1
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Vynck M, Chen Y, Gleerup D, Vandesompele J, Trypsteen W, Lievens A, Thas O, De Spiegelaere W. Digital PCR Partition Classification. Clin Chem 2023; 69:976-990. [PMID: 37401391 DOI: 10.1093/clinchem/hvad063] [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: 01/27/2023] [Accepted: 04/19/2023] [Indexed: 07/05/2023]
Abstract
BACKGROUND Partition classification is a critical step in the digital PCR data analysis pipeline. A range of partition classification methods have been developed, many motivated by specific experimental setups. An overview of these partition classification methods is lacking and their comparative properties are often unclear, likely impacting the proper application of these methods. CONTENT This review provides a summary of all available digital PCR partition classification approaches and the challenges they aim to overcome, serving as a guide for the digital PCR practitioner wishing to apply them. We additionally discuss strengths and weaknesses of these methods, which can further guide practitioners in vigilant application of these existing methods. This review provides method developers with ideas for improving methods or designing new ones. The latter is further stimulated by our identification and discussion of application gaps in the literature, for which there are currently no or few methods available. SUMMARY This review provides an overview of digital PCR partition classification methods, their properties, and potential applications. Ideas for further advances are presented and may bolster method development.
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Affiliation(s)
- Matthijs Vynck
- Digital PCR Consortium, Ghent University, Ghent, Belgium
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Yao Chen
- Digital PCR Consortium, Ghent University, Ghent, Belgium
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - David Gleerup
- Digital PCR Consortium, Ghent University, Ghent, Belgium
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Digital PCR Consortium, Ghent University, Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- CellCarta, Zwijnaarde, Belgium
| | - Wim Trypsteen
- Digital PCR Consortium, Ghent University, Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Antoon Lievens
- Digital PCR Consortium, Ghent University, Ghent, Belgium
- BASF Innovation Center Ghent, Zwijnaarde, Belgium
| | - Olivier Thas
- Digital PCR Consortium, Ghent University, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Data Science Institute, I-BioStat, Hasselt University, Hasselt, Belgium
- National Institute for Applied Statistics Research Australia, School of Mathematics and Applied Statistics, University of Wollongong, Wollongong, Australia
| | - Ward De Spiegelaere
- Digital PCR Consortium, Ghent University, Ghent, Belgium
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
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2
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Loskyll M, Podbiel D, Guber A, Hoffmann J. Partitioning and subsampling statistics in compartment-based quantification methods. PLoS One 2023; 18:e0285784. [PMID: 37186607 PMCID: PMC10184943 DOI: 10.1371/journal.pone.0285784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/01/2023] [Indexed: 05/17/2023] Open
Abstract
The precision of compartment-based quantification methods is subject to multiple effects, of which partitioning and subsampling play a major role. Partitioning is the process of aliquoting the sample liquid and consequently the contained target molecules, whereas subsampling denotes the fact that usually only a portion of a sample is analyzed. In this work, we present a detailed statistical description comprising the effects of partitioning and subsampling on the relative uncertainty of the test result. We show that the state-of-the-art binomial model does not provide accurate results for the level of subsampling present when analyzing the nucleic acid content of single specific cells. Hence, in this work we address partitioning and subsampling effects separately and subsequently combine them to derive the relative uncertainty of a test system and compare it for single cell content analysis and body fluid analysis. In point-of-care test systems the area for partitioning and detection is usually limited, which means that a trade-off between the number of partitions (related to a partitioning uncertainty) and the amount of analyzed volume (related to a subsampling uncertainty) might be inevitable. In case of low target concentration, the subsampling uncertainty is dominant whereas for high target concentration, the partitioning uncertainty increases, and a larger number of partitions is beneficial to minimize the combined uncertainty. We show, that by minimizing the subsampling uncertainty in the test system, the quantification uncertainty of low target concentrations in single cell content analysis is much smaller than in body fluid analysis. In summary, the work provides the methodological basis for a profound statistical evaluation of partitioning and subsampling effects in compartment-based quantification methods and paves the way towards an improved design of future digital quantification devices for highly accurate molecular diagnostic analysis at the point-of-care.
