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Ganguly R, Lee CS. A Poisson-Independent Approach to Precision Nucleic Acid Quantification in Microdroplets. ACS APPLIED BIO MATERIALS 2024; 7:3441-3451. [PMID: 38658190 DOI: 10.1021/acsabm.4c00350] [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] [Indexed: 04/26/2024]
Abstract
Digital PCR (dPCR) has become indispensable in nucleic acid (NA) detection across various fields, including viral diagnostics and mutant detection. However, misclassification of partitions in dPCR can significantly impact accuracy. Despite existing methods to minimize misclassification bias, accurate classification remains elusive, especially for nonamplified target partitions. To address these challenges, this study introduces an innovative microdroplet-based competitive PCR platform for nucleic acid quantification in microfluidic devices independent of Poisson statistics. In this approach, the target concentration (T) is determined from the concentration of competitor DNA (C) at the equivalence point (E.P.), where C/T is 1. Competitive PCR ensures that the ratio of target to competitor DNA remains constant during amplification, reflected in the resultant fluorescence intensity, allowing the quantification of target DNA concentration at the equivalence point. The unique amplification technique eliminates Poisson distribution, addressing misclassification challenges. Additionally, our approach reduces the need for post-PCR procedures and shortens analytical time. We envision this platform as versatile, reproducible, and easily adaptable for driving significant progress in molecular biology and diagnostics.
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Affiliation(s)
- Reya Ganguly
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Chang-Soo Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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2
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Cleveland MH, He HJ, Milavec M, Bae YK, Vallone PM, Huggett JF. Digital PCR for the characterization of reference materials. Mol Aspects Med 2024; 96:101256. [PMID: 38359699 DOI: 10.1016/j.mam.2024.101256] [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: 10/30/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
Well-characterized reference materials support harmonization and accuracy when conducting nucleic acid-based tests (such as qPCR); digital PCR (dPCR) can measure the absolute concentration of a specific nucleic acid sequence in a background of non-target sequences, making it ideal for the characterization of nucleic acid-based reference materials. National Metrology Institutes are increasingly using dPCR to characterize and certify their reference materials, as it offers several advantages over indirect methods, such as UV-spectroscopy. While dPCR is gaining widespread adoption, it requires optimization and has certain limitations and considerations that users should be aware of when characterizing reference materials. This review highlights the technical considerations of dPCR, as well as its role when developing and characterizing nucleic acid-based reference materials.
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Affiliation(s)
- Megan H Cleveland
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA.
| | - Hua-Jun He
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Young-Kyung Bae
- Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea
| | - Peter M Vallone
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Jim F Huggett
- National Measurement Laboratory (NML), LGC, Queens Road, Teddington, TW11 0LY, Middlesex, UK; School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, UK
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3
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Lin Y, Yang J, Wang X, Yang J, Dong L. Establishment of reference measurement procedure and reference material for Treponema pallidum. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1244-1251. [PMID: 38319302 DOI: 10.1039/d3ay01906c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Stem cell preparations, as a new type of biotherapeutic product, should be subject to strict quality control in terms of cell safety. The testing of stem cell donors and blood products used in stem cell cultures, including but not limited to Treponema pallidum, is needed to reduce the risk of transmission of infectious diseases by stem cell medical products. In this study, a reference measurement procedure (RMP) was established based on digital PCR (dPCR). A homogeneous reference material (RM) of TP containing the tpp47 gene has been developed and characterized. Two dPCR assays (A and B) show ideal linearity within five orders of magnitude. The limit of quantification (LoQ) for both assays is 57 copies/reaction; the limits of detection (LoD) are 9.69 and 9.59 copies/reaction, respectively. The quantitative results of the established duplex dPCR assay are in good agreement. The RM of TP containing the tpp47 gene has been developed and characterized. The reference value with its expanded uncertainty is (2.21 ± 0.22) × 106 copies per μL determined by the established dPCR RMP. The developed dPCR was validated by applying a simulated stem cell matrix, and no impact was observed on the accuracy of dPCR. By providing an accurate reference value for the absolute copy number of the target gene, the developed RM can be used to improve the reliability of TP testing in the production of stem cell preparations and clinical diagnostics.
