Cutting-edge nanopore devices have enabled scientists to sequence the genetic material of biological samples outside of the laboratory for decades. Portable devices, such as Oxford Nanopore Technologies’ MinION sequencer, can rapidly generate genomic sequences from biological samples, whether out in the field or inside a clinic. This kind of technology has been used for Ebola surveillance in West Arica, to profile microbial communities in the Arctic and to determine the coronavirus’s evolution during the current pandemic.
Typically, the raw data from these samples has required high-end computing to process. The numerous strings of genetic data need to be pieced into a single sequence, and this has needed the power of high-end servers or cloud systems.
The Genopo genomics app – developed by the Garvan Institute of Medical Research in collaboration with the University of Peradeniya in Sri Lanka – could be about to change all that. Condensing a number of bioinformatics tools into a single Android application, Genopo could now be used to make genomics research more accessible in remote or resource-limited regions. “Miniature devices like from Oxford Nanopore Technologies, such as the MinION – which is around the size of a USB stick – have enabled researchers to perform portable DNA sequencing in the field or clinic,” says Garvan’s Genomic Technologies Group head Dr Ira Deveson. “However, the resulting data is still large and complex, requiring (until now) powerful computers to analyse. Genopo takes the software required for this analysis and miniaturises it to work efficiently on a low-power device like a smartphone or tablet. This means the genomics analysis, not just the sequencing process itself, is now ultra-portable.”
An Android app for genomic data
The app was tested on the raw sequencing data of virus samples isolated from nine Australian patients infected with Covid-19. The viral RNA was extracted and amplified from a swab sample, and the amplified genomic data sequenced with a MinION, before the Genopo sequencing was trialled.
Genopo was trialled on Nokia, Huawei, LG and Sony phones. The app took an average of 27 minutes to determine the complete genome sequence from the raw data, which opens up the possibility of carrying out genomic analysis at the point-of-care, in real time.
Crucially, this could help clinicians in resource-limited settings fight more effectively against the Covid-19 pandemic.
“DNA sequencing and genomics analysis has become a really important tool in the global response to the Covid-19 pandemic,” Deveson says. “Researchers analyse the coronavirus genome in order to understand patterns of transmission within the community.
“Genopo is designed to make this process fast and portable, which means researchers can potentially perform these genomics experiments on the go, in the field, at the bedside and, in particular, in remote areas with limited access to computational resources and lab infrastructure.”
Beyond the novel coronavirus
The researchers were also able to demonstrate that Genopo could be used to profile DNA methylation – a modification which changes gene activity – in a human genome sample.
When performing DNA methylation profiling in human genome samples, Genopo was able to keep pace with the sequencing output of a MinION device. These analyses demonstrate Genopo’s suitability for rapid sequencing analysis on a generic Android smartphone.
The app also has potential to analyse genomic data from numerous infectious diseases – not just Covid-19.
Deveson says: “Genopo is not specifically designed for analysing genomics data from coronavirus – the app can be used to process data from any organism, including other viruses, bacteria or even humans. We anticipate the app could be useful for field-based virus research in existing human viruses that predominantly effect developing nations, such as dengue, Zika and Ebola.”
The free, open source application is now available to download through the Google Play store.