It’s hard to believe a year has passed since I last wrote up some personal highlights from the Nanopore Community Meeting in New York. Nevertheless, it’s been a year which has marked considerable progress within the world of nanopore sequencing – and in the ways we use nanopore sequencing in our lab.
Summaries of day 1 and day 2 are available here. This year’s meeting was packed with many, many talks from the user community and relatively few announcements of dramatic new tech directions. It seems right now is the time to polish many of the emerging strengths of nanopore sequencing.
To be honest, what is already being achieved is extremely impressive. Consider antimicrobial resistance as a case in point – a major societal challenge. Existing approaches take time. Time can cost lives, as bluntly demonstrated by Charles Chiu’s slide on time to effective antibiosis in sepsis. Several speakers showed how nanopore sequencing changes the dynamic: Patricia Simner reported detecting carbapenem antibiotic resistance genotypes within minutes of sequencing. I expect the next frontier is cost: where the tests are more expensive than many commonly prescribed antibiotics, the impact will be diluted. Low cost, application specific nanopore tools may well change this economic balance.
I think the highlight of the conference for me was that during an interactive plenary, discussion moved from technology itself to its societal implications of everyday genomics. If technologies such as nanopore sequencing are to be transformative for society, in what ways do we all wish society be transformed? Would we opt for our children to be sequenced at birth, and what would that mean for insurance? Or a future where your genome could be sequenced from a handshake and resynthesized in a genome foundry. Hypothetical for now, but the convergence of simplified sequencing, powerful computing and synthetic biology in a biohacker’s lab is one to watch.
This year I had the privilege of presenting in the microbial breakout session once more, reporting on our underground sequencing work. In two experiments in a coal mine, we demonstrated microbial identification using our lightweight metagenomad kit without benefit of power or internet. This experience has been useful in mounting our Arctic campaigns this summer, using rapid library preparations to characterize the microbial communities of the Greenland Ice Sheet while camped at the ice margin, achieving species level ID of cyanobacterial ecosystem engineers, and 16S rRNA gene sequencing on Svalbard to look at community responses to habitat changes on the glacier surface. Having shown in field metagenomics from sample-to-preprint publication within the likely doubling time of a glacier microbial community in 2016, it’s high time for me to consolidate a body of work in this area.
Cramming a little bit too much into the talk, I also presented our results from the lyophilized field kit on metagenomic sequencing. Until now the cold chain has been a significant constraint on deep field sequencing: essentially, in-field sequencing has moved the cold chain from sample return to lab to the deployment phase. It’s not going to be a problem for long. Using flow cells stored at +20*C for six days and freeze dried library reagents I was able to sequence a metagenome within two hours of Oxford Nanopore Technologies releasing the protocol. Although the “field site” was my kitchen table rather than the glacier – I’m very happy with the concordance between the field kit, nanopore rapid libraries and Illumina data from the same microbial community. I’ll post more about the lyophilized kit when I return to the UK, and release some data from a second experiment.