Long Overdue and Overly Short Notes on Clive's NCM 2019 Talk

A theme of the 2019 Nanopore Community Meeting in New York was the long and short of nanopore sequencing.  While the public sparring with Illumina/PacBio over the definitions of sequencing types wasn't explicitly discussed, certainly ONT wants to make sure that people understand they don't intend to ignore applications that are naturally short reads.  I've been slowly trying to get this summary to gel for awhile, with the usual distractions this time of year of some trips, planning for holidays and a bout with a virus.  Plus general procrastination. 

I'm just going to cover Clive's talk; there were some really spectacular presentations (including one by someone who remarked that they hoped their upcoming thesis committee meeting would go well! One of multiple excellent platform talks by very junior scientists) If you'd like to watch yourself, the video of Clive's talk is online. Watching it again is kind of fun, except for the distraction of seeing a guy with huge glasses trying to live tweet from the front row.  I've put in brackets rough timepoints for some of the topics; you may need to slide back or forth a bit to nail it exactly but they can land you near the right spot.

Merger Questions to Mull Over Your Cider

With the full FTC complaint against the Illumina-PacBio merger now out in the open but the holiday break bearing down like a reindeer on steroids, I want to leave you with a few questions to ponder over your wassail.  Because what holiday gathering is not enlightened by discussion on the Herfindahl-Hirschmann Index (HHI)?

FTC Slams Illumina-PacBio Merger, but Illumina Not Quitting Yet

Tonight I was intending to finally get out my summary of technical notes from the Oxford Nanopore Community Meeting, but yesterday the U.S. Federal Trade Commission issued a press release that they believe the proposed acquisition of Pacific Biosciences by Illumina would be grossly anticompetitive and cannot be approved in any form.  A more detailed report is promised but hasn't surfaced yet.  Curiously, not only did this ultimately move PacBio's stock very little, but today Illumina and Pacific Biosciences filed matching SEC documents that Illumina will continue to infuse cash into PacBio through March of next year.  Also, I should note that someone left a passionate defense of regulators in the comments on a prior piece, noting that the FTC decision shows that the CMA was justified in opposing the deal and not simply acting with a parochial eye on Oxford Nanopore.

Is ONT Really Going to Twist the Watch Stem Backwards?

I was in New York last week for the Nanopore Community Meeting.  I'll save some technical updates for tomorrow, for I wanted to focus today on a huge inflection point that Oxford Nanopore announced that they will really will punch through next year.  I'm going to do that with an extended comparison to Robert Bloch's wonderful short story That Hellbound Train.  I won't spoil that story, but if you want to first go find a copy to read (there is apparently now a graphic novel version) or spend a half hour on a decent narration of it, please do.  It's especially a joy if you're steeped in the lore of American railroading.

Should Patent Pool Save the ILMN-PACB Merger? ONT Doesn't Think So

Last week the UK’s CMA published a proposal submitted by Illumina and PacBio to save their merger. This was then published in a revised, seemingly more generous form on Wednesday.  Most strikingly, the proposal tackles head-on an elephant long in the room: is the CMA playing hardball because the biggest competitor in this space is not named Oslo Nanopore Technologies.

Genapsys Launches

Today Genapsys launches their sequencer into the U.S. market, with worldwide launch next year.  They also received a new round ($90M) of financing from a major firm, Foresite Capital.  In addition to the Press Release and Media Kit, Genapsys' PR team, provided me with answers to a set of questions I provided.  As a reminder, I previously covered their pre-print pushed out to BioRxiv six months ago.

CMA Drops the (Preliminary) Hammer on ILMN-PacBio

Today the United Kingdom's Competition and Merger Authority (CMA) issued their preliminary report on the proposed acquisition of Pacific Biosciences by Illumina.  The report has no dry British phrasing: they clearly state that the merger is anticompetitive and that the only legal remedy is to block the transaction.  Interestingly, today was also the scheduled Illumina Q3 earnings call, but the subject wasn't even broached there.

QIAGEN Quashes GeneReader

Two weeks ago QIAGEN announced they will discontinue development of their GeneReader short read instrument and move their portfolio of gene panel tests over to the Illumina MiSeq and NextSeq. Existing instrument owners will continue to be supported for an indefinite period.  Thus ends QIAGEN's effort to build a fully vertically integrated sample-to-answer diagnostic sequencing system, just short of 4 years from the system's launch. What can be learned from this and how does this reshape the sequencing market?

Illumina Throws PacBio An Extension and a Lifeline

Interesting news today on the PacBio front: as reported by GenomeWeb, Illumina announced that their walkaway date for the acquisition has been extended to March 31 of next year and that Illumina will be pumping significant cash into PacBio until either the merger occurs or is terminated.  In addition to publicly reinforcing Illumina's determination to get the deal done, the terms of the arrangement have interesting consequences should the deal fall through

Where U.K.'s CMA Missed the Plot

I've written far more than I expected to on the PacBio merger, with it dominating my output here this summer save that recent dip in the CCS boomerangs.  We still haven't heard from the U.S. FTC, which is the big hammer that could drop and the stock is still selling at a substantial discount to the price offered by Illumina.  While I've hinted at it, I've never quite detailed my major objection to the form of the UK CMA's analysis of the proposed acquisition.  I've missed the opportunity to lay that out during the period of public comment for the next round of the CMA.  Still, worth it to write it down.  Which was true about a month ago when I wrote this, then failed to actually push it to a post before I headed out for a rugged vacation in the American West.  And then forgot about it after returning.  And more news today to comment on -- so better finally get this out there.