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Affiliation(s)
- Manuel Loskyll
- Advanced Technologies and Microsystems, Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Renningen, Baden-Württemberg, Germany
| | - Daniel Podbiel
- Advanced Technologies and Microsystems, Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Renningen, Baden-Württemberg, Germany
| | - Andreas Guber
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Baden-Württemberg, Germany
- BioMEMS Consulting, Karlsruhe, Baden-Württemberg, Germany
| | - Jochen Hoffmann
- Advanced Technologies and Microsystems, Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Renningen, Baden-Württemberg, Germany
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3
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Hou Y, Chen S, Zheng Y, Zheng X, Lin JM. Droplet-based digital PCR (ddPCR) and its applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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4
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Emerging digital PCR technology in precision medicine. Biosens Bioelectron 2022; 211:114344. [DOI: 10.1016/j.bios.2022.114344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/23/2022] [Accepted: 05/03/2022] [Indexed: 12/20/2022]
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5
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Suchy FP, Nishimura T, Seki S, Wilkinson AC, Higuchi M, Hsu I, Zhang J, Bhadury J, Nakauchi H. Streamlined and quantitative detection of chimerism using digital PCR. Sci Rep 2022; 12:10223. [PMID: 35715477 PMCID: PMC9206010 DOI: 10.1038/s41598-022-14467-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/07/2022] [Indexed: 12/28/2022] Open
Abstract
Animal chimeras are widely used for biomedical discoveries, from developmental biology to cancer research. However, the accurate quantitation of mixed cell types in chimeric and mosaic tissues is complicated by sample preparation bias, transgenic silencing, phenotypic similarity, and low-throughput analytical pipelines. Here, we have developed and characterized a droplet digital PCR single-nucleotide discrimination assay to detect chimerism among common albino and non-albino mouse strains. In addition, we validated that this assay is compatible with crude lysate from all solid organs, drastically streamlining sample preparation. This chimerism detection assay has many additional advantages over existing methods including its robust nature, minimal technical bias, and ability to report the total number of cells in a prepared sample. Moreover, the concepts discussed here are readily adapted to other genomic loci to accurately measure mixed cell populations in any tissue.
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Affiliation(s)
- Fabian P Suchy
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Toshiya Nishimura
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Shinsuke Seki
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Experimental Animal Division, Bioscience Education and Research Support Center, Akita University, Akita, 010-8543, Japan
| | - Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Maimi Higuchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ian Hsu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jinyu Zhang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Joydeep Bhadury
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Institute of Biomedicine, Sahlgrenska University Hospital, University of Gothenburg, 41345, Gothenburg, SE, Sweden
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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6
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Usha SP, Manoharan H, Deshmukh R, Álvarez-Diduk R, Calucho E, Sai VVR, Merkoçi A. Attomolar analyte sensing techniques (AttoSens): a review on a decade of progress on chemical and biosensing nanoplatforms. Chem Soc Rev 2021; 50:13012-13089. [PMID: 34673860 DOI: 10.1039/d1cs00137j] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Detecting the ultra-low abundance of analytes in real-life samples, such as biological fluids, water, soil, and food, requires the design and development of high-performance biosensing modalities. The breakthrough efforts from the scientific community have led to the realization of sensing technologies that measure the analyte's ultra-trace level, with relevant sensitivity, selectivity, response time, and sampling efficiency, referred to as Attomolar Analyte Sensing Techniques (AttoSens) in this review. In an AttoSens platform, 1 aM detection corresponds to the quantification of 60 target analyte molecules in 100 μL of sample volume. Herein, we review the approaches listed for various sensor probe design, and their sensing strategies that paved the way for the detection of attomolar (aM: 10-18 M) concentration of analytes. A summary of the technological advances made by the diverse AttoSens trends from the past decade is presented.
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Affiliation(s)
- Sruthi Prasood Usha
- Biomedical Engineering, Department of Applied Mechanics, Indian Institute of Technology Madras (IITM), India.
| | - Hariharan Manoharan
- Biomedical Engineering, Department of Applied Mechanics, Indian Institute of Technology Madras (IITM), India.
| | - Rehan Deshmukh
- Biomedical Engineering, Department of Applied Mechanics, Indian Institute of Technology Madras (IITM), India.
| | - Ruslan Álvarez-Diduk
- Nanobioelectronics & Biosensors Group, Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Barcelona, Spain.
| | - Enric Calucho
- Nanobioelectronics & Biosensors Group, Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Barcelona, Spain.
