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Ge X, Zhou H, Shen F, Yang G, Zhang Y, Zhang X, Li H. SARS-CoV-2 subgenomic RNA: formation process and rapid molecular diagnostic methods. Clin Chem Lab Med 2024; 62:1019-1028. [PMID: 38000044 DOI: 10.1515/cclm-2023-0846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which caused coronavirus disease-2019 (COVID-19) is spreading worldwide and posing enormous losses to human health and socio-economic. Due to the limitations of medical and health conditions, it is still a huge challenge to develop appropriate discharge standards for patients with COVID-19 and to use medical resources in a timely and effective manner. Similar to other coronaviruses, SARS-CoV-2 has a very complex discontinuous transcription process to generate subgenomic RNA (sgRNA). Some studies support that sgRNA of SARS-CoV-2 can only exist when the virus is active and is an indicator of virus replication. The results of sgRNA detection in patients can be used to evaluate the condition of hospitalized patients, which is expected to save medical resources, especially personal protective equipment. There have been numerous investigations using different methods, especially molecular methods to detect sgRNA. Here, we introduce the process of SARS-CoV-2 sgRNA formation and the commonly used molecular diagnostic methods to bring a new idea for clinical detection in the future.
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Affiliation(s)
- Xiao Ge
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Huizi Zhou
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Fangyuan Shen
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Guimao Yang
- Department of Medical Laboratory, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P.R. China
| | - Yubo Zhang
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Xiaoyu Zhang
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Heng Li
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
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2
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Lechner A, Rai A, Rojas-Rudilla V, Kuang Y, Paweletz CP, Sholl LM, Dong F. Atypical Droplet Digital Polymerase Chain Reaction Patterns That Indicate Uncommon but Clinically Actionable EGFR Mutations in Lung Cancer. Arch Pathol Lab Med 2024; 148:553-558. [PMID: 37639432 DOI: 10.5858/arpa.2023-0088-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2023] [Indexed: 08/31/2023]
Abstract
CONTEXT Droplet digital polymerase chain reaction (ddPCR) is a sensitive method to detect common pathogenic EGFR mutations in non-small cell lung cancer. Although targeted assays have not been specifically designed to detect them, uncommon EGFR mutations have been linked to response to targeted therapy. OBJECTIVE To describe atypical ddPCR patterns that correspond to uncommon but clinically actionable EGFR mutations. DESIGN A cohort of 1134 consecutive non-small cell lung cancers that underwent targeted next-generation sequencing was reviewed. Uncommon EGFR mutations involving probe binding sites were evaluated by ddPCR. RESULTS Two hundred fifty-five of 1134 cancers (22.5%) harbored pathogenic EGFR mutations. One hundred eighty-six of 255 (72.9%) had canonical EGFR exon 19 deletion or exon 21 p.L858R variants designed for detection by ddPCR. An additional 25 of 255 cases (9.8%) had uncommon EGFR mutations within the probe-binding site, including 1 case with concurrent uncommon mutations in both exon 19 and exon 21. These mutations included uncommon EGFR exon 19 deletions (n = 6), EGFR exon 19 substitutions p.L747P (n = 3) and p.L747A (n = 1), dinucleotide substitutions leading to EGFR p.L858R (n = 5), EGFR exon 21 substitutions p.K860I (n = 1) and p.L861Q (n = 9), and EGFR p.[L858R;K860I] (n = 1). Droplet digital polymerase chain reaction generated atypical but reproducible signal for each of these uncommon variants. CONCLUSIONS Droplet digital polymerase chain reaction analysis of uncommon pathogenic EGFR variants can yield unique and reproducible results. Recognition of atypical patterns in EGFR ddPCR testing can prompt confirmatory molecular testing and aid appropriate targeted therapy selection for patients with non-small cell lung cancer.
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Affiliation(s)
- Adam Lechner
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Lechner, Rai, Rojas-Rudilla, Sholl, Dong)
- the University of Missouri School of Medicine, Columbia (Lechner)
| | - Anooja Rai
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Lechner, Rai, Rojas-Rudilla, Sholl, Dong)
| | - Vanesa Rojas-Rudilla
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Lechner, Rai, Rojas-Rudilla, Sholl, Dong)
| | - Yanan Kuang
- the Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute, Boston, Massachusetts(Kuang)
- the Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts(Kuang, Paweletz)
| | - Cloud P Paweletz
- the Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts(Kuang, Paweletz)
| | - Lynette M Sholl
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Lechner, Rai, Rojas-Rudilla, Sholl, Dong)
| | - Fei Dong
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Lechner, Rai, Rojas-Rudilla, Sholl, Dong)
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Chen Y, De Spiegelaere W, Trypsteen W, Gleerup D, Vandesompele J, Lievens A, Vynck M, Thas O. Benchmarking digital PCR partition classification methods with empirical and simulated duplex data. Brief Bioinform 2024; 25:bbae120. [PMID: 38555473 PMCID: PMC10981767 DOI: 10.1093/bib/bbae120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/09/2024] [Accepted: 02/26/2024] [Indexed: 04/02/2024] Open
Abstract
Digital PCR (dPCR) is a highly accurate technique for the quantification of target nucleic acid(s). It has shown great potential in clinical applications, like tumor liquid biopsy and validation of biomarkers. Accurate classification of partitions based on end-point fluorescence intensities is crucial to avoid biased estimators of the concentration of the target molecules. We have evaluated many clustering methods, from general-purpose methods to specific methods for dPCR and flowcytometry, on both simulated and real-life data. Clustering method performance was evaluated by simulating various scenarios. Based on our extensive comparison of clustering methods, we describe the limits of these methods, and formulate guidelines for choosing an appropriate method. In addition, we have developed a novel method for simulating realistic dPCR data. The method is based on a mixture distribution of a Poisson point process and a skew-$t$ distribution, which enables the generation of irregularities of cluster shapes and randomness of partitions between clusters ('rain') as commonly observed in dPCR data. Users can fine-tune the model parameters and generate labeled datasets, using their own data as a template. Besides, the database of experimental dPCR data augmented with the labeled simulated data can serve as training and testing data for new clustering methods. The simulation method is available as an R Shiny app.
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Affiliation(s)
- Yao Chen
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Belgium
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Ghent University, Belgium
- Ghent University Digital PCR Consortium, Ghent University, Belgium
| | - Ward De Spiegelaere
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Ghent University, Belgium
- Ghent University Digital PCR Consortium, Ghent University, Belgium
| | - Wim Trypsteen
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Ghent University, Belgium
- Ghent University Digital PCR Consortium, Ghent University, Belgium
- Department of Internal Medicine, Ghent University and University Hospital, Belgium
| | - David Gleerup
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Ghent University, Belgium
- Ghent University Digital PCR Consortium, Ghent University, Belgium
| | - Jo Vandesompele
- Ghent University Digital PCR Consortium, Ghent University, Belgium
- Department of Biomolecular Medicine, Ghent University and University Hospital, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University and University Hospital, Belgium
- Pxlence, Belgium
| | - Antoon Lievens
- Ghent University Digital PCR Consortium, Ghent University, Belgium
| | - Matthijs Vynck
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Ghent University, Belgium
- Ghent University Digital PCR Consortium, Ghent University, Belgium
| | - Olivier Thas
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Belgium
- Ghent University Digital PCR Consortium, Ghent University, Belgium
- I-BioStat, Data Science Institute, Hasselt University, Belgium
- National Institute for Applied Statistics Research Australia (NIASRA), University of Wollongong, Australia
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Roemen GMJM, Theunissen TEJ, Hoezen WWJ, Steyls ARM, Paulussen ADC, Mosterd K, Rahikkala E, zur Hausen A, Speel EJM, van Geel M. Detection of PTCH1 Copy-Number Variants in Mosaic Basal Cell Nevus Syndrome. Biomedicines 2024; 12:330. [PMID: 38397932 PMCID: PMC10886644 DOI: 10.3390/biomedicines12020330] [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: 12/28/2023] [Revised: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Basal cell nevus syndrome (BCNS) is an inherited disorder characterized mainly by the development of basal cell carcinomas (BCCs) at an early age. BCNS is caused by heterozygous small-nucleotide variants (SNVs) and copy-number variants (CNVs) in the Patched1 (PTCH1) gene. Genetic diagnosis may be complicated in mosaic BCNS patients, as accurate SNV and CNV analysis requires high-sensitivity methods due to possible low variant allele frequencies. We compared test outcomes for PTCH1 CNV detection using multiplex ligation-probe amplification (MLPA) and digital droplet PCR (ddPCR) with samples from a BCNS patient heterozygous for a PTCH1 CNV duplication and the patient's father, suspected to have a mosaic form of BCNS. ddPCR detected a significantly increased PTCH1 copy-number ratio in the index patient's blood, and the father's blood and tissues, indicating that the father was postzygotic mosaic and the index patient inherited the CNV from him. MLPA only detected the PTCH1 duplication in the index patient's blood and in hair and saliva from the mosaic father. Our data indicate that ddPCR more accurately detects CNVs, even in low-grade mosaic BCNS patients, which may be missed by MLPA. In general, quantitative ddPCR can be of added value in the genetic diagnosis of mosaic BCNS patients and in estimating the recurrence risk for offspring.
