Cold Spring Harbor Laboratory (CSHL) scientists have developed the world’s first mobile genome sequence analyser – a new iPhone app called iGenomics.
DNA sequencing technology
DNA sequencing technology over the past 30 years has progressed enormously. From the earliest approaches in the 1980s with Sanger sequencing, to the 2000s and high-throughput second-generation sequencing instruments. These technologies went from large bench-top instruments to more compact and simple designs. Nonetheless, these advances have been limited in their accessibility by most individual laboratories and citizen scientists. Currently, most alignment and analysis tools require expert knowledge.
In the past few years, Oxford Nanopore has introduced small inexpensive hand-held sequencing instruments that has enabled genomics experiments to be conducted in essentially any environment. For example, their technology was used during the Ebola outbreaks in remote areas of Africa. Nanopore sequencing has also played a role in monitoring the transmission of SARS-CoV-2.
The standard approach for analysing reads is to align them to a reference genome using high-end laptops, servers or even supercomputers. Unfortunately, these requirements may be out of reach for many researchers and citizen scientists. The ability to analyse data without high-end computing hardware is difficult, particularly in remote environments.
To address this critical gap, researchers developed iGenomics – an iOS application that allows anyone to easily align and analyse DNA sequences in a mobile environment. iGenomics uses the same high-performance algorithms for read alignment and variant calling as mainstream software. Using the advanced user interface features available in iOS, iGenomics allows for interactive visualisation and inspection of read alignments and variant calls. It also contains additional features for reviewing critical mutations of interest. Nonetheless, due to the lower amount of processing power in mobile devices, iGenomics is limited in the size of the genomes that can be processed. All alignment and analysis algorithms used by iGenomics have been tested on both real and simulated datasets to ensure consistent speed, accuracy and reliability of both alignments and variant calls.
iGenomics is the first comprehensive mobile genome analysis application. It has the capability to align reads, call variants and visualise the results entirely on an iOS device. The app is designed to complement the small hand-held DNA sequencing devices made by Oxford Nanopore. iGenomics is available open source and for free on Apple’s app store. iGenomics helps make genome studies more portable, accessible and affordable. Therefore, this development represents a step towards widespread DNA analysis.
In the journal Gigascience, the iGenomics algorithm is reported to quickly map DNA sequences of viral pathogens, such as Zika virus. It is also found to identify mutations important for diagnosis and treatment.
Excitingly, users can AirDrop sequencing data to each other, enabling DNA analysis in the most remote location. iGenomics could even potentially make it to space! Michael Schatz, adjunct associate professor at CSHL, stated:
“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.”
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