Readers of this space might have detected a significant slant towards skepticism in my coverage of Illumina Complete Long Reads (iCLR), exacerbated by now deposed Illumina CEO Francis deSouza claiming it isn't a synthetic read technology.  Illumina's posters on iCLR at AGBT this year seemed to reinforce my view that Illumina was marketing purely on short-read like terms - call SNPs in a few more hard-to-map regions of the genome, but not really compete head-to-head with the true long read platforms.  But now there is a preprint out on MedRxiv that reports iCLR results for a Genome In ..read more

A number of academic labs and startups have been trying to build new ways of parallel sequencing of large numbers of peptides using schemes that have significant resemblance in their logic to the highly parallel DNA sequencing schemes often highlighted in this space; QuantumSI is the first (and so far only) such company to actually commercialize in this space.  Resemblances to NGS but not identity - for a few important reasons. The biggest such challenge is the lack of anything resembling Watson-Crick basepairing in proteins. Sequencing chemistries almost invariably rely on basepairing ..read more

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 ..read more

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 pheno ..read more

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 ..read more

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.R ..read more

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

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!Read more ..read more

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 sequenc ..read more

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 Calpyso 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 c ..read more