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Affiliation(s)
- Guido M. J. M. Roemen
- Department of Pathology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands; (T.E.J.T.)
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
| | - Tom E. J. Theunissen
- Department of Pathology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands; (T.E.J.T.)
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
| | - Ward W. J. Hoezen
- Department of Dermatology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | - Anja R. M. Steyls
- Department of Clinical Genetics, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands;
| | - Aimee D. C. Paulussen
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
- Department of Clinical Genetics, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands;
| | - Klara Mosterd
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
- Department of Dermatology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | - Elisa Rahikkala
- Research Unit of Clinical Medicine, Department of Clinical Genetics, Medical Research Center Oulu, Oulu University Hospital, University of Oulu, 90570 Oulu, Finland
| | - Axel zur Hausen
- Department of Pathology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands; (T.E.J.T.)
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
| | - Ernst Jan M. Speel
- Department of Pathology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands; (T.E.J.T.)
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
| | - Michel van Geel
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
- Department of Dermatology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands;
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Svetina M, Šelb J, Lyons JJ, Korošec P, Rijavec M. Clinically accessible amplitude-based multiplex ddPCR assay for tryptase genotyping. Sci Rep 2024; 14:2416. [PMID: 38287122 PMCID: PMC10825142 DOI: 10.1038/s41598-024-52983-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/25/2024] [Indexed: 01/31/2024] Open
Abstract
Hereditary α tryptasemia (HαT) is an autosomal dominant trait characterized by increased TPSAB1 copy number (CN) encoding α-tryptase. The determination of HαT is being discussed as an important biomarker to be included in risk assessment models and future diagnostic algorithms for patients with mastocytosis and anaphylaxis. Due to the complex genetic structure at the human tryptase locus, genetic testing for tryptase gene composition is presently notably limited and infrequently pursued. This study aimed to develop, optimise and validate a multiplex droplet digital PCR (ddPCR) assay that can reliably quantify α- and β-tryptase encoding sequences in a single reaction. To optimise the ddPCR conditions and establish an amplitude-based multiplex ddPCR assay, additional primers and probes, a thermal gradient with varying annealing temperatures, different primers/probe concentrations, and various initial DNA quantities were tested. Results obtained from all 114 samples analysed using multiplex ddPCR were identical to those obtained through the use of original duplex assays. Utilizing this multiplex ddPCR assay, in contrast to conducting distinct duplex ddPCRs, presents noteworthy benefits for tryptase genotyping. These advantages encompass a substantial threefold decrease in material costs and considerable time savings. Consequently, this approach exhibits high suitability and particularly captures interest for routine clinical implementation.
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Affiliation(s)
- Manca Svetina
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Julij Šelb
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jonathan J Lyons
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | - Peter Korošec
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Matija Rijavec
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia.
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
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Calabrese S, Markl AM, Neugebauer M, Krauth SJ, Borst N, von Stetten F, Lehnert M. Reporter emission multiplexing in digital PCRs (REM-dPCRs): direct quantification of multiple target sequences per detection channel by population specific reporters. Analyst 2023; 148:5243-5254. [PMID: 37727114 DOI: 10.1039/d3an00191a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Digital PCRs (dPCRs) are widely used methods for the detection and quantification of rare abundant sequences relevant to fields such as liquid biopsy or oncology. In order to increase the information content and save valuable sample materials, there is a significant need for digital multiplexing methods that are easy to establish, analyse, and interpret, and ideally allow the usage of existing lab equipment. Herein, we present a novel reporter emission multiplexing approach for the digital PCR method (REM-dPCR), which meets these requirements. It further increases the multiplexing capacity of commercial dPCR devices. For example, we present a stepwise increase in multiplexing degrees from a monochrome two-plex assay in one detection channel to a six-plex REM-dPCR assay in a three-color dPCR device for KRAS/BRAF single nucleotide polymorphism (SNP) target sequences. The guidelines for the REM-dPCR design are presented, and the process from duplex to six-plex assay establishment, taking into account the target sequence-dependent effects on assay performance, is discussed. Furthermore, the assay-specific, sensitive and precise quantification of different fractions of KRAS mutant and wild-type DNA sequences in different ratios is demonstrated. To increase the device capacitance and the degree of multiplexing, the REM-dPCR uses the advantage of n target-independent reporter molecules in combination with target sequence-specific mediator probes. Different reporter types are labelled with fluorophores of different signal intensities but not necessarily different emission spectra. This leads to the generation of n independent single-positive populations in the dataspace, created by k detection channels, whereby n > k and n ≥ 2. By usage of target-independent but population-specific reporter types, a fixed set of six optimized signalling molecules could be defined. This reporter set enables the robust generation and precise differentiation of multiple fluorescence signals in dPCRs and can be transferred to new target panels. The set which enables stable signal generation and differentiation in a specified device would allow easy transfer to new target panels.
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Affiliation(s)
| | - Anja M Markl
- Hahn-Schickard, 79110 Freiburg, Germany.
- Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Maximilian Neugebauer
- Hahn-Schickard, 79110 Freiburg, Germany.
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany
| | - Stefanie J Krauth
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, UK
- School of Health and Wellbeing, General Practice and Primary Care, University of Glasgow, Glasgow, UK
| | - Nadine Borst
- Hahn-Schickard, 79110 Freiburg, Germany.
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany
| | - Felix von Stetten
- Hahn-Schickard, 79110 Freiburg, Germany.
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany
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Chatterton S, Schwinghamer TD, Pagé A, Davidson RB, Harding MW, Banniza S. Inoculum dose-disease response relationships for the pea root rot pathogen, Aphanomyces euteiches, are dependent on soil type and other pathogens. FRONTIERS IN PLANT SCIENCE 2023; 14:1115420. [PMID: 37235016 PMCID: PMC10205554 DOI: 10.3389/fpls.2023.1115420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 04/03/2023] [Indexed: 05/28/2023]
Abstract
The oomycete pathogen, Aphanomyces euteiches, was implicated for the first time in pea and lentil root rot in Saskatchewan and Alberta in 2012 and 2013. Subsequent surveys from 2014 to 2017 revealed that Aphanomyces root rot (ARR) was widespread across the Canadian prairies. The absence of effective chemical, biological, and cultural controls and lack of genetic resistance leave only one management option: avoidance. The objectives of this study were to relate oospore levels in autoclaved and non-autoclaved soils to ARR severity across soil types from the vast prairie landscape and to determine the relationship of measured DNA quantity of A. euteiches using droplet digital PCR or quantitative PCR to the initial oospore inoculum dose in soils. These objectives support a future end goal of creating a rapid assessment method capable of categorizing root rot risk in field soil samples to aid producers with pulse crop field selection decisions. The ARR severity to oospore dose relationship was statistically significantly affected by the soil type and location from which soils were collected and did not show a linear relationship. For most soil types, ARR did not develop at oospore levels below 100/g soil, but severity rose above this level, confirming a threshold level of 100 oospores/g soil for disease development. For most soil types, ARR severity was significantly higher in non-autoclaved compared to autoclaved treatments, demonstrating the role that other pathogens play in increasing disease severity. There was a significant linear relationship between DNA concentrations measured in soil and oospore inoculum concentration, although the strength of the relationship was better for some soil types, and in some soil types, DNA measurement results underestimated the number of oospores. This research is important for developing a root rot risk assessment system for the Canadian prairies based on soil inoculum quantification, following field validation of soil quantification and relationship to root rot disease severity.
