID: PMC10951391 DOI: 10.3389/fonc.2024.1332004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/07/2024] [Indexed: 03/22/2024] Open
Abstract
In clinical oncology, cell-free DNA (cfDNA) has shown immense potential in its ability to noninvasively detect cancer at various stages and monitor the progression of therapy. Despite the rapid improvements in cfDNA liquid biopsy approaches, achieving the required sensitivity to detect rare tumor-derived cfDNA still remains a challenge. For next-generation sequencing, the perceived presentation of cfDNA is strongly linked to the extraction and library preparation protocols. Conventional double-stranded DNA library preparation (dsDNA-LP) focuses on assessing ~167bp double-stranded mononucleosomal (mncfDNA) and its other oligonucleosomal cell-free DNA counterparts in plasma. However, dsDNA-LP methods fail to include short, single-stranded, or nicked DNA in the final library preparation, biasing the representation of the actual cfDNA populations in plasma. The emergence of single-stranded library preparation (ssDNA-LP) strategies over the past decade has now allowed these other populations of cfDNA to be studied from plasma. With the use of ssDNA-LP, single-stranded, nicked, and ultrashort cfDNA can be comprehensively assessed for its molecular characteristics and clinical potential. In this review, we overview the current literature on applications of ssDNA-LP on plasma cfDNA from a potential cancer liquid biopsy perspective. To this end, we discuss the molecular principles of single-stranded DNA adapter ligation, how library preparation contributes to the understanding of native cfDNA characteristics, and the potential for ssDNA-LP to improve the sensitivity of circulating tumor DNA detection. Additionally, we review the current literature on the newly reported species of plasma ultrashort single-stranded cell-free DNA plasma, which appear biologically distinct from mncfDNA. We conclude with a discussion of future perspectives of ssDNA-LP for liquid biopsy endeavors.
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Affiliation(s)
- Jordan C. Cheng
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
- Stanford Cancer Institute, Stanford University, Stanford, CA, United States
| | - Neeti Swarup
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - David T. W. Wong
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - David Chia
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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Smit DJ, Schneegans S, Pantel K. Clinical applications of circulating tumor cells in patients with solid tumors. Clin Exp Metastasis 2024:10.1007/s10585-024-10267-5. [PMID: 38281256 DOI: 10.1007/s10585-024-10267-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
The concept of liquid biopsy analysis has been established more than a decade ago. Since the establishment of the term, tremendous advances have been achieved and plenty of methods as well as analytes have been investigated in basic research as well in clinical trials. Liquid biopsy refers to a body fluid-based biopsy that is minimal-invasive, and most importantly, allows dense monitoring of tumor responses by sequential blood sampling. Blood is the most important analyte for liquid biopsy analyses, providing an easily accessible source for a plethora of cells, cell-derived products, free nucleic acids, proteins as well as vesicles. More than 12,000 publications are listed in PubMed as of today including the term liquid biopsy. In this manuscript, we critically review the current implications of liquid biopsy, with special focus on circulating tumor cells, and describe the hurdles that need to be addressed before liquid biopsy can be implemented in clinical standard of care guidelines.
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Affiliation(s)
- Daniel J Smit
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Fleur Hiege Center for Skin Cancer Research, Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Svenja Schneegans
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Klaus Pantel
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
- Fleur Hiege Center for Skin Cancer Research, Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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6
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van der Leest P, Schuuring E. Critical Factors in the Analytical Work Flow of Circulating Tumor DNA-Based Molecular Profiling. Clin Chem 2024; 70:220-233. [PMID: 38175597 DOI: 10.1093/clinchem/hvad194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 10/30/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Liquid biopsy testing, especially molecular tumor profiling of circulating tumor DNA (ctDNA) in cell-free plasma, has received increasing interest in recent years as it serves as a reliable alternative for the detection of tumor-specific aberrations to guide treatment decision-making in oncology. Many (commercially available) applications have been developed, however, broad divergences in (pre)analytical work flows and lack of universally applied guidelines impede routine clinical implementation. In this review, critical factors in the blood-based ctDNA liquid biopsy work flow are evaluated. CONTENT In the preanalytical phase, several aspects (e.g., blood collection tubes [BCTs], plasma processing, and extraction method) affect the quantity and quality of the circulating cell-free DNA (ccfDNA) applicable for subsequent molecular analyses and should meet certain standards to be applied in diagnostic work flows. Analytical considerations, such as analytical input and choice of assay, might vary based on the clinical application (i.e., screening, primary diagnosis, minimal residual disease [MRD], response monitoring, and resistance identification). In addition to practical procedures, variant interpretation and reporting ctDNA results should be harmonized. Collaborative efforts in (inter)national consortia and societies are essential for the establishment of standard operating procedures (SOPs) in attempts to standardize the plasma-based ctDNA analysis work flow. SUMMARY Development of universally applicable guidelines regarding the critical factors in liquid biopsy testing are necessary to pave the way to clinical implementation for routine diagnostics.
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Affiliation(s)
- Paul van der Leest
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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7
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Bronkhorst AJ, Holdenrieder S. A pocket companion to cell-free DNA (cfDNA) preanalytics. Tumour Biol 2024; 46:S297-S308. [PMID: 37840517 DOI: 10.3233/tub-230011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023] Open
Abstract
The cumulative pool of cell-free DNA (cfDNA) molecules within bodily fluids represents a highly dense and multidimensional information repository. This "biological mirror" provides real-time insights into the composition, function, and dynamics of the diverse genomes within the body, enabling significant advancements in personalized molecular medicine. However, effective use of this information necessitates meticulous classification of distinct cfDNA subtypes with exceptional precision. While cfDNA molecules originating from different sources exhibit numerous genetic, epigenetic, and physico-chemical variations, they also share common features that complicate analyses. Considerable progress has been achieved in mapping the landscape of cfDNA features, their clinical correlations, and optimizing extraction procedures, analytical approaches, bioinformatics pipelines, and machine learning algorithms. Nevertheless, preanalytical workflows, despite their profound impact on cfDNA measurements, have not progressed at a corresponding pace. In this perspective article, we emphasize the pivotal role of robust preanalytical procedures in the development and clinical integration of cfDNA assays, highlighting persistent obstacles and emerging challenges.
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Affiliation(s)
- Abel J Bronkhorst
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center, Technical University Munich, Munich, Germany
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8
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Devonshire A, Jones G, Gonzalez AF, Kofanova O, Trouet J, Pinzani P, Gelmini S, Bonin S, Foy C. Interlaboratory evaluation of quality control methods for circulating cell-free DNA extraction. N Biotechnol 2023; 78:13-21. [PMID: 37730172 DOI: 10.1016/j.nbt.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/07/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023]
Abstract
Analysis of circulating cell-free DNA (ccfDNA) isolated from liquid biopsies is rapidly being implemented into clinical practice. However, diagnostic accuracy is significantly impacted by sample quality and standardised approaches for assessing the quality of ccfDNA are not yet established. In this study we evaluated the application of nucleic acid "spike-in" control materials to aid quality control (QC) and standardisation of cfDNA isolation for use in in vitro diagnostic assays. We describe an approach for the design and characterisation of in-process QC materials, illustrating it with a spike-in material containing an exogenous Arabidopsis sequence and DNA fragments approximating to ccfDNA and genomic DNA lengths. Protocols for inclusion of the spike-in material in plasma ccfDNA extraction and quantification of its recovery by digital PCR (dPCR) were assessed for their suitability for process QC in an inter-laboratory study between five expert laboratories, using a range of blood collection devices and ccfDNA extraction methods. The results successfully demonstrated that spiking plasmid-derived material into plasma did not deleteriously interfere with endogenous ccfDNA recovery. The approach performed consistently across a range of commonly-used extraction protocols and was able to highlight differences in efficiency and variability between the methods, with the dPCR quantification assay performing with good repeatability (generally CV <5%). We conclude that initial findings demonstrate that this approach appears "fit for purpose" and spike-in recovery can be combined with other extraction QC metrics for monitoring the performance of a process over time, or in the context of external quality assessment.
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Affiliation(s)
- Alison Devonshire
- Molecular and Cell Biology Team, National Measurement Laboratory (NML), LGC, Teddington, Middlesex, UK.
| | - Gerwyn Jones
- Molecular and Cell Biology Team, National Measurement Laboratory (NML), LGC, Teddington, Middlesex, UK
| | - Ana Fernandez Gonzalez
- Molecular and Cell Biology Team, National Measurement Laboratory (NML), LGC, Teddington, Middlesex, UK
| | - Olga Kofanova
- Integrated BioBank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), 1, rue Louis Rech, L-3555 Dudelange, Luxembourg
| | - Johanna Trouet
- Integrated BioBank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), 1, rue Louis Rech, L-3555 Dudelange, Luxembourg
| | - Pamela Pinzani
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
| | - Stefania Gelmini
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
| | - Serena Bonin
- DSM-Dept. Medical Sciences, University of Trieste, Trieste, Italy
| | - Carole Foy
- Molecular and Cell Biology Team, National Measurement Laboratory (NML), LGC, Teddington, Middlesex, UK
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9
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Kim AK, Lin SY, Wang Z, Luu H, Hamilton JP, Song W, Su YH. Impact of Cell-Debris and Room-Temperature Storage on Urine Circulating Tumor DNA from Hepatocellular Carcinoma. J Mol Diagn 2023; 25:913-920. [PMID: 37813297 PMCID: PMC10734279 DOI: 10.1016/j.jmoldx.2023.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/01/2023] [Accepted: 08/25/2023] [Indexed: 10/11/2023] Open
Abstract
This study evaluated the impact of cell debris and 7-day room temperature storage on the quality and yield of transrenal DNA. Archived urine specimens collected from five hepatocellular carcinoma (HCC) patients and two pregnant women carrying male fetuses were used to assess the impact of cell debris on urine cell-free DNA (ucfDNA) isolation as measured by quantitative PCR for Y-chromosome DNA, or HCC-associated mutation and methylation markers, and by capillary electrophoresis. Prospectively collected urine from 21 HCC patients was aliquoted after collection for paired immediate freezing versus 7-day room temperature storage followed by freezing for further analysis. Cell debris contained more Y-chromosome DNA than supernatant in three of the six urine specimens tested from pregnant women, suggesting that cell debris can be associated with 20.6% to 84.9% of transrenal ucfDNA. Ninety-five percent (20 of 21) of frozen and room temperature urine pairs had overlapping DNA size distribution. ucfDNA quantity determined by quantitative PCR for TP53, CTNNB1, TERT, and HCC-associated urine circulating tumor DNA markers were statistically similar between room temperature and frozen samples. This suggests no significant difference in DNA degradation between the groups. The association of transrenal ucfDNA with cell debris and HCC circulating DNA stability at room temperature is significant to further the understanding of transrenal circulating tumor DNA pre-analytical handling for HCC screening.
