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Peng H, Pan M, Zhou Z, Chen C, Xing X, Cheng S, Zhang S, Zheng H, Qian K. The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples. Front Cell Dev Biol 2024; 12:1385041. [PMID: 38784382 PMCID: PMC11111958 DOI: 10.3389/fcell.2024.1385041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Cell-free DNA (cfDNA), a burgeoning class of molecular biomarkers, has been extensively studied across a variety of biomedical fields. As a key component of liquid biopsy, cfDNA testing is gaining prominence in disease detection and management due to the convenience of sample collection and the abundant wealth of genetic information it provides. However, the broader clinical application of cfDNA is currently impeded by a lack of standardization in the preanalytical procedures for cfDNA analysis. A number of fundamental challenges, including the selection of appropriate preanalytical procedures, prevention of short cfDNA fragment loss, and the validation of various cfDNA measurement methods, remain unaddressed. These existing hurdles lead to difficulties in comparing results and ensuring repeatability, thereby undermining the reliability of cfDNA analysis in clinical settings. This review discusses the crucial preanalytical factors that influence cfDNA analysis outcomes, including sample collection, transportation, temporary storage, processing, extraction, quality control, and long-term storage. The review provides clarification on achievable consensus and offers an analysis of the current issues with the goal of standardizing preanalytical procedures for cfDNA analysis.
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Affiliation(s)
- Hongwei Peng
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ming Pan
- Taihe Skills Training Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zongning Zhou
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Congbo Chen
- Department of Urology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xing Xing
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shaoping Cheng
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shanshan Zhang
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hang Zheng
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
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2
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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] [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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3
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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] [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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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] [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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Kramer A, Rubio-Alarcón C, van den Broek D, Vessies DCL, Van't Erve I, Meijer GA, Vink GR, Schuuring E, Fijneman RJA, Coupé VMH, Retèl VP. A scenario-drafting study to explore potential future implementation pathways of circulating tumor DNA testing in oncology. Mol Oncol 2023. [PMID: 38060377 DOI: 10.1002/1878-0261.13562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/17/2023] [Accepted: 12/05/2023] [Indexed: 01/13/2024] Open
Abstract
Circulating tumor DNA (ctDNA) detection has multiple promising applications in oncology, but the road toward implementation in clinical practice is unclear. We aimed to support the implementation process by exploring potential future pathways of ctDNA testing. To do so, we studied four ctDNA-testing applications in two cancer types and elicited opinions from 30 ctDNA experts in the Netherlands. Our results showed that the current available evidence differed per application and cancer type. Tumor profiling and monitoring treatment response were found most likely to be implemented in non-small cell lung cancer (NSCLC) within 5 years. For colorectal cancer, applications of ctDNA testing were found to be at an early stage in the implementation process. Demonstrating clinical utility was found a key aspect for successful implementation, but there was no consensus regarding the evidence requirements. The next step toward implementation is to define how clinical utility of biomarkers should be evaluated. Finally, these data indicate that specific challenges for each clinical application and tumor type should be appropriately addressed in a deliberative process involving all stakeholders to ensure implementation of ctDNA testing and timely access for patients.