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Affiliation(s)
- Syama Chatterton
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Timothy D. Schwinghamer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Antoine Pagé
- Aquatic and Crop Resource Development, National Research Council Canada, Montreal, QC, Canada
| | | | - Michael W. Harding
- Plant and Bee Health Surveillance, Alberta Ministry of Agriculture and Irrigation, Brooks, AB, Canada
| | - Sabine Banniza
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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Tsuriel S, Hannes V, Hasona A, Raz M, Hershkovitz D. Digital PCR-Based Method for Detecting CDKN2A Loss in Brain Tumours. Mol Diagn Ther 2022; 26:689-698. [PMID: 36129665 DOI: 10.1007/s40291-022-00610-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2022] [Indexed: 12/30/2022]
Abstract
INTRODUCTION CDKN2A is a key tumour suppressor gene and loss of CDKN2A can be found in many tumours. In astrocytoma grade IV, CDKN2A is deleted in more than 50% of tumours. In many instances, low-grade gliomas with homozygous loss of CDKN2A behave like high grade tumours. The available techniques for CDKN2A loss are laborious, expensive, unreliable, or unavailable in most pathology institutes. Therefore, although it is essential for accurate brain tumour diagnosis, the routine diagnosis does not include testing for CDKN2A deletion. METHODS We developed a digital polymerase chain reaction (dPCR) assay for CDKN2A loss detection. The assay is based on counting the copy number of CDKN2A gene and of a reference gene on the same chromosome. It was tested for the detection limit with regard to tumour content and minimal DNA quantity. It was then tested on 24 clinical samples with known CDKN2A status. Additionally, we tested 44 gliomas with unknown CDKN2A status. RESULTS We found that the newly developed assay is reliable in tissue with more than 50% tumour content and more than 0.4 ng of DNA. The validation cohort showed complete concordance, and we were able to detect homozygous loss in 16 gliomas with unknown CDKN2A status. DISCUSSION The method presented can give a fast, cost-effective, clinically reliable evaluation of CDKN2A loss in tissue with more than 50% tumour content. Its ability to work with old samples and with low amounts of DNA makes it the favoured assay in cases where other techniques fail.
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Affiliation(s)
- Shlomo Tsuriel
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel.
| | - Victoria Hannes
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel
| | - Asala Hasona
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel-Aviv, Israel
| | - Michal Raz
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel
| | - Dov Hershkovitz
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel.
- Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel-Aviv, Israel.
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9
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Droplet-based methods for tackling antimicrobial resistance. Curr Opin Biotechnol 2022; 76:102755. [PMID: 35841864 DOI: 10.1016/j.copbio.2022.102755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 11/21/2022]
Abstract
Application of droplet-based methods enables (i) faster detection, (ii) increased sensitivity, (iii) characterization of the level of heterogeneity in response to antibiotics by bacterial populations, and (iv) expanded screening of the effectiveness of antibiotic combinations. Hereby, we discuss the key steps and parameters of droplet-based experiments to investigate antimicrobial resistance. We also review recent findings accomplished with these methods and highlight their advantages and capacity to yield new insights into the problem of antimicrobial resistance.
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10
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von Ammon U, Averink T, Kumanan K, Brosnahan CL, Pochon X, Hutson KS, Symonds JE. An Efficient Tetraplex Surveillance Tool for Salmonid Pathogens. Front Microbiol 2022; 13:885585. [PMID: 35531301 PMCID: PMC9069008 DOI: 10.3389/fmicb.2022.885585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/01/2022] [Indexed: 12/22/2022] Open
Abstract
Fish disease surveillance methods can be complicated and time consuming, which limits their value for timely intervention strategies on aquaculture farms. Novel molecular-based assays using droplet digital Polymerase Chain Reaction (ddPCR) can produce immediate results and enable high sample throughput with the ability to multiplex several targets using different fluorescent dyes. A ddPCR tetraplex assay was developed for priority salmon diseases for farmers in New Zealand including New Zealand Rickettsia-like organism 1 (NZ-RLO1), NZ-RLO2, Tenacibaculum maritimum, and Yersinia ruckeri. The limit of detection in singleplex and tetraplex assays was reached for most targets at 10−9 ng/μl with, respectively, NZ-RLO1 = 0.931 and 0.14 copies/μl, NZ-RLO2 = 0.162 and 0.21 copies/μl, T. maritimum = 0.345 and 0.93 copies/μl, while the limit of detection for Y. ruckeri was 10−8 with 1.0 copies/μl and 0.7 copies/μl. While specificity of primers was demonstrated in previous studies, we detected cross-reactivity of T. maritimum with some strains of Tenacibaculum dicentrarchi and Y. ruckeri with Serratia liquefaciens, respectively. The tetraplex assay was applied as part of a commercial fish disease surveillance program in New Zealand for 1 year to demonstrate the applicability of tetraplex tools for the salmonid aquaculture industry.
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Affiliation(s)
- Ulla von Ammon
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
- *Correspondence: Ulla von Ammon,
| | - Tessa Averink
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
| | - Karthiga Kumanan
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Cara L. Brosnahan
- Institute of Marine Science, University of Auckland, Warkworth, New Zealand
| | - Xavier Pochon
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
- Animal Health Laboratory, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - Kate S. Hutson
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Jane E. Symonds
- Aquaculture & Marine Biosecurity, Cawthron Institute, Nelson, New Zealand
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11
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Wen T, Zhang X, Lippuner C, Schiff M, Stuber F. Development and Evaluation of a Droplet Digital PCR Assay for 8p23 β-Defensin Cluster Copy Number Determination. Mol Diagn Ther 2021; 25:607-615. [PMID: 34327613 PMCID: PMC8320422 DOI: 10.1007/s40291-021-00546-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2021] [Indexed: 12/01/2022]
Abstract
Introduction It has been proposed that the copy number (CN) variation (CNV) in β-defensin genes (DEFB) on human chromosome 8p23 determines phenotypic differences in inflammatory diseases. However, no method for accurate and easy DEFB CN quantification is yet available. Objective Droplet digital polymerase chain reaction (ddPCR) is a novel method for CNV quantification and has been used for genes such as CCL4L, CCL3L1, AMY1, and HER2. However, to date, no ddPCR assay has been available for DEFB CN determination. In the present study, we aimed to develop and evaluate such a ddPCR assay. Methods The assay was designed using DEFB4 and RPP30 as the target and the reference gene, respectively. To evaluate the assay, 283 DNA samples with known CNs previously determined using the multiple ligation-dependent probe amplification (MLPA) method, the current gold standard, were used as standards. To discover the optimal DNA template amount, we tested 80 to 2.5 ng DNA by a serial of one to two dilutions of eight samples. To evaluate the reproducibility of the assay, 31 samples were repeated to calculate the intra- and inter-assay variations. To further validate the reliability of the assay, the CNs of all 283 samples were determined using ddPCR. To compare results with those using quantitative PCR (qPCR), DEFB CNs for 48 samples were determined using qPCR with the same primers and probes. Results In a one-dimensional plot, the positive and negative droplets were clearly separated in both DEFB4 and RPP30 detection channels. In a two-dimensional plot, four populations of droplets were observed. The 20 ng template DNA proved optimal, with either high (80 ng) or low (10, 5, 2.5 ng) template input leading to ambiguous or inaccurate results. For the 31 standard samples, DEFB CNs were accurately determined with small intra- and inter-assay variations (coefficient of variation < 0.04 for both). In the validation cohort, ddPCR provided the correct CN for all 283 samples with high confidence. qPCR measurements for the 48 samples produced noisy data with high uncertainty and low accuracy. Conclusions ddPCR is an accurate, reproducible, easy-to-use, cheap, high-throughput method for DEFB CN determination. ddPCR could be applied to DEFB CN quantification in large-scale case–control studies. Supplementary Information The online version contains supplementary material available at 10.1007/s40291-021-00546-2.