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Affiliation(s)
- Amy K Kim
- Division of Gastroenterology and Hepatology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | | | - Zhili Wang
- JBS Science, Inc., Doylestown, Pennsylvania
| | - Harry Luu
- Division of Gastroenterology and Hepatology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - James P Hamilton
- Division of Gastroenterology and Hepatology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Wei Song
- JBS Science, Inc., Doylestown, Pennsylvania
| | - Ying-Hsiu Su
- Baruch S. Blumberg Institute, Doylestown, Pennsylvania.
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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Keup C, Kimmig R, Kasimir-Bauer S. The Diversity of Liquid Biopsies and Their Potential in Breast Cancer Management. Cancers (Basel) 2023; 15:5463. [PMID: 38001722 PMCID: PMC10670968 DOI: 10.3390/cancers15225463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Analyzing blood as a so-called liquid biopsy in breast cancer (BC) patients has the potential to adapt therapy management. Circulating tumor cells (CTCs), extracellular vesicles (EVs), cell-free DNA (cfDNA) and other blood components mirror the tumoral heterogeneity and could support a range of clinical decisions. Multi-cancer early detection tests utilizing blood are advancing but are not part of any clinical routine yet. Liquid biopsy analysis in the course of neoadjuvant therapy has potential for therapy (de)escalation.Minimal residual disease detection via serial cfDNA analysis is currently on its way. The prognostic value of blood analytes in early and metastatic BC is undisputable, but the value of these prognostic biomarkers for clinical management is controversial. An interventional trial confirmed a significant outcome benefit when therapy was changed in case of newly emerging cfDNA mutations under treatment and thus showed the clinical utility of cfDNA analysis for therapy monitoring. The analysis of PIK3CA or ESR1 variants in plasma of metastatic BC patients to prescribe targeted therapy with alpesilib or elacestrant has already arrived in clinical practice with FDA-approved tests available and is recommended by ASCO. The translation of more liquid biopsy applications into clinical practice is still pending due to a lack of knowledge of the analytes' biology, lack of standards and difficulties in proving clinical utility.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45147 Essen, Germany
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van der Leest P, Janning M, Rifaela N, Azpurua MLA, Kropidlowski J, Loges S, Lozano N, Sartori A, Irwin D, Lamy PJ, Hiltermann TJN, Groen HJM, Pantel K, van Kempen LC, Wikman H, Schuuring E. Detection and Monitoring of Tumor-Derived Mutations in Circulating Tumor DNA Using the UltraSEEK Lung Panel on the MassARRAY System in Metastatic Non-Small Cell Lung Cancer Patients. Int J Mol Sci 2023; 24:13390. [PMID: 37686200 PMCID: PMC10487510 DOI: 10.3390/ijms241713390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Analysis of circulating tumor DNA (ctDNA) is a potential minimally invasive molecular tool to guide treatment decision-making and disease monitoring. A suitable diagnostic-grade platform is required for the detection of tumor-specific mutations with high sensitivity in the circulating cell-free DNA (ccfDNA) of cancer patients. In this multicenter study, the ccfDNA of 72 patients treated for advanced-stage non-small cell lung cancer (NSCLC) was evaluated using the UltraSEEK® Lung Panel on the MassARRAY® System, covering 73 hotspot mutations in EGFR, KRAS, BRAF, ERBB2, and PIK3CA against mutation-specific droplet digital PCR (ddPCR) and routine tumor tissue NGS. Variant detection accuracy at primary diagnosis and during disease progression, and ctDNA dynamics as a marker of treatment efficacy, were analyzed. A multicenter evaluation using reference material demonstrated an overall detection rate of over 90% for variant allele frequencies (VAFs) > 0.5%, irrespective of ccfDNA input. A comparison of UltraSEEK® and ddPCR analyses revealed a 90% concordance. An 80% concordance between therapeutically targetable mutations detected in tumor tissue NGS and ccfDNA UltraSEEK® analysis at baseline was observed. Nine of 84 (11%) tumor tissue mutations were not covered by UltraSEEK®. A decrease in ctDNA levels at 4-6 weeks after treatment initiation detected with UltraSEEK® correlated with prolonged median PFS (46 vs. 6 weeks; p < 0.05) and OS (145 vs. 30 weeks; p < 0.01). Using plasma-derived ccfDNA, the UltraSEEK® Lung Panel with a mid-density set of the most common predictive markers for NSCLC is an alternative tool to detect mutations both at diagnosis and during disease progression and to monitor treatment response.
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Affiliation(s)
- Paul van der Leest
- Department of Pathology (EA10), University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (P.v.d.L.); (N.R.); (M.L.A.A.); (L.C.v.K.)
| | - Melanie Janning
- German Cancer Research Center (DKFZ)-Hector Cancer Institute, University Medical Center Mannheim, 68167 Mannheim, Germany;
- Division of Personalized Medical Oncology (A420), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
- Department of Personalized Oncology, University Hospital Mannheim, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (J.K.); (K.P.); (H.W.)
| | - Naomi Rifaela
- Department of Pathology (EA10), University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (P.v.d.L.); (N.R.); (M.L.A.A.); (L.C.v.K.)
| | - Maria L. Aguirre Azpurua
- Department of Pathology (EA10), University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (P.v.d.L.); (N.R.); (M.L.A.A.); (L.C.v.K.)
| | - Jolanthe Kropidlowski
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (J.K.); (K.P.); (H.W.)
| | - Sonja Loges
- Division of Personalized Medical Oncology (A420), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
- Department of Personalized Oncology, University Hospital Mannheim, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Nicolas Lozano
- Institut d’Analyse Génomique Imagenome, Labosud, 34070 Montpellier, France
| | | | | | - Pierre-Jean Lamy
- Institut d’Analyse Génomique Imagenome, Labosud, 34070 Montpellier, France
- Department of Clinical Research, Clinique BeauSoleil, 34070 Montpellier, France
| | - T. Jeroen N. Hiltermann
- Department of Pulmonary Medicine, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (T.J.N.H.); (H.J.M.G.)
| | - Harry J. M. Groen
- Department of Pulmonary Medicine, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (T.J.N.H.); (H.J.M.G.)
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (J.K.); (K.P.); (H.W.)
| | - Léon C. van Kempen
- Department of Pathology (EA10), University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (P.v.d.L.); (N.R.); (M.L.A.A.); (L.C.v.K.)
| | - Harriet Wikman
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (J.K.); (K.P.); (H.W.)
| | - Ed Schuuring
- Department of Pathology (EA10), University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (P.v.d.L.); (N.R.); (M.L.A.A.); (L.C.v.K.)
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Cheema PK, Banerji SO, Blais N, Chu QSC, Juergens RA, Leighl NB, Sacher A, Sheffield BS, Snow S, Vincent M, Wheatley-Price PF, Yip S, Melosky BL. Canadian Consensus Recommendations on the Management of KRAS G12C-Mutated NSCLC. Curr Oncol 2023; 30:6473-6496. [PMID: 37504336 PMCID: PMC10377814 DOI: 10.3390/curroncol30070476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023] Open
Abstract
Activating mutations in Kirsten rat sarcoma viral oncogene homologue (KRAS), in particular, a point mutation leading to a glycine-to-cysteine substitution at codon 12 (G12C), are among the most frequent genomic alterations in non-small cell lung cancer (NSCLC). Several agents targeting KRAS G12C have recently entered clinical development. Sotorasib, a first-in-class specific small molecule that irreversibly inhibits KRAS G12C, has since obtained Health Canada approval. The emergence of novel KRAS-targeted therapies warrants the development of evidence-based consensus recommendations to help clinicians better understand and contextualize the available data. A Canadian expert panel was convened to define the key clinical questions, review recent evidence, and discuss and agree on recommendations for the treatment of advanced KRAS G12C-mutated NSCLC. The panel agreed that testing for KRAS G12C should be performed as part of a comprehensive panel that includes current standard-of-care biomarkers. Sotorasib, the only approved KRAS G12C inhibitor in Canada, is recommended for patients with advanced KRAS G12C-mutated NSCLC who progressed on guideline-recommended first-line standard of care for advanced NSCLC without driver alterations (immune-checkpoint inhibitor(s) [ICIs] +/- chemotherapy). Sotorasib could also be offered as second-line therapy to patients who progressed on ICI monotherapy that are not candidates for a platinum doublet and those that received first-line chemotherapy with a contraindication to ICIs. Preliminary data indicate the activity of KRAS G12C inhibitors in brain metastases; however, the evidence is insufficient to make specific recommendations. Regular liver function monitoring is recommended when patients are prescribed KRAS G12C inhibitors due to risk of hepatotoxicity.
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Affiliation(s)
- Parneet K. Cheema
- Division of Medical Oncology, William Osler Health System, University of Toronto, Brampton, ON L6R 3J7, Canada
- Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shantanu O. Banerji
- CancerCare Manitoba Research Institute, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
| | - Normand Blais
- Department of Medicine, Centre Hospitalier de l’Université de Montréal, University of Montreal, Montreal, QC H2X 3E4, Canada;
| | - Quincy S.-C. Chu
- Division of Medical Oncology, Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB T6G 1Z2, Canada;
| | - Rosalyn A. Juergens
- Department of Medical Oncology, Juravinski Cancer Centre, McMaster University, Hamilton, ON L8V 5C2, Canada;
| | - Natasha B. Leighl
- Department of Medicine, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5S 1A8, Canada; (N.B.L.); (A.S.)
| | - Adrian Sacher
- Department of Medicine, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5S 1A8, Canada; (N.B.L.); (A.S.)
| | - Brandon S. Sheffield
- Department of Laboratory Medicine, William Osler Health System, Brampton, ON L6R 3J7, Canada
| | - Stephanie Snow
- Division of Medical Oncology, Department of Medicine, QEII Health Sciences Centre, Dalhousie University, Halifax, NS B3H 2Y9, Canada;
| | - Mark Vincent
- Department of Medical Oncology, London Regional Cancer Program, London, ON N6A 5W9, Canada;
| | - Paul F. Wheatley-Price
- Department of Medicine, The Ottawa Hospital Research Institute, The Ottawa Hospital, University of Ottawa, Ottawa, ON K1H 8L6, Canada;
| | - Stephen Yip
- BC Cancer, Vancouver, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
| | - Barbara L. Melosky
- Department of Medical Oncology, BC Cancer-Vancouver Centre, Vancouver, BC V5Z 4E6, Canada;
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Richter F, Henssen C, Steiert TA, Meissner T, Mehdorn AS, Röcken C, Franke A, Egberts JH, Becker T, Sebens S, Forster M. Combining Solid and Liquid Biopsy for Therapy Monitoring in Esophageal Cancer. Int J Mol Sci 2023; 24:10673. [PMID: 37445849 DOI: 10.3390/ijms241310673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 07/15/2023] Open
Abstract
Esophageal cancer (EC) has one of the highest mortality rates among cancers, making it imperative that therapies are optimized and dynamically adapted to individuals. In this regard, liquid biopsy is an increasingly important method for residual disease monitoring. However, conflicting detection rates (14% versus 60%) and varying cell-free circulating tumor DNA (ctDNA) levels (0.07% versus 0.5%) have been observed in previous studies. Here, we aim to resolve this discrepancy. For 19 EC patients, a complete set of cell-free DNA (cfDNA), formalin-fixed paraffin-embedded tumor tissue (TT) DNA and leukocyte DNA was sequenced (139 libraries). cfDNA was examined in biological duplicates and/or longitudinally, and TT DNA was examined in technical duplicates. In baseline cfDNA, mutations were detected in 12 out of 19 patients (63%); the median ctDNA level was 0.4%. Longitudinal ctDNA changes were consistent with clinical presentation. Considerable mutational diversity was observed in TT, with fewer mutations in cfDNA. The most recurrently mutated genes in TT were TP53, SMAD4, TSHZ3, and SETBP1, with SETBP1 being reported for the first time. ctDNA in blood can be used for therapy monitoring of EC patients. However, a combination of solid and liquid samples should be used to help guide individualized EC therapy.