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Affiliation(s)
- Yanmin Lin
- College of Food Science and Technology, Shanghai Ocean University, 201306, Shanghai, P. R. China.
- Center for Advanced Measurement of Science, National Institute of Metrology, 100029, Beijing, P. R. China.
| | - Jiayi Yang
- Center for Advanced Measurement of Science, National Institute of Metrology, 100029, Beijing, P. R. China.
| | - Xia Wang
- Center for Advanced Measurement of Science, National Institute of Metrology, 100029, Beijing, P. R. China.
| | - Jingya Yang
- College of Food Science and Technology, Shanghai Ocean University, 201306, Shanghai, P. R. China.
- Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, 201306, Shanghai, P. R. China
| | - Lianhua Dong
- Center for Advanced Measurement of Science, National Institute of Metrology, 100029, Beijing, P. R. China.
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4
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Berden P, Wiederkehr RS, Lagae L, Michiels J, Stakenborg T, Fauvart M, Van Roy W. Amplification Efficiency and Template Accessibility as Distinct Causes of Rain in Digital PCR: Monte Carlo Modeling and Experimental Validation. Anal Chem 2022; 94:15781-15789. [DOI: 10.1021/acs.analchem.2c03534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Pieter Berden
- Imec, Leuven 3001, Belgium
- Department of Physics and Astronomy, KU Leuven, Leuven 3001, Belgium
- Department of Molecular and Microbial Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven 3001, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven 3001, Belgium
| | | | - Liesbet Lagae
- Imec, Leuven 3001, Belgium
- Department of Physics and Astronomy, KU Leuven, Leuven 3001, Belgium
| | - Jan Michiels
- Department of Molecular and Microbial Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven 3001, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven 3001, Belgium
| | | | - Maarten Fauvart
- Imec, Leuven 3001, Belgium
- Department of Molecular and Microbial Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven 3001, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven 3001, Belgium
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5
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Recent advances in integrated microfluidics for liquid biopsies and future directions. Biosens Bioelectron 2022; 217:114715. [PMID: 36174359 DOI: 10.1016/j.bios.2022.114715] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 07/20/2022] [Accepted: 09/09/2022] [Indexed: 12/12/2022]
Abstract
Liquid biopsies have piqued the interest of researchers as a new tumor diagnosis technique due to their unique benefits of non-invasiveness, sensitivity, and convenience. Recent advances in microfluidic technology have integrated separation, purification, and detection, allowing for high-throughput, high-sensitivity, and high-controllability detection of specific biomarkers in liquid biopsies. With the increasing demand for tumor detection and individualized treatment, new challenges are emerging for the ever-improving microfluidic technology. The state-of-the-art microfluidic design and fabrications have been reviewed in this manuscript, and how this technology can be applied to liquid biopsies from the point of view of the detection process. The primary discussion objectives are circulating tumor cells (CTCs), exosomes, and circulating nucleic acid (ctDNA). Furthermore, the challenges and future direction of microfluidic technology in detecting liquid biomarkers have been discussed.