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Affiliation(s)
- Tingting Wen
- Department of Anesthesiology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xianghong Zhang
- Department of Cardiac Intensive Care Unit, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Heath, Hangzhou, Zhejiang, China.
| | - Christoph Lippuner
- Department of Anesthesiology and Pain Medicine, Bern University Hospital, Inselspital, Bern, Switzerland
| | - Marcel Schiff
- Department of Anesthesiology and Pain Medicine, Bern University Hospital, Inselspital, Bern, Switzerland
| | - Frank Stuber
- Department of Anesthesiology and Pain Medicine, Bern University Hospital, Inselspital, Bern, Switzerland
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12
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Bidshahri R, Fakhfakh K, McNeil K, Won JR, Wolber R, Hughesman C, Haynes C. Analysis of
KRAS
G12
/
G13
in colorectal cancer using an economical digital
PCR
assay that unequivocally differentiates missense and synonymous alleles. CAN J CHEM ENG 2021. [DOI: 10.1002/cjce.24243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Roza Bidshahri
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Biomedical Engineering Program University of British Columbia Vancouver British Columbia Canada
| | - Kareem Fakhfakh
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Department of Chemical and Biological Engineering University of British Columbia Vancouver British Columbia Canada
| | - Kelly McNeil
- Department of Genetics and Molecular Diagnostics British Columbia Cancer Agency Vancouver British Columbia Canada
| | - Jennifer R. Won
- Canadian Immunohistochemistry Quality Control, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver British Columbia Canada
| | - Robert Wolber
- Canadian Immunohistochemistry Quality Control, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver British Columbia Canada
- Department of Pathology Lion's Gate Hospital North Vancouver British Columbia Canada
| | - Curtis Hughesman
- Cancer Genetics and Genomics Lab British Columbia Cancer Agency Vancouver British Columbia Canada
| | - Charles Haynes
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Biomedical Engineering Program University of British Columbia Vancouver British Columbia Canada
- Department of Chemical and Biological Engineering University of British Columbia Vancouver British Columbia Canada
- Genome Sciences and Technology Program Vancouver British Columbia Canada
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13
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Schlenker F, Kipf E, Borst N, Hutzenlaub T, Zengerle R, von Stetten F, Juelg P. Virtual Fluorescence Color Channels by Selective Photobleaching in Digital PCR Applied to the Quantification of KRAS Point Mutations. Anal Chem 2021; 93:10538-10545. [PMID: 34279918 DOI: 10.1021/acs.analchem.1c01488] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Multiplexing of analyses is essential to reduce sample and reagent consumption in applications with large target panels. In applications such as cancer diagnostics, the required degree of multiplexing often exceeds the number of available fluorescence channels in polymerase chain reaction (PCR) devices. The combination of photobleaching-sensitive and photobleaching-resistant fluorophores of the same color can boost the degree of multiplexing by a factor of 2 per channel. The only additional hardware required to create virtual fluorescence color channels is a low-cost light-emitting diode (LED) setup for selective photobleaching. Here, we present an assay concept for fluorescence color multiplexing in up to 10 channels (five standard channels plus five virtual channels) using the mediator probe PCR with universal reporter (UR) fluorogenic oligonucleotides. We evaluate the photobleaching characteristic of 21 URs, which cover the whole spectral range from blue to crimson. This comprehensive UR data set is employed to demonstrate the use of three virtual channels in addition to the three standard channels of a commercial dPCR device (blue, green, and red) targeting cancer-associated point mutations (KRAS G12D and G12V). Moreover, a LOD (limit of detection) analysis of this assay confirms the high sensitivity of the multiplexing method (KRAS G12D: 16 DNA copies/reaction in the standard red channel and KRAS G12V: nine DNA copies/reaction in the virtual red channel). Based on the presented data set, optimal fluorogenic reporter combinations can be easily selected for the application-specific creation of virtual channels, enabling a high degree of multiplexing at low optical and technical effort.
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Affiliation(s)
| | - Elena Kipf
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Nadine Borst
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.,Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Tobias Hutzenlaub
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.,Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Roland Zengerle
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.,Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Felix von Stetten
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.,Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Peter Juelg
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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14
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Srisutham S, Suwannasin K, Sugaram R, Dondorp AM, Imwong M. Measurement of gene amplifications related to drug resistance in Plasmodium falciparum using droplet digital PCR. Malar J 2021; 20:120. [PMID: 33639924 PMCID: PMC7916280 DOI: 10.1186/s12936-021-03659-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy number variations (CNVs) of the Plasmodium falciparum multidrug resistance 1 (pfmdr1), P. falciparum plasmepsin2 (pfplasmepsin2) and P. falciparum GTP cyclohydrolase 1 (pfgch1) genes are associated with anti-malarial drug resistance in P. falciparum malaria. Droplet digital PCR (ddPCR) assays have been developed for accurate assessment of CNVs in several human genes. The aim of the present study was to develop and validate ddPCR assays for detection of the CNVs of P. falciparum genes associated with resistance to anti-malarial drugs. METHODS A multiplex ddPCR assay was developed to detect the CNVs in the pfmdr1 and pfplasmepsin2 genes, while a duplex ddPCR assay was developed to detect CNV in the pfgch1 gene. The gene copy number (GCN) quantification limit, as well as the accuracy and precision of the ddPCR assays were determined and compared to conventional quantitative PCR (qPCR). In order to reduce the cost of testing, a multiplex ddPCR assay of two target genes, pfmdr1 and pfplasmepsin2, was validated. In addition, the CNVs of genes of field samples collected from Thailand from 2015 to 2019 (n = 84) were assessed by ddPCR and results were compared to qPCR as the reference assay. RESULTS There were no significant differences between the GCN results obtained from uniplex and multiplex ddPCR assays for detection of CNVs in the pfmdr1 and pfplasmepsin2 genes (p = 0.363 and 0.330, respectively). Based on the obtained gene copy number quantification limit, the accuracy and percent relative standard deviation (%RSD) value of the multiplex ddPCR assay were 95% and 5%, respectively, for detection of the CNV of the pfmdr1 gene, and 91% and 5% for detection of the CNV of the pfplasmepsin2 gene. There was no significant difference in gene copy numbers assessed by uniplex or duplex ddPCR assays regarding CNV in the pfgch1 gene (p = 0.276). The accuracy and %RSD value of the duplex ddPCR assay were 95% and 4%, respectively, regarding pfgch1 GCN. In the P. falciparum field samples, pfmdr1 and pfplasmepsin2 GCNs were amplified in 15% and 27% of samples from Ubon Ratchathani, Thailand, while pfgch1 GCN was amplified in 50% of samples from Yala, Thailand. There was 100% agreement between the GCN results obtained from the ddPCR and qPCR assays (κ = 1.00). The results suggested that multiplex ddPCR assay is the optional assay for the accurate detection of gene copy number without requiring calibration standards, while the cost and required time are reduced. Based on the results of this study, criteria for GCN detection by ddPCR analysis were generated. CONCLUSIONS The developed ddPCR assays are simple, accurate, precise and cost-effective tools for detection of the CNVs in the pfmdr1, pfplasmepsin2 and pfgch1 genes of P. falciparum. The ddPCR assay is a useful additional tool for the surveillance of anti-malarial drug resistance.
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Affiliation(s)
- Suttipat Srisutham
- Department of Clinical Microscopy, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Kanokon Suwannasin
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rungniran Sugaram
- Division of Vector Borne Diseases, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mallika Imwong
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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15
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Oladipo EK, Ajayi AF, Odeyemi AN, Akindiya OE, Adebayo ET, Oguntomi AS, Oyewole MP, Jimah EM, Oladipo AA, Ariyo OE, Oladipo BB, Oloke JK. Laboratory diagnosis of COVID-19 in Africa: availability, challenges and implications. Drug Discov Ther 2020; 14:153-160. [PMID: 32908070 DOI: 10.5582/ddt.2020.03067] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The COVID-19 infection has been a matter of urgency to tackle around the world today, there exist 200 countries around the world and 54 countries in Africa that the COVID-19 infection cases have been confirmed. This situation prompted us to look into the challenges African laboratories are facing in the diagnosis of novel COVID-19 infection. A limited supply of essential laboratory equipment and test kits are some of the challenges faced in combatting the novel virus in Africa. Also, there is inadequate skilled personnel, which might pose a significant danger in case there is a surge in COVID-19 infection cases. The choice of diagnostic method in Africa is limited as there are only two available diagnostic methods being used out of the six methods used globally, thereby reducing the opportunity of supplementary diagnosis, which will further lead to inappropriate diagnosis and affect the accuracy of diagnostic reports. Furthermore, challenges like inadequate power supply, the method used in sample collection, storage and transportation of specimens are also significant as they also pose their respective implication. From the observations, there is an urgent need for more investment into the laboratories for proper, timely, and accurate diagnosis of COVID-19.
