Preprint
Nanopore sequencing in microgravity
bioRxiv.org
10 Dec 2015
Abstract
Rapid DNA sequencing and analysis has been a long-sought goal in remote research and point-of-care medicine. In microgravity, DNA sequencing can facilitate novel astrobiological research and close monitoring of crew health, but spaceflight places stringent restrictions on the mass and volume of instruments, crew operation time, and instrument functionality. The recent emergence of portable, nanopore-based tools with streamlined sample preparation protocols finally enables DNA sequencing on missions in microgravity. As a first step toward sequencing in space and aboard the International Space Station (ISS), we tested the Oxford Nanopore Technologies MinION during a parabolic flight to understand the effects of variable gravity on the instrument and data. In a successful proof-of-principle experiment, we found that the instrument generated DNA reads over the course of the flight, including the first ever sequenced in microgravity, and additional reads measured after the flight concluded its parabolas. Here we detail modifications to the sample-loading procedures to facilitate nanopore sequencing aboard the ISS and in other microgravity environments. We also evaluate existing analysis methods and outline two new approaches, the first based on a wave-fingerprint method and the second on entropy signal mapping. Computationally light analysis methods offer the potential for in situ species identification, but are limited by the error profiles (stays, skips, and mismatches) of older nanopore data. Higher accuracies attainable with modified sample processing methods and the latest version of flow cells will further enable the use of nanopore sequencers for diagnostics and research in space.
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Details
- Title
- Nanopore sequencing in microgravity
- Creators
- Alexa B. R. McIntyre - Triinst Training Program Computat Biol & Med, New York, NY USALindsay Rizzardi - Johns Hopkins Univ, Sch Med, Ctr Epigenet, Baltimore, MD 21205 USAAngela M. Yu - Triinst Training Program Computat Biol & Med, New York, NY USAGail L. Rosen - Drexel University, Electrical and Computer EngineeringNoah Alexander - Weill Cornell MedicineDouglas J. Botkin - JES Tech, Houston, TX USAKristen K. John - NASA, Johnson Space Ctr, Astromat Res & Explorat Sci Div, Explorat Integrat & Sci Directorate, Houston, TX 77058 USASarah L. Castro-Wallace - NASA, Johnson Space Ctr, Biomed Res & Environm Sci Div, Houston, TX USAAaron S. Burton - NASA, Johnson Space Ctr, Astromat Res & Explorat Sci Div, Explorat Integrat & Sci Directorate, Houston, TX 77058 USAAndrew P. Feinberg - Johns Hopkins Univ, Sch Med, Ctr Epigenet, Baltimore, MD 21205 USAChristopher E. Mason - Weill Cornell Medicine
- Publication Details
- bioRxiv.org
- Publisher
- American Physical Society (APS)
- Grant note
- OPP1151054 / Bill & Melinda Gates Foundation Grand Challenges Explorations Initiative R01ES021006 / NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Environmental Health Sciences (NIEHS) R01 NS076465 / NINDS NIH HHS; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Neurological Disorders & Stroke (NINDS) R01 ES021006 / NIEHS NIH HHS; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Environmental Health Sciences (NIEHS) R25EB020393 / NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Biomedical Imaging & Bioengineering (NIBIB) R01AI125416 / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Allergy & Infectious Diseases (NIAID) T32 GM083937 / NIGMS NIH HHS; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS) R01 AI125416 / NIAID NIH HHS; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Allergy & Infectious Diseases (NIAID) R25 EB020393 / NIBIB NIH HHS; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Biomedical Imaging & Bioengineering (NIBIB) T32GM083937 / NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS) R01NS076465 / NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKE; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Neurological Disorders & Stroke (NINDS)
- Resource Type
- Preprint
- Language
- English
- Academic Unit
- Electrical and Computer Engineering
- Other Identifier
- 991021881815704721