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Affiliation(s)
- Florian Richter
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein Campus Kiel, 24105 Kiel, Germany
| | - Clara Henssen
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany
| | | | - Tobias Meissner
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, SD 57105, USA
| | - Anne-Sophie Mehdorn
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein Campus Kiel, 24105 Kiel, Germany
| | - Christoph Röcken
- Department of Pathology, University Hospital Schleswig-Holstein Campus Kiel, 24105 Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany
| | - Jan-Hendrik Egberts
- Department of Surgery, Israelitisches Krankenhaus Hamburg, 22297 Hamburg, Germany
| | - Thomas Becker
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein Campus Kiel, 24105 Kiel, Germany
| | - Susanne Sebens
- Institute for Experimental Cancer Research, Kiel University, University Hospital Schleswig-Holstein Campus Kiel, 24105 Kiel, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany
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Cohen R, Platell CF, McCoy MJ, Meehan K, Fuller K. Circulating tumour DNA in colorectal cancer management. Br J Surg 2023; 110:773-783. [PMID: 37190784 PMCID: PMC10364542 DOI: 10.1093/bjs/znad126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/17/2023] [Accepted: 04/28/2023] [Indexed: 05/17/2023]
Abstract
Circulating tumour DNA analysis can be performed using two opposing paradigms: tumour-informed and tumour-agnostic approaches. The first requires sequencing data from the primary tumour sample to identify tumour DNA in circulation, whereas the latter occurs without previous primary tumour genetic profiling.
Several preanalytical and laboratory considerations need to be taken into account before proceeding with in-house circulating tumour DNA analysis.
Detection of circulating tumour DNA after curative resection is associated with a significant risk of recurrence. For those with stage II disease and detectable postoperative circulating tumour DNA, administration of adjuvant chemotherapy results in a reduction in the number of patients receiving chemotherapy while providing non-inferior recurrence-free survival compared with standard histopathological decision-making algorithms.
Monitoring circulating tumour DNA during post-treatment surveillance may provide a significantly earlier diagnosis of recurrence.
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Affiliation(s)
- Ryan Cohen
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
- Colorectal Cancer Unit, St John of God Subiaco Hospital, Perth, Western Australia, Australia
| | - Cameron F Platell
- Colorectal Cancer Unit, St John of God Subiaco Hospital, Perth, Western Australia, Australia
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Melanie J McCoy
- Colorectal Cancer Unit, St John of God Subiaco Hospital, Perth, Western Australia, Australia
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Katie Meehan
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Kathy Fuller
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
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Trinidad EM, Juan-Ribelles A, Pisano G, Castel V, Cañete A, Gut M, Heath S, Font de Mora J. Evaluation of circulating tumor DNA by electropherogram analysis and methylome profiling in high-risk neuroblastomas. Front Oncol 2023; 13:1037342. [PMID: 37251933 PMCID: PMC10213460 DOI: 10.3389/fonc.2023.1037342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
Background Liquid biopsy has emerged as a promising, non-invasive diagnostic approach in oncology because the analysis of circulating tumor DNA (ctDNA) reflects the precise status of the disease at diagnosis, progression, and response to treatment. DNA methylation profiling is also a potential solution for sensitive and specific detection of many cancers. The combination of both approaches, DNA methylation analysis from ctDNA, provides an extremely useful and minimally invasive tool with high relevance in patients with childhood cancer. Neuroblastoma is an extracranial solid tumor most common in children and responsible for up to 15% of cancer-related deaths. This high death rate has prompted the scientific community to search for new therapeutic targets. DNA methylation also offers a new source for identifying these molecules. However, the limited blood sample size which can be obtained from children with cancer and the fact that ctDNA content may occasionally be diluted by non-tumor cell-free DNA (cfDNA) complicate optimal quantities of material for high-throughput sequencing studies. Methods In this article, we present an improved method for ctDNA methylome studies of blood-derived plasma from high-risk neuroblastoma patients. We assessed the electropherogram profiles of ctDNA-containing samples suitable for methylome studies, using 10 ng of plasma-derived ctDNA from 126 samples of 86 high-risk neuroblastoma patients, and evaluated several bioinformatic approaches to analyze DNA methylation sequencing data. Results We demonstrated that enzymatic methyl-sequencing (EM-seq) outperformed bisulfite conversion-based method, based on the lower proportion of PCR duplicates and the higher percentage of unique mapping reads, mean coverage, and genome coverage. The analysis of the electropherogram profiles revealed the presence of nucleosomal multimers, and occasionally high molecular weight DNA. We established that 10% content of the mono-nucleosomal peak is sufficient ctDNA for successful detection of copy number variations and methylation profiles. Quantification of mono-nucleosomal peak also showed that samples at diagnosis contained a higher amount of ctDNA than relapse samples. Conclusions Our results refine the use of electropherogram profiles to optimize sample selection for subsequent high-throughput analysis and support the use of liquid biopsy followed by enzymatic conversion of unmethylated cysteines to assess the methylomes of neuroblastoma patients.
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Affiliation(s)
- Eva María Trinidad
- Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
| | - Antonio Juan-Ribelles
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
- Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
| | - Giulia Pisano
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
- Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
| | - Victoria Castel
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
- Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
| | - Adela Cañete
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
- Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
- School of Medicine, University of Valencia, Valencia, Spain
| | - Marta Gut
- National Center for Genomic Analysis – Centre for Genomic Regulation (CNAG-CRG), Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Simon Heath
- National Center for Genomic Analysis – Centre for Genomic Regulation (CNAG-CRG), Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jaime Font de Mora
- Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
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Khan SR, Scheffler M, Soomar SM, Rashid YA, Moosajee M, Ahmad A, Raza A, Uddin S. Role of circulating-tumor DNA in the early-stage non-small cell lung carcinoma as a predictive biomarker. Pathol Res Pract 2023; 245:154455. [PMID: 37054576 DOI: 10.1016/j.prp.2023.154455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 04/15/2023]
Abstract
Lung cancer is one of the most common solid malignancies. Tissue biopsy is the standard method for accurately diagnosing lung and many other malignancies over decades. However, molecular profiling of tumors leads to establishing a new horizon in the field of precision medicine, which has now entered the mainstream in clinical practice. In this context, a minimally invasive complementary method has been proposed as a liquid biopsy (LB) which is a blood-based test that is gaining popularity as it provides the opportunity to test genotypes in a unique, less invasive manner. Circulating tumor cells (CTC) captivating the Circulating-tumor DNA (Ct-DNA) are often present in the blood of lung cancer patients and are the fundamental concept behind LB. There are multiple clinical uses of Ct-DNA, including its role in prognostic and therapeutic purposes. The treatment of lung cancer has drastically evolved over time. Therefore, this review article mainly focuses on the current literature on circulating tumor DNA and its clinical implications and future goals in non-small cell lung cancer.
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Affiliation(s)
- Saqib Raza Khan
- Medical Oncology Department, Aga Khan University Hospital, Karachi, Pakistan.
| | - Matthias Scheffler
- Internal Medicine Department, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | | | - Yasmin Abdul Rashid
- Medical Oncology Department, Aga Khan University Hospital, Karachi, Pakistan
| | - Munira Moosajee
- Medical Oncology Department, Aga Khan University Hospital, Karachi, Pakistan
| | - Aamir Ahmad
- Translational Research Institute & Dermatology Institute, Hamad Medical Corporation, Doha, Qatar
| | - Afsheen Raza
- College of Health Sciences, Abu Dhabi University, Abu Dhabi, United Arab Emirates
| | - Shahab Uddin
- Translational Research Institute & Dermatology Institute, Hamad Medical Corporation, Doha, Qatar.
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Moser T, Kühberger S, Lazzeri I, Vlachos G, Heitzer E. Bridging biological cfDNA features and machine learning approaches. Trends Genet 2023; 39:285-307. [PMID: 36792446 DOI: 10.1016/j.tig.2023.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 02/15/2023]
Abstract
Liquid biopsies (LBs), particularly using circulating tumor DNA (ctDNA), are expected to revolutionize precision oncology and blood-based cancer screening. Recent technological improvements, in combination with the ever-growing understanding of cell-free DNA (cfDNA) biology, are enabling the detection of tumor-specific changes with extremely high resolution and new analysis concepts beyond genetic alterations, including methylomics, fragmentomics, and nucleosomics. The interrogation of a large number of markers and the high complexity of data render traditional correlation methods insufficient. In this regard, machine learning (ML) algorithms are increasingly being used to decipher disease- and tissue-specific signals from cfDNA. Here, we review recent insights into biological ctDNA features and how these are incorporated into sophisticated ML applications.
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Affiliation(s)
- Tina Moser
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Stefan Kühberger
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Isaac Lazzeri
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Georgios Vlachos
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria.