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Affiliation(s)
- Elijah Kolawole Oladipo
- Department of Microbiology, Laboratory of Molecular Biology, Bioinformatics and Immunology, Adeleke University, Ede, Osun State, Nigeria.,Genomics Unit, Helix Biogen Consult, Ogbomosho, Oyo State, Nigeria
| | - Ayodeji Folorunsho Ajayi
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomosho, Oyo State, Nigeria
| | - Aduragbemi Noah Odeyemi
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomosho, Oyo State, Nigeria
| | - Olawumi Elizabeth Akindiya
- Department of Biological Science, Ondo State University of Science and Technology, Okitipupa, Ondo State, Nigeria
| | - Emmanuel Tayo Adebayo
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomosho, Oyo State, Nigeria
| | | | | | - Esther Moradeyo Jimah
- Genomics Unit, Helix Biogen Consult, Ogbomosho, Oyo State, Nigeria.,Department of Medical Microbiology and Parasitology, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Abayomi Adio Oladipo
- Department of Haematology and Blood Grouping Serology, Obafemi Awolowo University Teaching Hospital Complex, Ile Ife Wesley Guild Hospital Wing, Osun State, Nigeria
| | - Olumuyiwa Elijah Ariyo
- Department of Medicine, Infectious Diseases and Tropical Medicine Unit, Federal Teaching Hospital, Ido-Ekiti, Ekiti State, Nigeria
| | - Bukola Bisola Oladipo
- Department of Clinical Nursing, Bowen University Teaching Hospital, Ogbomosho, Oyo State, Nigeria
| | - Julius Kola Oloke
- Department of Natural Science, Precious Cornerstone University, Ibadan, Oyo State, Nigeria
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16
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Evaluating the quantity, quality and size distribution of cell-free DNA by multiplex droplet digital PCR. Sci Rep 2020; 10:12564. [PMID: 32724107 PMCID: PMC7387491 DOI: 10.1038/s41598-020-69432-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/07/2020] [Indexed: 01/06/2023] Open
Abstract
Cell-free DNA (cfDNA) has become a comprehensive biomarker in the fields of non-invasive cancer detection and monitoring, organ transplantation, prenatal genetic testing and pathogen detection. While cfDNA samples can be obtained using a broad variety of approaches, there is an urgent need to standardize analytical tools aimed at assessing its basic properties. Typical methods to determine the yield and fragment size distribution of cfDNA samples are usually either blind to genomic DNA contamination or the presence of enzymatic inhibitors, which can confound and undermine downstream analyses. Here, we present a novel droplet digital PCR assay to identify suboptimal samples and aberrant cfDNA size distributions, the latter typically associated with high levels of circulating tumour DNA (ctDNA). Our assay was designed to promiscuously cross-amplify members of the human olfactory receptor (OR) gene family and includes a customizable diploid locus for the determination of absolute cfDNA concentrations. We demonstrate here the utility of our assay to estimate the yield and quality of cfDNA extracts and deduce fragment size distributions that correlate well with those inferred by capillary electrophoresis and high throughput sequencing. The assay described herein is a powerful tool to establish quality controls and stratify cfDNA samples based on presumed ctDNA levels, then facilitating the implementation of robust, cost-effective and standardized analytical workflows into clinical practice.
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17
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Lee KH, Lee TH, Choi MK, Kwon IS, Bae GE, Yeo MK. Identification of a Clinical Cutoff Value for Multiplex KRAS G12/G13 Mutation Detection in Colorectal Adenocarcinoma Patients Using Digital Droplet PCR, and Comparison with Sanger Sequencing and PNA Clamping Assay. J Clin Med 2020; 9:jcm9072283. [PMID: 32708359 PMCID: PMC7409004 DOI: 10.3390/jcm9072283] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/08/2020] [Accepted: 07/16/2020] [Indexed: 12/17/2022] Open
Abstract
KRAS (Kirsten rat sarcoma 2 viral oncogene homolog) is a major predictive marker for anti-epidermal growth factor receptor treatment, and determination of KRAS mutational status is crucial for successful management of colorectal adenocarcinoma. More standardized and accurate methods for testing KRAS mutation, which is vital for therapeutic decision-making, are required. Digital droplet polymerase chain reaction (ddPCR) is an advanced digital PCR technology developed to provide absolute quantitation of target DNA. In this study, we validated the clinical performance of ddPCR in determination of KRAS mutational status, and compared ddPCR results with those obtained by Sanger sequencing and peptide nucleic acid-clamping. Of 81 colorectal adenocarcinoma tissue samples, three repeated sets of KRASG12/G13 mutation were measured by ddPCR, yielding high consistency (ICC = 0.956). Receiver operating characteristic (ROC) curves were constructed to determine KRASG12/G13 mutational status based on mutant allele frequency generated by ddPCR. Using the best threshold cutoff (mutant allele frequency of 7.9%), ddPCR had superior diagnostic sensitivity (100%) and specificity (100%) relative to the two other techniques. Thus, ddPCR is effective for detecting the KRASG12/G13 mutation in colorectal adenocarcinoma tissue samples. By allowing definition of the optimal cutoff, ddPCR represents a potentially useful diagnostic tool that could improve diagnostic sensitivity and specificity.
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Affiliation(s)
- Kyung Ha Lee
- Department of Surgery, Chungnam National University Hospital, Daejeon 282, Korea;
| | - Tae Hee Lee
- The Biobank of Chungnam National University Hospital, Daejeon 282, Korea;
| | - Min Kyung Choi
- Department of Pathology, Chungnam National University School of Medicine, Daejeon 266, Korea; (M.K.C.); (G.E.B.)
| | - In Sun Kwon
- Clinical Trials Center of Chungnam National University Hospital, Daejeon 282, Korea;
| | - Go Eun Bae
- Department of Pathology, Chungnam National University School of Medicine, Daejeon 266, Korea; (M.K.C.); (G.E.B.)
| | - Min-Kyung Yeo
- Department of Pathology, Chungnam National University School of Medicine, Daejeon 266, Korea; (M.K.C.); (G.E.B.)
- Correspondence: ; Tel.: +82-42-280-7196; Fax: +82-42-580-8231
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18
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A review of predictive, prognostic and diagnostic biomarkers for brain tumours: towards personalised and targeted cancer therapy. JOURNAL OF RADIOTHERAPY IN PRACTICE 2019. [DOI: 10.1017/s1460396919000955] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
AbstractBackground:Brain tumours are relatively rare disease but present a large medical challenge as there is currently no method for early detection of the tumour and are typically not diagnosed until patients have progressed to symptomatic stage which significantly decreases chances of survival and also minimises treatment efficacy. However, if brain cancers can be diagnosed at early stages and also if clinicians have the potential to prospectively identify patients likely to respond to specific treatments, then there is a very high potential to increase patients’ treatment efficacy and survival. In recent years, there have been several investigations to identify biomarkers for brain cancer risk assessment, early detection and diagnosis, the likelihood of identifying which group of patients will benefit from a particular treatment and monitoring patient response to treatment.Materials and methods:This paper reports on a review of 21 current clinical and emerging biomarkers used in risk assessment, screening for early detection and diagnosis, and monitoring the response of treatment of brain cancers.Conclusion:Understanding biomarkers, molecular mechanisms and signalling pathways can potentially lead to personalised and targeted treatment via therapeutic targeting of specific genetic aberrant pathways which play key roles in malignant brain tumour formation. The future holds promising for the use of biomarker analysis as a major factor for personalised and targeted brain cancer treatment, since biomarkers have the potential to measure early disease detection and diagnosis, the risk of disease development and progression, improved patient stratification for various treatment paradigms, provide accurate information of patient response to a specific treatment and inform clinicians about the likely outcome of a brain cancer diagnosis independent of the treatment received.
