As a 14-year-old intern at Cold Spring Harbor Laboratory, Aspyn Palatnick identified a gap in the genomics industry. Eight years later, he has now filled that gap with an iPhone app he named iGenomics.
iGenomics is the world’s first mobile genome sequence analyzer, reminiscent of the "tricorder” featured in Star Trek. The app runs entirely on iPhone’s operating system, eliminating the need for laptops, servers or other high-tech computers usually needed for the analysis of DNA reads.
DNA sequencing has changed exponentially over the past 20 years, advancing from a specialty lab-based process that required hundreds of millions of dollars to mobile, handheld equipment that costs less than $1,000. Illumina led the charge to make DNA sequencing more accessible at a laboratory level, while Oxford Nanopore Technologies pioneered the first pocket-sized sequencer.
Palatnick developed the iGenomics app to complement the tiny DNA sequencing devices being made now—and in the future—by Oxford Nanopore and others.
"As the sequencers continued to get even smaller, there were no technologies available to let you study that DNA on a mobile device,” says Palatnick. “iGenomics is leading the shift of DNA analysis software and sequencing tools towards mobile devices and marks a great leap forward towards widespread DNA analysis by non-bioinformatician students, researchers, and citizen scientists.”
Typically, high-end laptops or even supercomputers are used to analyze reads. iGenomics, however, just requires the sequenced reads to be uploaded from the phone itself, the Internet, or elsewhere. This approach allows anyone to perform sequence analysis and mutation identification, according to Palatnick’s paper, published in Gigascience.
Since today’s iPhones and iPads have power and memory close to that of an advanced laptop, iGenomics is able to use the same high-performance algorithms for read alignment and analysis as mainstream software. Thus, the novelty of the iGenomics application is not the DNA sequencing algorithms themselves, but rather how they can be easily applied in a mobile environment.
Palatnick and study co-authors, including CSHL professor Michael Schatz, tested the efficiency and accuracy of iGenomics running on an iPhone 8 using several simulated datasets. Compared with whole genome sequencing, almost all datasets showed positive correlation of iGenomics’s results, demonstrating well over 90% accuracy. Additionally, analysis runtime for iGenomics was clocked at under 3 seconds, which is 4 to 5x faster than current methods.
The research team also tested iGenomics on influenza samples to see if it could differentiate between the three distinct viral types.
“The results of this experiment show that we have a >93% identification rate, meaning that in most cases this simple process can accurately and quickly determine the type and subtype of the flu genome entirely on a mobile device,” the researchers explain in their paper.
The mobile analysis of viral genomes, like influenza, Ebola, Zika and more, is obviously the biggest draw for iGenomics. With the ability to “AirDrop” sequencing data to others, iGenomics could be a game changer for scientists and users in remote areas. It’s especially applicable now as the world continues to fight COVID-19. Palatnick and Schatz even designed an online tutorial for the analysis of SARS-CoV-2 using the mobile platform. But the accessible technology can go far beyond biology. Schatz is looking into getting it on the International Space Station, as he says there is “a lot of interest” in performing DNA sequencing in space.
Essentially, the researchers see a future in which the app is useful to almost everyone.
“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,” said Schatz.
iGenomics is available open-source and free of cost in Apple’s App Store.
Photo: Aspyn Palatnick holding the world's first mobile genetics laboratory at Cold Spring Harbor Laboratory's 125th anniversary Open House. Credit: CSHL