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Published, Version of Record (VoR)CC BY V4.0, Open
Journal article
Nanopore sequencing in microgravity
NPJ microgravity, v 2(1), pp 16035-16035
20 Oct 2016
PMID: 28725742
Featured in Collection : UN Sustainable Development Goals @ Drexel
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 - Cornell UniversityLindsay Rizzardi - Johns Hopkins MedicineAngela M Yu - Tri-Institutional PhD Program in Chemical BiologyNoah Alexander - Cornell UniversityGail L Rosen - Drexel UniversityDouglas J Botkin - JES TechSarah E Stahl - JES TechKristen K John - Johnson Space CenterSarah L Castro-Wallace - Johnson Space CenterKen McGrath - Australian Genome Research FacilityAaron S Burton - Johnson Space CenterAndrew P Feinberg - Johns Hopkins MedicineChristopher E Mason - Cornell University
- Publication Details
- NPJ microgravity, v 2(1), pp 16035-16035
- Publisher
- Nature Publishing Group
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Electrical and Computer Engineering
- Web of Science ID
- WOS:000385972200001
- Scopus ID
- 2-s2.0-85029004739
- Other Identifier
- 991019168131204721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Biotechnology & Applied Microbiology