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6
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International co-validation on absolute quantification of single nucleotide variants of KRAS by digital PCR. Anal Bioanal Chem 2022; 414:5899-5906. [DOI: 10.1007/s00216-022-04155-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/15/2022] [Accepted: 05/31/2022] [Indexed: 11/01/2022]
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7
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Abramovic I, Vrhovec B, Skara L, Vrtaric A, Nikolac Gabaj N, Kulis T, Stimac G, Ljiljak D, Ruzic B, Kastelan Z, Kruslin B, Bulic-Jakus F, Ulamec M, Katusic-Bojanac A, Sincic N. MiR-182-5p and miR-375-3p Have Higher Performance Than PSA in Discriminating Prostate Cancer from Benign Prostate Hyperplasia. Cancers (Basel) 2021; 13:cancers13092068. [PMID: 33922968 PMCID: PMC8123314 DOI: 10.3390/cancers13092068] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/16/2021] [Accepted: 04/22/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Prostate cancer (PCa) is the most prevalent neoplasia among men worldwide but is commonly “mimicked” by benign prostate hyperplasia (BPH). Their discrimination by the prostate-specific antigen (PSA) is often uncertain, resulting in lengthy diagnostic protocols and recurrent tissue biopsies. The development of more appropriate biomarkers, possibly present in liquid biopsy, would significantly improve PCa and BPH patient management. To address this challenge, in this study miR-375-3p, miR-182-5p, miR-21-5p, and miR-148a-3p were analyzed by ddPCR in blood plasma and seminal plasma of patients with PCa and BPH prior to tissue biopsy. Among other findings, miR-182-5p and miR-375-3p were found to have statistically significantly higher expression in PCa patients compared to BPH in blood, with a combined specificity of 90.2% to predict positive or negative biopsy results. The data presented emphasize the great potential of miRNAs as liquid biopsy biomarkers for PCa. Abstract Prostate cancer (PCa) is the most commonly diagnosed neoplasm among men. Since it often resembles benign prostate hyperplasia (BPH), biomarkers with a higher differential value than PSA are required. Epigenetic biomarkers in liquid biopsies, especially miRNA, could address this challenge. The absolute expression of miR-375-3p, miR-182-5p, miR-21-5p, and miR-148a-3p were quantified in blood plasma and seminal plasma of 65 PCa and 58 BPH patients by digital droplet PCR. The sensitivity and specificity of these microRNAs were determined using ROC curve analysis. The higher expression of miR-182-5p and miR-375-3p in the blood plasma of PCa patients was statistically significant as compared to BPH (p = 0.0363 and 0.0226, respectively). Their combination achieved a specificity of 90.2% for predicting positive or negative biopsy results, while PSA cut-off of 4 µg/L performed with only 1.7% specificity. In seminal plasma, miR-375-3p, miR-182-5p, and miR-21-5p showed a statistically significantly higher expression in PCa patients with PSA >10 µg/L compared to ones with PSA ≤10 µg/L. MiR-182-5p and miR-375-3p in blood plasma show higher performance than PSA in discriminating PCa from BPH. Seminal plasma requires further investigation as it represents an obvious source for PCa biomarker identification.
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Affiliation(s)
- Irena Abramovic
- Department of Medical Biology, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (I.A.); (L.S.); (F.B.-J.); (A.K.-B.)
- Group for Research on Epigenetic Biomarkers (Epimark), University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (T.K.); (G.S.); (B.R.); (Z.K.); (M.U.)
- Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (A.V.); (N.N.G.); (B.K.)
| | - Borna Vrhovec
- Department of Urology, University Clinical Hospital Center Sestre Milosrdnice, 10000 Zagreb, Croatia;
| | - Lucija Skara
- Department of Medical Biology, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (I.A.); (L.S.); (F.B.-J.); (A.K.-B.)
- Group for Research on Epigenetic Biomarkers (Epimark), University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (T.K.); (G.S.); (B.R.); (Z.K.); (M.U.)
- Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (A.V.); (N.N.G.); (B.K.)
| | - Alen Vrtaric
- Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (A.V.); (N.N.G.); (B.K.)
- Department of Clinical Chemistry, University Clinical Hospital Center Sestre Milosrdnice, 10000 Zagreb, Croatia
| | - Nora Nikolac Gabaj
- Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (A.V.); (N.N.G.); (B.K.)
- Department of Clinical Chemistry, University Clinical Hospital Center Sestre Milosrdnice, 10000 Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
| | - Tomislav Kulis
- Group for Research on Epigenetic Biomarkers (Epimark), University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (T.K.); (G.S.); (B.R.); (Z.K.); (M.U.)
- Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (A.V.); (N.N.G.); (B.K.)
- Department of Urology, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
| | - Goran Stimac
- Group for Research on Epigenetic Biomarkers (Epimark), University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (T.K.); (G.S.); (B.R.); (Z.K.); (M.U.)
- Department of Urology, University Clinical Hospital Center Sestre Milosrdnice, 10000 Zagreb, Croatia;
| | - Dejan Ljiljak
- Department of Gynecology and Obstetrics, University Clinical Hospital Center Sestre Milosrdnice, 10000 Zagreb, Croatia;
| | - Boris Ruzic
- Group for Research on Epigenetic Biomarkers (Epimark), University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (T.K.); (G.S.); (B.R.); (Z.K.); (M.U.)
- Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (A.V.); (N.N.G.); (B.K.)
- Department of Urology, University Clinical Hospital Center Sestre Milosrdnice, 10000 Zagreb, Croatia;
| | - Zeljko Kastelan
- Group for Research on Epigenetic Biomarkers (Epimark), University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (T.K.); (G.S.); (B.R.); (Z.K.); (M.U.)
- Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (A.V.); (N.N.G.); (B.K.)
- Department of Urology, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
| | - Bozo Kruslin
- Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (A.V.); (N.N.G.); (B.K.)
- Ljudevit Jurak Clinical Department of Pathology and Cytology, University Clinical Hospital Center Sestre Milosrdnice, 10000 Zagreb, Croatia
| | - Floriana Bulic-Jakus
- Department of Medical Biology, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (I.A.); (L.S.); (F.B.-J.); (A.K.-B.)
- Group for Research on Epigenetic Biomarkers (Epimark), University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (T.K.); (G.S.); (B.R.); (Z.K.); (M.U.)
- Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (A.V.); (N.N.G.); (B.K.)
| | - Monika Ulamec
- Group for Research on Epigenetic Biomarkers (Epimark), University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (T.K.); (G.S.); (B.R.); (Z.K.); (M.U.)
- Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (A.V.); (N.N.G.); (B.K.)
- Ljudevit Jurak Clinical Department of Pathology and Cytology, University Clinical Hospital Center Sestre Milosrdnice, 10000 Zagreb, Croatia
- Department of Pathology, School of Dental Medicine and School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Ana Katusic-Bojanac
- Department of Medical Biology, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (I.A.); (L.S.); (F.B.-J.); (A.K.-B.)
- Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (A.V.); (N.N.G.); (B.K.)
| | - Nino Sincic
- Department of Medical Biology, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (I.A.); (L.S.); (F.B.-J.); (A.K.-B.)
- Group for Research on Epigenetic Biomarkers (Epimark), University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (T.K.); (G.S.); (B.R.); (Z.K.); (M.U.)
- Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; (A.V.); (N.N.G.); (B.K.)
- Correspondence: ; Tel.: +385-145-66-806
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8
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Li J, Zhang L, Li L, Li X, Zhang X, Zhai S, Gao H, Li Y, Wu G, Wu Y. Development of Genomic DNA Certified Reference Materials for Genetically Modified Rice Kefeng 6. ACS OMEGA 2020; 5:21602-21609. [PMID: 32905288 PMCID: PMC7469412 DOI: 10.1021/acsomega.0c02274] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
The application of certified reference materials (CRMs) to genetically modified organism (GMO) detection is essential for guaranteeing the accuracy, comparability, and traceability of quantitative results over time and among laboratories. Clean leaves from GM rice Kefeng 6 were used as raw materials to develop a batch of genomic DNA (gDNA) CRMs. The optimized KF6/PLD duplex digital PCR was used for collaborative characterization of Kefeng 6 gDNA CRMs by eight qualified laboratories; this batch of gDNA CRMs was certified for two property values, namely, copy number ratio and copy number concentration, which were 1.03 ± 0.04 and (1.60 ± 0.11) × 105 copies/μL, respectively. The gDNA CRMs displayed good between-vial homogeneity when the minimum sample intake of 2 μL was taken into account. Stability studies indicated that the gDNA CRMs should be transported below 25 °C, and cold chain transport was recommended. Shelf life was assessed to be at least 12 months, and when using gDNA CRMs, freeze-thaw should not exceed 10 cycles. Compared to the available gDNA CRMs in the market, this batch of gDNA CRMs has accurate property values with combined uncertainties, providing user-friendly calibrators for GM rice Kefeng 6 inspection and monitoring. The development and characterization of Kefeng 6 gDNA CRMs contribute to the establishment of a copy number-based reference system for GMO detection.