Amazon Needs Another Training Track

I spent a day recently taking Amazon's "AWS Technical Essentials" course.  I had originally opted not to go, but a summons went out that we had already paid for seats and that everyone using AWS should really go.  I've been in far worse courses and certainly had no complaints with our instructor, a former mechanical engineer who knew his stuff and was never in salesman mode.  Indeed, many of the tips I extracted had to do with how to save money.  No, the problem is that the course is designed for a very, very different use case than anyone in my shoes is interested in.  It's a use case that I'm sure Amazon has a few bazillion customers for, but I'm just not one of them.

Mirror, Mirror Have You Leads, On My Strange HiFi Reads?

A core purpose of this space is to explore the current state of genomics technology.  Much of the time this is via distilling news reports, press releases and interviews with persons in the field.  But even more fun is to dive into actual data.  Such data is often accessed via the generosity of researchers who deposit open access datasets.  But it is also true that part of my professional responsibilities is to determine when new technologies and methods have applications at my day job, so I'm also charged in the day job with contemplating experiments to plumb sequencing systems.  Only by doing so can we ensure that we maximize our ability to perform cutting-edge synthetic biology.  A recent such experiment generated some curious data which I have obtained permission to share a subset of it publicly, as I'm scratching my head and hope that someone out in the community has insight.

Wall Street Bets Illumina Won't Acquire PacBio

The proposed PacBio-ILMN Merger remains an interesting spectator sport, with the UK's CMA looking for public input for the next round.  I don't usually pay attention to stock prices, but PacBio's current state presents too juicy a situations.  Just to be clear though: I do not hold any individual stock position in PacBio or Illumina (the bulk of my investing is in broad mutual funds, some of which certainly have bits of these companies).

UK CMA & ILMN/PACB: The Inconvenience of Being Earnest.

As part two of a yet-to-be-determined number of pieces on the UK's CMA preliminary analysis of the proposed Pacific Biosciences acquisition by Illumina, I'd like to briefly explore the surprising authority of this agency to plumb internal documents at the two companies.

UK CMA's Write-up of PacBio Acquisition by Illumina Makes for XXX Reading; Clearly They Believe XXX and XXX

After writing my two recent pieces on the business side of the long read industry I planned, after a recent extended family vacation, to try to get back to science.  Particularly after my chagrin when various correspondents pointed out a fact from each I should have found and didn't: in my ONT piece I failed to discover that ONT has two share classes and the Woodford fund's shares cannot be used to gain control of the company and in the PacBio piece that there is a $100M breakup fee due PacBio if for any reason the deal doesn't go thru.  I'm particularly red faced on that one, as a breakup fee would play importantly into PacBio's financial health should the deal go south; $100M would buy perhaps two quarters time.

But then a bunch of people threw my way the UK Competition and Mergers Authority (CMA) report on the merger and I foolishly opened the document.  It makes for interesting reading, but that is hampered by the fact it is highly redacted -- like my title. Reserving the right to comment on the contents substance at a future date (or never), I'd just like to give a tour around some of the redactions.

Will Regulators Scotch PacBio Acquisition?

When Illumina announced its proposed acquisition of Pacific Biosciences last fall, an immediate question arose as to whether the deal would pass antitrust review.  Illumina must have been optimistic, as they originally expected the deal to close in "mid-2019".  That timetable has now been rolled back to late 2019 in the face of the UK agency with jurisdiction over mergers deciding to go for a second round of review and no word yet from the U.S.'s Federal Trade Commission.

ONT & The Woodford Liquidity Squeeze

There's an unfortunate chain of events that may end up causing a headache for Oxford Nanopore, and it's completely outside their control.  One of the their key investors has just had his luck - or perhaps more critically his reputation -- at stock picking disintegrate.  Because of some unusual choices, that has potential repercussions for ONT.

The Genius of Plongle

I noted in my roundup of Oxford Nanopore technical announcements that I loved the Plongle concept.  This is really both a new application-specific integrated circuit (ASIC) and using it to build a 96-well sequencer.  Let me expand on what there is to love.

ONT's Horrid Data Storage Folly

In the coverage of ONT's announcements at London Calling, I specifically left out one of Clive's Skunk Works projects.  This would be a device to use nanopores to write digital information.  I'll give him points for creativity, but the reason I held this for here is I truly and sincerely hate the concept and didn't want my vitriol to distract within the other piece.  But here I will let loose.

ONT's London Calling Announcements, Pass One

The annual big Clive Brown London Calling talk had a twist this year  Brown introduced a set of senior lieutenants at Oxford Nanopore and then tacked on a few "and one more thing" moments at the end.  If you're looking for the TL;DR version from me, it is that there were a lot of sensible but non-Earth shattering updates from the team followed by Clive updating on one prior crazy idea and throwing out two more -- one of which I love and the other I believe should be thrown out posthaste.