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Affiliation(s)
- Astrid Kramer
- Department of Epidemiology and Data Science, Amsterdam UMC, The Netherlands
| | - Carmen Rubio-Alarcón
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan C L Vessies
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Iris Van't Erve
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Geraldine R Vink
- Department of Medical Oncology, University Medical Center Utrecht, University of Utrecht, The Netherlands
- Department of Research and Development, IKNL, Utrecht, The Netherlands
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University Medical Center Groningen, The Netherlands
| | - Remond J A Fijneman
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Veerle M H Coupé
- Department of Epidemiology and Data Science, Amsterdam UMC, The Netherlands
| | - Valesca P Retèl
- Department of Psychosocial Research and Epidemiology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Erasmus School of Health Policy and Management, Erasmus University Rotterdam, The Netherlands
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6
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Ntzifa A, Lianidou E. Pre-analytical conditions and implementation of quality control steps in liquid biopsy analysis. Crit Rev Clin Lab Sci 2023; 60:573-594. [PMID: 37518938 DOI: 10.1080/10408363.2023.2230290] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023]
Abstract
Over the last decade, great advancements have been made in the field of liquid biopsy through extensive research and the development of new technologies that facilitate the use of liquid biopsy for cancer patients. This is shown by the numerous liquid biopsy tests that gained clearance by the US Food and Drug Administration (FDA) in recent years. Liquid biopsy has significantly altered cancer treatment by providing clinicians with powerful and immediate information about therapeutic decisions. However, the clinical integration of liquid biopsy is still challenging and there are many critical factors to consider prior to its implementation into routine clinical practice. Lack of standardization due to technical challenges and the definition of the clinical utility of specific assays further complicates the establishment of Standard Operating Procedures (SOPs) in liquid biopsy. Harmonization of laboratories to established guidelines is of major importance to overcome inter-lab variabilities observed. Quality control assessment in diagnostic laboratories that offer liquid biopsy testing will ensure that clinicians can base their therapeutic decisions on robust results. The regular participation of laboratories in external quality assessment schemes for liquid biopsy testing aims to promptly pinpoint deficiencies and efficiently educate laboratories to improve their quality of services. Accreditation of liquid biopsy diagnostic laboratories based on the ISO15189 standard in Europe or by CLIA/CAP accreditation procedures in the US is the best way to achieve the adaptation of liquid biopsy into the clinical setting by assuring reliable results for the clinicians and their cancer patients. Nowadays, various organizations from academia, industry, and regulatory agencies collaborate to set a framework that will include all procedures from the pre-analytical phase and the analytical process to the final interpretation of results. In this review, we underline several challenges in the analysis of circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) concerning standardization of protocols, quality control assessment, harmonization of laboratories, and compliance to specific guidelines that need to be thoroughly considered before liquid biopsy enters the clinic.
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Affiliation(s)
- Aliki Ntzifa
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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7
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Ruppert T, Roth A, Kollmeier J, Mairinger T, Frost N. Cell-free DNA extraction from urine of lung cancer patients and healthy individuals: Evaluation of a simple method using sample volume up-scaling. J Clin Lab Anal 2023; 37:e24984. [PMID: 37991151 PMCID: PMC10749489 DOI: 10.1002/jcla.24984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Urine holds promise as a source for cell-free DNA (cfDNA) analysis of cancer genetics due to its nature as a self-collectable biospecimen available in large quantities. However, pre-analytical variables such as preservation of cfDNA or efficiency of up-scaling specimen volume need to be better explored to increase analysis sensitivity. PATIENTS AND METHODS Initially effects of pH levels on cfDNA stability of urine preserved with EDTA were investigated in three healthy probands. Furthermore, the efficiency of urine volume up-scaling was examined using a simple DNA extraction method and cfDNA in urine of 32 individuals. Quantification was performed by PCR detection of three relevant targets used for EGFR and KRAS gene mutational analysis. RESULTS Only samples preserved with EDTA at alkaline pH levels showed cfDNA stability of up to 10 days at room temperature. Moreover, it was found that increasing the volume up to 100 mL was highly efficient. A similar amount of copies was detected in three different gene sites in all specimens indicating both a good availability and a non-random distribution pattern across genes. Since the median cfDNA copy number was 1642 copies/mL, abundance of cfDNA in this type of liquid biopsy is low. CONCLUSION Predictable sensitivities with different urine volumes on the ground of detectable cfDNA in our study population revealed that up-scaling (>5 mL) is mandatory if the mutation allele frequency is less than 1%.