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Affiliation(s)
- Jun Li
- Key
Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil
Crops Research Institute, Chinese Academy
of Agricultural Sciences, Wuhan 430062, China
| | - Li Zhang
- School
of Life Science, South-Central University
for Nationalities, Wuhan 430074, China
| | - Liang Li
- Biotechnology
Research Institute, Chinese Academy of Agricultural
Sciences, Beijing 100081, China
| | - Xiaying Li
- Development
Center of Science and Technology, Ministry
of Agriculture and Rural Affairs P. R. China, Beijing 100025, China
| | - Xiujie Zhang
- Development
Center of Science and Technology, Ministry
of Agriculture and Rural Affairs P. R. China, Beijing 100025, China
| | - Shanshan Zhai
- Key
Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil
Crops Research Institute, Chinese Academy
of Agricultural Sciences, Wuhan 430062, China
| | - Hongfei Gao
- Key
Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil
Crops Research Institute, Chinese Academy
of Agricultural Sciences, Wuhan 430062, China
| | - Yunjing Li
- Key
Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil
Crops Research Institute, Chinese Academy
of Agricultural Sciences, Wuhan 430062, China
| | - Gang Wu
- Key
Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil
Crops Research Institute, Chinese Academy
of Agricultural Sciences, Wuhan 430062, China
| | - Yuhua Wu
- Key
Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil
Crops Research Institute, Chinese Academy
of Agricultural Sciences, Wuhan 430062, China
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Kline MC, Duewer DL. Evaluating digital PCR for the quantification of human nuclear DNA: determining target strandedness. Anal Bioanal Chem 2020; 412:4749-4760. [PMID: 32474725 DOI: 10.1007/s00216-020-02733-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/13/2020] [Accepted: 05/20/2020] [Indexed: 01/28/2023]
Abstract
Digital polymerase chain reaction (dPCR) methodology has been asserted to be a "potentially primary" analytical approach for assigning DNA concentration. The essence of dPCR measurements is the independent dispersal of fragments into multiple reaction partitions, amplifying fragments containing a target nucleotide sequence until the signal from all partitions containing at least one such fragment rises above threshold, and then determining the proportion of partitions with an above-threshold signal. Should originally double-stranded DNA (dsDNA) fragments be converted into two single strands (ssDNA) prior to dispersal, the dPCR measurements could be biased high by as much as a factor of two. Realizing dPCR's metrological potential therefore requires analytical methods for determining the proportion of ssDNA in nominally dsDNA samples. To meet this need, we have investigated several approaches to this determination: A260 ratio, dPCR ratio, cdPCR staircase, and ddPCR enzyme. In our hands, only the endonuclease-based approach provides adequately accurate estimates for relatively small ssDNA proportions. We present four (enzyme, assay) pairs that provide self-consistent results for human nuclear DNA extracts. However, the proportion of ssDNA differs by as much as 50% between assays, apparently related to the guanine-cytosine (GC) content of the fragment near the assay's target sequence. While materials extracted by us have no more than 6% ssDNA content even after long storage, a commercially obtained PCR assay calibrant contains ≈18% ssDNA. Graphical abstract.
