Abstract
The ability to perform remote, in situ sequencing and diagnostics has been a long-sought goal for point-of-care medicine and portable DNA/RNA measurements. This technological advancement extends to missions beyond Earth as well, both for crew health and astrobiology applications. However, most commercially available sequencing technologies are ill-suited for space flight for a variety of reasons, including excessive volume and mass, and insufficient ruggedization for spaceflight. Portable and lightweight nanopore-based sequencers, which analyze nucleic acids electrochemically, are inherently much better suited to spaceflight, and could potentially be incorporated into future missions with only minimal modification. As a first step toward evaluating the performance of nanopore sequencers in a microgravity environment, we tested the Oxford Nanopore Technologies MinION™ in a parabolic flight simulator to examine the effect of reduced gravity on DNA sequencing. The instrument successfully generated three reads, averaging 2,371 bases. However, the median current was shifted across all reads and the error profiles changed compared with operation of the sequencer on the ground, indicating that distinct computational methods may be needed for such data. We evaluated existing methods and propose two new methods; the first new method is based on a wave-fingerprint method similar to that of the Shazam model for matching periodicity information in music, and the second is based on entropy signal mapping. These tools provide a unique opportunity for nucleic acid sequencing in reduced gravity environments. Finally, we discuss the lessons learned from the parabolic flight as they would apply to performing DNA sequencing with the MinION™ aboard the International Space Station.
Footnotes
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 would to like to thank the Alfred P. Sloan Foundation (2015-13964), the Bert L. and N. Kuggie Vallee Foundation, the Irma T. Hirschl and Monique Weill-Caulier Charitable Trusts, the WorldQuant Foundation, the STARR Consortium (I7-A765, I9-A9-071), and support from the National Institutes of Health (R25EB020393, R01NS076465), as well as support from NASA (NNX14AH50G) and the collaborators of the NASA Twins Study.
The authors would like to acknowledge Edward Oakeley for initial discussions on using Shazam for nanopore data.
Contributions: D.J.B. prepared the sample libraries. K.K.J., S.L.C and A.S.B. developed the operations concepts for in-flight loading, and modified the software settings to allow sequencing in-flight. N.A. consulted on sequencing protocols. L.R. and A.F. ran sequencing in-flight. A.B.R.M. performed analysis and developed novel methods along with A.M.Y., G.L.R. and C.E.M.
