There is a very funny tweet by Matthew Hankins about the over-use of “paradigm shift” in articles in Scopus between 1962-2014 which clearly suggest we over-use the term:
Percentage of shifts described as paradigm shifts, 1962-2014 pic.twitter.com/nHLuBUrH0H
— Matthew Hankins (@mc_hankins) January 23, 2016
However, last week there was a genuine shift in DNA sequencing published in bioRxiv by Matt Loose called “Real time selective sequencing using nanopore technology“. So what makes this paper special? Why is this a genuine paradigm shift?
Well, this is the first example, ever, of a DNA sequencer selecting regions of the input genome to sequence. To be more accurate, Matt demonstrates the MinION sequencing DNA molecules and analyzing them in real time; testing whether they come from a region of the genome he is interested in; and if they are not, rejecting them (“spitting them out”) and making the nanopore available for the next read.
This has huge applications from human health through to pathogen genomics and microbiome research. There are many applications in genomics where you are only interested in a subset of the DNA molecules in your sample. For example, exome sequencing, or other sequence capture experiments – at the moment a separate capture reaction needs to take place and this can actually be more expensive than the sequencing. Or pathogen diagnostics – here most of what you sequence would be host DNA, which you could ask the sequencer to reject, leaving only the pathogen to sequence; or flip it round – human saliva samples can have up to 40% oral microbiome DNA, which is wasted if what you want to sequence is the host. I have worked with piRNA and siRNA datasets from insects where less than 1% of the Illumina reads are those I actually want. If you want to know if a particular bacterial infection is resistant to antibiotics, you only actually need to sequence the antibiotic-resistance genes/islands/plasmids, not the entire genome. etc etc etc
Of course, we still have a bit of a way to go – Matt demonstrates so-called “read until” on Lambda, a relatively small, simple genome – but this is an amazing proof-of-principle of an incredible idea – that you can tell your sequencer what to sequence. The paper deserves your attention. Please read it and fire up your imagination!