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Affiliation(s)
- Margaret C Kline
- Biomolecular Measurement Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899-8314, USA
| | - David L Duewer
- Chemical Sciences Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8390, Gaithersburg, MD, 20899-8390, USA.
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10
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He HJ, Das B, Cleveland MH, Chen L, Camalier CE, Liu LC, Norman KL, Fellowes AP, McEvoy CR, Lund SP, Almeida J, Steffen CR, Karlovich C, Williams PM, Cole KD. Development and interlaboratory evaluation of a NIST Reference Material RM 8366 for EGFR and MET gene copy number measurements. Clin Chem Lab Med 2020; 57:1142-1152. [PMID: 31112502 PMCID: PMC6875440 DOI: 10.1515/cclm-2018-1306] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/21/2019] [Indexed: 01/04/2023]
Abstract
Background The National Institute of Standards and Technology (NIST) Reference Material RM 8366 was developed to improve the quality of gene copy measurements of EGFR (epidermal growth factor receptor) and MET (proto-oncogene, receptor tyrosine kinase), important targets for cancer diagnostics and treatment. The reference material is composed of genomic DNA prepared from six human cancer cell lines with different levels of amplification of the target genes. Methods The reference values for the ratios of the EGFR and MET gene copy numbers to the copy numbers of reference genes were measured using digital PCR. The digital PCR measurements were confirmed by two additional laboratories. The samples were also characterized using Next Generation Sequencing (NGS) methods including whole genome sequencing (WGS) at three levels of coverage (approximately 1 ×, 5 × and greater than 30 ×), whole exome sequencing (WES), and two different pan-cancer gene panels. The WES data were analyzed using three different bioinformatic algorithms. Results The certified values (digital PCR) for EGFR and MET were in good agreement (within 20%) with the values obtained from the different NGS methods and algorithms for five of the six components; one component had lower NGS values. Conclusions This study shows that NIST RM 8366 is a valuable reference material to evaluate the performance of assays that assess EGFR and MET gene copy number measurements.
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Affiliation(s)
- Hua-Jun He
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, 100 Bureau Drive, MS 8312, Gaithersburg, MD 20899, USA, Phone: +301-975-2169, Fax: +301-330-3447
| | - Biswajit Das
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Megan H Cleveland
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Li Chen
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Corinne E Camalier
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | | | | | | | - Steve P Lund
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Jamie Almeida
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Carolyn R Steffen
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Chris Karlovich
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - P Mickey Williams
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kenneth D Cole
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, 100 Bureau Drive, MS 8312, Gaithersburg, MD 20899, USA, Phone: +301-975-2169, Fax: +301-330-3447
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11
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Wu Y, Li J, Li X, Zhai S, Gao H, Li Y, Zhang X, Wu G. Development and strategy of reference materials for the DNA-based detection of genetically modified organisms. Anal Bioanal Chem 2019; 411:1729-1744. [DOI: 10.1007/s00216-019-01576-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 12/21/2018] [Accepted: 01/03/2019] [Indexed: 12/11/2022]
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Milosevic D, Mills JR, Campion MB, Vidal-Folch N, Voss JS, Halling KC, Highsmith WE, Liu MC, Kipp BR, Grebe SKG. Applying Standard Clinical Chemistry Assay Validation to Droplet Digital PCR Quantitative Liquid Biopsy Testing. Clin Chem 2018; 64:1732-1742. [DOI: 10.1373/clinchem.2018.291278] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/23/2018] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Droplet digital PCR (ddPCR) is an emerging technology for quantitative cell-free DNA oncology applications. However, assay performance criteria must be established in a standardized manner to harness this potential. We reasoned that standard protocols used in clinical chemistry assay validation should be able to fill this need.
