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Nanopore DNA Sequencing and Genome Assembly on the International Space Station

Sarah L. Castro-Wallace, Charles Y. Chiu, Kristen K. John, Sarah E. Stahl, Kathleen H. Rubins, Alexa B. R. McIntyre, Jason P. Dworkin, Mark L. Lupisella, David J Smith, Douglas J. Botkin, Timothy A. Stephenson, Sissel Juul, Daniel J. Turner, Fernando Izquierdo, Scot Federman, Doug Stryke, Sneha Somasekar, Noah Alexander, Guixia Yu, Christopher E. Mason, Aaron S Burton
doi: https://doi.org/10.1101/077651
Sarah L. Castro-Wallace
1Biomedical Research and Environmental Sciences Division, NASA JSC, Houston, TX
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Charles Y. Chiu
2Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
3UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA
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Kristen K. John
4NASA Postdoctoral Program, NASA Johnson Space Center (JSC), Houston, TX
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Sarah E. Stahl
5JES Tech, Houston, TX
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Kathleen H. Rubins
6Astronaut Office, NASA JSC, Houston, TX
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Alexa B. R. McIntyre
7Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY
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Jason P. Dworkin
8Solar System Exploration Division, NASA Goddard Space Flight Center (GSFC), Greenbelt, MD
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Mark L. Lupisella
9Exploration Systems Projects Office, NASA GSFC, Greenbelt, MD
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David J Smith
10Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA
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Douglas J. Botkin
11Formerly JES Tech, Houston, TX
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Timothy A. Stephenson
12Applied Engineering and Technology Directorate, NASA GSFC, Greenbelt, MD 20771
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Sissel Juul
13Oxford Nanopore Technologies, Oxford, UK
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Daniel J. Turner
13Oxford Nanopore Technologies, Oxford, UK
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Fernando Izquierdo
13Oxford Nanopore Technologies, Oxford, UK
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Scot Federman
2Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
3UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA
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Doug Stryke
2Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
3UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA
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Sneha Somasekar
2Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
3UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA
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Noah Alexander
7Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY
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Guixia Yu
2Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
3UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA
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Christopher E. Mason
7Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY
14The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
15The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY
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Aaron S Burton
16Astromaterials Research and Exploration Science Division, NASA JSC, Houston, TX
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  • For correspondence: aaron.burton@nasa.gov
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Abstract

The emergence of nanopore-based sequencers greatly expands the reach of sequencing into low-resource field environments, enabling in situ molecular analysis. In this work, we evaluated the performance of the MinION DNA sequencer (Oxford Nanopore Technologies) in-flight on the International Space Station (ISS), and benchmarked its performance off-Earth against the MinION, Illumina MiSeq, and PacBio RS II sequencing platforms in terrestrial laboratories. Samples contained mixtures of genomic DNA extracted from lambda bacteriophage, Escherichia coli (strain K12) and Mus musculus (BALB/c). The in-flight sequencing experiments generated more than 80,000 total reads with mean 2D accuracies of 85 – 90%, mean 1D accuracies of 75 – 80%, and median read lengths of approximately 6,000 bases. We were able to construct directed assemblies of the ~4.7 Mb E. coli genome, ~48.5 kb lambda genome, and a representative M. musculus sequence (the ~16.3 kb mitochondrial genome), at 100%, 100%, and 96.7% pairwise identity, respectively, and de novo assemblies of the lambda and E. coli genomes generated solely from nanopore reads yielded 100% and 99.8% genome coverage, respectively, at 100% and 98.5% pairwise identity. Across all surveyed metrics (base quality, throughput, stays/base, skips/base), no observable decrease in MinION performance was observed while sequencing DNA in space. Simulated runs of in-flight nanopore data using an automated bioinformatic pipeline and cloud or laptop based genomic assembly demonstrated the feasibility of real-time sequencing analysis and direct microbial identification in space. Applications of sequencing for space exploration include infectious disease diagnosis, environmental monitoring, evaluating biological responses to spaceflight, and even potentially the detection of extraterrestrial life on other planetary bodies.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 27, 2016.
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Nanopore DNA Sequencing and Genome Assembly on the International Space Station
Sarah L. Castro-Wallace, Charles Y. Chiu, Kristen K. John, Sarah E. Stahl, Kathleen H. Rubins, Alexa B. R. McIntyre, Jason P. Dworkin, Mark L. Lupisella, David J Smith, Douglas J. Botkin, Timothy A. Stephenson, Sissel Juul, Daniel J. Turner, Fernando Izquierdo, Scot Federman, Doug Stryke, Sneha Somasekar, Noah Alexander, Guixia Yu, Christopher E. Mason, Aaron S Burton
bioRxiv 077651; doi: https://doi.org/10.1101/077651
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Nanopore DNA Sequencing and Genome Assembly on the International Space Station
Sarah L. Castro-Wallace, Charles Y. Chiu, Kristen K. John, Sarah E. Stahl, Kathleen H. Rubins, Alexa B. R. McIntyre, Jason P. Dworkin, Mark L. Lupisella, David J Smith, Douglas J. Botkin, Timothy A. Stephenson, Sissel Juul, Daniel J. Turner, Fernando Izquierdo, Scot Federman, Doug Stryke, Sneha Somasekar, Noah Alexander, Guixia Yu, Christopher E. Mason, Aaron S Burton
bioRxiv 077651; doi: https://doi.org/10.1101/077651

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