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19
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Davidson M, Aronson LI, Howard-Reeves J, Bryant H, Cutts RJ, Hulkki-Wilson S, Kouvelakis K, Kalaitzaki E, Watkins D, Starling N, Rao S, Cardenosa ML, Begum R, Rana I, Lazaro-Alcausi R, Terlizzo M, Wotherspoon A, Brown G, Swansbury J, Lord CJ, Cunningham D, Chau I, Chong IY. Clonal diversity of MYC amplification evaluated by fluorescent in situ hybridisation and digital droplet polymerase chain reaction in oesophagogastric cancer: Results from a prospective clinical trial screening programme. Eur J Cancer 2019; 122:12-21. [PMID: 31606655 DOI: 10.1016/j.ejca.2019.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/19/2019] [Accepted: 09/03/2019] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The MYC proto-oncogene is among the most commonly dysregulated genes in human cancers. We report screening data from the iMYC trial, an ongoing phase II study assessing ibrutinib monotherapy in advanced pretreated MYC- and/or HER2-amplified oesophagogastric cancer, representing the first attempt to prospectively identify MYC amplifications in this tumour type for the purposes of therapeutic targeting. METHODS Screening utilising a fluorescent in situ hybridisation (FISH) assay for assessment of tumour MYC amplification has been instituted. An experimental digital droplet polymerase chain reaction (ddPCR) assay to assess MYC amplification in both tumour and circulating-tumour (ct)DNA has been developed and investigated. RESULTS One hundred thirty-five archival tumour specimens have undergone successful FISH analysis with 23% displaying evidence of MYC amplification. Intertumour heterogeneity was observed, with the percentage of cancer cells harbouring MYC amplification ranging widely between samples (median 51%, range 11-94%). Intratumoural clonal diversity of MYC amplification was also observed, with a significant degree of variance in amplification ratios (Bartlett's test for equal variance p < 0.001), and an association between greater variance in MYC amplification and improved outcome with prior first-line chemotherapy. ddPCR was most accurate in quantifying MYC amplification in tumour-derived DNA from cases with a high proportion (>70%) of amplified cells within the tumour specimen but was not reliable in samples containing a low proportion of amplified cells or in ctDNA. CONCLUSIONS Our results illustrate the utility of FISH to assess MYC amplification prospectively for a biomarker-selected trial by providing reliable and reproducible results in real time, with a high degree of heterogeneity of MYC amplification observed. We show that ddPCR can potentially detect high-level MYC amplifications in tumour tissue.
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Affiliation(s)
- Michael Davidson
- Royal Marsden NHS Foundation Trust, Downs Road, Surrey, SM2 5PT, UK
| | - Lauren I Aronson
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | | | - Hanna Bryant
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Rosalind J Cutts
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | | | | | | | - David Watkins
- Royal Marsden NHS Foundation Trust, Downs Road, Surrey, SM2 5PT, UK
| | - Naureen Starling
- Royal Marsden NHS Foundation Trust, Downs Road, Surrey, SM2 5PT, UK
| | - Sheela Rao
- Royal Marsden NHS Foundation Trust, Downs Road, Surrey, SM2 5PT, UK
| | | | - Ruwaida Begum
- Royal Marsden NHS Foundation Trust, Downs Road, Surrey, SM2 5PT, UK
| | - Isma Rana
- Royal Marsden NHS Foundation Trust, Downs Road, Surrey, SM2 5PT, UK
| | | | - Monica Terlizzo
- Royal Marsden NHS Foundation Trust, Downs Road, Surrey, SM2 5PT, UK
| | | | - Gina Brown
- Royal Marsden NHS Foundation Trust, Downs Road, Surrey, SM2 5PT, UK
| | - John Swansbury
- Royal Marsden NHS Foundation Trust, Downs Road, Surrey, SM2 5PT, UK
| | - Christopher J Lord
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK; The Breast Cancer Now Toby Robins Research Centre, 237 Fulham Road, London, SW3 6JB, UK
| | - David Cunningham
- Royal Marsden NHS Foundation Trust, Downs Road, Surrey, SM2 5PT, UK
| | - Ian Chau
- Royal Marsden NHS Foundation Trust, Downs Road, Surrey, SM2 5PT, UK.
| | - Irene Y Chong
- Royal Marsden NHS Foundation Trust, Downs Road, Surrey, SM2 5PT, UK; Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
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20
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Brink BG, Meskas J, Brinkman RR. ddPCRclust: an R package and Shiny app for automated analysis of multiplexed ddPCR data. Bioinformatics 2019. [PMID: 29534153 PMCID: PMC6061851 DOI: 10.1093/bioinformatics/bty136] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Motivation Droplet digital PCR (ddPCR) is an emerging technology for quantifying DNA. By partitioning the target DNA into ∼20 000 droplets, each serving as its own PCR reaction compartment, a very high sensitivity of DNA quantification can be achieved. However, manual analysis of the data is time consuming and algorithms for automated analysis of non-orthogonal, multiplexed ddPCR data are unavailable, presenting a major bottleneck for the advancement of ddPCR transitioning from low-throughput to high-throughput. Results ddPCRclust is an R package for automated analysis of data from Bio-Rad’s droplet digital PCR systems (QX100 and QX200). It can automatically analyze and visualize multiplexed ddPCR experiments with up to four targets per reaction. Results are on par with manual analysis, but only take minutes to compute instead of hours. The accompanying Shiny app ddPCRvis provides easy access to the functionalities of ddPCRclust through a web-browser based GUI. Availability and implementation R package: https://github.com/bgbrink/ddPCRclust; Interface: https://github.com/bgbrink/ddPCRvis/; Web: https://bibiserv.cebitec.uni-bielefeld.de/ddPCRvis/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Benedikt G Brink
- International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes" and Biodata Mining Group, Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Justin Meskas
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada
| | - Ryan R Brinkman
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada.,Department Medical Genetics, University of British Columbia, Vancouver, Canada
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21
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Lee KS, Nam SK, Seo SH, Park KU, Oh HK, Kim DW, Kang SB, Kim WH, Lee HS. Digital polymerase chain reaction for detecting c-MYC copy number gain in tissue and cell-free plasma samples of colorectal cancer patients. Sci Rep 2019; 9:1611. [PMID: 30733532 PMCID: PMC6367402 DOI: 10.1038/s41598-018-38415-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 12/28/2018] [Indexed: 02/07/2023] Open
Abstract
We focused on the utility of the droplet digital polymerase chain reaction (ddPCR) for detecting c-MYC gene copy number (GCN) gain in cell-free plasma and tumor tissue of colorectal cancer (CRC) patients. c-MYC GCN status was determined using dual-color silver in situ hybridization (SISH) and ddPCR in retrospective cohort 1 (192 CRC patients) and prospective cohort 2 (64 CRC patients). In cohort 1, c-MYC GCN gain was observed in 34 (17.5%) patients by SISH, and in 7 (3.6%) patients by ddPCR. c-MYC GCN by SISH significantly correlated with ddPCR results (ρ = 0.532, P < 0.001). Although 40 cases (20.7%) showed intratumoral genetic heterogeneity, it did not cause discordance in results obtained by the two methods. c-MYC GCN gain, by both SISH and ddPCR was independently correlated with worst prognosis (P = 0.002). In cohort 2, c-MYC GCN estimation in tissue by ddPCR was also significantly associated with results obtained by SISH (ρ = 0.349, P = 0.005), but correlated with plasma ddPCR with borderline significance (ρ = 0.246, P = 0.050). Additionally, detecting c-MYC GCN gain in plasma with ddPCR might have relatively low sensitivity but high specificity. Our study suggests that ddPCR can be a useful tool for detecting c-MYC GCN gain as a potential prognostic biomarker in CRC tissue samples; however, this will need further verification in plasma samples.