METHODS
We validated KRAS, EGFR, and BRAF quantitative ddPCR assays based on the Clinical Laboratory Improvement Act regulations for laboratory-developed tests in clinical chemistry and the matching Clinical and Laboratory Standards Institute guidelines. This included evaluation of limit of the blank (LOB), limit of detection (LOD), limit of quantification (LOQ), intraassay and interassay imprecision, analytical range, dilution linearity, accuracy (including comparison with orthogonal platforms), reference range study, interference, and stability studies.
RESULTS
For the ddPCR assays, the LOB was 4 mutant copies, LODs were 12 to 22 copies, and LOQs were 35 to 64 copies. The upper limit of the dynamic range was 30000 copies, and dilutions were linear down to the LOQs with good accuracy of spike recovery of Horizon reference material. Method comparisons with next-generation sequencing and an alternative ddPCR platform showed complete qualitative agreement and quantitative concordance, with slopes of 0.73 to 0.97 and R2s of 0.83 to 0.99. No substantial interferences were discovered. Wild-type copy numbers in plasma ranged from 462 to 6169/mL in healthy individuals.
CONCLUSIONS
Standard clinical chemistry assay validation protocols can be applied to quantitative ddPCR assays. This should facilitate comparison of the performance of different assays and allow establishment of minimal significant change thresholds in monitoring applications.
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Affiliation(s)
- Dragana Milosevic
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN
| | - John R Mills
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN
| | - Michael B Campion
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Noemi Vidal-Folch
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Jesse S Voss
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Kevin C Halling
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - W Edward Highsmith
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Minetta C Liu
- Department of Laboratory Meidicne and Pathology, Division of Anatomic Pathology, Mayo Clinic, Rochester, MN
- Department of Oncology, Division of Medical Oncology Mayo Clinic, Rochester, MN
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Stefan K G Grebe
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN
- Department of Medicine, Division of Endocrinology, Mayo Clinic, Rochester, MN
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Evaluating droplet digital PCR for the quantification of human genomic DNA: converting copies per nanoliter to nanograms nuclear DNA per microliter. Anal Bioanal Chem 2018; 410:2879-2887. [PMID: 29556737 DOI: 10.1007/s00216-018-0982-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/05/2018] [Accepted: 02/22/2018] [Indexed: 12/19/2022]
Abstract
The highly multiplexed polymerase chain reaction (PCR) assays used for forensic human identification perform best when used with an accurately determined quantity of input DNA. To help ensure the reliable performance of these assays, we are developing a certified reference material (CRM) for calibrating human genomic DNA working standards. To enable sharing information over time and place, CRMs must provide accurate and stable values that are metrologically traceable to a common reference. We have shown that droplet digital PCR (ddPCR) limiting dilution end-point measurements of the concentration of DNA copies per volume of sample can be traceably linked to the International System of Units (SI). Unlike values assigned using conventional relationships between ultraviolet absorbance and DNA mass concentration, entity-based ddPCR measurements are expected to be stable over time. However, the forensic community expects DNA quantity to be stated in terms of mass concentration rather than entity concentration. The transformation can be accomplished given SI-traceable values and uncertainties for the number of nucleotide bases per human haploid genome equivalent (HHGE) and the average molar mass of a nucleotide monomer in the DNA polymer. This report presents the considerations required to establish the metrological traceability of ddPCR-based mass concentration estimates of human nuclear DNA. Graphical abstract The roots of metrological traceability for human nuclear DNA mass concentration results. Values for the factors in blue must be established experimentally. Values for the factors in red have been established from authoritative source materials. HHGE stands for "haploid human genome equivalent"; there are two HHGE per diploid human genome.
