Tuesday, April 23, 2024

Bruker Wins NanoString Auction

NanoString declaring bankruptcy on the eve of 2024's edition of AGBT was a shock to many at the meeting and then there was confusion: would one of the sponsors have a dark booth? The aggressive 10X Genomics legal strategy that forced the bankruptcy raised a degree of polite ire. But NanoString marketing carried on and CSO Joe Beecham delivered a fiery speech saying "we're not going anywhere". Then an investment firm, Patient Square Capital, appeared to be the front runner for acquiring the assets, with speculation they would combine NanoString with their other spatial omics portfolio company, Resolve Biosciences.  But last week, as the genomics world was still processing PacBio's turmoil, news broke that Bruker had significantly outbid Patient Square - $392.6M vs $220M.  So Bruker takes NanoString home - and I gives me an entree to float an ontology of spatial technologies I've been fermenting, as Bruker will now have instruments in the four major spatial approaches.  And 10X now has a more formidable opponent in the ongoing patent wars.

Wednesday, April 17, 2024

PacBio Plummets

PacBio announced preliminary earnings yesterday, and the nearly immediate result was a 50% plunge in their share price.  Along with the earnings, the company announced significant cost cutting.  The details of those cuts were not made available, but some clever tea leave parsers noted a significant omission from what the company said it would continue.  The ASeq Discord channel on PacBio absolutely blew up, with opinions ranging from PacBio is in a death spiral to PacBio must be for sale, with significant numbers of "Christian Henry won't be CEO by year's end".  

Wednesday, April 10, 2024

Thoughts on RNU4-2 Mutation Paper

A new preprint based on Genomics UK data has identified a set of single base insertion mutations (predominantly a specific A insertion)  in a spliceosomal RNA which is responsible for about 0.5% of previously undiagnosed genetic cases of syndromic neurodevelopmental disorders . That's a remarkably high frequency mutation which has gone unnoticed to date, but the fact it was hiding in a non-protein-coding RNA (a spliceosome component called RNU4-2) had much to do with that - this gene won't be in any exome panels. The mutation always appears to be de novo and therefore the pathogenic phenotype is dominant.   I'd like to write down a few other thoughts - mostly in the form of questions --  with the caveat that I've never worked on a rare disease project and to describe me as a detached armchair voyeur of the field would be far too generous.

Thursday, March 28, 2024

Post-AGBT: VizGen & Scale Biosciences Partner

It's been just a few weeks since I sat poolside at AGBT with VizGen CEO Terry Lo and Scale Biosciences CEO Giovanna Prout to discuss the two companies' new partnership.  Well, that would have been accurate about a month ago; getting the last AGBT threads together has been buried under post-AGBT day work, some family business, another vacation - and let's be serious, mega-scale procrastination and writer's block (and that's just a euphemism here for more procrastination).  But that shouldn't detract from what these two RNA (and more!) profiling companies are trying to build together.  Plus this is my last "Post-AGBT" tag for the year; now I can move on to "inspired by AGBT" that is a bit less tied to the meeting (and less obviously overdue)

Monday, March 11, 2024

BioNano In Peril Again

While I still have a pair of pre-AGBT and AGBT interviews to write up - plus a long list of post ideas inspired by AGBT - breaking news about BioNano Genomics takes precedence.  The company has announced a major restructuring, with about 30% of its employees being laid off.  I've been laid off twice and it's never enjoyable, so I hope what I write here is appropriately sensitive - but won't be surprised if I still commit a faux pas.  Even with the restructuring, one analyst who likes BioNano estimated they will have about three quarters of cash - this is indeed a perilous time.

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.

Post-AGBT: Element AVITI Sequencing Updates

Element has been very busy over the past year and in the Silver Sponsor presentation covered updates since last AGBT as well as a number of completely new items.  I covered their Teton approach to multiomic analysis of cell culture in the last piece; in this one I'll cover their sequencing platform evolution.  Element was kind enough to loan me key members of their technical braintrust for an hour in the week before AGBT, which sadly I repaid by allowing their lunch to be scheduled over.  Thankfully, they do have a recording available!

Tuesday, February 27, 2024

Post-AGBT: Both Element & Singular Want Spatial to Go With The Flow(cells)

Element Biosciences and Singular Genomics have often appeared to be on roughly parallel trajectories, though with key differences.  Both companies launched sequencing instruments with NextSeq 2000-like specifications and largely aimed at the academic core lab and small biotech company market.  At AGBT, both announced upgrades to their sequencing instruments that allow the instrument to perform spatial omics while still functioning as a sequencer.  But there are key differences in their approach and what we know about each company and their degree of success so far in the sequencer market.

Tuesday, February 20, 2024

AGBT Follow-up: Ultima Genomics UG100, Volta Labs Callisto, N6Tec iconPCR

A confusion of ideas for AGBT follow-up have collided with the inevitable post-AGBT return-to-ordinary-life requirements.  To try to avoid a huge project that never gets completed, I'm breaking these up into multiple pieces.  First off, a look at reaction to the three big pieces I wrote before the conference or early during the conference: Ultima Genomics, Volta Labs Callisto and N6Tec iconPCR.  My comments are based on further thoughts on my part, discussions with other AGBT attendees and feedback I've gotten via social media, blog comments and emails/DMs.  Please keep it coming!  One of the great values of writing this is getting feedback - it illuminates questions I haven't considered and highlights gaps in my thinking. 

