ShinyCurves, a shiny web application to analyse multisource qPCR amplification data: a COVID-19 case study

S Olaechea-Lázaro,Nora Fernandez-Jimenez,I Badiola,J R Pineda,Jose Ramon Bilbao,S Alonso,I García-Santisteban

doi:10.1186/s12859-021-04392-1

S Olaechea-Lázaro, Nora Fernandez-Jimenez + Show 5 more

Open Access

https://doi.org/10.1186/s12859-021-04392-1

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Abstract

BackgroundQuantitative, reverse transcription PCR (qRT-PCR) is currently the gold-standard for SARS-CoV-2 detection and it is also used for detection of other virus. Manual data analysis of a small number of qRT-PCR plates per day is a relatively simple task, but automated, integrative strategies are needed if a laboratory is dealing with hundreds of plates per day, as is being the case in the COVID-19 pandemic.ResultsHere we present shinyCurves, an online shiny-based, free software to analyze qRT-PCR amplification data from multi-plate and multi-platform formats. Our shiny application does not require any programming experience and is able to call samples Positive, Negative or Undetermined for viral infection according to a number of user-defined settings, apart from providing a complete set of melting and amplification curve plots for the visual inspection of results.ConclusionsshinyCurves is a flexible, integrative and user-friendly software that speeds-up the analysis of massive qRT-PCR data from different sources, with the possibility of automatically producing and evaluating melting and amplification curve plots.

Highlights

Quantitative, reverse transcription PCR is currently the goldstandard for SARS-CoV-2 detection and it is used for detection of other virus
Depending on the amount of viral mRNA detected by the qRT-PCR system, a sample is assigned as Positive, Negative or Undetermined
Most healthcare providers rely on automated detection procedures that make use of proprietary reagents and software and offer limited options for parameter set-up, with special emphasis on Olaechea‐Lázaro et al BMC Bioinformatics (2021) 22:476 those recommended by World Health Organization (WHO) (CFX Manager 3.1 from BioRad) and by the Food and Drug Agency (FDA) (Food and Drug Administration)

Summary

Introduction

Quantitative, reverse transcription PCR (qRT-PCR) is currently the goldstandard for SARS-CoV-2 detection and it is used for detection of other virus. Most healthcare providers rely on automated detection procedures that make use of proprietary reagents and software and offer limited options for parameter set-up, with special emphasis on Olaechea‐Lázaro et al BMC Bioinformatics (2021) 22:476 those recommended by WHO (CFX Manager 3.1 from BioRad) and by the FDA (Food and Drug Administration) (the SDS 1.4 software from Applied Biosystems). In this context, research laboratories worldwide are developing alternative diagnostic protocols that do not depend on commercial kits and their accompanying software. In order to discard samples with unspecific amplification products, a software for accurate qRT-PCR analysis should allow the inspection of amplification and melting curves

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