Thursday, February 29, 2024

Post-AGBT: Sequencing Hardware Roundup

Some updates on the sequencing instrument vendors, save Ultima Genomics and Element Biosciences which I've covered already.


Illumina was really, really quiet this year.  Sure, they had a booth and they had some posters, but not much talk about either as there wasn't much news.  Some of the posters were on the Illumina Complete Long Reads (ICLR) and did nothing to dispel my attitude that Illumina is treating ICLR as a product to hold onto a few wavering customers who aren't already committed to true long read platforms - the posters seemed to discuss only SNP calling and not any sort of structural rearrangements.  Other posters were on DRAGEN.

Particularly striking is the fact that new CEO Jacob Thayssen did not make an appearance.  If Illumina wanted to reassure the research genomics community that the new regime is still interested in them, this wasn't the way to go.  In contrast, it was very hard to miss the old Illumina braintrust of Jay Flatley, Mostafa Ronaghi and Gary Schroth as they moved about.  

Pacific Biosciences

Pacific Biosciences also had a relatively quiet AGBT, and I don't just mean they didn't host a pop concert.  New library prep automation for Hamilton robots was announced as well as HiFi Prep Kit 96 and HiFi Plex Prep Kit 96 said to lower waste and packaging.  With Plex Prep Kit 96,384 validated barcoding adapters are now available, which could enable 1536 samples on a Revio.  PacBio is proposing these kits will be of interest for microbial, metagenomic and low-pass mammalian projects.

CEO Christian Henry was recently on Mendelspod and mentioned the various hardware in development - population-scale short reads via the Apton technology, benchtop long reads and population-scale long reads - but no updates on timeframes.

Part of me feels I'm going easy on PacBio and hard on Illumina (especially during more pointed mental drafts of the Illumina section), but there is a key difference -- PacBio hasn't just had a major shakeup in upper management.

Deviating a bit from my form here, one exciting PacBio sample prep announcement (well, beyond the Volta Labs Callisto instrument) is seqWell's LongPlex product, which uses tagmentation to both shear HMW DNA to HiFi size range (<25Kb) and add barcodes to it so samples can be pooled upstream of HiFi library prep.  And since HiFi library prep is labor intensive, that could be a big savings.  Or if you are sequencing microbes on a Revio, then I could imagine using LongPlex on entire plates of extracted DNA, pool that and then prep each pool on Callisto.

Singular Genomics

Singular's focus was on the G4X spatial chemistry.  On the sequencing side, they released specs on the F4 flowcell which is slated for release in the second half of the year.  F4 is slated to deliver 600-800 million read pairs per flowcell and since the G4 instrument can host four flowcells at once, the F4 gives the instrument the potential to generate up to 3.2 billion read pairs.

I was interested to hear that Singular's Eli Glezer is very upfront about their precarious financial position: only about 20 instruments placed and perhaps two years of cash runway - Singular should be reporting financials in the next few weeks which will allow revising that estimate.    

Complete Genomics

Complete Genomics' biggest AGBT news is confirming they plan to launch a benchtop instrument called G800 that will use the CoolMPS antibody-based detection method to deliver 400-600 basepair single end reads.    Complete claims the data will be Q40, even at the end of the read.  Makes one wonder (and ditto with Element's Q50 chemistry), if the data is that good then how much farther until it drops to Q30?  What is the ultimate read length limit with these chemistries if long haplotypes are your priority and not per base accuracy?

One of the most curious answers I've ever gotten from a sales rep was the one I got in the Complete booth: a ubiquitous question is how many instruments they've placed in the US, and the answer I got was "less than fifty".  Never before had a sales type give me a ceiling on their market presence!

Oxford Nanopore

Oxford Nanopore had one huge, shocking announcement at AGBT - that Oxford Nanopore was a sponsor at AGBT!!!  Granted, the lowest tier with a booth far from the metallic sponsors, but still this is radical. 

Novel Technologies

No novel technologies at all on the sequencing tech side; neither talks nor posters.  One prior AGBT I remember thinking I was perhaps the only person outside the poster author(s) who had ever heard of Auger electron spectroscopy; sadly I've never seen that tech again.  There was no strange application of magnets to unzipper DNA, variations on nanopores, electron microscopes, quantum trickery or anything other exotic approach.  Ahh, the good old days of yore.  


Anonymous said...

There are a couple of places where "million" is missing from the throughout numbers.

Anonymous said...

I am always in awe of the money spent and wasted at this particular conference. If what I hear is true on the cost of sponsorships for about 1000 attendees, it is a wonder any financial department says yes to it. Better off spending the money on traditional sales/marketing.