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Whale AS, Jones GM, Pavšič J, Dreo T, Redshaw N, Akyürek S, Akgöz M, Divieto C, Sassi MP, He HJ, Cole KD, Bae YK, Park SR, Deprez L, Corbisier P, Garrigou S, Taly V, Larios R, Cowen S, O'Sullivan DM, Bushell CA, Goenaga-Infante H, Foy CA, Woolford AJ, Parkes H, Huggett JF, Devonshire AS. Assessment of Digital PCR as a Primary Reference Measurement Procedure to Support Advances in Precision Medicine. Clin Chem 2018; 64:1296-1307. [PMID: 29903874 DOI: 10.1373/clinchem.2017.285478] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/24/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND Genetic testing of tumor tissue and circulating cell-free DNA for somatic variants guides patient treatment of many cancers. Such measurements will be fundamental in the future support of precision medicine. However, there are currently no primary reference measurement procedures available for nucleic acid quantification that would support translation of tests for circulating tumor DNA into routine use. METHODS We assessed the accuracy of digital PCR (dPCR) for copy number quantification of a frequently occurring single-nucleotide variant in colorectal cancer (KRAS c.35G>A, p.Gly12Asp, from hereon termed G12D) by evaluating potential sources of uncertainty that influence dPCR measurement. RESULTS Concentration values for samples of KRAS G12D and wild-type plasmid templates varied by <1.2-fold when measured using 5 different assays with varying detection chemistry (hydrolysis, scorpion probes, and intercalating dyes) and <1.3-fold with 4 commercial dPCR platforms. Measurement trueness of a selected dPCR assay and platform was validated by comparison with an orthogonal method (inductively coupled plasma mass spectrometry). The candidate dPCR reference measurement procedure showed linear quantification over a wide range of copies per reaction and high repeatability and interlaboratory reproducibility (CV, 2%-8% and 5%-10%, respectively). CONCLUSIONS This work validates dPCR as an SI-traceable reference measurement procedure based on enumeration and demonstrates how it can be applied for assignment of copy number concentration and fractional abundance values to DNA reference materials in an aqueous solution. High-accuracy measurements using dPCR will support the implementation and traceable standardization of molecular diagnostic procedures needed for advancements in precision medicine.
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Affiliation(s)
| | - Gerwyn M Jones
- Molecular and Cell Biology Team, LGC, Teddington, Middlesex, UK
| | - Jernej Pavšič
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Tanja Dreo
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
| | | | - Sema Akyürek
- TUBITAK National Metrology Institute (TUBITAK UME), Bioanalysis Laboratory, Gebze, Kocaeli, Turkey
| | - Müslüm Akgöz
- TUBITAK National Metrology Institute (TUBITAK UME), Bioanalysis Laboratory, Gebze, Kocaeli, Turkey
| | - Carla Divieto
- INRIM Istituto Nazionale di Ricerca Metrologica, Turin, Italy
| | | | - Hua-Jun He
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD
| | - Kenneth D Cole
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD
| | - Young-Kyung Bae
- Center for Bioanalysis, KRISS, Yuseong-gu, Daejeon, Republic of Korea
| | - Sang-Ryoul Park
- Center for Bioanalysis, KRISS, Yuseong-gu, Daejeon, Republic of Korea
| | - Liesbet Deprez
- Directorate for Health, Consumers and Reference Materials, Joint Research Centre (JRC), European Commission, Geel, Belgium
| | - Philippe Corbisier
- Directorate for Health, Consumers and Reference Materials, Joint Research Centre (JRC), European Commission, Geel, Belgium
| | - Sonia Garrigou
- INSERM UMR-S1147, CNRS SNC5014, Equipe labellisée Ligue Nationale contre le cancer, Paris Descartes University, Paris, France
| | - Valérie Taly
- INSERM UMR-S1147, CNRS SNC5014, Equipe labellisée Ligue Nationale contre le cancer, Paris Descartes University, Paris, France
| | - Raquel Larios
- Inorganic Analysis Team, LGC, Teddington, Middlesex, UK
| | - Simon Cowen
- Statistics Team, LGC, Teddington, Middlesex, UK
| | | | | | | | - Carole A Foy
- Molecular and Cell Biology Team, LGC, Teddington, Middlesex, UK
| | | | - Helen Parkes
- Molecular and Cell Biology Team, LGC, Teddington, Middlesex, UK
| | - Jim F Huggett
- Molecular and Cell Biology Team, LGC, Teddington, Middlesex, UK; .,School of Biosciences and Medicine, Faculty of Health and Medical Science, University of Surrey, Guildford, UK