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Diaz IM, Nocon A, Held SAE, Kobilay M, Skowasch D, Bronkhorst AJ, Ungerer V, Fredebohm J, Diehl F, Holdenrieder S, Holtrup F. Pre-Analytical Evaluation of Streck Cell-Free DNA Blood Collection Tubes for Liquid Profiling in Oncology. Diagnostics (Basel) 2023; 13:diagnostics13071288. [PMID: 37046506 PMCID: PMC10093569 DOI: 10.3390/diagnostics13071288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Excellent pre-analytical stability is an essential precondition for reliable molecular profiling of circulating tumor DNA (ctDNA) in oncological diagnostics. Therefore, in vitro degradation of ctDNA and the additional release of contaminating genomic DNA from lysed blood cells must be prevented. Streck Cell-Free DNA blood collection tubes (cfDNA BCTs) have proposed advantages over standard K2EDTA tubes, but mainly have been tested in healthy individuals. Blood was collected from cancer patients (n = 53) suffering from colorectal (n = 21), pancreatic (n = 11), and non-small-cell lung cancer (n = 21) using cfDNA BCT tubes and K2EDTA tubes that were processed immediately or after 3 days (BCTs) or 6 hours (K2EDTA) at room temperature. The cfDNA isolated from these samples was characterized in terms of yield using LINE-1 qPCR; the level of gDNA contamination; and the mutation status of KRAS, NRAS, and EGFR genes using BEAMing ddPCR. CfDNA yield and gDNA levels were comparable in both tube types and were not affected by prolonged storage of blood samples for at least 3 days in cfDNA BCTs or 6 hours in K2EDTA tubes. In addition, biospecimens collected in K2EDTA tubes and cfDNA BCTs stored for up to 3 days demonstrated highly comparable levels of mutational load across all respective cancer patient cohorts and a wide range of concentrations. Our data support the applicability of clinical oncology specimens collected and stored in cfDNA BCTs for up to 3 days for reliable cfDNA and mutation analyses.
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Dameri M, Cirmena G, Ravera F, Ferrando L, Cuccarolo P, Stabile M, Fanelli GN, Nuzzo PV, Calabrese M, Tagliafico A, Ballestrero A, Zoppoli G. Standard Operating Procedures (SOPs) for non-invasive multiple biomarkers detection in an academic setting: a critical review of the literature for the RENOVATE study protocol. Crit Rev Oncol Hematol 2023; 185:103963. [PMID: 36931614 DOI: 10.1016/j.critrevonc.2023.103963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 03/17/2023] Open
Abstract
Liquid biopsy has the potential to drastically change clinical practice, paving the way to a novel non-invasive approach for cancer diagnosis and treatment. One of the limitations for the implementation of liquid biopsy in clinical practice is the lack of shared and reproducible standard operating procedures (SOPs) for sample collection, processing and storage. Here, we present a critical review of the literature focusing on the available SOPs to guide liquid biopsy management in research settings and describe SOPs that our laboratory developed and employed in the context of a prospective clinical-translational trial (RENOVATE, NCT04781062). The main aim of this manuscript is to address common issues, towards the implementation of interlaboratory shared protocols for optimized preanalytical handling of blood and urine samples. To our knowledge, this work is one of the few up-to-date, freely available comprehensive reports on trial-level procedures for the handling of liquid biopsy.
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Affiliation(s)
- Martina Dameri
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy
| | | | - Francesco Ravera
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, 10044, New York, NY, USA
| | | | - Paola Cuccarolo
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy
| | - Mario Stabile
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy
| | - Giuseppe Nicolò Fanelli
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 10021, New York, NY, USA; First Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
| | - Pier Vitale Nuzzo
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, 10044, New York, NY, USA
| | | | - Alberto Tagliafico
- IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy; Department of Health Sciences DISSAL, University of Genoa, 16132, Genoa, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy; IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - Gabriele Zoppoli
- Department of Internal Medicine and Medical Specialties DiMI, University of Genoa, 16132, Genoa, Italy; IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy.
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21
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Heidrich I, Deitert B, Werner S, Pantel K. Liquid biopsy for monitoring of tumor dormancy and early detection of disease recurrence in solid tumors. Cancer Metastasis Rev 2023; 42:161-82. [PMID: 36607507 DOI: 10.1007/s10555-022-10075-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023]
Abstract
Cancer is one of the three leading causes of death worldwide. Even after successful therapy and achieving remission, the risk of relapse often remains. In this context, dormant residual cancer cells in secondary organs such as the bone marrow constitute the cellular reservoir from which late tumor recurrences arise. This dilemma leads the term of minimal residual disease, which reflects the presence of tumor cells disseminated from the primary lesion to distant organs in patients who lack any clinical or radiological signs of metastasis or residual tumor cells left behind after therapy that eventually lead to local recurrence. Disseminated tumor cells have the ability to survive in a dormant state following treatment and linger unrecognized for more than a decade before emerging as recurrent disease. They are able to breakup their dormant state and to readopt their proliferation under certain circumstances, which can finally lead to distant relapse and cancer-associated death. In recent years, extensive molecular and genetic characterization of disseminated tumor cells and blood-based biomarker has contributed significantly to our understanding of the frequency and prevalence of tumor dormancy. In this article, we describe the clinical relevance of disseminated tumor cells and highlight how latest advances in different liquid biopsy approaches can be used to detect, characterize, and monitor minimal residual disease in breast cancer, prostate cancer, and melanoma patients.
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22
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Terp SK, Stoico MP, Dybkær K, Pedersen IS. Early diagnosis of ovarian cancer based on methylation profiles in peripheral blood cell-free DNA: a systematic review. Clin Epigenetics 2023; 15:24. [PMID: 36788585 PMCID: PMC9926627 DOI: 10.1186/s13148-023-01440-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/05/2023] [Indexed: 02/16/2023] Open
Abstract
Patients diagnosed with epithelial ovarian cancer (OC) have a 5-year survival rate of 49%. For early-stage disease, the 5-year survival rate is above 90%. However, advanced-stage disease accounts for most cases as patients with early stages often are asymptomatic or present with unspecific symptoms, highlighting the need for diagnostic tools for early diagnosis. Liquid biopsy is a minimal invasive blood-based approach that utilizes circulating tumor DNA (ctDNA) shed from tumor cells for real-time detection of tumor genetics and epigenetics. Increased DNA methylation of promoter regions is an early event during tumorigenesis, and the methylation can be detected in ctDNA, accentuating the promise of methylated ctDNA as a biomarker for OC diagnosis. Many studies have investigated multiple methylation biomarkers in ctDNA from plasma or serum for discriminating OC patients from patients with benign diseases of the ovaries and/or healthy females. This systematic review summarizes and evaluates the performance of the currently investigated DNA methylation biomarkers in blood-derived ctDNA for early diagnosis of OC. PubMed's MEDLINE and Elsevier's Embase were systematically searched, and essential results such as methylation frequency of OC cases and controls, performance measures, as well as preanalytical factors were extracted. Overall, 29 studies met the inclusion criteria for this systematic review. The most common method used for methylation analysis was methylation-specific PCR, with half of the studies using plasma and the other half using serum. RASSF1A, BRCA1, and OPCML were the most investigated gene-specific methylation biomarkers, with OPCML having the best performance measures. Generally, methylation panels performed better than single gene-specific methylation biomarkers, with one methylation panel of 103,456 distinct regions and 1,116,720 CpGs having better performance in both training and validation cohorts. However, the evidence is still limited, and the promising methylation panels, as well as gene-specific methylation biomarkers highlighted in this review, need validation in large, prospective cohorts with early-stage asymptomatic OC patients to assess the true diagnostic value in a clinical setting.
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Affiliation(s)
- Simone Karlsson Terp
- Department of Molecular Diagnostics, Aalborg University Hospital, 9000, Aalborg, Denmark.
- Department of Clinical Medicine, Aalborg University, 9000, Aalborg, Denmark.
| | - Malene Pontoppidan Stoico
- Department of Molecular Diagnostics, Aalborg University Hospital, 9000, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, 9000, Aalborg, Denmark
| | - Karen Dybkær
- Department of Clinical Medicine, Aalborg University, 9000, Aalborg, Denmark
- Department of Hematology, Aalborg University Hospital, 9000, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, 9000, Aalborg, Denmark
| | - Inge Søkilde Pedersen
- Department of Molecular Diagnostics, Aalborg University Hospital, 9000, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, 9000, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, 9000, Aalborg, Denmark
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23
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Papadimitriou MA, Levis P, Kotronopoulos G, Stravodimos K, Avgeris M, Scorilas A. Preoperative Cell-Free DNA (cfDNA) in Muscle-Invasive Bladder Cancer Treatment Outcome. Clin Chem 2023; 69:399-410. [PMID: 36738246 DOI: 10.1093/clinchem/hvac218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/22/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Tumor heterogeneity and lack of personalized prognosis leads to bladder cancer (BlCa) patients' lifelong surveillance with invasive interventions, highlighting the need for modern minimally invasive tools for disease management. Herein, we have evaluated the clinical utility of preoperative serum cell-free DNA (cfDNA) in ameliorating patients' risk-stratification and prognosis. METHODS cfDNA was purified from 190 preoperative BlCa patients and 26 healthy individuals' serum samples and quantified by 2 assays: an in-house quantitative real-time PCR (qPCR) assay using LEP as reference control and a direct fluorometric assay using Qubit HS dsDNA. Capillary electrophoresis was performed in 31 samples for cfDNA fragment profiling. Tumor relapse/progression and metastasis/death were used as clinical endpoints for non-muscle-invasive bladder cancer and muscle-invasive bladder cancer (MIBC), respectively. RESULTS cfDNA profiling by capillary electrophoresis highlighted that total and fragment-related cfDNA levels were significantly increased in BlCa and associated with advance disease stages. Evaluation of cfDNA levels by both Qubit/qPCR displayed highly consistent results (rs = 0.960; P < 0.001). Higher cfDNA was correlated with MIBC and stronger risk for early metastasis (Qubit:hazard ratio [HR] = 3.016, P = 0.009; qPCR:HR = 2.918, P = 0.004) and poor survival (Qubit:HR = 1.898, P = 0.042; qPCR:HR = 1.888, P = 0.026) of MIBC patients. Multivariate cfDNA-fitted models led to superior risk stratification and net benefit for MIBC prognosis compared to disease established markers. CONCLUSIONS Elevated preoperative cfDNA levels are strongly associated with higher risk for short-term metastasis and poor outcome of MIBC, supporting modern noninvasive disease prognosis and management.
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Affiliation(s)
- Maria-Alexandra Papadimitriou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Levis
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Kotronopoulos
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Stravodimos
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece.,Laboratory of Clinical Biochemistry - Molecular Diagnostics, Second Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, "P. & A. Kyriakou" Children's Hospital, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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24
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Qi T, Pan M, Shi H, Wang L, Bai Y, Ge Q. Cell-Free DNA Fragmentomics: The Novel Promising Biomarker. Int J Mol Sci 2023; 24:ijms24021503. [PMID: 36675018 PMCID: PMC9866579 DOI: 10.3390/ijms24021503] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Cell-free DNA molecules are released into the plasma via apoptotic or necrotic events and active release mechanisms, which carry the genetic and epigenetic information of its origin tissues. However, cfDNA is the mixture of various cell fragments, and the efficient enrichment of cfDNA fragments with diagnostic value remains a great challenge for application in the clinical setting. Evidence from recent years shows that cfDNA fragmentomics' characteristics differ in normal and diseased individuals without the need to distinguish the source of the cfDNA fragments, which makes it a promising novel biomarker. Moreover, cfDNA fragmentomics can identify tissue origins by inferring epigenetic information. Thus, further insights into the fragmentomics of plasma cfDNA shed light on the origin and fragmentation mechanisms of cfDNA during physiological and pathological processes in diseases and enhance our ability to take the advantage of plasma cfDNA as a molecular diagnostic tool. In this review, we focus on the cfDNA fragment characteristics and its potential application, such as fragment length, end motifs, jagged ends, preferred end coordinates, as well as nucleosome footprints, open chromatin region, and gene expression inferred by the cfDNA fragmentation pattern across the genome. Furthermore, we summarize the methods for deducing the tissue of origin by cfDNA fragmentomics.