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Affiliation(s)
- Kyu Sang Lee
- Department of Pathology, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Soo Kyung Nam
- Department of Pathology, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Soo Hyun Seo
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Heung-Kwon Oh
- Department of Surgery, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-707, Republic of Korea
| | - Duck-Woo Kim
- Department of Surgery, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-707, Republic of Korea
| | - Sung-Bum Kang
- Department of Surgery, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-707, Republic of Korea
| | - Woo Ho Kim
- Department of Pathology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Hye Seung Lee
- Department of Pathology, Seoul National University Bundang Hospital, 173-82 Gumi-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea. .,Department of Pathology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
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22
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Gao M, Callari M, Beddowes E, Sammut SJ, Grzelak M, Biggs H, Jones L, Boumertit A, Linn SC, Cortes J, Oliveira M, Baird R, Chin SF, Caldas C. Next Generation-Targeted Amplicon Sequencing (NG-TAS): an optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA. Genome Med 2019; 11:1. [PMID: 30609936 PMCID: PMC6320579 DOI: 10.1186/s13073-018-0611-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/17/2018] [Indexed: 01/05/2023] Open
Abstract
Circulating tumour DNA (ctDNA) detection and monitoring have enormous potential clinical utility in oncology. We describe here a fast, flexible and cost-effective method to profile multiple genes simultaneously in low input cell-free DNA (cfDNA): Next Generation-Targeted Amplicon Sequencing (NG-TAS). We designed a panel of 377 amplicons spanning 20 cancer genes and tested the NG-TAS pipeline using cell-free DNA from two HapMap lymphoblastoid cell lines. NG-TAS consistently detected mutations in cfDNA when mutation allele fraction was > 1%. We applied NG-TAS to a clinical cohort of metastatic breast cancer patients, demonstrating its potential in monitoring the disease. The computational pipeline is available at https://github.com/cclab-brca/NGTAS_pipeline .
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Affiliation(s)
- Meiling Gao
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
| | - Maurizio Callari
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
| | - Emma Beddowes
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
- Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 2QQ UK
| | - Stephen-John Sammut
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
| | - Marta Grzelak
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
| | - Heather Biggs
- Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 2QQ UK
| | - Linda Jones
- Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 2QQ UK
| | - Abdelhamid Boumertit
- Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 2QQ UK
| | - Sabine C. Linn
- Netherland Cancer Institute, 1006 BE Amsterdam, Netherlands
| | - Javier Cortes
- Ramon y Cajal University Hospital, 28034 Madrid, Spain
- Vall d’Hebron Institute of Oncology, 08035 Barcelona, Spain
| | | | - Richard Baird
- Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 2QQ UK
| | - Suet-Feung Chin
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
- Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 2QQ UK
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Malic L, Daoud J, Geissler M, Boutin A, Lukic L, Janta M, Elmanzalawy A, Veres T. Epigenetic subtyping of white blood cells using a thermoplastic elastomer-based microfluidic emulsification device for multiplexed, methylation-specific digital droplet PCR. Analyst 2019; 144:6541-6553. [DOI: 10.1039/c9an01316d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Digital droplet PCR for epigenetic leukocyte subtyping from clinically relevant samples is implemented using a thermoplastic elastomer microfluidic droplet generator as a first step towards an economical, customizable and easily deployable system.
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Affiliation(s)
- Lidija Malic
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Jamal Daoud
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Matthias Geissler
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Alex Boutin
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Ljuboje Lukic
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Mojra Janta
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | | | - Teodor Veres
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
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24
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A Novel Multiplex Droplet Digital PCR Assay to Identify and Quantify KRAS Mutations in Clinical Specimens. J Mol Diagn 2018; 21:214-227. [PMID: 30472330 DOI: 10.1016/j.jmoldx.2018.09.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 09/03/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023] Open
Abstract
Recurrent activating point mutations in KRAS are critical drivers in pancreatic cancer and have been attributed to resistance to anti-epidermal growth factor receptor therapy in colorectal cancer. Although KRAS genotyping provides limited clinical utility in the diagnosis and management of pancreatic cancer patients at present, inferences about the fractional abundance of KRAS mutations may inform on tumor purity in traditionally challenging clinical specimens and their potential use in precision medicine. KRAS genetic testing has indeed become an essential tool to guide treatment decisions in colorectal cancer, but an unmet need for methods standardization exists. Here, we present a unique droplet digital PCR method that enables the simultaneous detection and quantification of KRAS exon 2, 3, and 4 point mutations and copy number alterations. We have validated 13 mutations (G12S, G12R, G12D, G12A, G12V, G12C, G13D, G60V, Q61H, Q61L, A146V, A146T, and A146P) and focal KRAS amplifications by conducting this assay in a cohort of 100 DNA samples extracted from fresh frozen tumor biopsies, formaldehyde-fixed, paraffin-embedded tissue, and liquid biopsy specimens. Despite its modest lower limit of detection (approximately 1%), this assay will be a rapid cost-effective means to infer the purity of biopsy specimens carrying KRAS mutations and can be used in noninvasive serial monitoring of circulating tumor DNA to evaluate clinical response and/or detect early signs of relapse.
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25
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Lu XJD, Liu KYP, Zhu YS, Cui C, Poh CF. Using ddPCR to assess the DNA yield of FFPE samples. BIOMOLECULAR DETECTION AND QUANTIFICATION 2018; 16:5-11. [PMID: 30560062 PMCID: PMC6287546 DOI: 10.1016/j.bdq.2018.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/04/2018] [Accepted: 10/24/2018] [Indexed: 12/24/2022]
Abstract
Objectives Detection of genomic alterations in diseases can be achieved with current molecular technologies. However, the molecules extracted from formalin-fixed, paraffin-embedded (FFPE) bio-samples are often limited possibly due to DNA fragmentation and crosslinking caused by the sample fixation and processing. The study objective was to design a droplet digital PCR (ddPCR) assay to assess the quality and quantity of DNA derived from various DNA extraction conditions on FFPE samples. Methods We used 10 μm-thick sections from 5 FFPE oral tumoral blocks, each consisting of 10–15 sections. The protocol variables tested included: 1) tissue staining; 2) duration and 3) temperature of post-digestion heat treatment; and 4) DNA extraction method. DNA quantity was assessed using the NanoDrop 2000 (Thermo Fisher Scientific, USA), the Qubit fluorometer (Thermo Fisher Scientific, USA), and a ddPCR-based assay. DNA quality was assessed using a ddPCR assay for the degree of fragmentation and the effectiveness of removing crosslinks with varying guanine-cytosine (GC)-content. Results Deparaffinization with xylene helped to increase the DNA yield. Tissue staining (methyl green staining, pH 6) prior to microdissection, comparing to no staining, caused additional DNA fragmentation. Compared to column-based method, DNA extracted with phenol chloroform and ethanol precipitation increased the degree of fragmentation and lowered the yield of amplifiable DNA. The cross-linking derived from GC-contents may not be the only factor impacting on the DNA quality. Conclusions Samples undergoing different pre-treatment conditions prior to extraction can impact the yield of amplifiable DNA. Our ddPCR assay can be used to assess for both DNA quantity and quality.
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Affiliation(s)
- X J David Lu
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.,Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Kelly Y P Liu
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.,Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Yuqi Sarah Zhu
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Cindy Cui
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Catherine F Poh
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.,Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
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Molecular Minimal Residual Disease Testing in Acute Myeloid Leukemia: A Review for the Practicing Clinician. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2018; 18:636-647. [PMID: 30006258 DOI: 10.1016/j.clml.2018.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 11/21/2022]
Abstract
Minimal residual disease (MRD) testing in acute myeloid leukemia is increasingly being used to assess treatment response and stratify the risk of relapse for individual patients. Molecular methods for MRD testing began with PCR-based assays for individual recurrent mutations. To date, there is robust evidence for testing NPM1, CBFB-MYH11, and RUNX1/RUNXT1 mutations using this approach, though the best timing and threshold level for each mutation varies. More recent approaches have been with PCR-based multigene panels, occasionally combined with flow cytometric techniques, and next-generation sequencing techniques. This review outlines the various techniques used in molecular approaches to MRD, the evidence behind individual mutation testing, and the novel approaches for evaluating multigene MRD so that clinicians can understand and incorporate these evaluations into their practice.
