World's first mobile genetics laboratory launched as an iPhone app

A new iPhone app developed by researchers at Cold Spring Harbor Laboratory (CSHL) in Long Island, New York, enables scientists and others to access a hand-held mobile genetics laboratory in the field. 

The app, called iGenomics, can be paired with an Oxford Nanopore sequencer to map and analyze DNA sequences on the go. This can be accomplished even in remote locations lacking internet access.

iGenomics can also identify mutations in a virus, which is important for diagnosis and treatment.

The app is open source and available GitHub and the iOS App Store, as detailed in the Dec. 7 issue of Gigascience.

The iGenomics software was developed by a high school intern, Aspyn Palatnick, as he worked in the laboratory of computational biologist Michael Shatz at CSHL.

Palatnick told Current Science Daily how he first became involved in the work: "I started interning at the Schatz Lab when I was 14. By that time, I had a lot of experience building iOS apps (mainly games with fun interfaces), but had never done anything related to genomics.

"Mike took me under his wing and taught me about various bioinformatics algorithms. For context, at this time, traditional bioinformatics software mainly ran on high-performance computers or server clusters. And with DNA sequencers shrinking from being refrigerator-size to thumb drive-size, there was no analysis platform being built to complement those increasingly portable sequencers.

"Eventually we came to realize that with my iOS programming skills and his guidance, we’d be able to create the first ever mobile DNA analysis app."

DNA sequencers

DNA sequencers have become much more compact over the years, and now the Oxford Nanopore sequencing platform has an inexpensive hand-held version. This allows analysis of a genome, virtually anywhere, without sophisticated equipment.

The Oxford Nanopore system measures the change in ionic current as a DNA molecule is passed through a nanopore. A nanopore is a nano-scale hole set in an electrically resistant polymer membrane. The current changes as the bases G, A, T and C of a physical DNA sample pass through the pore in different combinations.

The problem CSHL researchers wanted to solve is how to analyze the DNA data without bulky computer equipment after it was collected. They aimed to create stand-alone genomics analysis software usable on any iOS device that could be paired with the Oxford Nanopore.

Palatnick told Current Science Daily that the key advance of iGenomics is to "give citizen scientists and researchers alike the ability to align and analyze DNA on a mobile device for the first time."

Simple to use

CSHL also designed iGenomics to be simple to use.

"Even with its advanced capabilities, iGenomics is built to have almost no learning curve, allowing anybody to become a DNA researcher with just their iPhone or iPad," Palatnick said. "Furthermore, when used with certain flu genomes, iGenomics can suggest what antivirals would not be effective in treating that strain of the flu, opening the door to the future of DNA-based medical tools."

Without an internet connection, iGenomics is still able to quickly compute "detailed genetic information about specific mutations within different viral or bacterial genomes," the researchers say. Someone in the field could analyze mutations of a coronavirus, for example, in just a few seconds.

iGenomics uses the Airdrop app to import or export data. This is an Apple technology that allows data transfer between iOS devices without Internet access.

A real life 'tricorder'

Current Science Daily asked Palatnick what he finds most exciting about this work:

"iGenomics," he said, "proves that analyzing DNA and mutations on a mobile device is both feasible, accurate, and, with viral genomes like the flu or COVID-19, takes just a few seconds. The question has moved from `If mobile DNA analysis were possible, how would that affect genomics research?' to `We now know mobile DNA analysis is possible, how do we make this the new reality?'

"iGenomics paired with a mobile sequencer is like a real life 'tricorder' from Star Trek."

The GigaScience article explains the software development process and its capabilities. To take one example: iGenomics comes preloaded with a file of known mutations in the influenza genome that make it resistant to some antiviral agents. This can aid the user in selecting a treatment for a particular virus.

What's next?

As for what's next with iGenomics, Palatnick told Current Science Daily: "For a while, there was this notion that aligning DNA and identifying mutations on a mobile device would take so long that it wouldn’t be practical, and for a while that was true. Now, with iGenomics, mobile DNA analysis both exists and is practical from a software standpoint."

"Ideally, this will inspire others to extend our research and develop the new reality where mobile DNA analysis is common across citizen scientists, researchers, medical professionals, astronauts, and more," Palatnick said.

Palatnick is now a software engineer at Facebook.