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Affiliation(s)
- Ting Qi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Min Pan
- School of Medicine, Southeast University, Nanjing 210097, China
| | - Huajuan Shi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Liangying Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Correspondence: ; Tel./Fax: +86-025-83792396
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25
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Takousis P, Devonshire AS, Redshaw N, von Baumgarten L, Whale AS, Jones GM, Fernandez-Gonzalez A, Martin J, Foy CA, Alexopoulos P, Huggett JF, Perneczky R. A standardised methodology for the extraction and quantification of cell-free DNA in cerebrospinal fluid and application to evaluation of Alzheimer's disease and brain cancers. N Biotechnol 2022; 72:97-106. [PMID: 36202346 DOI: 10.1016/j.nbt.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 09/23/2022] [Accepted: 10/01/2022] [Indexed: 11/27/2022]
Abstract
Cerebrospinal fluid (CSF) is a source of diagnostic biomarkers for a range of neurological conditions. Cell-free DNA (cfDNA) is detected in CSF and differences in the concentration of cell-free mitochondrial DNA have been reported in studies of neurodegenerative disorders including Alzheimer's disease (AD). However, the influence of pre-analytical steps has not been investigated for cfDNA in CSF and there is no standardised approach for quantification of total cfDNA (copies of nuclear genome or mitochondria-derived gene targets). In this study, the suitability of four extraction methods was evaluated: QIAamp Circulating Nucleic Acid (Qiagen), Quick-cfDNA Serum & Plasma (Zymo), NucleoSnap® DNA Plasma (Macherey-Nagel) and Plasma/Serum Circulating DNA Purification Mini (Norgen) kits, for cfDNA extraction from CSF of controls and AD dementia patients, utilising a spike-in control for extraction efficiency and fragment size. One of the optimal extraction methods was applied to a comparison of cfDNA concentrations in CSF from control subjects, AD dementia and primary and secondary brain tumour patients. Extraction efficiency based on spike-in recovery was similar in all three groups whilst both endogenous mitochondrial and nucleus-derived cfDNA was significantly higher in CSF from cancer patients compared to control and AD groups, which typically contained < 100 genome copies/mL. This study shows that it is feasible to measure low concentration nuclear and mitochondrial gene targets in CSF and that normalisation of extraction yield can help control pre-analytical variability influencing biomarker measurements.
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Affiliation(s)
- Petros Takousis
- Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College London, London, UK
| | - Alison S Devonshire
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK.
| | - Nicholas Redshaw
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Louisa von Baumgarten
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany; Department of Neurosurgery, University Hospital, LMU Munich, Munich, Germany
| | - Alexandra S Whale
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Gerwyn M Jones
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Ana Fernandez-Gonzalez
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Jan Martin
- Department of Anaesthesiology and Intensive Care Medicine, Technical University Munich, Munich, Germany
| | - Carole A Foy
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Panagiotis Alexopoulos
- Department of Psychiatry, University of Patras, Rion Patras, Greece; Department of Psychiatry and Psychotherapy, Technical University Munich, Munich, Germany
| | - Jim F Huggett
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK; School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Robert Perneczky
- Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College London, London, UK; Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
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26
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Verderio P, Ciniselli CM, Gaignaux A, Pastori M, Saracino S, Kofanova O, Betsou F. External Quality Assurance programs for processing methods provide evidence on impact of preanalytical variables. N Biotechnol 2022; 72:29-37. [PMID: 36049650 DOI: 10.1016/j.nbt.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/09/2022] [Accepted: 08/28/2022] [Indexed: 12/14/2022]
Abstract
An annual External Quality Assurance (EQA) program has been provided to processing laboratories over the last ten years, allowing them to assess the performance of their processing methods, such as nucleic acid extractions or peripheral blood mononuclear cell (PBMC) isolation and cryopreservation. The objective of this study was to perform a global analysis on almost 1000 EQA scheme/participant data in order to assess (i) the impact of critical preanalytical factors on quantitative or qualitative attributes of different types of specimens and (ii) laboratory performance pattern over time. Statistical analysis was performed within each EQA scheme based on categorized preanalytical data provided by the participants and on centralized measurements of relevant quality attributes of the produced specimens (z-scores): DNA, cell-free (cf)DNA or RNA extraction from blood, DNA or RNA extraction from formalin fixed tissue, DNA or RNA extraction from frozen tissue, DNA extraction from saliva or stool, viable PBMC isolation and cryopreservation. The most critical preanalytical factors in nucleic acid extraction schemes were the nucleic acid extraction method and kit, the elution buffer, the enzymes used during extraction, the input material quantity and the storage temperature. Several indications of laboratory performance improvement over time could be seen. The conclusions are that EQA for processing methods provides unique evidence-based insights into the impact of preanalytical factors and the comparative performance of different processing methods and kits, while supporting laboratories in validating their processing methods.
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Affiliation(s)
- Paolo Verderio
- Unit of Bioinformatics and Biostatistics, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy
| | - Chiara Maura Ciniselli
- Unit of Bioinformatics and Biostatistics, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy
| | - Amélie Gaignaux
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health, 1 rue Louis Rech, 3555, Luxembourg
| | - Marta Pastori
- Unit of Bioinformatics and Biostatistics, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy
| | - Sabrina Saracino
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health, 1 rue Louis Rech, 3555, Luxembourg
| | - Olga Kofanova
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health, 1 rue Louis Rech, 3555, Luxembourg.
| | - Fay Betsou
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health, 1 rue Louis Rech, 3555, Luxembourg; Institut Pasteur, Université Paris Cité, CRBIP, F-75015 Paris, France
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27
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Zhou X, Zheng H, Fu H, Dillehay McKillip KL, Pinney SM, Liu Y. CRAG: de novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing. Genome Med 2022; 14:138. [PMID: 36482487 PMCID: PMC9733064 DOI: 10.1186/s13073-022-01141-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
The fine-scale cell-free DNA fragmentation patterns in early-stage cancers are poorly understood. We developed a de novo approach to characterize the cell-free DNA fragmentation hotspots from plasma whole-genome sequencing. Hotspots are enriched in open chromatin regions, and, interestingly, 3'end of transposons. Hotspots showed global hypo-fragmentation in early-stage liver cancers and are associated with genes involved in the initiation of hepatocellular carcinoma and associated with cancer stem cells. The hotspots varied across multiple early-stage cancers and demonstrated high performance for the diagnosis and identification of tissue-of-origin in early-stage cancers. We further validated the performance with a small number of independent case-control-matched early-stage cancer samples.
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Affiliation(s)
- Xionghui Zhou
- grid.239573.90000 0000 9025 8099Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.35155.370000 0004 1790 4137Present address: Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 China
| | - Haizi Zheng
- grid.239573.90000 0000 9025 8099Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Hailu Fu
- grid.239573.90000 0000 9025 8099Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Kelsey L. Dillehay McKillip
- grid.24827.3b0000 0001 2179 9593University of Cincinnati Cancer Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA
| | - Susan M. Pinney
- grid.24827.3b0000 0001 2179 9593University of Cincinnati Cancer Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA
| | - Yaping Liu
- grid.239573.90000 0000 9025 8099Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593University of Cincinnati Cancer Center, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Electrical Engineering and Computing Sciences, University of Cincinnati College of Engineering and Applied Science, Cincinnati, OH 45229 USA
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28
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Malapelle U, Pisapia P, Pepe F, Russo G, Buono M, Russo A, Gomez J, Khorshid O, Mack PC, Rolfo C, Troncone G. The evolving role of liquid biopsy in lung cancer. Lung Cancer 2022; 172:53-64. [PMID: 35998482 DOI: 10.1016/j.lungcan.2022.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 07/22/2022] [Accepted: 08/05/2022] [Indexed: 12/20/2022]
Abstract
Liquid biopsy has revolutionized the management of cancer patients. In particular, liquid biopsy-based testing has proven to be highly beneficial for identifying actionable cancer markers, especially when solid tissue biopsies are insufficient or unattainable. Beyond the predictive role, liquid biopsy may be a useful tool for comprehensive tumor genotyping, identification of emergent resistance mechanisms, monitoring of minimal residual disease, early detection, and cancer interception. The application of next generation sequencing to liquid biopsy has led to the "quantum leap" of predictive molecular pathology. Here, we review the evolving role of liquid biopsy in lung cancer.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy.
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mauro Buono
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Jorge Gomez
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
| | - Ola Khorshid
- National Cancer Institute, Cairo University, Cairo, Egypt
| | - Philip C Mack
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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29
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Bronkhorst AJ, Ungerer V, Oberhofer A, Gabriel S, Polatoglou E, Randeu H, Uhlig C, Pfister H, Mayer Z, Holdenrieder S. New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:2147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
Abstract
Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.
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Duffy MJ, Crown J. Circulating Tumor DNA as a Biomarker for Monitoring Patients with Solid Cancers: Comparison with Standard Protein Biomarkers. Clin Chem 2022; 68:1381-1390. [PMID: 35962648 DOI: 10.1093/clinchem/hvac121] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/21/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND Protein-based biomarkers are widely used in monitoring patients with diagnosed cancer. These biomarkers however, lack specificity for cancer and have poor sensitivity in detecting early recurrences and monitoring therapy effectiveness. Emerging data suggest that the use of circulating tumor DNA (ctDNA) has several advantages over standard biomarkers. CONTENT Following curative-intent surgery for cancer, the presence of ctDNA is highly predictive of early disease recurrence, while in metastatic cancer an early decline in ctDNA following the initiation of treatment is predictive of good outcome. Compared with protein biomarkers, ctDNA provides greater cancer specificity and sensitivity for detecting early recurrent/metastatic disease. Thus, in patients with surgically resected colorectal cancer, multiple studies have shown that ctDNA is superior to carcinoembryonic antigen (CEA) in detecting residual disease and early recurrence. Similarly, in breast cancer, ctDNA was shown to be more accurate than carbohydrate antigen 15-3 (CA 15-3) in detecting early recurrences. Other advantages of ctDNA over protein biomarkers in monitoring cancer patients include a shorter half-life in plasma and an ability to predict likely response to specific therapies and identify mechanisms of therapy resistance. However, in contrast to proteins, ctDNA biomarkers are more expensive to measure, less widely available, and have longer turnaround times for reporting. Furthermore, ctDNA assays are less well standardized. SUMMARY Because of their advantages, it is likely that ctDNA measurements will enter clinical use in the future, where they will complement existing biomarkers and imaging in managing patients with cancer. Hopefully, these combined approaches will lead to a better outcome for patients.