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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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Stein EV, Duewer DL, Farkas N, Romsos EL, Wang L, Cole KD. Steps to achieve quantitative measurements of microRNA using two step droplet digital PCR. PLoS One 2017; 12:e0188085. [PMID: 29145448 PMCID: PMC5690473 DOI: 10.1371/journal.pone.0188085] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/31/2017] [Indexed: 12/29/2022] Open
Abstract
Droplet digital PCR (ddPCR) is being advocated as a reference method to measure rare genomic targets. It has consistently been proven to be more sensitive and direct at discerning copy numbers of DNA than other quantitative methods. However, one of the largest obstacles to measuring microRNA (miRNA) using ddPCR is that reverse transcription efficiency depends upon the target, meaning small RNA nucleotide composition directly effects primer specificity in a manner that prevents traditional quantitation optimization strategies. Additionally, the use of reagents that are optimized for miRNA measurements using quantitative real-time PCR (qRT-PCR) appear to either cause false positive or false negative detection of certain targets when used with traditional ddPCR quantification methods. False readings are often related to using inadequate enzymes, primers and probes. Given that two-step miRNA quantification using ddPCR relies solely on reverse transcription and uses proprietary reagents previously optimized only for qRT-PCR, these barriers are substantial. Therefore, here we outline essential controls, optimization techniques, and an efficacy model to improve the quality of ddPCR miRNA measurements. We have applied two-step principles used for miRNA qRT-PCR measurements and leveraged the use of synthetic miRNA targets to evaluate ddPCR following cDNA synthesis with four different commercial kits. We have identified inefficiencies and limitations as well as proposed ways to circumvent identified obstacles. Lastly, we show that we can apply these criteria to a model system to confidently quantify miRNA copy number. Our measurement technique is a novel way to quantify specific miRNA copy number in a single sample, without using standard curves for individual experiments. Our methodology can be used for validation and control measurements, as well as a diagnostic technique that allows scientists, technicians, clinicians, and regulators to base miRNA measures on a single unit of measurement rather than a ratio of values.
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Affiliation(s)
- Erica V. Stein
- Biosystems and Biomaterials Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America
- * E-mail:
| | - David L. Duewer
- Chemical Sciences Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America
| | - Natalia Farkas
- Engineering Physics Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America
| | - Erica L. Romsos
- Biomolecular Measurement Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America
| | - Lili Wang
- Biosystems and Biomaterials Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America
| | - Kenneth D. Cole
- Biosystems and Biomaterials Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America
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Droplet volume variability as a critical factor for accuracy of absolute quantification using droplet digital PCR. Anal Bioanal Chem 2017; 409:6689-6697. [PMID: 28921124 PMCID: PMC5670190 DOI: 10.1007/s00216-017-0625-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/30/2017] [Accepted: 09/05/2017] [Indexed: 11/13/2022]
Abstract
Accurate and precise nucleic-acid quantification is crucial for clinical and diagnostic decisions, as overestimation or underestimation can lead to misguided treatment of a disease or incorrect labelling of the products. Digital PCR is one of the best tools for absolute nucleic-acid copy-number determination. However, digital PCR needs to be well characterised in terms of accuracy and sources of uncertainty. With droplet digital PCR, discrepancies between the droplet volume assigned by the manufacturer and measured by independent laboratories have already been shown in previous studies. In the present study, we report on the results of an inter-laboratory comparison of different methods for droplet volume determination that is based on optical microscopy imaging and is traceable to the International System of Units. This comparison was conducted on the same DNA material, with the examination of the influence of parameters such as droplet generators, supermixes, operators, inter-cartridge and intra-cartridge variability, and droplet measuring protocol. The mean droplet volume was measured using a QX200™ AutoDG™ Droplet Digital™ PCR system and two QX100™ Droplet Digital™ PCR systems. The data show significant volume differences between these two systems, as well as significant differences in volume when different supermixes are used. We also show that both of these droplet generator systems produce droplets with significantly lower droplet volumes (13.1%, 15.9%, respectively) than stated by the manufacturer and previously measured by other laboratories. This indicates that to ensure precise quantification, the droplet volumes should be assessed for each system.
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Gil BM, Valero D. NUEVAS TECNOLOGÍAS PARA EL DIAGNÓSTICO GENÉTICO. REVISTA MÉDICA CLÍNICA LAS CONDES 2017. [DOI: 10.1016/j.rmclc.2017.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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