Omicsomics.blogspot.com

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. 

I'm in the airport getting set to jet off to London Calling - already spotted a kindred spirit at Logan doing the same, but I could be easily be going somewhere else - or staying home.  There are three major 'omics conferences this week, all in incompatible geographies and overlapping.  Then there is a major vendor announcement day - also in London and perhaps about nanopores and conflicting.  There's also a pub meetup in London that thankfully doesn't  Back in Boston, there's also two free NGS vendor events I might have gone to. Читать дальше...

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... Читать дальше...

Technologies vying for state-of-the-art in human genome analysis are a recurrent theme in this space, and there are many ideas on this in the collection I really need to get out over the next two weeks before my brain is overwhelmed by London Calling.  Up today: Dovetail Genomics popping back on the scene (as a subsidiary of Cantata Bio)  with an AACR poster several weeks ago showing early results from a "LinkPrep" kit that will commercialize tagmentation (in vitro transposition to fragment DNA and add adapters) for Hi-C library generation... Читать дальше...

Liquid biopsies - the idea of peering into the disease state somewhere in the body by looking at “cell-free DNA” in the blood - is quite the rage these days.  There are a host of companies and approaches, and I haven’t quite found the discipline to start trying to build a census of all of them.  The field started with Non-Invasive Prenatal Testing (NIPT), and then some early NIPT cases had odd DNA that looked like oncogenic in healthy mothers - who turned out to actually have the cancer. Oncology has been the primary focus... Читать дальше...

An exciting aspect of true single molecule sequencing has been the detection of methylated bases.  Both Oxford Nanopore and Pacific Biosciences technology generate altered signals if methylated bases are present.  For Oxford Nanopore this is hardly surprising, as it would seem any change in the DNA should alter the complex interaction with the protein pore and it should become just a computational challenge of recognizing that signal.  PacBio is a bit more surprising, but the kinetics of base incorporation... Читать дальше...

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. Читать дальше...

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.

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... Читать дальше...

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... Читать дальше...