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Affiliation(s)
- Michael J Duffy
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,UCD Clinical Research Centre, St. Vincent's University Hospital, Dublin, Ireland
| | - John Crown
- Department of Medical Oncology, St Vincent's University Hospital, Dublin, Ireland
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Heidrich I, Pantel K. Liquid biopsy: blood-based analyses of circulating cell-free DNA in xenografts. EMBO Mol Med 2022; 14:e16326. [PMID: 35903952 PMCID: PMC9358390 DOI: 10.15252/emmm.202216326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 11/09/2022] Open
Abstract
The liquid biopsy concept has been introduced for circulating tumor cells more than 10 years ago (Pantel & Alix-Panabieres, 2010) and rapidly extended to cell-free DNA released from tumor cells (ctDNA; Lo et al, 2021) and other tumor-derived products such as circulating cell-free RNA (noncoding and messenger RNA), extracellular vesicles, or tumor-educated platelets (Alix-Panabières & Pantel, 2021). In this issue of EMBO Molecular Medicine, the report of Sauer et al (2022) demonstrates the feasibility of longitudinal monitoring of disease burden and response using ctDNA from dried blood spots in xenograft models.
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Affiliation(s)
- Isabel Heidrich
- Department of Tumor Biology, University Medical, Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Dermatology and Venereology, Skin Cancer Center, University Hospital Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Klaus Pantel
- Department of Tumor Biology, University Medical, Center Hamburg-Eppendorf, Hamburg, Germany
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Cox DR, Wong BKL, Lee E, Testro A, Muralidharan V, Dobrovic A, Goh SK. Evaluating DNA recovery efficiency following bisulphite modification from plasma samples submitted for cell-free DNA methylation analysis. Epigenetics 2022; 17:1956-1960. [PMID: 35763697 DOI: 10.1080/15592294.2022.2091821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The detection of methylated templates in cell-free DNA (cfDNA) is increasingly recognized as a valuable, non-invasive tool for diagnosis, monitoring and prognostication in a range of medical contexts. The importance of controlling pre-analytical conditions in laboratory workflows prior to cfDNA quantification is well-established. Significant variations in the recovery of DNA following processes such as cfDNA extraction and sodium bisulphite modification may confound downstream analysis, particularly when accurate quantification of templates is required. Given the wealth of potential applications for this emerging molecular technology, attention has turned to the requirement to recognize and minimize pre-analytical variables prior to cfDNA methylation analysis. We recently described the development of an approach using an exogenous DNA construct to evaluate the recovery efficiency of cfDNA following the extraction and bisulphite modification steps (CEREBIS). Here, we report our experience in the practical application of this technique in 107 consecutive patient plasma samples submitted for quantitative cfDNA methylation analysis. The mean recovery of cfDNA (as estimated using cerebis), following extraction and bisulphite modification, was 37% ± 7%. Nine (8.4%) of the 107 samples were found to be outside of control limits, where the recovery of cerebis indicated significant differences in the efficiency of the pre-analytical processing of these samples. Recognition of these out-of-control samples precluded subsequent molecular analysis. Implementation of data-driven quality control measures, such as the one described, has the potential to improve the quality of liquid biopsy methylation analysis, interpretation and reporting.
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Affiliation(s)
- Daniel Ra Cox
- Department of Surgery (Austin Precinct), The University of Melbourne, Heidelberg, Australia.,Translational Genomics and Epigenomics Laboratory, Department of Surgery (Austin Precinct), The University of Melbourne, Heidelberg, Australia.,Hepatopancreatobiliary and Transplant Surgery Unit, Austin Health, Heidelberg, Australia
| | - Boris Ka Leong Wong
- Translational Genomics and Epigenomics Laboratory, Department of Surgery (Austin Precinct), The University of Melbourne, Heidelberg, Australia
| | - Eunice Lee
- Department of Surgery (Austin Precinct), The University of Melbourne, Heidelberg, Australia.,Hepatopancreatobiliary and Transplant Surgery Unit, Austin Health, Heidelberg, Australia
| | - Adam Testro
- Liver Transplant Unit, Austin Health, Heidelberg, Australia
| | - Vijayaragavan Muralidharan
- Department of Surgery (Austin Precinct), The University of Melbourne, Heidelberg, Australia.,Hepatopancreatobiliary and Transplant Surgery Unit, Austin Health, Heidelberg, Australia
| | - Alexander Dobrovic
- Department of Surgery (Austin Precinct), The University of Melbourne, Heidelberg, Australia.,Translational Genomics and Epigenomics Laboratory, Department of Surgery (Austin Precinct), The University of Melbourne, Heidelberg, Australia
| | - Su Kah Goh
- Department of Surgery (Austin Precinct), The University of Melbourne, Heidelberg, Australia.,Hepatopancreatobiliary and Transplant Surgery Unit, Austin Health, Heidelberg, Australia
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Pascual J, Attard G, Bidard FC, Curigliano G, De Mattos-Arruda L, Diehn M, Italiano A, Lindberg J, Merker JD, Montagut C, Normanno N, Pantel K, Pentheroudakis G, Popat S, Reis-Filho JS, Tie J, Seoane J, Tarazona N, Yoshino T, Turner NC. ESMO recommendations on the use of circulating tumour DNA assays for patients with cancer: a report from the ESMO Precision Medicine Working Group. Ann Oncol 2022; 33:750-768. [PMID: 35809752 DOI: 10.1016/j.annonc.2022.05.520] [Citation(s) in RCA: 164] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 12/16/2022] Open
Abstract
Circulating tumour DNA (ctDNA) assays conducted on plasma are rapidly developing a strong evidence base for use in patients with cancer. The European Society for Medical Oncology convened an expert working group to review the analytical and clinical validity and utility of ctDNA assays. For patients with advanced cancer, validated and adequately sensitive ctDNA assays have utility in identifying actionable mutations to direct targeted therapy, and may be used in routine clinical practice, provided the limitations of the assays are taken into account. Tissue based testing remains the preferred test for many cancer patients, due to limitations of ctDNA assays detecting fusion events and copy number changes, although ctDNA assays may be routinely used when faster results will be clinically important, or when tissue biopsies are not possible or inappropriate. Reflex tumour testing should be considered following a non-informative ctDNA result, due to false negative results with ctDNA testing. In patients treated for early-stage cancers, detection of molecular residual disease (MRD) or molecular relapse (MR), has high evidence of clinical validity in anticipating future relapse in many cancers. MRD/MR detection cannot be recommended in routine clinical practice, as currently there is no evidence for clinical utility in directing treatment. Additional potential applications of ctDNA assays, under research development and not recommended for routine practice, include identifying patients not responding to therapy with early dynamic changes in ctDNA levels, monitoring therapy for the development of resistance mutations prior to clinical progression, and in screening asymptomatic people for cancer. Recommendation for reporting of results, future development of ctDNA assays, and future clinical research are made.
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Affiliation(s)
- Javier Pascual
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Malaga, Spain
| | - Gerhardt Attard
- Urological Cancer Research, University College London, London, UK
| | - François-Clément Bidard
- Department of Medical Oncology, Institut Curie, Paris, France; University of Versailles Saint-Quentin-en-Yvelines (UVSQ)/Paris-Saclay University, Saint Cloud, France
| | - Giuseppe Curigliano
- Department of Oncology and Hemato-Oncology, University of Milano, Milano, Italy; Division of Early Drug Development, European Institute of Oncology, IRCCS, Milano, Italy
| | - Leticia De Mattos-Arruda
- IrsiCaixa, Hospital Universitari Trias i Pujol, Badalona, Spain; Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, US
| | - Antoine Italiano
- Early Phase Trials and Sarcoma Units, Institut Bergonie, Bordeaux, France; DITEP, Gustave Roussy, Villejuif, France; Faculty of Medicine, University of Bordeaux, Bordeaux, France
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden
| | - Jason D Merker
- Departments of Pathology and Laboratory Medicine & Genetics, UNC School of Medicine, Chapel Hill, NC, US
| | - Clara Montagut
- Medical Oncology Department, Hospital del Mar-IMIM, CIBERONC, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, 'Fondazione G. Pascale' - IRCCS, Naples, Italy
| | - Klaus Pantel
- Institute for Tumour Biology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - George Pentheroudakis
- Scientific and Medical Division, European Society for Medical Oncology, Lugano, Switzerland
| | - Sanjay Popat
- Royal Marsden Hospital, London, UK; Institute of Cancer Research, London, UK
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, US
| | - Jeanne Tie
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia; Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Joan Seoane
- Preclinical and Translational Research Programme, Vall d'Hebron Institute of Oncology (VHIO), ICREA, CIBERONC, Barcelona, Spain,; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Noelia Tarazona
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia, Spain; Instituto de Salud Carlos III, CIBERONC, Madrid, Spain
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Nicholas C Turner
- Royal Marsden Hospital, London, UK; Institute of Cancer Research, London, UK
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Krasic J, Skara L, Bojanac AK, Ulamec M, Jezek D, Kulis T, Sincic N. The utility of cfDNA in TGCT patient management: a systematic review. Ther Adv Med Oncol 2022; 14:17588359221090365. [PMID: 35656387 PMCID: PMC9152191 DOI: 10.1177/17588359221090365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/10/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Testicular germ cell tumors (TGCTs) are the most common young male malignancy with a steadily rising incidence. Standard clinical practice is radical orchidectomy of suspicious lumps followed by histopathological diagnosis and tumor subtyping. This practice can lead to complications and quality of life issues for the patients. Liquid biopsies, especially cell-free DNA (cfDNA), promised to be true surrogates for tissue biopsies, which are considered dangerous to perform in cases of testicular tumors. In this study, we have performed a systematic review on the potential of cfDNA in TGCT patient management, its potential challenges in translation to clinical application and possible approaches in further research. Materials & Methods: The review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines on EuropePMC and PUBMED electronic databases, with the last update being on October 21, 2021. Due to the high heterogeneity in identified research articles, we have performed an overview of their efficacy. Results: Eight original articles have been identified on cfDNA in TGCT patients published from 2004 to 2021, of which six had more than one TGCT patient enrolled and were included in the final analysis. Three studies investigated cfDNA methylation, one has investigated mutations in cfDNA, two have investigated cfDNA amount, and one has investigated cfDNA integrity in TGCT. The sensitivity of cfDNA for TGCT was found to be higher than in serum tumor markers and lower than miR-371a-3p, with comparable specificity. cfDNA methylation analysis has managed to accurately detect teratoma in TGCT patients. Conclusion: Potential challenges in cfDNA application to TGCT patient management were identified. The challenges relating to the biology of TGCT with its low mutational burden and low cfDNA amounts in blood plasma make next-generation sequencing (NGS) methods especially challenging. We have also proposed possible approaches to help find clinical application, including a focus on cfDNA methylation analysis, and potentially solving the challenge of teratoma detection.