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Demeke T, Dobnik D. Critical assessment of digital PCR for the detection and quantification of genetically modified organisms. Anal Bioanal Chem 2018; 410:4039-4050. [PMID: 29574561 PMCID: PMC6010488 DOI: 10.1007/s00216-018-1010-1] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/06/2018] [Accepted: 03/08/2018] [Indexed: 12/21/2022]
Abstract
The number of genetically modified organisms (GMOs) on the market is steadily increasing. Because of regulation of cultivation and trade of GMOs in several countries, there is pressure for their accurate detection and quantification. Today, DNA-based approaches are more popular for this purpose than protein-based methods, and real-time quantitative PCR (qPCR) is still the gold standard in GMO analytics. However, digital PCR (dPCR) offers several advantages over qPCR, making this new technique appealing also for GMO analysis. This critical review focuses on the use of dPCR for the purpose of GMO quantification and addresses parameters which are important for achieving accurate and reliable results, such as the quality and purity of DNA and reaction optimization. Three critical factors are explored and discussed in more depth: correct classification of partitions as positive, correctly determined partition volume, and dilution factor. This review could serve as a guide for all laboratories implementing dPCR. Most of the parameters discussed are applicable to fields other than purely GMO testing. Graphical abstract There are generally three different options for absolute quantification of genetically modified organisms (GMOs) using digital PCR: droplet- or chamber-based and droplets in chambers. All have in common the distribution of reaction mixture into several partitions, which are all subjected to PCR and scored at the end-point as positive or negative. Based on these results GMO content can be calculated.
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Affiliation(s)
- Tigst Demeke
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, MB, R3C3G8, Canada
| | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.
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He HJ, Stein EV, DeRose P, Cole KD. Limitations of methods for measuring the concentration of human genomic DNA and oligonucleotide samples. Biotechniques 2018; 64:59-68. [PMID: 29571283 PMCID: PMC6157598 DOI: 10.2144/btn-2017-0102] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/04/2018] [Indexed: 02/02/2023] Open
Abstract
We compared different methods (absorbance, fluorescent dye-binding, and digital PCR) for measuring the concentrations of human genomic DNA from cultured cells and absorbance measurements of a synthetic DNA oligonucleotide. NIST Standard Reference Material (SRM) 2082, a pathlength absorbance standard, was used to benchmark the absorbance measurements done with microvolume spectrophotometers and a microvolume plate reader. Control absorbance values were measured on a high accuracy spectrophotometer and a NIST calibrated pathlength cuvette. Measurements of the human genomic DNA sample were done with several types of fluorescent dye binding assays using different DNA calibrators. The fluorescent dye binding methods gave different results for genomic DNA depending upon the type of DNA calibrator and the fluorescent dye that was used. The human genomic DNA sample was also characterized by using six different droplet digital PCR assays (amplicons located on different chromosomes) to measure the average copy number. Conversion of the digital PCR data to copy numbers was sensitive to the droplet size used for calculations and conversion to mass concentration was dependent upon the molecular weight of the human genome used for the calculations. The results from the different methods were compared and the caveats for each measurement method were discussed.
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Affiliation(s)
- Hua-Jun He
- The Biosystems and Biomaterials Division, The National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899
| | - Erica V. Stein
- The Biosystems and Biomaterials Division, The National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899
| | - Paul DeRose
- The Biosystems and Biomaterials Division, The National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899
| | - Kenneth D. Cole
- The Biosystems and Biomaterials Division, The National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899
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