Tuesday, May 21, 2024

Thoughts on A Decade of Oxford Nanopore Sequencing

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. 

Monday, May 20, 2024

FOMO Index at All Time High This Week

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.  Not only can't I attend them all, I can't attend most - and it will be impossible to monitor Twitter in real time much of the time.

Business travel is always a two-sided coin.  On the one hand I enjoy seeing new sights and revisiting other favorites.  I've been lucky that I've fit some sort of fun into just about every business trip I've taken, even if it's meant riding a nearly empty cable car to a deserted Fisherman's Wharf.  Two exceptions were both day trips, but how I couldn't sneak in excitement at Monmouth Junction New Jersey or East Haven Connecticut won't exactly haunt me.  But I'm also torn about travel: home is where the dog is.  Also the spouse and F1.  

Conferences are also an exhausting rush; London Calling isn't as bad as AGBT in this regard as it is shorter, there's only a late evening one night and there's not afterparties or European friends defeating your well intentioned plans to sleep by bringing a bottle of port and fine Dutch chocolates.  But it's always intense trying to catch talks, make meetings, visit demonstrations and booths, catch up with friends you only see at a specific meeting and take notes to share with colleagues and have a shot at writing something coherent for this space.  I'm not complaining - I could always quit, but I won't anytime soon.  This year London Calling is three days of talks instead of the usual two, so a bit more of the thrilling grind.

And of course,  at least for the next several weeks, there's my current day job to attend to.  Conferences are great and often lead to valuable connections and information; at AGBT i even tried on a Business Development persona which seems to have yielded multiple legitimate leads four our enzyme discovery & engineering business. But in the end, the team I'm on plus myself would like to see progress on the projects I've taken on, and I'm many solar orbits past the age where I can conference all day and code all night.

This year London is also featuring a Diagnostics Day from Roche on Wednesday.  There have been persistent rumors that Roche will finally, over a decade since acquiring Genia and four years after acquiring Stratos, announce a nanopore sequencing platform.  Or maybe not.  But counterprogramming that against London Calling is downright annoying!

If you are in London for either event, the folks at Plasmidosaurus have announced a pub night on Thursday at The Court.   It's over near University College London, which isn't very close to Old Billingsgate where London Calling is, but it appears to be a simple tube ride around the Circle Line. 

There's a list of conferences I'd like to attend but the timing never works; the Biology of Genomes has been "I'll go next year" for two decades.  SFAF is higher on the list, given the location - I love the American West scenery and Santa Fe can be such a great launchpad for so many interesting adventures - plus it sounds like a great conference.  SFAF has a reputation for taking on more of the early stage commercialization technologies that don't have a strong home at AGBT anymore.   Last year it was bumped for the practical concerns of a college graduation, moving the F1 back home and a celebratory trip.  Now it's in conflict with London Calling and put off for another year.

If I'd stayed in Boston, I might have thought about catching  NextFlow Summit.  Understanding workflow languages is becoming critical in bioinformatics (don't ask if I've followed that advice), and NextFlow is one of the leaders.

Back home, PacBio has the Boston edition of their PRISMBoston edition of their PRISM series -- I caught it two years ago and the talks were very good, but last year some schedule conflict of another caught me.  Complete Genomics is having a grand opening celebration at their new "Customer Experience Center" in Framingham, the biomedically biomedically immortal Boston suburb. I won't begin to claim I've checked other geographies; I did see a Nanostring event in central Europe going on this week also.

So I'm off to Gatwick in under an hour.  It horrified my British colleague I mentioned this to - Heathrow does have cachet plus often great views of Windsor Castle on approach - but I pointed out she's the one who got me hooked on picking up delectables at Borough Market, and if you get off the train from Gatwick one stop early at London Bridge the market is almost under the station. I'll get there just around the time it opens - and it's a quite reasonable walk to my hotel near The Tower of London from there.  JetBlue made it even easier last year by sending my bag to Heathrow and then delivering it, but I can't count on such service on a regular basis!

Going to London Calling or the pub outing?  Look for my hat celebrating the birthplace of Taq polymerase and please do say hi! 

Friday, May 17, 2024

HiFi WGS As A (Nearly) Unified Tool For Rare Genetic Disease Diagnosis

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 technology can cover a few types of mutations but miss others.  So this is good snapshot of the current state of human genomics technology with hints of where it might be going.  And Hoischen made a strong case that many other technologies  - but not all of them - can be retired if PacBio HiFi sequencing is the lead approach.  A longer, similar talk is also available as a PacBio-sponsored webinar given by Lissenka Vissers from the same institution and some of the data is in a preprint linked below.

Sunday, May 12, 2024

DoveTail Transposes Their Hi-C Methodology

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, with the promise of enabling short read sequencing to deliver both SNVs as well as long-range structural information all from the same library.  

Friday, May 10, 2024

AQTUAL: Arthritis Drug Selection Via Assaying Cell Free Chromatin

[Note: after I initially released this, Dr. Abdueva spotted some glitches; I pulled it back for editing & then got swept into London Calling; this revised version is finally emerging]

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, but there’s been many hints that liquid biopsies may be valuable in a wide range of diseases.  A bit over a week ago, Dr. Diana Abdueva founder and CEO of AQTUAL, walked me through (over Zoom) that company’s liquid biopsy approach to inflammatory disease management.

Tuesday, May 07, 2024

On The Expanding Versatility of Single Molecule Sequencing for Detecting Anomalous DNA

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 are apparently sensitive to the complementary base.  I wanted to point out, though without much deep analysis, three recent preprints that demonstrate detection of other modifications to DNA and thereby enable some interesting applications (and of course, some wild speculations on my part).  It's also interesting because of the overlap between the papers, as they are interconnected to a degree in their methods.

Wednesday, May 01, 2024

First Illumina Complete Long Reads Preprint

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 A Bottle (GIAB) sample as well as seven samples from individuals wiith potential genetic diseases of unresolved cause.  The GIAB sample was also sequenced with some of the latest Oxford Nanopore chemistry (Duplex R10.4.1) and as HiFi libraries on PacBio Revio - enabling comparisons of the platforms.  The preprint is probably going to be revised and expanded - I'm certainly hoping some of my comments are found constructive - but is very useful to see.  And perhaps it will soften positions such as mine on iCLR's utility.