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Affiliation(s)
- Jure Krasic
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Group for Research on Epigenetic Biomarkers (Epimark), School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Lucija Skara
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Group for Research on Epigenetic Biomarkers (Epimark), School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Ana Katusic Bojanac
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Monika Ulamec
- Group for Research on Epigenetic Biomarkers (Epimark), School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Ljudevit Jurak Clinical Department of Pathology and Cytology, University Clinical Hospital Center Sestre Milosrdnice, Zagreb, Croatia
- Department of Pathology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Davor Jezek
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Histology and Embryology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Tomislav Kulis
- Group for Research on Epigenetic Biomarkers (Epimark), School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Urology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Nino Sincic
- Department of Medical Biology, School of Medicine, University of Zagreb, Šalata 3, Zagreb, 10 000, Croatia
- Group for Research on Epigenetic Biomarkers (Epimark), School of Medicine, University of Zagreb, Šalata 3, Zagreb, 10 000, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, Zagreb, 10 000, Croatia
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Donker HC, Schuuring E, Heitzer E, Groen HJ. Decoding circulating tumor DNA to identify durable benefit from immunotherapy in lung cancer. Lung Cancer 2022; 170:52-57. [DOI: 10.1016/j.lungcan.2022.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 11/28/2022]
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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] [What about the content of this article? (0)] [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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Haselmann V, Hedtke M, Neumaier M. Liquid Profiling for Cancer Patient Stratification in Precision Medicine—Current Status and Challenges for Successful Implementation in Standard Care. Diagnostics (Basel) 2022; 12:diagnostics12030748. [PMID: 35328301 PMCID: PMC8947441 DOI: 10.3390/diagnostics12030748] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 12/13/2022] Open
Abstract
Circulating tumor DNA (ctDNA), accurately described by the term liquid profiling (LP), enables real-time assessment of the tumor mutational profile as a minimally invasive test and has therefore rapidly gained traction, particular for the management of cancer patients. By LP, tumor-specific genetic alterations can be determined as part of companion diagnostics to guide selection of appropriate targeted therapeutics. Because LP facilitates longitudinal monitoring of cancer patients, it can be used to detect acquired resistant mechanisms or as a personalized biomarker for earlier detection of disease recurrence, among other applications. However, LP is not yet integrated into routine care to the extent that might be expected. This is due to the lack of harmonization and standardization of preanalytical and analytical workflows, the lack of proper quality controls, limited evidence of its clinical utility, heterogeneous study results, the uncertainty of clinicians regarding the value and appropriate indications for LP and its interpretation, and finally, the lack of reimbursement for most LP tests. In this review, the value proposition of LP for cancer patient management and treatment optimization, the current status of implementation in standard care, and the main challenges that need to be overcome are discussed in detail.
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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 DOI: 10.1016/j.esmoop.2022.100399] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [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. LB is a rapidly evolving diagnostic tool that may be an adjunct or an alternative to TB in clinic. Pragmatic scenarios for ctDNA mutation testing to identify actionable targets in NSCLC are explored. ctDNA mutation testing may identify resistance mechanisms, discordant clinical history, and intertumor/intratumor heterogeneity. ctDNA mutation testing may be useful if the tumor location is hard to biopsy or if an insufficient tumor sample was taken. Proper implementation of ctDNA mutation testing in routine clinical practice is envisioned in the near future.
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40
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Hudecova I, Smith CG, Hänsel-Hertsch R, Chilamakuri CS, Morris JA, Vijayaraghavan A, Heider K, Chandrananda D, Cooper WN, Gale D, Garcia-Corbacho J, Pacey S, Baird RD, Rosenfeld N, Mouliere F. Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA. Genome Res 2022; 32:215-227. [PMID: 34930798 PMCID: PMC8805718 DOI: 10.1101/gr.275691.121] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 12/16/2021] [Indexed: 11/24/2022]
Abstract
Current evidence suggests that plasma cell-free DNA (cfDNA) is fragmented around a mode of 166 bp. Data supporting this view has been mainly acquired through the analysis of double-stranded cfDNA. The characteristics and diagnostic potential of single-stranded and damaged double-stranded cfDNA in healthy individuals and cancer patients remain unclear. Here, through a combination of high-affinity magnetic bead-based DNA extraction and single-stranded DNA sequencing library preparation (MB-ssDNA), we report the discovery of a large proportion of cfDNA fragments centered at ∼50 bp. We show that these "ultrashort" cfDNA fragments have a greater relative abundance in plasma of healthy individuals (median = 19.1% of all sequenced cfDNA fragments, n = 28) than in plasma of patients with cancer (median = 14.2%, n = 21, P < 0.0001). The ultrashort cfDNA fragments map to accessible chromatin regions of blood cells, particularly in promoter regions with the potential to adopt G-quadruplex (G4) DNA secondary structures. G4-positive promoter chromatin accessibility is significantly enriched in ultrashort plasma cfDNA fragments from healthy individuals relative to patients with cancers (P < 0.0001), in whom G4-cfDNA enrichment is inversely associated with copy number aberration-inferred tumor fractions. Our findings redraw the landscape of cfDNA fragmentation by identifying and characterizing a novel population of ultrashort plasma cfDNA fragments. Sequencing of MB-ssDNA libraries could facilitate the characterization of gene regulatory regions and DNA secondary structures via liquid biopsy. Our data underline the diagnostic potential of ultrashort cfDNA through classification for cancer patients.
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Affiliation(s)
- Irena Hudecova
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Christopher G Smith
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Robert Hänsel-Hertsch
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Center for Molecular Medicine Cologne CMMC, University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital Cologne, 50931 Cologne, Germany
- Institute of Human Genetics, University Hospital Cologne, 50931 Cologne, Germany
| | - Chandra S Chilamakuri
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - James A Morris
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Aadhitthya Vijayaraghavan
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Katrin Heider
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Dineika Chandrananda
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Wendy N Cooper
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Davina Gale
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Javier Garcia-Corbacho
- Clinical Trials Unit, Clinic Institute of Hematological and Oncological Diseases, Hospital Clinic, 170 08036 Barcelona, Spain
| | - Simon Pacey
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Richard D Baird
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Florent Mouliere
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Centre Amsterdam, 1081 HV Amsterdam, The Netherlands
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Cisneros-Villanueva M, Hidalgo-Pérez L, Rios-Romero M, Cedro-Tanda A, Ruiz-Villavicencio CA, Page K, Hastings R, Fernandez-Garcia D, Allsopp R, Fonseca-Montaño MA, Jimenez-Morales S, Padilla-Palma V, Shaw JA, Hidalgo-Miranda A. Cell-free DNA analysis in current cancer clinical trials: a review. Br J Cancer 2022; 126:391-400. [PMID: 35027672 PMCID: PMC8810765 DOI: 10.1038/s41416-021-01696-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/06/2021] [Accepted: 12/23/2021] [Indexed: 12/13/2022] Open
Abstract
Cell-free DNA (cfDNA) analysis represents a promising method for the diagnosis, treatment selection and clinical follow-up of cancer patients. Although its general methodological feasibility and usefulness has been demonstrated, several issues related to standardisation and technical validation must be addressed for its routine clinical application in cancer. In this regard, most cfDNA clinical applications are still limited to clinical trials, proving its value in several settings. In this paper, we review the current clinical trials involving cfDNA/ctDNA analysis and highlight those where it has been useful for patient stratification, treatment follow-up or development of novel approaches for early diagnosis. Our query included clinical trials, including the terms 'cfDNA', 'ctDNA', 'liquid biopsy' AND 'cancer OR neoplasm' in the FDA and EMA public databases. We identified 1370 clinical trials (FDA = 1129, EMA = 241) involving liquid-biopsy analysis in cancer. These clinical trials show promising results for the early detection of cancer and confirm cfDNA as a tool for real-time monitoring of acquired therapy resistance, accurate disease-progression surveillance and improvement of treatment, situations that result in a better quality of life and extended overall survival for cancer patients.
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Affiliation(s)
- M Cisneros-Villanueva
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - L Hidalgo-Pérez
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - M Rios-Romero
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - A Cedro-Tanda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - C A Ruiz-Villavicencio
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - K Page
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - R Hastings
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - D Fernandez-Garcia
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - R Allsopp
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - M A Fonseca-Montaño
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - S Jimenez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - V Padilla-Palma
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - J A Shaw
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - A Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico.
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Weber S, van der Leest P, Donker HC, Schlange T, Timens W, Tamminga M, Hasenleithner SO, Graf R, Moser T, Spiegl B, Yaspo ML, Terstappen LWMM, Sidorenkov G, Hiltermann TJN, Speicher MR, Schuuring E, Heitzer E, Groen HJM. Dynamic Changes of Circulating Tumor DNA Predict Clinical Outcome in Patients With Advanced Non-Small-Cell Lung Cancer Treated With Immune Checkpoint Inhibitors. JCO Precis Oncol 2022; 5:1540-1553. [PMID: 34994642 DOI: 10.1200/po.21.00182] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
PURPOSE Immune checkpoint inhibitors (ICIs) are increasingly being used in non-small-cell lung cancer (NSCLC), yet biomarkers predicting their benefit are lacking. We evaluated if on-treatment changes of circulating tumor DNA (ctDNA) from ICI start (t0) to after two cycles (t1) assessed with a commercial panel could identify patients with NSCLC who would benefit from ICI. PATIENTS AND METHODS The molecular ctDNA response was evaluated as a predictor of radiographic tumor response and long-term survival benefit of ICI. To maximize the yield of ctDNA detection, de novo mutation calling was performed. Furthermore, the impact of clonal hematopoiesis (CH)-related variants as a source of biologic noise was investigated. RESULTS After correction for CH-related variants, which were detected in 75 patients (44.9%), ctDNA was detected in 152 of 167 (91.0%) patients. We observed only a fair agreement of the molecular and radiographic response, which was even more impaired by the inclusion of CH-related variants. After exclusion of those, a ≥ 50% molecular response improved progression-free survival (10 v 2 months; hazard ratio [HR], 0.55; 95% CI, 0.39 to 0.77; P = .0011) and overall survival (18.4 v 5.9 months; HR, 0.44; 95% CI, 0.31 to 0.62; P < .0001) compared with patients not achieving this end point. After adjusting for clinical variables, ctDNA response and STK11/KEAP1 mutations (HR, 2.08; 95% CI, 1.4 to 3.0; P < .001) remained independent predictors for overall survival, irrespective of programmed death ligand-1 expression. A landmark survival analysis at 2 months (n = 129) provided similar results. CONCLUSION On-treatment changes of ctDNA in plasma reveal predictive information for long-term clinical benefit in ICI-treated patients with NSCLC. A broader NSCLC patient coverage through de novo mutation calling and the use of a variant call set excluding CH-related variants improved the classification of molecular responders, but had no significant impact on survival.