| | - V V R Sai
- Biomedical Engineering, Department of Applied Mechanics, Indian Institute of Technology Madras (IITM), India.
| | - Arben Merkoçi
- Nanobioelectronics & Biosensors Group, Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Barcelona, Spain. .,ICREA, Institució Catalana de Recercai Estudis Avançats, Barcelona, Spain
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7
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Zhang Y, Li H, Shang S, Meng S, Lin T, Zhang Y, Liu H. Evaluation validation of a qPCR curve analysis method and conventional approaches. BMC Genomics 2021; 22:680. [PMID: 34789146 PMCID: PMC8596907 DOI: 10.1186/s12864-021-07986-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 09/07/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Reverse Transcription quantitative polymerase chain reaction (RT-qPCR) is a sensitive and reliable method for mRNA quantification and rapid analysis of gene expression from a large number of starting templates. It is based on the statistical significance of the beginning of exponential phase in real-time PCR kinetics, reflecting quantitative cycle of the initial target quantity and the efficiency of the PCR reaction (the fold increase of product per cycle). RESULTS We used the large clinical biomarker dataset and 94-replicates-4-dilutions set which was published previously as research tools, then proposed a new qPCR curve analysis method--CqMAN, to determine the position of quantitative cycle as well as the efficiency of the PCR reaction and applied in the calculations. To verify algorithm performance, 20 genes from biomarker and partial data with concentration gradients from 94-replicates-4-dilutions set of MYCN gene were used to compare our method with various publicly available methods and established a suitable evaluation index system. CONCLUSIONS The results show that CqMAN method is comparable to other methods and can be a feasible method which applied to our self-developed qPCR data processing and analysis software, providing a simple tool for qPCR analysis.
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Affiliation(s)
- Yashu Zhang
- Department of Information Science and Engineering, Ocean University of China, Qingdao, China
| | - Hongping Li
- Department of Information Science and Engineering, Ocean University of China, Qingdao, China.
| | - Shucheng Shang
- Department of Information Science and Engineering, Ocean University of China, Qingdao, China
| | - Shuoyu Meng
- Department of Information Science and Engineering, Ocean University of China, Qingdao, China
| | - Ting Lin
- Apexbio Biotechnology (Suzhou) Co., Ltd, Suzhou, China
| | - Yanhui Zhang
- Apexbio Biotechnology (Suzhou) Co., Ltd, Suzhou, China
| | - Haixing Liu
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
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8
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Cao L, Guo X, Mao P, Ren Y, Li Z, You M, Hu J, Tian M, Yao C, Li F, Xu F. A Portable Digital Loop-Mediated Isothermal Amplification Platform Based on Microgel Array and Hand-Held Reader. ACS Sens 2021; 6:3564-3574. [PMID: 34606243 DOI: 10.1021/acssensors.1c00603] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Digital polymerase chain reaction (dPCR) has found widespread applications in molecular diagnosis of various diseases owing to its sensitive single-molecule detection capability. However, the existing dPCR platforms rely on the auxiliary procedure to disperse DNA samples, which needs complicated operation, expensive apparatus, and consumables. Besides, the complex and costly dPCR readers also impede the applications of dPCR for point-of-care testing (POCT). Herein, we developed a portable digital loop-mediated isothermal amplification (dLAMP) platform, integrating a microscale hydrogel (microgel) array chip for sample partition, a miniaturized heater for DNA amplification, and a hand-held reader for digital readout. In the platform, the chip with thousands of isolated microgels holds the capability of self-absorption and partition of DNA samples, thus avoiding auxiliary equipment and professional personnel operations. Using the integrated dLAMP platform, λDNA templates have been quantified with a good linear detection range of 2-1000 copies/μL and a detection limit of 1 copy/μL. As a demonstration, the epidermal growth factor receptor L858R gene mutation, a crucial factor for the susceptibility of the tyrosine kinase inhibitor in non-small-cell lung cancer treatment, has been accurately identified by the dLAMP platform with a spiked plasma sample. This work shows that the developed dLAMP platform provides a low-cost, facile, and user-friendly solution for the absolute quantification of DNA, showing great potential for the POCT of nucleic acids.
