Nanopore DNA Sequencing and Genome Assembly on the International Space Station

Abstract

We evaluated the performance of the MinION DNA sequencer 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 equimolar mixtures of genomic DNA from lambda bacteriophage, Escherichia coli (strain K12, MG1655) and Mus musculus (female BALB/c mouse). Nine sequencing runs were performed aboard the ISS over a 6-month period, yielding a total of 276,882 reads with no apparent decrease in performance over time. From sequence data collected aboard the ISS, we constructed directed assemblies of the ~4.6 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% consensus pairwise identity, respectively; de novo assembly of the E. coli genome from raw reads yielded a single contig comprising 99.9% of the genome at 98.6% consensus pairwise identity. Simulated real-time analyses of in-flight sequence data using an automated bioinformatic pipeline and laptop-based genomic assembly demonstrated the feasibility of sequencing analysis and microbial identification aboard the ISS. These findings illustrate the potential for sequencing applications including disease diagnosis, environmental monitoring, and elucidating the molecular basis for how organisms respond to spaceflight.

First Identification of Human Adenovirus Subtype 21a in China With MinION and Illumina Sequencers

“…Nanopore sequencing technology has an advantage of extremely long-read output (>2.3 Mb according to ONT website) over current NGS platforms. This characteristic has promoted rapid identification of pathogens in the field (McIntyre et al, 2016;Castro-Wallace et al, 2017;Johnson et al, 2017;Edwards et al, 2019), especially for bacteria and viruses. Human adenoviruses usually have 35-36 kb in their genomes, which could be captured and covered by ONT with a single read.…”

“…When compared to the next-generation sequencing (NGS) methods, nanopore sequencing technology has advantages such as real time, long reads, short turnaround time, and simple sample preparation procedures (van Dijk et al, 2018;Ameur et al, 2019). In particular, the ONT platform MinION, also characterized by portability and low cost in addition to the above advantages, can well handle rapid pathogen detection in the field (McIntyre et al, 2016;Castro-Wallace et al, 2017;Johnson et al, 2017;Edwards et al, 2019). MinION has been widely employed in pathogen identification from human clinical samples to identify Chikungunya virus, hepatitis C virus, and enterovirus Imai et al, 2018;Xu et al, 2018).…”

The utility and perspectives of NGS-based methods in BSL-3 and BSL-4 laboratory – sequencing and analysis strategies

“…For working it have to be plug into a PC or laptop by the USB cable. That made it also possible to take it into International Space Station [35,36] or in the Antarctic Dry Valleys [37] so it is also possible to implement it also in the BSL-3 and 4 laboratory environment and prepare all the sequencing steps inside the BSC. It would be also possible to use MinION in the field laboratory e.g.…”

Portable sequencer in the fight against infectious disease

“…The portable sequencer, MinION, can be transported to countries or locations where performing sequencing is difficult or transferring samples to other countries or locations is forbidden. For example, MinION has been taken to a remote rainforest of Tanzania [17], Ecuador [18], the Canadian high Arctic [19], and even the International Space Station [20]. MinION helped the surveillance and sequencing of Zika virus in the 2016 Brazil outbreak [21].…”