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Affiliation(s)
- Sabrina Weber
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Paul van der Leest
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, the Netherlands
| | - Hylke C Donker
- Department of Pulmonary Diseases, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, the Netherlands
| | - Menno Tamminga
- Department of Pulmonary Diseases, University Medical Center Groningen, Groningen, the Netherlands
| | - Samantha O Hasenleithner
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Ricarda Graf
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Tina Moser
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Benjamin Spiegl
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Marie-Laure Yaspo
- Max Plank Institute for Molecular Genetics, Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Berlin, Germany
| | | | - Grigory Sidorenkov
- Department of Epidemiology, University Medical Center Groningen, Groningen, the Netherlands
| | - T Jeroen N Hiltermann
- Department of Pulmonary Diseases, University Medical Center Groningen, Groningen, the Netherlands
| | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, the Netherlands
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Harry J M Groen
- Department of Pulmonary Diseases, University Medical Center Groningen, Groningen, the Netherlands
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Abstract
Broad molecular profiling by next-generation sequencing of solid tumors has become a critical tool for clinical decision-making in the era of precision oncology. In addition to many already approved targeted therapies, more than half of ongoing oncology-related clinical trials are biomarker-driven. Therefore, accurate and reliable assays are needed to assess the genetic make-up of tumor cells and guide clinicians in the therapy decision process. In order to obtain high-quality NGS data for variant detection, certain preanalytical steps and quality metrics should be followed. These include assessment of sample types, choice of extraction method, library preparation technology, sequencing platform, and finally sequencing quality control. Each of these steps has certain challenges and pitfalls that need to be addressed and overcome, respectively. In this chapter, we address the preanalytical quality control and how each of the involved steps may influence the final result. Following these guidelines and QC metrics may help in obtaining optimal results that will allow the precise and robust assessment of genetic variants in a clinical setting.
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Affiliation(s)
- Ilaria Alborelli
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Philip M Jermann
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.
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47
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Žvirblytė J, Mažutis L. Microfluidics for Cancer Biomarker Discovery, Research, and Clinical Application. Microfluidics and Biosensors in Cancer Research 2022; 1379:499-524. [DOI: 10.1007/978-3-031-04039-9_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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48
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Bang-Christensen SR, Katerov V, Jørgensen AM, Gustavsson T, Choudhary S, Theander TG, Salanti A, Allawi HT, Agerbæk MØ. Detection of VAR2CSA-Captured Colorectal Cancer Cells from Blood Samples by Real-Time Reverse Transcription PCR. Cancers (Basel) 2021; 13:5881. [PMID: 34884994 DOI: 10.3390/cancers13235881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/18/2021] [Accepted: 11/21/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Circulating tumor cells are cancer cells that have entered blood or lymphatic vessels wherefrom they might get access to distant body parts and form metastases. The presence of cancer cells in a blood sample can be exploited for non-invasive diagnostic purposes. However, as blood consists of a vast number of healthy red and white blood cells the task of identifying the few potential cancer cells in a sample is a technical challenge. In this study we explore strategies for detecting circulating tumor cells after a pre-enrichment through binding to VAR2CSA protein coupled to magnetic beads. We evaluate the performance of a novel workflow that recognizes and detects the cancer cells based on their gene expression and compare this with the more traditional detection strategy using antibodies for cell staining. The highly sensitive assay presented here could potentially provide a novel strategy for early cancer detection. Abstract Analysis of circulating tumor cells (CTCs) from blood samples provides a non-invasive approach for early cancer detection. However, the rarity of CTCs makes it challenging to establish assays with the required sensitivity and specificity. We combine a highly sensitive CTC capture assay exploiting the cancer cell binding recombinant malaria VAR2CSA protein (rVAR2) with the detection of colon-related mRNA transcripts (USH1C and CKMT1A). Cancer cell transcripts are detected by RT-qPCR using proprietary Target Enrichment Long-probe Quantitative Amplified Signal (TELQAS) technology. We validate each step of the workflow using colorectal cancer (CRC) cell lines spiked into blood and compare this with antibody-based cell detection. USH1C and CKMT1A are expressed in healthy colon tissue and CRC cell lines, while only low-level expression can be detected in healthy white blood cells (WBCs). The qPCR reaction shows a near-perfect amplification efficiency for all primer targets with minimal interference of WBC cDNA. Spike-in of 10 cancer cells in 3 mL blood can be detected and statistically separated from control blood using the RT-qPCR assay after rVAR2 capture (p < 0.01 for both primer targets, Mann-Whitney test). Our results provide a validated workflow for highly sensitive detection of magnetically enriched cancer cells.
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van der Leest P, Hiddinga B, Miedema A, Aguirre Azpurua ML, Rifaela N, ter Elst A, Timens W, Groen HJM, van Kempen LC, Hiltermann TJN, Schuuring E. Circulating tumor DNA as a biomarker for monitoring early treatment responses of patients with advanced lung adenocarcinoma receiving immune checkpoint inhibitors. Mol Oncol 2021; 15:2910-2922. [PMID: 34449963 PMCID: PMC8564646 DOI: 10.1002/1878-0261.13090] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/27/2021] [Accepted: 08/25/2021] [Indexed: 11/07/2022] Open
Abstract
Immunotherapy for metastasized non-small-cell lung cancer (NSCLC) can show long-lasting clinical responses. Selection of patients based on programmed death-ligand 1 (PD-L1) expression shows limited predictive value for durable clinical benefit (DCB). We investigated whether early treatment effects as measured by a change in circulating tumor DNA (ctDNA) level is a proxy of early tumor response to immunotherapy according to response evaluation criteria in solid tumors v1.1 criteria, progression-free survival (PFS), DCB, and overall survival (OS). To this aim, blood tubes were collected from advanced-stage lung adenocarcinoma patients (n = 100) receiving immune checkpoint inhibitors (ICI) at baseline (t0 ) and prior to first treatment evaluation (4-6 weeks; t1 ). Nontargetable (driver) mutations detected in the pretreatment tumor biopsy were used to quantify tumor-specific ctDNA levels using droplet digital PCR. We found that changes in ctDNA levels were strongly associated with tumor response. A > 30% decrease in ctDNA at t1 correlated with a longer PFS and OS. In total, 80% of patients with a DCB of ≥ 26 weeks displayed a > 30% decrease in ctDNA levels. For patients with a PD-L1 tumor proportion score of ≥ 1%, decreasing ctDNA levels were associated with a higher frequency a DCB (80%) and a prolonged median PFS (85 weeks) and OS (101 weeks) compared with patients with no decrease in ctDNA (34%; 11 and 39 weeks, respectively). This study shows that monitoring of ctDNA dynamics is an easy-to-use and promising tool for assessing PFS, DCB, and OS for ICI-treated NSCLC patients.
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Affiliation(s)
- Paul van der Leest
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Birgitta Hiddinga
- Department of Pulmonary DiseasesUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Anneke Miedema
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Maria L. Aguirre Azpurua
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Naomi Rifaela
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Arja ter Elst
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Wim Timens
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Harry J. M. Groen
- Department of Pulmonary DiseasesUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Léon C. van Kempen
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - T. Jeroen N. Hiltermann
- Department of Pulmonary DiseasesUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Ed Schuuring
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
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Krasic J, Abramovic I, Vrtaric A, Nikolac Gabaj N, Kralik-Oguic S, Katusic Bojanac A, Jezek D, Sincic N. Impact of Preanalytical and Analytical Methods on Cell-Free DNA Diagnostics. Front Cell Dev Biol 2021; 9:686149. [PMID: 34552921 PMCID: PMC8451956 DOI: 10.3389/fcell.2021.686149] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/13/2021] [Indexed: 01/18/2023] Open
Abstract
While tissue biopsy has for the longest time been the gold-standard in biomedicine, precision/personalized medicine is making the shift toward liquid biopsies. Cell-free DNA (cfDNA) based genetic and epigenetic biomarkers reflect the molecular status of its tissue-of-origin allowing for early and non-invasive diagnostics of different pathologies. However, selection of preanalytical procedures (including cfDNA isolation) as well as analytical methods are known to impact the downstream results. Calls for greater standardization are made continuously, yet comprehensive assessments of the impact on diagnostic parameters are lacking. This study aims to evaluate the preanalytic and analytic factors that influence cfDNA diagnostic parameters in blood and semen. Text mining analysis has been performed to assess cfDNA research trends, and identify studies on isolation methods, preanalytical and analytical impact. Seminal and blood plasma were tested as liquid biopsy sources. Traditional methods of cfDNA isolation, commercial kits (CKs), and an in-house developed protocol were tested, as well as the impact of dithiothreitol (DTT) on cfDNA isolation performance. Fluorimetry, qPCR, digital droplet PCR (ddPCR), and bioanalyzer were compared as cfDNA quantification methods. Fragment analysis was performed by qPCR and bioanalyzer while the downstream application (cfDNA methylation) was analyzed by pyrosequencing. In contrast to blood, semen as a liquid biopsy source has only recently begun to be reported as a liquid biopsy source, with almost half of all publications on it being review articles. Experimental data revealed that cfDNA isolation protocols give a wide range of cfDNA yields, both from blood and seminal plasma. The addition of DTT to CKs has improved yields in seminal plasma and had a neutral/negative impact in blood plasma. Capillary electrophoresis and fluorometry reported much higher yields than PCR methods. While cfDNA yield and integrity were highly impacted, cfDNA methylation was not affected by isolation methodology or DTT. In conclusion, NucleoSnap was recognized as the kit with the best overall performance. DTT improved CK yields in seminal plasma. The in-house developed protocol has shown near-kit isolation performance. ddPCR LINE-1 assay for absolute detection of minute amounts of cfDNA was established and allowed for quantification of samples inhibited in qPCR. cfDNA methylation was recognized as a stable biomarker unimpacted by cfDNA isolation method. Finally, semen was found to be an abundant source of cfDNA offering potential research opportunities and benefits for cfDNA based biomarkers development related to male reproductive health.
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Affiliation(s)
- Jure Krasic
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Irena Abramovic
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Alen Vrtaric
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Clinical Chemistry, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
| | - Nora Nikolac Gabaj
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Clinical Chemistry, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Sasa Kralik-Oguic
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Clinical Institute of Laboratory Diagnostics, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Ana Katusic Bojanac
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Davor Jezek
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Histology and Embryology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Nino Sincic
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
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