Researchers at Cold Spring Harbor Laboratory (CSHL) say they have developed the world’s first mobile genome sequence analyzer, a new iPhone app called iGenomics. By pairing an iPhone with a handheld DNA sequencer, users can create a mobile genetics laboratory, 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 ecology workers, noted the scientists. Aspyn Palatnick programmed iGenomics in the laboratory of Michael Schatz, PhD, adjunct associate professor, over a period of eight years, starting when he was a 14-year-old high school intern.
The iPhone app was developed to complement the tiny DNA sequencing devices being made by Oxford Nanopore. Palatnick, now a software engineer at Facebook, was already experienced at building iPhone apps when joining the Schatz laboratory.
He and Schatz realized that: “As the sequencers continued to get even smaller, there were no technologies available to let you study that DNA on a mobile device. Most of the studying of DNA—aligning, analyzing—is done on large server clusters or high-end laptops.”
Schatz recognized that scientists studying pandemics were “flying in suitcases full of Nanopores and laptops and other servers to do that analysis in the remote fields.” iGenomics helps by making genome studies more portable, accessible, and affordable, said Schatz.
Users can AirDrop sequencing data to each other, enabling DNA analysis in remote locations—even those without internet access. iGenomics may soon even find its way into the hands of astronauts.
According to Schatz: “There’s a lot of interest to do DNA sequencing in space. I’m trying to see if there’s a way we can get iGenomics up there. There’s a lot of people that are interested to do that. It’s a real testament about how it would be impossible to do, you know, any sort of analysis on regular computers. It’s just impossible to bring them with you.”
Published in the journal Gigascience, in an article titled, “iGenomics: Comprehensive DNA sequence analysis on your Smartphone,” Palatnick and Schatz reported that the iGenomics algorithm can quickly map DNA sequences of viral pathogens, such as a flu virus or Zika virus, and identify mutations important for diagnosis and treatment. They also provided an online tutorial for analyzing other viral genomes, such as from a SARS-CoV-2 patient.
“Following the miniaturization of integrated circuitry and other computer hardware over the past several decades, DNA sequencing is on a similar path. Leading this trend is the Oxford Nanopore sequencing platform, which currently offers the hand-held MinION instrument and even smaller instruments on the horizon. This technology has been used in several important applications, including the analysis of genomes of major pathogens in 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 align reads, call variants, and visualize the results entirely on an iOS device. Implemented in Objective-C using the FM-index, banded dynamic programming, and other high-performance bioinformatics techniques, iGenomics is optimized to run in a mobile environment. We benchmark iGenomics using a variety of real and simulated Nanopore sequencing datasets of viral and bacterial genomes and show that iGenomics has performance comparable to the popular BWA-MEM/SAMtools/IGV suite, without necessitating a laptop or server cluster.”
Schatz dreams that this device will help field workers and citizen scientists alike: “Today, we all carry professional cameras in our pockets, so it’s not that hard to imagine in the next couple years, all of us carrying our own DNA sequencers on our smartphones, as well. There’s just so many opportunities to do measurements of our environment and look for pathogens, maybe even do scans of yourself.”
iGenomics is available open source (github.com/stuckinaboot/iGenomics) and for free on Apple’s App Store (apple.co/2HCplzr).
