Wednesday, 8 April 2015

Rise of the Nanopore

Nature Methods recently carried a News & Views article from Nick Loman and Mick Watson: “Successful test launch for nanopore sequencing”, in which they discuss the early reports of MinION usage; including a paper in the same issue of Nature Methods (Jain et al). They recall the initial “launch” by Clive Brown at AGBT 2012; this caused a huge amount of excitement, which has been tempered by the slightly longer wait than many were hoping for. Nick ‘n’ Mick suggest that a “new branch of bioinformatics” is coming dedicated to the nanopore data (k-mers), which is very different compared to Sanger or NGS data (bases).

Jain et al: The paper in Nature Metohds from Mark Akeson’s lab at UCSC presents the sequencing of the 7.2kb genome of M13mp18 (42%GC) and reported 99% of 2D MinION reads (the highest quality reads) mapping to the reference at 85% raw accuracy. They presented a SNP detection tool that increased the SNP-call accuracy up to 99%. To achieve this they modelled the error rate in this small genome at high-coverage; 100% accuracy might be impossible in homopolymer regions where the transition between k-mers is very very difficult to interpret, but for much of the genome MinION looks like it will be usable. Whether this approach will work for targeted sequencing of Human genomes will be something I’ll be working on myself.

In the paper they also reported very long-read sequencing of a putative 50-kb assembly gap on human Xq24 containing a 4,861-bp tandem repeat cluster. They sequenced a BAC clone and obtained 9 2D reads that spanned the gap allowing them to determine the presence of 8 repeats, confirmed by PFGE and “short” 10kb-reads from fragmented BAC DNA. 

The future looks bright for MinION: Jain et al discuss the rapid rate of improvement in MinION data quality, and Nick ‘n’ Mick also mention this when talking about why they're so upbeat about the MinION (hear it directly, both are speaking at the ONT "London Calling" conference). Their main reason is the success of the MinION Access Program in its first year (e.g. Jain et al reported the increase in 2D reads due to changes in sequencing chemistry from June (66%), July (70%), October (78%) and November (85%); and Loman published a bacterial genome after just 3 months in the MAP demonstrating the improvements in chemistry); they also point out that very long-reads allow access to regions of the genome off-limits to short-read technologies; and they mention the hope of direct base-modification analysis, direct RNA-seq and protein sequencing. Jain et al also discuss the possibilities of detecting epigenetic modifications, etc. These all seem a very long way off to me, but with so many labs participating in the MAP who knows how soon we’ll be reading about these applications? 

Jain et al and Nick ‘n’ Mick both mention the miniature size of the MinION and its portability. It is certainly small, I accidentally took mine home after a meeting because it was in my pocket! If this portability can move sequencing from the bench-to-bedside then MinION could be the first point-of-care diagnostic sequencer. It may be premature to suggest this, but many cancer researchers would love to sequence DNA directly from blood with as little time in-between collection and sequencing – if Clive’s AGBT 2012 claim “that sequencing can be accomplished directly from blood” proves to be accurate then this may just be a matter of technology (mainly sample prep) maturation.

I agree that the future looks bright for MinION. ONT tried something quite different with the MAP, this was a risk but is one that seems to be paying off. Year two is likely to see many many more publications from the large number of MAPpers.

Disclosure: I am a participant in the MinION Access Program.

PS: You can find a few MinION’s on the Google Map of NGS.

1 comment:

  1. Got MinION?
    Get ready for LomanION see: