Novel App Can Analyze Coronavirus Genome

Novel mobile app Genopo can analyze the genome of SARS-CoV-2 virus on a smartphone in less than half an hour.

The report on the app Genopo is published in the journal Communications Biology.

Nanopore devices have led scientists to read the genetic sequence outside a laboratory. However, analyzing raw data until now has required high-end computing power.

‘Researchers developed a new app that could execute bioinformatics workflows on nanopore sequencing datasets that are downloaded to a smartphone. The app Genopo can analyze the genome of the novel Coronavirus in 27 minutes.’

"Fast, real-time genomic analysis is more crucial today than ever, as a central method for tracking the spread of coronavirus. Our app makes the genomic analysis more accessible, literally placing the technology into the pockets of scientists around the world," said Dr Ira Deveson.

Taking Genome Analysis Off-Line

Portable devices like the Oxford Nanopore Technologies MinION sequencer has the ability to rapidly generate genomic sequences from a sample in the clinic or field.

This technology has been used in West Africa for Ebola surveillance, in the Artic to profile microbial communities and to determine the evolution of coronavirus during the current pandemic.

Analyzing genome sequencing data requires powerful computation. Scientists also need to piece many strings of genetic letters from the raw data into a single sequence and pinpoint the instances of genetic variation. The genetic variations shed light on how a virus evolves.

"The app Genopo combines several available bioinformatics tools into a single Android application, 'miniaturized' to work on the processing power of a consumer Android device," said Hasindu Gamaarachchi.

Coronavirus testing

The app was tested on the raw sequencing data of virus samples. This data was isolated from 9 Sydney patients who were infected with SARS-COV-2.

The isolation process involved the extraction and amplification of the SARS-CoV-2 virus RNA from a swab sample. The amplified DNA was sequenced with a MinION device. The data was analyzed on a smartphone.

The app was tested on different Android devices, such as models of Nokia, Huawei, LG and Sony.

The researchers found that the app to an average of 27 minutes to determine the complete SARS-CoV-2 genome sequence from the raw data. This opens the possibility to do genomic analysis at the point of care, in real-time.

The researchers also showed that the app could be used to profile DNA methylation in a sample of the human genome. DNA methylation is a modification which changes the activity of the gene.

"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," says Dr Deveson.

Genopo is a free, open-source application available through the Google Play store.



Source: Medindia