Covid-19 virus genome analysed by app in under 30 minutes
Image credit: Dr Ira Deveson
Researchers at Australia’s Garvan Institute of Medical Research have developed an app, Genopo, which carries out speedy genome sequence analysis on a smartphone.
Portable nanopore devices – which measure changes in current as a DNA or RNA strand passes through a nanopore – allow scientists and clinicians to sequence the genome of viruses such as the Covid-19 or Ebola viruses outside laboratory settings.
However, advances in in situ genomics will require the parallel development of portable, offline tools to analyse the data gathered by these tools. At present, analysis of these data requires access to high-end computing power. During Ebola surveillance in West Africa, for instance, field research was disrupted by internet connectivity issues in which they were forced to slowly upload large datasets via 2G for analysis elsewhere.
“Not everyone has access to the high-power computing resources that are required for DNA and RNA analysis, but most people have access to a smartphone,” said the Garvan Institute’s Ira Deveson, co-senior author of the Communications Biology paper describing the project. “Fast, real-time genomic analysis is more crucial today than ever, as a central method for tracking the spread of coronavirus.
“Our app makes genomic analysis more accessible, literally placing the technology into the pockets of scientists around the world.”
During genome sequence analysis, the strings of genetic code from raw data are pieced together into a single sequence, from which genetic variations indicating viral mutation can be identified.
“Until now, genomic analysis has required the processing power of high-end server computers or cloud services. We set out to change that,” said co-senior author Hasindu Gamaarachichi, a computer engineer at the Garvan Institute.
The researchers – collaborating with engineers from Sri Lanka’s University of Peradeniya – developed an app which could execute bioinformatics workflows on genetic datasets downloaded to a smartphone, adapting to the resource constraints in smartphones. The app combines several available bioinformatics tools into a single app, 'miniaturised' to work on the processing power of a typical consumer Android phone.
They tested the Genopo app on the raw sequencing data of virus samples isolated from nine Covid-19 patients in Sydney and sequenced with a MinION nanopore device. They tested it on various Android devices, including standard Nokia, Huawei, LG and Sony models. On average, the Genopo app took 27 minutes to determine the complete SARS-CoV-2 genome sequence from the raw dataset, opening up the possibility to perform genomic analysis at the point of core and in real time.
Genopo was also found to be able to profile DNA methylation – a modification which alters gene activity – in a human genome sample.
“This illustrates a flexible, efficient architecture that is suitable to run many popular bioinformatics tools and accommodate small or large genomes,” said Deveson. “We hope this will make genomics much more accessible to researchers to unlock the information in DNA or RNA to the benefit of human health, including in the current pandemic.”
Genopo has been made free and open-source and is available through the Google Play store.
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