TY - JOUR
T1 - Nanopore sequencing in microgravity
AU - McIntyre, Alexa B.R.
AU - Rizzardi, Lindsay
AU - Yu, Angela M.
AU - Alexander, Noah
AU - Rosen, Gail L.
AU - Botkin, Douglas J.
AU - Stahl, Sarah E.
AU - John, Kristen K.
AU - Castro-Wallace, Sarah L.
AU - McGrath, Ken
AU - Burton, Aaron S.
AU - Feinberg, Andrew P.
AU - Mason, Christopher E.
N1 - Funding Information:
We acknowledge Edward Oakeley for initial discussions on using Shazam for nanopore data. Support was provided by the Tri-Institutional Training Program in Computational Biology and Medicine (via NIH training grant T32GM083937 in part), the International Space Station Program office, and the NASA Postdoctoral Program administered through a contract with Oak Ridge Associated Universities. For C.E.M we thank the Epigenomics Core Facility at Weill Cornell Medicine, as well as the Starr Cancer Consortium grants (I7-A765, I9-A9–071) and funding from the Irma T. Hirschl and Monique Weill-Caulier Charitable Trusts, Bert L and N Kuggie Vallee Foundation, the WorldQuant Foundation, The Pershing Square Sohn Cancer Research Alliance, NASA (NNX14AH50G, 15-15Omni2-0063), the National Institutes of Health (R25EB020393, R01NS076465, R01AI125416, R01ES021006), the Bill and Melinda Gates Foundation (OPP1151054), the Alfred P. Sloan Foundation (G-2015–13964), and the collaborators of the NASA Twins Study.
Publisher Copyright:
© 2016 Macmillan Publishers Limited.
PY - 2016/1/7
Y1 - 2016/1/7
N2 - 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.
AB - 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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U2 - 10.1038/npjmgrav.2016.35
DO - 10.1038/npjmgrav.2016.35
M3 - Article
AN - SCOPUS:85029004739
SN - 2373-8065
VL - 2
JO - npj Microgravity
JF - npj Microgravity
M1 - 16035
ER -