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Affiliation(s)
- Lei Cao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Xiaojin Guo
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
- Department of Chemistry, School of Science, Xi’an Jiaotong University, Xi’an 710049, China
| | - Ping Mao
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Yulin Ren
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Minli You
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Jie Hu
- Suzhou DiYinAn Biotechnology Company Ltd., Suzhou 215000, China
| | - Miao Tian
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Chunyan Yao
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Fei Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
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9
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Huggett JF. The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020. Clin Chem 2021; 66:1012-1029. [PMID: 32746458 DOI: 10.1093/clinchem/hvaa125] [Citation(s) in RCA: 210] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/18/2020] [Indexed: 12/17/2022]
Abstract
Digital PCR (dPCR) has developed considerably since the publication of the Minimum Information for Publication of Digital PCR Experiments (dMIQE) guidelines in 2013, with advances in instrumentation, software, applications, and our understanding of its technological potential. Yet these developments also have associated challenges; data analysis steps, including threshold setting, can be difficult and preanalytical steps required to purify, concentrate, and modify nucleic acids can lead to measurement error. To assist independent corroboration of conclusions, comprehensive disclosure of all relevant experimental details is required. To support the community and reflect the growing use of dPCR, we present an update to dMIQE, dMIQE2020, including a simplified dMIQE table format to assist researchers in providing key experimental information and understanding of the associated experimental process. Adoption of dMIQE2020 by the scientific community will assist in standardizing experimental protocols, maximize efficient utilization of resources, and further enhance the impact of this powerful technology.
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10
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Direct plasmonic detection of circulating RAS mutated DNA in colorectal cancer patients. Biosens Bioelectron 2020; 170:112648. [PMID: 33010708 DOI: 10.1016/j.bios.2020.112648] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/01/2020] [Accepted: 09/21/2020] [Indexed: 12/11/2022]
Abstract
RAS mutations in the blood of colorectal cancer (CRC) patients are emerging as biomarkers of acquired resistance to Epidermal Growth Factor Receptor therapy. Unfortunately, reliable assays granting fast, real-time monitoring of treatment response, capable of refining retrospective, tissue-based analysis, are still needed. Recently, several methods for detecting blood RAS mutations have been proposed, generally relying on multi-step and PCR-based, time-consuming and cost-ineffective procedures. By exploiting a liquid biopsy approach, we developed an ultrasensitive nanoparticle-enhanced plasmonic method for detecting ~1 aM RAS single nucleotide variants (SNVs) in the plasma of CRC patients. The assay does not require the extraction of tumor DNA from plasma and detects it in volumes as low as 40 μL of plasma, which is at least an order of magnitude smaller than that required by state of the art liquid biopsy technologies. The most prevalent RAS mutations are detected in DNA from tumor tissue with 100% sensitivity and 83.33% specificity. Spike-in experiments in human plasma further encouraged assay application on clinical specimens. The assay was proven in plasma from CRC patients and healthy donors, and full discrimination between mutated DNA from patients over wild-type DNA from healthy volunteers was obtained thus demonstrating its promising avenue for cancer monitoring based on liquid biopsy.
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11
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Development of certified reference material NMIJ CRM 6205-a for the validation of DNA quantification methods: accurate mass concentrations of 600-bp DNA solutions having artificial sequences. Anal Bioanal Chem 2019; 411:6091-6100. [PMID: 31289897 DOI: 10.1007/s00216-019-01992-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/03/2019] [Accepted: 06/18/2019] [Indexed: 10/26/2022]
Abstract
Two 600-bp DNA solutions (DNA600-G and DNA600-T) were developed as certified reference material, NMIJ CRM 6205-a, for the validation of DNA quantification methods. Both DNA600-G and DNA600-T are ideal as "spike-in control" because these materials have artificial nucleic acid sequences. The certified values were determined as the mass concentration of total DNA (whole DNA materials in sample solution regardless of sequence) at 25 °C by formic acid hydrolysis/liquid chromatography-isotope dilution mass spectrometry (LC-IDMS) and inductively coupled plasma-mass spectrometry (ICP-MS) based on the amount of phosphorus. DNAs were synthesized, and plasmids including the synthesized DNAs were cloned into Escherichia coli DH5α. The amplified plasmids were digested with a restriction enzyme and highly purified. Then, the purified DNAs were diluted with water to approximately 1 ng/μL. By using the CRM-validated methods in fields where DNA quantification is required, the reliability of DNA quantification could be improved. Graphical abstract.