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Affiliation(s)
- Tilman Ruppert
- Department of PathologyHelios Klinikum Emil von BehringBerlinGermany
| | - Andreas Roth
- Department of PathologyHelios Klinikum Emil von BehringBerlinGermany
| | - Jens Kollmeier
- Department of PneumologyHelios Klinikum Emil von BehringBerlinGermany
| | - Thomas Mairinger
- Department of PathologyHelios Klinikum Emil von BehringBerlinGermany
| | - Nikolaj Frost
- Department of PneumologyCharité ‐ Universitätsmedizin BerlinBerlinGermany
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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: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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9
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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: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [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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Global Trends in Research on Cell-Free Nucleic Acids in Obstetrics and Gynecology during 2017–2021. J Clin Med 2022; 11:jcm11195545. [PMID: 36233412 PMCID: PMC9572904 DOI: 10.3390/jcm11195545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/14/2022] [Accepted: 09/18/2022] [Indexed: 11/16/2022] Open
Abstract
Objectives. The objectives of this study were to identify global trends in research on cell-free deoxyribonucleic acid (cfDNA) from a bibliometric perspective and provide researchers with new research hotspots. Methods. In all, we extracted 5038 pieces of literature from PubMed and 527 articles from the Web of Science Core Collection (WoSCC) database related to cfDNA published from 1 January 2017 to 31 December 2021. For PubMed literature, we employed co-word, biclustering, and strategic diagram analysis to describe the trends in research on cfDNA in the said five years. Then, we used VOSviewer analysis for the WoSCC database to display the trends in research on cfDNA in obstetrics and gynecology during 2017–2021. Results. Strategy diagram analysis of 95 major Medical Subject Headings terms extracted from 5038 pieces of literature indicated that cfDNA sequence analysis for non-invasive prenatal and genetic testing and its application in the fields of neoplasm genetics and diagnosis is a newly emerging immature theme of cfDNA. VOSviewer analysis of 527 articles showed the global trends in research on cfDNA in obstetrics and gynecology, for example, in terms of most influential authors, institutions, countries, journals, and five research hotspots: (1) cfDNA application in prenatal screening and prenatal diagnosis, (2) cfDNA application in assisted reproductive technology, (3) cfDNA application in pre-eclampsia, DNA methylation, etc., (4) cfDNA application in placental dysfunction and fetal growth restriction, and (5) cfDNA application in fetal chromosomal abnormalities (fetal aneuploidy). Conclusions. Comprehensive visual analysis provides information regarding authors, organizations, countries/regions, journals, research hotspots, and emerging topics in the field of cfDNA for obstetrics and gynecology research. This comprehensive study could make it easier to find a partner for project development and build a network of knowledge on this emerging topic.
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Seong H, Park J, Bae M, Shin S. Rapid and Efficient Extraction of Cell-Free DNA Using Homobifunctional Crosslinkers. Biomedicines 2022; 10:biomedicines10081883. [PMID: 36009429 PMCID: PMC9405790 DOI: 10.3390/biomedicines10081883] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/31/2022] [Accepted: 08/01/2022] [Indexed: 11/25/2022] Open
Abstract
Since its discovery in circulating blood seven decades ago, cell-free DNA (cfDNA) has become a highly focused subject in cancer management using liquid biopsy. Despite its clinical utility, the extraction of cfDNA from blood has many technical difficulties, including a low efficiency of recovery and long processing times. We introduced a magnetic bead-based cfDNA extraction method using homobifunctional crosslinkers, including dimethyl suberimidate dihydrochloride (DMS). Owing to its bifunctional nature, DMS can bind to DNA through either covalent or electrostatic bonding. By adopting amine-conjugated magnetic beads, DMS–DNA complexes can be rapidly isolated from blood plasma. Using standard washing and eluting processes, we successfully extracted cfDNA from plasma within 10 min. This method yielded a 56% higher extraction efficiency than that of a commercial product (QIAamp kit). Furthermore, the instant binding mechanism of amine coupling between the microbeads and DMS–DNA complexes significantly reduced the processing time. These results highlight the potential of this magnetic bead-based homobifunctional crosslinker platform for extraction of cfDNA from blood plasma.
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Affiliation(s)
- HyeonAh Seong
- School of Mechanical engineering, Korea University, Seoul 02841, Korea
| | - Junsoo Park
- Department of Micro-Nano Engineering, Korea University, Seoul 02841, Korea
| | - Minju Bae
- School of Mechanical engineering, Korea University, Seoul 02841, Korea
| | - Sehyun Shin
- School of Mechanical engineering, Korea University, Seoul 02841, Korea
- Department of Micro-Nano Engineering, Korea University, Seoul 02841, Korea
- Engineering Research Center for Biofluid Biopsy, Seoul 02841, Korea
- Correspondence: ; Tel.: +82-10-4506-2825
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