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27
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Chin SF, Santonja A, Grzelak M, Ahn S, Sammut SJ, Clifford H, Rueda OM, Pugh M, Goldgraben MA, Bardwell HA, Cho EY, Provenzano E, Rojo F, Alba E, Caldas C. Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers. Exp Mol Pathol 2018; 104:161-169. [PMID: 29608913 PMCID: PMC5993858 DOI: 10.1016/j.yexmp.2018.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
Pathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised due to the low amount and quality of extracted nucleic acids. We profiled the copy number landscape of 356 breast cancer patients using DNA extracted FFPE tissues by shallow whole genome sequencing. We generated a total of 491 sequencing libraries from 2 kits and obtained data from 98.4% of libraries with 86.4% being of good quality. We generated libraries from as low as 3.8 ng of input DNA and found that the success was independent of input DNA amount and quality, processing site and age of the fixed tissues. Since copy number alterations (CNA) play a major role in breast cancer, it is imperative that we are able to use FFPE archives and we have shown in this study that sWGS is a robust method to do such profiling.
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Affiliation(s)
- Suet-Feung Chin
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK.
| | - Angela Santonja
- Medical Oncology Service, Hospital Universitario Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain; Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain
| | - Marta Grzelak
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Soomin Ahn
- Department of Pathology, Seoul National University Bundang Hospital, 82, Gumi-ro 173 Beon-gil, Bundang-gu, Seongnam, Gyeonggi 13620, Republic of Korea; Inivata, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Stephen-John Sammut
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK
| | - Harry Clifford
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Oscar M Rueda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK
| | - Michelle Pugh
- Inivata UK, The Portway Building, Granta Park, Cambridge CB21 6GS, UK
| | - Mae A Goldgraben
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Helen A Bardwell
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Eun Yoon Cho
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 50 Irwon-dong, Gangnam-gu, Seoul 135-710, Republic of Korea
| | - Elena Provenzano
- Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK
| | - Federico Rojo
- Pathology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain; GEICAM-Spanish Breast Cancer Research Group, Madrid, Spain
| | - Emilio Alba
- Medical Oncology Service, Hospital Universitario Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain; GEICAM-Spanish Breast Cancer Research Group, Madrid, Spain; Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK.
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28
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Liu KYP, Lu XJD, Cheng YSL, Klieb H, Ng S, McNeil K, Karsan A, Poh CF. An actionable test using loss of heterozygosity in identifying high-risk oral premalignant lesions. Oral Surg Oral Med Oral Pathol Oral Radiol 2017; 126:S2212-4403(17)31208-7. [PMID: 29428696 DOI: 10.1016/j.oooo.2017.10.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 10/03/2017] [Accepted: 10/12/2017] [Indexed: 01/18/2023]
Abstract
OBJECTIVES To develop an actionable test using fluorescence capillary electrophoresis (FCE) to assess loss of heterozygosity (LOH) of histologically similar low-grade lesions (LGLs) to identify high-risk lesions for oral cancer progression. STUDY DESIGN To determine the cutoffs of LOH, the FCE results of 52 surgical margin samples were used to compare with the existing LOH results from the previously validated 32 P-GE approach. Using the developed FCE workflow, an independent set of 102 LGLs with known progression status was used to determine the LOH molecular risk (MR) patterns and associated risk of progression. RESULTS Using 65% cutoff LOH-FCE, the agreement of LOH-32 P-GE had an average of 82.3% (76.8-87.8). Compared with nonprogressors (n = 61), anatomic site and MR patterns (LOH at 9 p21, 3 p14, or 17 p13) were independent risk factors. High-risk profile of tongue and MR3 (LOH at 9 p21 and/or 3 p14 and 17 p13) was significantly associated with progression (hazard ratio [HR] 6.7; 95% confidence interval [CI] 2.6-17.6) with specificity of 98.4% at identifying progressors. CONCLUSIONS We have developed an objective test using LOH to stratify the risk of LGLs. With further validation, it can be used in the clinical settings to provide clinicians additional information guiding the management of these lesions.
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Affiliation(s)
- Kelly Y P Liu
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada; Department of Integrative Oncology, BC Cancer Agency, Vancouver, BC, Canada
| | - X J David Lu
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada; Department of Integrative Oncology, BC Cancer Agency, Vancouver, BC, Canada
| | - Yi-Shing L Cheng
- Diagnostic Sciences, Texas A&M University College of Dentistry, Dallas, TX, USA
| | - Hagen Klieb
- Department of Anatomic Pathology and Department of Dentistry, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Samson Ng
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - Kelly McNeil
- Cancer Genetics Laboratory, Pathology and Laboratory Medicine, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, Canada
| | - Aly Karsan
- Cancer Genetics Laboratory, Pathology and Laboratory Medicine, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, Canada
| | - Catherine F Poh
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada; Department of Integrative Oncology, BC Cancer Agency, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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29
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Hughesman CB, Lu XJD, Liu KYP, Zhu Y, Towle RM, Haynes C, Poh CF. Detection of clinically relevant copy number alterations in oral cancer progression using multiplexed droplet digital PCR. Sci Rep 2017; 7:11855. [PMID: 28928368 PMCID: PMC5605662 DOI: 10.1038/s41598-017-11201-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023] Open
Abstract
Copy number alterations (CNAs), a common genomic event during carcinogenesis, are known to affect a large fraction of the genome. Common recurrent gains or losses of specific chromosomal regions occur at frequencies that they may be considered distinctive features of tumoral cells. Here we introduce a novel multiplexed droplet digital PCR (ddPCR) assay capable of detecting recurrent CNAs that drive tumorigenesis of oral squamous cell carcinoma. Applied to DNA extracted from oral cell lines and clinical samples of various disease stages, we found good agreement between CNAs detected by our ddPCR assay with those previously reported using comparative genomic hybridization or single nucleotide polymorphism arrays. Furthermore, we demonstrate that the ability to target specific locations of the genome permits detection of clinically relevant oncogenic events such as small, submicroscopic homozygous deletions. Additional capabilities of the multiplexed ddPCR assay include the ability to infer ploidy level, quantify the change in copy number of target loci with high-level gains, and simultaneously assess the status and viral load for high-risk human papillomavirus types 16 and 18. This novel multiplexed ddPCR assay therefore may have clinical value in differentiating between benign oral lesions from those that are at risk of progressing to oral cancer.
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Affiliation(s)
- Curtis B Hughesman
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - X J David Lu
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Kelly Y P Liu
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Yuqi Zhu
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Rebecca M Towle
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Charles Haynes
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
| | - Catherine F Poh
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, V6T 2B5, Canada.
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30
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Taylor SC, Laperriere G, Germain H. Droplet Digital PCR versus qPCR for gene expression analysis with low abundant targets: from variable nonsense to publication quality data. Sci Rep 2017; 7:2409. [PMID: 28546538 PMCID: PMC5445070 DOI: 10.1038/s41598-017-02217-x] [Citation(s) in RCA: 319] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/07/2017] [Indexed: 01/23/2023] Open
Abstract
Quantitative PCR (qPCR) has become the gold standard technique to measure cDNA and gDNA levels but the resulting data can be highly variable, artifactual and non-reproducible without appropriate verification and validation of both samples and primers. The root cause of poor quality data is typically associated with inadequate dilution of residual protein and chemical contaminants that variably inhibit Taq polymerase and primer annealing. The most susceptible, frustrating and often most interesting samples are those containing low abundant targets with small expression differences of 2-fold or lower. Here, Droplet Digital PCR (ddPCR) and qPCR platforms were directly compared for gene expression analysis using low amounts of purified, synthetic DNA in well characterized samples under identical reaction conditions. We conclude that for sample/target combinations with low levels of nucleic acids (Cq ≥ 29) and/or variable amounts of chemical and protein contaminants, ddPCR technology will produce more precise, reproducible and statistically significant results required for publication quality data. A stepwise methodology is also described to choose between these complimentary technologies to obtain the best results for any experiment.
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Affiliation(s)
- Sean C Taylor
- Bio-Rad Laboratories, Inc., Hercules, CA, 94547, USA.
| | - Genevieve Laperriere
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 boul. des Forges, Trois-Rivières, QC, G9A 5H7, Canada
| | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 boul. des Forges, Trois-Rivières, QC, G9A 5H7, Canada
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