I'm always excited by sequencing technology going bigger.  Every time the technology can generate significantly more data, experiments that previously could only be run as proof-of-concept can move to routine, and what was previously completely impractical enters the realm of proof-of-concept.  These shifts have steadily enabled scientists to look farther and broader into biology - though the complexity of the living world always dwarves our approaches.  So it was easy to say yes several weeks ago to an overture from Scale Bio to again chat with CEO Giovanna Prout about their ne ..read more

A maxim from the great but fictional advertising executive Don Draper: "if you don't like what people are saying, change the conversation".  In an online strategy update presented two weeks ago ( Slides / Replay  ), Illumina announced they'd like a new conversation around sequencing costs.  No longer will they tout reagent cost per basepair, but instead will be focused on the total cost of sequencing workflows.  The obvious cynical response is that Illumina is conceding defeat on the raw cost, having been severely beaten by Ultima Genomics (and Complete Genomics aka MGI, bu ..read more

I recently tried to place a claim that I had first conceived Oxford Nanopore's "6b4" strategy for solving homopolymers, but that appropriately brought a number of citations for the concept that predated my blog piece.  Not one to give up easily (and as hinted in that piece), I'm going to spend part of this piece trying to stake claim on some new concepts for fixing Oxford Nanopore's homopolymer issues - and PacBio's trouble with polypurine stretches.  To be honest, much of this piece will consist of me posing questions I haven't bothered to try to chase down if they've already been a ..read more

One of the most important enzymes in the sequencing world, one which enables spectacular creativity on the part of novel assay designers, is Tn5 transposase.  Personally, I spend many times each month thinking about how to use Tn5 and its ability to tagment - both tag and fragment - input DNA. There’s even reports that Tn5 can tagment RNA-DNA hybrids such as from reverse transcription or even long single-stranded DNA.  I’ve covered seqWell in the past,with their fully kitted reagents; now the company (which just turned ten) is launching a Tagify product line that is focused on e ..read more

Oxford Nanopore is in the process of morphing into a product-focused company, and so must identify specific markets in which they believe nanopore sequencing can compete or even dominate.  One such market that was spotlighted this year at London Calling is the quality control of mRNA therapeutics, where nanopore sequencing may be able to replace a kitchen sink of technologies and often provide superior data. Pharmaceutical and diagnostic quality control is both similar and very different to research.  While many sequencing research experiments are to some degree a fishing expedition ..read more

Scale Bioscience officially rolled out today - their rep was already talking about it at the Boston Single Cell Symposium I attended yesterday - a new cell indexing reagent called ScalePlex to streamline single cell 3' RNA sequencing of multiple samples.  Read more ..read more

London Calling isn't nearly as exhausting as AGBT, but the first day of talks is packed and then follows with the social event that goes late - this year with CEO Gordon Sanghera living out his dream of being the frontman for a band.  Then if you'd like you can follow the crowd to a pub to drink on ONT's tab (that and crashing the ONT wrap-up dinner is the extent of my drawing personal benefit from ONT, contrary to a commenter on the prior piece who wrongfully believes they fund my LC expenses), and when that pub closes to another one (I peeled off after the first pub).  So one can b ..read more

London Calling was a particularly good opportunity to take stock of Oxford Nanopore's progress to a "fire-and-forget" sample-to-answer solution for "applied markets" such as food safety, public health and biotherapeutics quality control.   ElysION (formerly Project TurBOT) and TraxION represent very different approaches targeting different subsets of this broad market opportunity - and I heard from some interested parties that neither is quite what they want.  That doesn't mean they aren't right, but it does mean ONT may need to think of more approaches. The broad concept is to ..read more

I'm writing this the eve of Oxford Nanopore's London Calling conference.  This is a big one, as this summer marks the 10th anniversary of ONT releasing devices into the wild.  It's been a long, interesting journey and I'm much too jet-lagged to try to review old posts or even link to them, but a bunch of thoughts have been in my head the last few days.  Read more ..read more

What is now way back in February, Alexander Hoischen presented a talk at AGBT which described early results from an effort to apply PacBio HiFi sequencing at scale for solving rare disease cases.  Hoischen passionately made the case for how providing a diagnosis can change affected families.  It's also worth noting how important rare disease genetics has been to the history of biology, illuminating new processes and entire pathways.  Something I hadn't appreciated until his presentation is how many technologies are currently thrown at a case in current workflows because each tec ..read more