Wednesday, February 07, 2024

VoltaLabs Launches Callisto for DNA Extraction & Library Prep

Here at AGBT, VoltaLabs has unveiled their 24-sample DNA extraction and NGS library prep Callisto instrument, which is particularly suited for long read applications but is also suited for short read work. Volta has matured liquid handling automation to a novel open top electrowetting technology. Priced at $125K and planning to ship in the second quarter, Callisto is designed as a walk-away solution requiring no human interaction during a run. Personally, not only do I love the a new medium-throughput instrument for HMW DNA extraction and manipulation, but I also can at least pretend I helped steer the company In that directions

Tuesday, February 06, 2024

iconPCR: Super-Flexible qPCR Thermocycler Oft Dreamed, Now Delivered

Has there ever been a product you’ve just wanted to have, but it doesn’t exist? That keeps popping up in discussions - “if only we had X this project would go so much faster!”. Well, N6 Tec’s automation-friendly $99K i96 well iconPCR thermocycler is that to me. Launching at AGBT, it’s the gadget I’ve wanted repeatedly at Codon Devices, Warp Drive Bio and now Ginkgo Bioworks. It won’t solve all your PCR challenges, but it certainly gives new options to customize PCR like never before. And for many NGS labs, it offers major streamlining of PCR-based library construction protocols while also delivering superior data. How? By being a thermocycler where every well can run its own thermal profile and each well can go dormant once a desired level of amplification is achieved 

Monday, February 05, 2024

Want to Build A Sequencer? 454.bio Opens Up Their Plans

Just as the AGBT hype cycle was firing up (with me contributing multiple sparks), serial entrepreneur Jonathan Rothberg's latest sequencing startup 454.bio fully de-stealthed their technology this weekend, going so far as to release open source plans to build an instrument prototype.  454.bio  is aiming to build a Keurig-sized device to retail for $100, with sequencing runs in the $20 range.  To accomplish this, they're attempting a novel twist on sequencing-by-synthesis.  It's an unconventional strategy by someone who has succeeded twice before in DNA sequencing (454 and Ion Torrent) and has multiple other companies going (if I've counted correctly)  - QuantumSI in protein sequencing (a future topic for this space, I promise!), ButterflyNetworks with inexpensive, compact diagnostics ultrasound and Hyperfine with inexpensive, compact MRI diagnostic devices.  Then I went to the 4Catalyzer site - Rothberg's incubator - and discovered a bunch of companies I hadn't heard of or had forgotten about -- Protein Evolution in synthetic biology for plastics production, Detect for home-based diagnostics instruments, AI Therapeutics in the rare disease space and Liminal with what looks like consumer brain scanning.  That's quite a series of companies!   But the one closest to my heart (sorry QuantumSI :-) is  454.bio, and their announcements have many interesting facets which I'll dive into.

[2024-02-06 01:41 - 'used"--> iSeq fix -- stupid autocorrect!]

Thursday, February 01, 2024

Ultima Launches

As part of the run-up to Gold sponsorship at AGBT, Ultima Genomics held a multi-day event in early December, with tours of the headquarters facility and factory floor in the Bay Area and a day at a beautiful Wine Country resort. The resort session included talks from the company, early access collaborators and a pair of big name early backers, with a few hundred current customers and many contemplating the leap.  So confident was the company in their product, they even invited a blogger to moderate one of the panel discussions!  The UG100 is now officially launched as a fully commercial product, with ambitions to replace panels, exomes and microarrays with whole genome sequences at $100 apiece.  All in an instrument package designed for continuous industrial-scale operation.  Please note that Ultima did review this piece to ensure I didn’t disclose information they did not wish public, but for the most part just gave me some very good proofreading support.  Photos are my own, except as noted.

Monday, January 29, 2024

On Illumina's Moats Past & Present

Studying how Illumina came to dominate sequencing markets is certainly worthy of at least a Harvard Business School case study, and perhaps an entire graduate thesis.  But I wanted to give a quick review of some of my thoughts on the matter, spurred by Nava Whiteford's repeated savaging of a piece in another space but also because many of these themes will show up in a flurry of pieces I'm planning (one's even nearly done!) in the next few weeks due to AGBT and some non-AGBT news.  

Friday, January 05, 2024

2024: A Look Ahead

It's January, and that means the J.P. Morgan Healthcare Conference looms next week -- followed by AGBT just a month later.  Indeed, I've been trying to mark out the "can't miss" talks for AGBT so I can resist over-scheduling them with meet-ups -- but many talks lack titles so that's not easy.  JP Morgan seems to have Illumina, 10X and Nanostring -- and not much else in the way of sequencing-space companies.  But time to prognosticate before all the news happens!