The new mobile application made it possible to analyze the genome of the SARS-CoV-2 virus on a smartphone in less than half an hour. Scientists at the Garvan Institute for Medical Research, Australia, reported their development in the journal Communications Biology.
State-of-the-art nanopore devices have allowed scientists to read, or “sequence” genetic material in a biological sample outside the laboratory. But analyzing raw data has always required access to high-performance computing power – until now.
Developed by the Garvan Institute for Medical Research in collaboration with the University of Peradeniya in Sri Lanka, Genopo is making genomics more accessible in remote regions or hospitals with limited resources.
“Not everyone has access to the powerful computing power needed to analyze DNA and RNA, but most people do have access to a smartphone,” explains study co-author Dr. Ira Deveson, who leads the genomic technology group at Garvan Clinical Genomics Center. “Fast, real-time genomic analysis is more important than ever. It is the central method for tracking the spread of the coronavirus. Our application makes genomic analysis more accessible by literally putting technology in the pockets of scientists around the world. ”
To enable genomic sequencing and in situ analysis in real time and without a large laboratory infrastructure, scientists have developed an app that can run bioinformatics workflows for nanopore sequencing datasets downloaded to a smartphone. In the process of reengineering, scientists had to overcome a number of technical problems associated with various resource constraints in smartphones. The Genopo app brings together a range of available bioinformatics tools into a single Android app.
The researchers tested Genopo on raw sequencing data from virus samples isolated from nine Sydney patients infected with SARS-CoV-2, which included extracting and amplifying viral RNA from a smear sample, sequencing the amplified DNA using a MinION device, and analyzing the data on a smartphone. The researchers tested their app on a variety of Android devices, including Nokia, Huawei, LG and Sony models.
It took the Genopo app an average of 27 minutes to determine the complete sequence of the SARS-CoV-2 genome from the raw data, which the researchers said opens up the possibility of real-time, point-of-care genomic analysis. The researchers also showed that Genopo can be used to profile DNA methylation – a modification that alters gene activity – in a sample of the human genome.
“We hope this will make genomics much more accessible for researchers to uncover information in DNA or RNA for the benefit of human health, including in the current pandemic,” concludes Dr. Dewedson.
Genopo is a free open source application available on the Google Play store.