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Researchers at the Cold Spring Harbor Laboratory (CSHL) say they have developed the world’s first mobile genomic sequence analyzer, a new iPhone app called iGenomics. By pairing an iPhone with a portable DNA sequencer, users can create a mobile genetics lab, reminiscent of the “tricorder” featured in Star Trek.
The iGenomics app runs entirely on the iOS device, reducing the need for laptops or large equipment in the field, which is useful for pandemic and environmental workers, the scientists noted. Aspyn Palatnick programmed iGenomics in the lab of Assistant Associate Professor Michael Schatz, PhD, over a period of eight years, starting at the age of 14, a high school intern.
The iPhone app was developed to complement the tiny DNA sequencing devices manufactured by Oxford Nanopore. Palatnick, now a software engineer at Facebook, was already experienced in creating iPhone apps when he joined the Schatz lab.
He and Schatz realized that, “As the sequencers kept getting even smaller, there was no technology available to allow you to study this DNA on a mobile device. Most of the DNA study – alignment, analysis – is done on large clusters of high-end servers or laptops. “
Schatz acknowledged that scientists studying pandemics “were flying in suitcases full of nanopores, laptops and other servers to do this analysis in remote fields.” iGenomics is helping by making genome studies more portable, accessible and affordable, said Schatz.
Users can sequence data by AirDrop with each other, allowing DNA analysis in remote locations, even those without internet access. iGenomics may even soon find its place in the hands of astronauts.
According to Schatz: “There is a lot of interest in doing DNA sequencing in space. I’m trying to see if there’s a way to get iGenomics up. There are a lot of people who are interested in doing this. It’s a real testament to how impossible it would be to do, you know, any kind of analysis on ordinary computers. It is simply not possible to bring them with you.
Published in the newspaper Gigascience, in an article titled “iGenomics: Comprehensive DNA Sequence Analysis on Your Smartphone,” Palatnick and Schatz reported that the iGenomics algorithm can quickly map the DNA sequences of viral pathogens, such as a influenza or Zika virus, and identify mutations important for diagnosis and treatment. They also provided an online tutorial to analyze other viral genomes, such as that of a SARS-CoV-2 patient.
“With the miniaturization of integrated circuits and other computer hardware over the past decades, DNA sequencing is on a similar path. The Oxford Nanopore sequencing platform is at the forefront of this trend, which currently offers the portable MinION instrument and even smaller instruments on the horizon. This technology has been used in several important applications, including analysis of the genomes of major pathogens at remote stations around the world, ”the authors wrote. “However, despite the simplicity of the sequencer, an equally simple and portable analysis platform is not yet available.
“IGenomics is the first comprehensive mobile genome analysis application, with capabilities to line up reads, call up variants, and view results entirely on an iOS device. Implemented in Objective-C using FM index, dynamic band programming, and other high performance bioinformatics techniques, iGenomics is optimized to operate in a mobile environment. We compare iGenomics using various real and simulated Nanopore sequencing datasets of viral and bacterial genomes and show that iGenomics performs comparable to the popular BWA-MEM / SAMtools / IGV suite, without requiring a computer laptop or cluster of servers.
Schatz dreams that this device will help field workers and citizen scientists: “Today we all carry professional cameras in our pockets, so it’s not that hard to imagine in the next two years, carrying us all of our own DNA sequencers on our smartphones, as well as. There are so many opportunities to take measurements of our environment and look for pathogens, maybe even do some testing yourself.
iGenomics is available as open source (github.com/stuckinaboot/iGenomics) and free from the Apple App Store (apple.co/2HCplzr).
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