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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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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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Abstract
The PCR technique has been known to the general public since the pandemic outbreak of COVID-19. This technique has progressed through three stages: from simple PCR to real-time fluorescence PCR to digital PCR. Among them, the microfluidic-based droplet digital PCR technique has attracted much attention and has been widely applied due to its advantages of high throughput, high sensitivity, low reagent consumption, low cross-contamination, and absolute quantification ability. In this review, we introduce various designs of microfluidic-based ddPCR developed within the last decade. The microfluidic-based droplet generation methods, thermal cycle strategies, and signal counting approaches are described, and the applications in the fields of single-cell analysis, disease diagnosis, and pathogen detection are introduced. Further, the challenges and prospects of microfluidic-based ddPCR are discussed. We hope that this review can contribute to the further development of the microfluidic-based ddPCR technique.
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Affiliation(s)
- Danfeng Xu
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China.
| | - Weifei Zhang
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China.
| | - Hongmei Li
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China.
| | - Nan Li
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), China.
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), China.
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Fisher T, Ford CE, Warton K. Recovery Efficiency of Cell-Free DNA After Bisulfite Conversion. Clin Chem 2022; 68:1219-1220. [PMID: 35853844 DOI: 10.1093/clinchem/hvac107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Teagan Fisher
- Gynaecological Cancer Research Group, Adult Cancer Program, Department of Obstetrics and Gynaecology, School of Clinical Medicine, Faculty of Medicine and Health, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
| | - Caroline E Ford
- Gynaecological Cancer Research Group, Adult Cancer Program, Department of Obstetrics and Gynaecology, School of Clinical Medicine, Faculty of Medicine and Health, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
| | - Kristina Warton
- Gynaecological Cancer Research Group, Adult Cancer Program, Department of Obstetrics and Gynaecology, School of Clinical Medicine, Faculty of Medicine and Health, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
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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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Hodges A, Boral D. Spiking the Punch: CEREBIS for Standardizing cfDNA Recovery Efficiencies. Clin Chem 2021; 67:1169-1171. [PMID: 34323994 DOI: 10.1093/clinchem/hvab119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 06/17/2021] [Indexed: 11/12/2022]
Affiliation(s)
- Alan Hodges
- Center for Immunotherapy Research, Cancer Center of Excellence, Houston Methodist Research Institute, Houston, TX.,Texas A&M University System Health Science Center College of Medicine, Bryan, TX
| | - Debasish Boral
- Center for Immunotherapy Research, Cancer Center of Excellence, Houston Methodist Research Institute, Houston, TX
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