iPhone Genomics: beaming us up to the “tricorder” era
The first comprehensive mobile genome analysis application, iGenomics, is now available for download and use on an iOS smartphone. By pairing an smartphone with a handheld DNA sequencer, users will be able to create a mobile genetics laboratory, reminiscent of the Star Trek’s “tricorder”.
Just published is an article presenting iGenomics, the first DNA sequencing toolkit that can run on a smartphone. The work carried out by researchers at Cold Spring Harbor Laboratory takes us one step closer to making the tricorder envisioned by Star Trek a reality. While hand-held DNA sequencers have been available since 2014 (an event marked by our Data Note of the first complete E. coli genome sequenced by a handheld nanopore sequencer), an equally simple and portable analysis platform has not been available until now. We’ve previously showcased studies sequencing biodiversity in the jungle, but this still required a backpack of computer and other gear. iGenomics takes this a step further by providing applications to align reads, call variants, and visualize the results entirely on an iOS smartphone.
The project that led to iGenomics started out as a high school internship at Cold Spring Harbor Laboratory in New York State, when GigaScience Editorial Board Member Professor Michael Schatz noted the brilliance of a young high school student, Aspyn Palatnick.
Aspyn says of how the project got started: “In junior high school, I spent a lot of time making iOS apps, mainly games with fun interfaces. When I was 14, I started interning under Mike and he taught me the ropes of DNA sequence alignment and analysis. At some point, Mike had the realization that with my iOS app making skills and his mentorship, we could work together to build a solution in this space.”
Analysing genomes on a phone is intuitively different from doing so on a computer. A phone app requires a suitable graphical user interface with touch-related functions that are natural to anyone who has ever used a touch screen mobile device. For carrying out its analyses, iGenomics also has an option to export mutations and analysis data via email, Dropbox, Airdrop, or sharing via installed apps such as Google Drive.
Aspyn describes the potential uses for an app of this type: “We’ve targeted iGenomics towards the analysis of small viral genomes like influenza. Given this, with the support of Elodie Ghedin, we’ve used iGenomics for identifying which mutations in a strain of influenza would signal a resistance to particular antivirals. In simpler terms, we’ve demonstrated that iGenomics could be used to determine which drug classes would be ineffective in treating influenza.”
Another important use case of iGenomics was carrying out the first analysis of coronavirus mutations within a few seconds. To support this capability, the authors have provided a tutorial using the tool to compare the first published SARS-CoV2 patient and the consensus genome from a bat SARS-like coronavirus isolate (MG772934.1/).
Aspyn describes the potential uses for an app of this type: “We’ve targeted iGenomics towards the analysis of small viral genomes like influenza. Given this, with the support of Elodie Ghedin, we’ve used iGenomics for identifying which mutations in a strain of influenza would signal a resistance to particular antivirals. In simpler terms, we’ve demonstrated that iGenomics could be used to determine which drug classes would be ineffective in treating influenza.”
Aspyn adds on the portability side: “iGenomics solves the software-side of shifting the genomics field to be mobile; the final piece for completely portable DNA analysis is a sequencer that can read DNA directly into a mobile device and perform basecalling. iGenomics already has support for importing reads and references from external apps so, as soon as a mobile sequencer exists, iGenomics can take advantage of it right away. Oxford Nanopore has been actively working on a mobile sequencer for the past few years so we expect these to be available to the public in the not too distant future.”
Supervisor of the project Professor Michael Schatz adds: “iGenomics has been in our culture for decades, ever since we saw Dr. “Bones” McCoy use a tricorder to get an instant readout of the DNA and other molecules around him on Star Trek. iGenomics makes a really important step forward towards making this real by allowing for the analysis of viruses and microbes within a few seconds all on your iPhone. And while the concept has been around for several decades, it took Aspyn’s brilliance and creativity to make it come to life all within an easy-to-use app.”
iGenomics is open-source and available for free on Apple’s App Store: https://apple.co/2HCplzr
A youtube video of Aspyn Palatnick presenting the tool is available in our youtube channel.
References
Aspyn Palatnick, Bin Zhou, Elodie Ghedin, Michael C. Schatz. iGenomics: Comprehensive DNA Sequence Analysis on your Smartphone. GigaScience, Volume 9, Issue 12, December 2020, giaa133 https://doi.org/10.1093/gigascience/giaa138
