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Researchers Develop Handheld DNA Sequencer
Dec 8, 2020 by News Staff / Source
By pairing a new app called iGenomics with a handheld DNA sequencer, users can easily align and analyze relatively small genomes, like those of viral pathogens.
Aspyn Palatnick holding the world’s first mobile genetics laboratory at Cold Spring Harbor Laboratory’s 125th anniversary Open House. Image credit: Cold Spring Harbor Laboratory.
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.
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.
“As the sequencers continued to get even smaller, there were no technologies available to let you study that DNA on a mobile device,” said Aspyn Palatnick, software engineer at Facebook who programmed iGenomics in Cold Spring Harbor Laboratory.
“Most of the studying of DNA: aligning, analyzing, is done on large server clusters or high-end laptops.”
“Scientists studying pandemics were flying in suitcases full of Nanopores and laptops and other servers to do that analysis in the remote fields,” said Dr. Michael Schatz, a researcher at Cold Spring Harbor Laboratory and the Departments of Computer Science and Biology at Johns Hopkins University.
iGenomics helps by making genome studies more portable, accessible, and affordable.
Users can AirDrop sequencing data to each other, enabling DNA analysis in the most remote locations — even those without Internet access.
iGenomics may soon even find its way into the hands of astronauts.
“There’s a lot of interest to do DNA sequencing in space,” Dr. Schatz said.
“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.”
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.
“We dream that this device will help field workers and citizen scientists alike,” Dr. Schatz said.
“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.”
The team’s paper was published in the journal Gigascience.
_____
Aspyn Palatnick et al. 2020. iGenomics: Comprehensive DNA sequence analysis on your Smartphone. GigaScience 9 (12): giaa138; doi: 10.1093/gigascience/giaa138
http://www.sci-news.com/genetics/igenomics-09128.html?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+BreakingScienceNews+%28Breaking+Science+News%29
Thanks to: http://www.sci-news.com
Dec 8, 2020 by News Staff / Source
By pairing a new app called iGenomics with a handheld DNA sequencer, users can easily align and analyze relatively small genomes, like those of viral pathogens.
Aspyn Palatnick holding the world’s first mobile genetics laboratory at Cold Spring Harbor Laboratory’s 125th anniversary Open House. Image credit: Cold Spring Harbor Laboratory.
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.
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.
“As the sequencers continued to get even smaller, there were no technologies available to let you study that DNA on a mobile device,” said Aspyn Palatnick, software engineer at Facebook who programmed iGenomics in Cold Spring Harbor Laboratory.
“Most of the studying of DNA: aligning, analyzing, is done on large server clusters or high-end laptops.”
“Scientists studying pandemics were flying in suitcases full of Nanopores and laptops and other servers to do that analysis in the remote fields,” said Dr. Michael Schatz, a researcher at Cold Spring Harbor Laboratory and the Departments of Computer Science and Biology at Johns Hopkins University.
iGenomics helps by making genome studies more portable, accessible, and affordable.
Users can AirDrop sequencing data to each other, enabling DNA analysis in the most remote locations — even those without Internet access.
iGenomics may soon even find its way into the hands of astronauts.
“There’s a lot of interest to do DNA sequencing in space,” Dr. Schatz said.
“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.”
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.
“We dream that this device will help field workers and citizen scientists alike,” Dr. Schatz said.
“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.”
The team’s paper was published in the journal Gigascience.
_____
Aspyn Palatnick et al. 2020. iGenomics: Comprehensive DNA sequence analysis on your Smartphone. GigaScience 9 (12): giaa138; doi: 10.1093/gigascience/giaa138
http://www.sci-news.com/genetics/igenomics-09128.html?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+BreakingScienceNews+%28Breaking+Science+News%29
Thanks to: http://www.sci-news.com
