Literature DB >> 27351921

The Future of Digital Polymerase Chain Reaction in Virology.

Matthijs Vynck1, Wim Trypsteen2, Olivier Thas1,3, Linos Vandekerckhove2, Ward De Spiegelaere4.   

Abstract

Driven by its potential benefits over currently available methods, and the recent development of commercial platforms, digital polymerase chain reaction (dPCR) has received increasing attention in virology research and diagnostics as a tool for the quantification of nucleic acids. The current technologies are more precise and accurate, but may not be much more sensitive, compared with quantitative PCR (qPCR) applications. The most promising applications with the current technology are the analysis of mutated sequences, such as emerging drug-resistant mutations. Guided by the recent literature, this review focuses on three aspects that demonstrate the potential of dPCR for virology researchers and clinicians: the applications of dPCR within both virology research and clinical virology, the benefits of the technique over the currently used real-time qPCR, and the importance and availability of specific data analysis approaches for dPCR. Comments are provided on current drawbacks and often overlooked pitfalls that need further attention to allow widespread implementation of dPCR as an accurate and precise tool within the field of virology.

Mesh:

Year:  2016        PMID: 27351921     DOI: 10.1007/s40291-016-0224-1

Source DB:  PubMed          Journal:  Mol Diagn Ther        ISSN: 1177-1062            Impact factor:   4.074


  74 in total

1.  A short history of the polymerase chain reaction.

Authors:  John M S Bartlett; David Stirling
Journal:  Methods Mol Biol       Date:  2003

2.  Digital PCR provides absolute quantitation of viral load for an occult RNA virus.

Authors:  Richard Allen White; Stephen R Quake; Kenneth Curr
Journal:  J Virol Methods       Date:  2011-09-29       Impact factor: 2.014

3.  Elimination of amplification artifacts in real-time reverse transcription PCR using laser capture microdissected samples.

Authors:  Ward De Spiegelaere; Tim Erkens; Jurgen De Craene; Christian Burvenich; Luc Peelman; Wim Van den Broeck
Journal:  Anal Biochem       Date:  2008-07-15       Impact factor: 3.365

Review 4.  Standardization of Nucleic Acid Tests for Clinical Measurements of Bacteria and Viruses.

Authors:  Jernej Pavšič; Alison S Devonshire; Helen Parkes; Heinz Schimmel; Carole A Foy; Maria Karczmarczyk; Ion Gutiérrez-Aguirre; Isobella Honeyborne; Jim F Huggett; Timothy D McHugh; Mojca Milavec; Heinz Zeichhardt; Jana Žel
Journal:  J Clin Microbiol       Date:  2014-11-12       Impact factor: 5.948

5.  Rational design of digital assays.

Authors:  Pawel R Debski; Kamil Gewartowski; Magdalena Sulima; Tomasz S Kaminski; Piotr Garstecki
Journal:  Anal Chem       Date:  2015-08-05       Impact factor: 6.986

6.  Quantifying EGFR alterations in the lung cancer genome with nanofluidic digital PCR arrays.

Authors:  Jun Wang; Ramesh Ramakrishnan; Zhe Tang; Weiwen Fan; Amy Kluge; Afshin Dowlati; Robert C Jones; Patrick C Ma
Journal:  Clin Chem       Date:  2010-03-05       Impact factor: 8.327

7.  Optimising droplet digital PCR analysis approaches for detection and quantification of bacteria: a case study of fire blight and potato brown rot.

Authors:  Tanja Dreo; Manca Pirc; Živa Ramšak; Jernej Pavšič; Mojca Milavec; Jana Zel; Kristina Gruden
Journal:  Anal Bioanal Chem       Date:  2014-08-31       Impact factor: 4.142

8.  Quantitative analysis of viral load per haploid genome revealed the different biological features of Merkel cell polyomavirus infection in skin tumor.

Authors:  Satoshi Ota; Shumpei Ishikawa; Yutaka Takazawa; Akiteru Goto; Takeshi Fujii; Ken-ichi Ohashi; Masashi Fukayama
Journal:  PLoS One       Date:  2012-06-29       Impact factor: 3.240

9.  Integrated and Total HIV-1 DNA Predict Ex Vivo Viral Outgrowth.

Authors:  Maja Kiselinova; Ward De Spiegelaere; Maria Jose Buzon; Eva Malatinkova; Mathias Lichterfeld; Linos Vandekerckhove
Journal:  PLoS Pathog       Date:  2016-03-03       Impact factor: 6.823

10.  Detection of Rare Drug Resistance Mutations by Digital PCR in a Human Influenza A Virus Model System and Clinical Samples.

Authors:  Alexandra S Whale; Claire A Bushell; Paul R Grant; Simon Cowen; Ion Gutierrez-Aguirre; Denise M O'Sullivan; Jana Žel; Mojca Milavec; Carole A Foy; Eleni Nastouli; Jeremy A Garson; Jim F Huggett
Journal:  J Clin Microbiol       Date:  2015-12-09       Impact factor: 5.948

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  10 in total

Review 1.  Applications of Digital PCR for Clinical Microbiology.

Authors:  Jane Kuypers; Keith R Jerome
Journal:  J Clin Microbiol       Date:  2017-03-15       Impact factor: 5.948

Review 2.  The Role of BEAMing and Digital PCR for Multiplexed Analysis in Molecular Oncology in the Era of Next-Generation Sequencing.

Authors:  Jérôme Alexandre Denis; Erell Guillerm; Florence Coulet; Annette K Larsen; Jean-Marc Lacorte
Journal:  Mol Diagn Ther       Date:  2017-12       Impact factor: 4.074

3.  Superiority of Digital Reverse Transcription-PCR (RT-PCR) over Real-Time RT-PCR for Quantitation of Highly Divergent Human Rhinoviruses.

Authors:  Ruth Hall Sedlak; Thuy Nguyen; Isabel Palileo; Keith R Jerome; Jane Kuypers
Journal:  J Clin Microbiol       Date:  2016-11-23       Impact factor: 5.948

4.  Streamlined and quantitative detection of chimerism using digital PCR.

Authors:  Fabian P Suchy; Toshiya Nishimura; Shinsuke Seki; Adam C Wilkinson; Maimi Higuchi; Ian Hsu; Jinyu Zhang; Joydeep Bhadury; Hiromitsu Nakauchi
Journal:  Sci Rep       Date:  2022-06-17       Impact factor: 4.996

5.  Digital PCR Panel for Sensitive Hematopoietic Chimerism Quantification after Allogeneic Stem Cell Transplantation.

Authors:  Tanja Stahl; Caroline Rothe; Manja U Böhme; Aloisa Kohl; Nicolaus Kröger; Boris Fehse
Journal:  Int J Mol Sci       Date:  2016-09-09       Impact factor: 5.923

Review 6.  Digital PCR as a tool to measure HIV persistence.

Authors:  Sofie Rutsaert; Kobus Bosman; Wim Trypsteen; Monique Nijhuis; Linos Vandekerckhove
Journal:  Retrovirology       Date:  2018-01-30       Impact factor: 4.602

7.  Evaluation of bisulfite kits for DNA methylation profiling in terms of DNA fragmentation and DNA recovery using digital PCR.

Authors:  Sam Kint; Ward De Spiegelaere; Jonas De Kesel; Linos Vandekerckhove; Wim Van Criekinge
Journal:  PLoS One       Date:  2018-06-14       Impact factor: 3.240

8.  Development of sensitive ddPCR assays to reliably quantify the proviral DNA reservoir in all common circulating HIV subtypes and recombinant forms.

Authors:  Kobus J Bosman; Annemarie Mj Wensing; Aster E Pijning; Wilco J van Snippenberg; Petra M van Ham; Dorien Mc de Jong; Andy Im Hoepelman; Monique Nijhuis
Journal:  J Int AIDS Soc       Date:  2018-09       Impact factor: 5.396

9.  Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR.

Authors:  Diego R Hijano; Jessica Brazelton de Cardenas; Gabriela Maron; Cherilyn D Garner; Jose A Ferrolino; Ronald H Dallas; Zhengming Gu; Randall T Hayden
Journal:  PLoS One       Date:  2019-09-03       Impact factor: 3.240

10.  Digital PCR is a sensitive new technique for SARS-CoV-2 detection in clinical applications.

Authors:  Yanfang Jiang; Haifeng Wang; Sijia Hao; Yukun Chen; Jiaxue He; Yong Liu; Liguo Chen; Yuanhua Yu; Shucheng Hua
Journal:  Clin Chim Acta       Date:  2020-11-04       Impact factor: 3.786

  10 in total

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