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12
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Emslie KR, H McLaughlin JL, Griffiths K, Forbes-Smith M, Pinheiro LB, Burke DG. Droplet Volume Variability and Impact on Digital PCR Copy Number Concentration Measurements. Anal Chem 2019; 91:4124-4131. [PMID: 30775910 DOI: 10.1021/acs.analchem.8b05828] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Digital polymerase chain reaction (dPCR) is increasingly being adopted by reference material producers and metrology institutes for value assignment, and for homogeneity and stability studies of nucleic acid reference materials. A reference method procedure should fulfill several requirements, and the uncertainty and biases should be completely understood. A bias in target concentration when inaccurate droplet volume is used in the droplet dPCR measurement equation has previously been documented. In this study, we characterize both intrawell and interwell droplet volume variability using optical microscopy and determine the impact of these two sources of variability on target concentration estimates. A small optical distortion across the image was measured which, without correction, biased droplet volume measurements. Longitudinal monitoring of interwell droplet volume over 39 weeks using several lots of Mastermix demonstrated a mean droplet volume of 0.786 nL and intermediate precision of 1.7%. The frequency distribution of intrawell droplet volumes varied. Some wells displayed a skewed distribution which resulted in a small bias in estimated target concentration for a simulated dPCR with target concentrations of between 62 and 8000 copies μL-1. The size and direction of this bias was influenced by the distribution pattern of the droplet volumes within the well. The proportion of Mastermix in dPCR mix affected droplet volume. A pipetting error of 10% during mixing of the premix and Mastermix resulted in a 2.6% change in droplet volume and, consequently, a bias in concentration measurements highlighting the advantages of gravimetric preparation of dPCR mixes for high accuracy measurements.
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Affiliation(s)
- Kerry R Emslie
- National Measurement Institute , Lindfield , New South Wales 2070 , Australia
| | | | - Kate Griffiths
- National Measurement Institute , Lindfield , New South Wales 2070 , Australia
| | | | - Leonardo B Pinheiro
- National Measurement Institute , Lindfield , New South Wales 2070 , Australia
| | - Daniel G Burke
- National Measurement Institute , Lindfield , New South Wales 2070 , Australia
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13
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Huynh T, Byrnes SA, Chang TC, Weigl BH, Nichols KP. General methods for quantitative interpretation of results of digital variable-volume assays. Analyst 2019; 144:7209-7219. [DOI: 10.1039/c9an01479a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In digital assays, devices typically require precisely controlled volumes since variation can cause biases in concentration estimates. Here, we develop methods to correct bias when compartment volumes are variable.
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Affiliation(s)
- Toan Huynh
- Intellectual Ventures Laboratory
- Bellevue
- USA
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14
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Vynck M, Vandesompele J, Thas O. On determining the power of digital PCR experiments. Anal Bioanal Chem 2018; 410:5731-5739. [PMID: 29961092 DOI: 10.1007/s00216-018-1212-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 11/28/2022]
Abstract
The experimental design that will be carried out to evaluate a nucleic acid quantification hypothesis determines the cost and feasibility of digital polymerase chain reaction (digital PCR) studies. Experiment design involves the calculation of the number of technical measurement replicates and the determination of the characteristics of those replicates, and this in accordance with the capabilities of the available digital PCR platform. Available digital PCR power analyses suffer from one or more of the following limitations: narrow scope, unrealistic assumptions, no sufficient detail for replication, lack of source code and user-friendly software. Here, we discuss the nature of six parameters that affect the statistical power, i.e., desired effect size, total number of partitions, fraction of positive partitions, number of replicate measurements, between-replicate variance, and significance level. We also show to what extent these parameters affect power, and argue that careful design of experiments is needed to achieve the desired power. A web tool, dPowerCalcR, that allows interactive calculation of statistical power and optimization of the experimental design is available.
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Affiliation(s)
- Matthijs Vynck
- Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.,Bioinformatics Institute Ghent: from Nucleotides to Networks (BIG N2N), Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.,Biogazelle, Technologiepark 3, 9052, Zwijnaarde, Belgium
| | - Olivier Thas
- Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,Bioinformatics Institute Ghent: from Nucleotides to Networks (BIG N2N), Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, University of Wollongong, Wollongong, NSW, 2522, Australia
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