Can ONT Maintain Grip on Burgeoning Flowcell Herd?

A notion dawned on me when I was mentally planning my write-up of the Nanopore Community Meeting, but I decided to put off fleshing it out until a later date.  After a bit of procrastination plus a crush of other ideas, here it is: Oxford Nanopore flowcell lineup has been a bit complicated for a while, but it's probably going to get worse.  There's always been serious issues with the current level of complexity and it's hard to believe this will do anything but escalate.

An Ultimately Tufnellian Look At Oxford Nanopore R10.0 Homopolymer Performance

Homopolymeric sequences have never been easy for any sequencing platform, but single molecule sequencers struggle the most with this.  Oxford Nanopore has made remarkable strides in both raw an consensus accuracy via chemistry and software improvements, but still is challenged by systematic problems with homopolymers.  The R10 series of pores is intended to significantly improve performance by having a longer narrow region to interact with more bases, and at the Nanopore Community Meeting there were several slides touting improved performance.  Nanopore's slides have an X-axis that goes to 8.  By happy circumstance, around that time we generated a large dataset on R10 and got results very similar to ONT's.  Plus there's a dataset available from Mads Albertsen's group to support their updated pre-print on using Unique Molecular Identifiers (UMIs) to generate high quality consensus sequences.  But our internal dataset is  the best, as ours goes to eleven!

UST Bets on TELL-Seq

I've made a few references recently to TELL-Seq, both in my flawed analysis of BioNano Genomics (I missed a key business development in their raising $18M in October; I stand by the science comments and fear that the fund raise buys them about a year of time) and on 10X Genomics discontinuing their genome assay kits.  Now to actually dig into that technology -- a bit late given the preprint came out last fall, but better late than never.  So put on your sunglasses and hoodies, conjure up the image of early television chefs and key up the theme music for The Lone Ranger, because here I go.

Can BioNano Genomics Map A Way Past Twin Perils?

When playing with the structure of this piece in my mind, it occurred to me that Norman Maclean's thoughts about fly fishing apply just as well to biotechnology companies

It is also interesting that thoughts about fishing are often carried on in dialogue form where Hope and Fear -- or, many times, two Fears -- try to outweigh each other

The executive team at BioNano Genomics may well be gripped by this situation, as they are faced with two great perils: their finances and their markets.

Genia: It's Alive!

Once in a while I get the thrill of someone sending me a really good tip - that surge that comes with knowing that I know something that most people don't.  That rush of knowing that soon I'll get to spill the beans.  It's great, even if it upends my widely disseminated opinions.  Even if a moment later I realize that if I had thought harder I would have unearthed the nugget on my own.  All of which is the case here -- my tea leaf reading that Roche partnering with Illumina on diagnostics indicated that Genia is no more -- well, that interpretation is no more.  Because I got a hot and verifiable tip that Genia is very much still an active project at Roche.  And the verification is how I could I found this independently.

10X Genomics Exits Genomes

10X Genomics original product was a kit for generating linked reads from genomic DNA.  The idea had been kicking around for a while, partitioning long DNA into compartments and generating tagged libraries from each compartment.  This enabled both genome assembly and haplotyping from very small amounts of DNA.  When first reviewing 10X's slides from J.P. Morgan I had this thought "where's the genome kits" but then forgot to include it in my write-up.  Now I'm even more chagrined to discover that the explanation had been posted days before the conference: 10X has told their customers that their genome library kits are in the process of being discontinued.

JPM20 Loose Ends: Agilent, ThermoFisher, 10X Genomics, NanoString - plus PacBio & ONT

Time to close out  J.P. Morgan season with a grab bag of kvetches and kibbitzing on multiple 'omics companies that presented.  Much of this has been stimulated by Twitter discussions, with particular credit going to Varro Analytics and Albert Vilella.   While I've never been to J.P. Morgan physically and am skeptical I'll ever go, reviewing all this is a great prep for AGBT -- which I'm happy to be returning to this year for it's last Marco Island appearance for many years (forever?).

Bold Genapsys Talk at JPM20

Genapsys' CEO Hesaam Esfandyarpour presented today at the JPM Morgan Conference and delivered an expansive vision of where the company is going both this year an the long term.  This includes planned commercial launch of the 144M chip this year, an aggressive expansion into international markets and another round of "pre-IPO" financing.

JPM20: Roche Links with Illumina On Diagnostics

Another bit of Illumina news released at J.P. Morgan today is that Roche Diagnostics is partnering with Illumina.  The 15 year partnership (same duration as with QIAGEN) will place Roche diagnostic assays on Illumina clinical-grade sequencers as well as the two will jointly work for regulatory approval of Illumina's TruSight Oncology assays.  Roche has extensive experience in oncology, particularly since they own Foundation Medicine. This suggests that Roche is happy with a two pronged strategy in oncology diagnostics, selling assays on their own through the partnership while their Foundation arm offers an all-in service.   But it also stirs the tea leaves in the genomics M&A pot.

JPM20: Illumina Launches Super Resolution Instruments

Illumina presented this morning at the J.P. Morgan Healthcare Conference (presentation, slides & breakout).  For us sequencing geeks, the biggest news is the launch of a pair of new sequencers -- but not where either myself or Shawn Baker anticipated.  Rather than doing something about the low end of their line (as I predicted) or replacing the MiSeq as Shawn guessed, Illumina perceived a need for desktop instruments to span the range between the existing NextSeq 550 and the NovaSeq and has christened the new instruments NextSeq 1000 and NextSeq 2000.  They also come with some slick new technologies embedded.

Is Illumina Vulnerable At The Bottom?

According to both the FTC and CMA, Illumina holds a nearly complete monopoly on the sequencing market, with other players (Ion Torrent, Oxford Nanopore) holding on to toehold niches.  Illumina has held that position for an extended period, so what might upset it?  I'm going to explore the case that they may have some serious inroads at the bottom of their line.

Might Illumina Shave NovaSeq Run Times?

I've had some people asking, either privately or via Twitter, what might come from Illumina next week at JP Morgan (8:30 am PST on Monday).  I have another post in the works (ideally going out not long after this one) on one aspect of their business, but then I thought of something else.  Something in the great tradition of proposing a plan while being quite unaware of all the critical details that the plan relies on!

A Le Mans for Clinical Genomics?

If you haven't seen Ford v Ferrari (or Le Mans '66 in parts of Europe), I strongly suggest you do so if it is still in a local theater.  I'm neither a gearhead nor a fan of watching automobile races, but while the movie is centered on an attempt to win the  1966 24 Hours at Le Mans, there is so much more going on.  Designer Carroll Shelby (Matt Damon) must not only project manage a difficult task, but also deal with unreliable allies (as one wag put it, the biggest villain in the title isn't Ferrari) and a cantankerous star driver named Ken Miles (Christian Bale).  One touching aspect of the movie is the portrayal of Miles' relationship with his young son, an audience proxy who idolizes but sees all sides of his father.  

Illumina & PacBio Throw In The Towel

I had planned to post this morning a "preview of 2020" piece I had drafted in my head on the ski slopes the previous two days, but never got around to actually committing it to bits and bytes.  Today's announcement that the Pacific Biosciences acquisition from Illumina is officially dead means the first item of that piece is mostly going uncaptured.