Tuesday, June 30, 2015

June 2015: Busting Out All Over with Genomics Technology

This month I again entered the prime of my life, though next year my programming brother points out that next year I (and the first Apollo manned missions) hit the big 30.  Beyond my personal milestone, it's been a busy last couple of weeks on the genomics technology front. Despite a lack of conferences or other traditional venues, big news has poured out from Pacific Biosciences, BioNano Genomics, Genapsys, BGI (which had another announcement earlier in the month), 10X Genomics and a pair from Oxford Nanopore.

A multi-institutional team which included PacBio and BioNano demonstrated the generation of a high quality diploid human genomic sequence using no prior information and no cloning.  PacBio reads were assembled using a number of innovative technologies developed by PacBio and collaborators, and the resulting contigs were then scaffolded with BioNano's optical mapping technology, yielding a final genome with N50 values higher than the original published human genome.  The fact that diploids can be sequenced and assembled to high contiguity without any cloning represents a true landmark, enabling both more extensive studies of structural variation and the possibility of generating reference genomes for most living organisms rapidly.  Undoubtedly the next (and final?) mountain for these technologies to summit are very large polyploid genomes.  PacBio has a nice write-up on their blog in case you don't (as I don't) have access to the paper in Nature Genetics.

It's worth taking a moment to enjoy this, and to marvel at both of these technologies. Both image single DNA molecules!  PacBio measures the kinetics of individual polymerase enzymes in real time!  It is much too easy to forget just how much like science fiction these ideas seemed less than a generation ago.

Genapsys made a flashy presentation at AGBT two years ago touting an iPad-sized device running an Ion Torrent-like chemistry, but since then had been very quiet (engendering wonders as to their ongoing existence).  Now they and Sigma-Aldrich have announced a partnership to commercialize the GENIUS sequencer.  Brashly claiming to be the first all-electronic sequencer (which I'm sure both Ion Torrent and Oxford Nanopore representatives would challenge) and making lots ocromises ("substantial reduction in capital cost", "your run will be completed in a matter of hours, not days")  but nothing of real substance.  

Another hazy entry into the desktop sequencer market was made by BGI, which announced their BGISEQ-500 sequencer, which apparently uses the same Complete Genomics chemistry as their big Revolocity machine.  Performance and pricing (or for that matter, anything beyond it will run one of their non-invasive prenatal testing panels) won't be released until October.  

10X Genomics, which I had covered remotely during AGBT has announced they are shipping their GemCode platform for generating long-range information on the Illumina short read platform. 

Finally, Oxford Nanopore has been busy.  First, they released the pricing information for MinION flowcells, enabling all sorts of fun discussions about how these fit next to other platforms.  With a range from $500 to $900 (depending on the volume ordered) and the actual yield of data and the application (Oxford is now giving a warranty on the number of active pores on a flowcell, but data yield is critically dependent on library quality), some see Oxford as more expensive than PacBio and others see it cheaper. They're both right if you are at an institution in which the PacBio instrument (and its space and keepers) are considered a paid-for asset and you are charged only the consumables cost, then Oxford is more expensive per megabase.  On the other hand, for commercial users who are buying on the open market in which overhead and depreciation/cost-of-capital are priced in, Oxford could look like a bargain.  Of course, one must first convince oneself that the two are functionally equivalent for a given task, which is not yet the case.  (see also Mad Mike's take).  In any case, MinION is starting to condense into a real product, which now can be analyzed on very open and real terms as far as cost effectiveness relative to other real competition.

Oxford's other announcement is the initiation of the PromethION Early Access Program, or PEAP. To be eligible, applicants must first be in the MinION access program (MAP).  While that only set you back $1K, PEAP requires plunking a $75K deposit and $25K fee to enter (optionally waived by ONT), but as with MAP that will get you one instrument and consumables.  

Oxford did not release any of the goodies that were touted at the recent London Calling conference, with the "fast mode" (500base/second DNA translocation vs. 40 base/second now) expected to be first.  Well, that's not here -- but if you want to inhale the vapors all of the London Calling talks are now online (with registration)

Will this spate of announcements bring others out, or will we have to wait until the fall brings fresh conferences?  Stay tuned!


Dan Udwary said...

"Big 30", eh? Think you missed a few decades there, bud.

Heath said...

News to me that the Appolo program started in 1986!

Jonathan Badger said...

"This month I again entered the prime of my life, though next year my programming brother points out that next year I (and the first Apollo manned missions) hit the big 30."

Brilliant! Why haven't I heard of using hexadecimal to measure one's age before?

Jonathan Jacobs said...

Looking forward to the Genapsys system - especially if I/we can get it running on batteries.