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Implementation of an open-source robotic platform for SARS-CoV-2 testing by real-time RT-PCR

The current global pandemic due to the SARS-CoV-2 has pushed the limits of global health systems across all aspects of clinical care, including laboratory diagnostics. Supply chain disruptions and rapidly-shifting markets have resulted in flash-scarcity of commercial laboratory reagents; this has mo...

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Autores principales: Villanueva-Cañas, José Luis, Gonzalez-Roca, Eva, Gastaminza Unanue, Aitor, Titos, Esther, Martínez Yoldi, Miguel Julián, Vergara Gómez, Andrea, Puig-Butillé, Joan Anton
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8279358/
https://www.ncbi.nlm.nih.gov/pubmed/34260637
http://dx.doi.org/10.1371/journal.pone.0252509
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author Villanueva-Cañas, José Luis
Gonzalez-Roca, Eva
Gastaminza Unanue, Aitor
Titos, Esther
Martínez Yoldi, Miguel Julián
Vergara Gómez, Andrea
Puig-Butillé, Joan Anton
author_facet Villanueva-Cañas, José Luis
Gonzalez-Roca, Eva
Gastaminza Unanue, Aitor
Titos, Esther
Martínez Yoldi, Miguel Julián
Vergara Gómez, Andrea
Puig-Butillé, Joan Anton
author_sort Villanueva-Cañas, José Luis
collection PubMed
description The current global pandemic due to the SARS-CoV-2 has pushed the limits of global health systems across all aspects of clinical care, including laboratory diagnostics. Supply chain disruptions and rapidly-shifting markets have resulted in flash-scarcity of commercial laboratory reagents; this has motivated health care providers to search for alternative workflows to cope with the international increase in demand for SARS-CoV-2 testing. The aim of this study is to present a reproducible workflow for real time RT-PCR SARS-CoV-2 testing using OT-2 open-source liquid-handling robots (Opentrons, NY). We have developed a framework that includes a code template which is helpful for building different stand-alone robotic stations, capable of performing specific protocols. Such stations can be combined together to create a complex multi-stage workflow, from sample setup to real time RT-PCR. Using our open-source code, it is easy to create new stations or workflows from scratch, adapt existing templates to update the experimental protocols, or to fine-tune the code to fit specific needs. Using this framework, we developed the code for two different workflows and evaluated them using external quality assessment (EQA) samples from the European Molecular Genetics Quality Network (EMQN). The affordability of this platform makes automated SARS-CoV-2 PCR testing accessible for most laboratories and hospitals with qualified bioinformatics personnel. This platform also allows for flexibility, as it is not dependent on any specific commercial kit, and thus it can be quickly adapted to protocol changes, reagent, consumable shortages, or any other temporary material constraints.
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spelling pubmed-82793582021-07-31 Implementation of an open-source robotic platform for SARS-CoV-2 testing by real-time RT-PCR Villanueva-Cañas, José Luis Gonzalez-Roca, Eva Gastaminza Unanue, Aitor Titos, Esther Martínez Yoldi, Miguel Julián Vergara Gómez, Andrea Puig-Butillé, Joan Anton PLoS One Research Article The current global pandemic due to the SARS-CoV-2 has pushed the limits of global health systems across all aspects of clinical care, including laboratory diagnostics. Supply chain disruptions and rapidly-shifting markets have resulted in flash-scarcity of commercial laboratory reagents; this has motivated health care providers to search for alternative workflows to cope with the international increase in demand for SARS-CoV-2 testing. The aim of this study is to present a reproducible workflow for real time RT-PCR SARS-CoV-2 testing using OT-2 open-source liquid-handling robots (Opentrons, NY). We have developed a framework that includes a code template which is helpful for building different stand-alone robotic stations, capable of performing specific protocols. Such stations can be combined together to create a complex multi-stage workflow, from sample setup to real time RT-PCR. Using our open-source code, it is easy to create new stations or workflows from scratch, adapt existing templates to update the experimental protocols, or to fine-tune the code to fit specific needs. Using this framework, we developed the code for two different workflows and evaluated them using external quality assessment (EQA) samples from the European Molecular Genetics Quality Network (EMQN). The affordability of this platform makes automated SARS-CoV-2 PCR testing accessible for most laboratories and hospitals with qualified bioinformatics personnel. This platform also allows for flexibility, as it is not dependent on any specific commercial kit, and thus it can be quickly adapted to protocol changes, reagent, consumable shortages, or any other temporary material constraints. Public Library of Science 2021-07-14 /pmc/articles/PMC8279358/ /pubmed/34260637 http://dx.doi.org/10.1371/journal.pone.0252509 Text en © 2021 Villanueva-Cañas et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Villanueva-Cañas, José Luis
Gonzalez-Roca, Eva
Gastaminza Unanue, Aitor
Titos, Esther
Martínez Yoldi, Miguel Julián
Vergara Gómez, Andrea
Puig-Butillé, Joan Anton
Implementation of an open-source robotic platform for SARS-CoV-2 testing by real-time RT-PCR
title Implementation of an open-source robotic platform for SARS-CoV-2 testing by real-time RT-PCR
title_full Implementation of an open-source robotic platform for SARS-CoV-2 testing by real-time RT-PCR
title_fullStr Implementation of an open-source robotic platform for SARS-CoV-2 testing by real-time RT-PCR
title_full_unstemmed Implementation of an open-source robotic platform for SARS-CoV-2 testing by real-time RT-PCR
title_short Implementation of an open-source robotic platform for SARS-CoV-2 testing by real-time RT-PCR
title_sort implementation of an open-source robotic platform for sars-cov-2 testing by real-time rt-pcr
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8279358/
https://www.ncbi.nlm.nih.gov/pubmed/34260637
http://dx.doi.org/10.1371/journal.pone.0252509
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