Tuesday, January 19, 2021

J.P. Morgan: PacBio

PacBio CEO Christian Henry’s presentation at J.P. Morgan wasn't rich in technical specifics. But he gave a very bullish portrait of a company aiming for the stars.  A conflict reminder: he’s a member of the Board of the Strain Factory that employs me, though I haven’t yet had the pleasure of meeting him.

The biggest news is a broad partnership with Invitae four clinical human genome sequencing. The only specific here is that this is not the whole enchilada; platform development will take place both within the Invitae collaboration and outside it. What might that development be?

Between Henry’s comments in the Q&A and a few info crumbs on slides there will be pushed to further tune all the canister. Her mentioned efforts on dyes and further improving SMRTcell loading efficiency. There was chatter on Twitter about an overdue update to improve HiFi yields.

Henry talked of the importance of increasing ZMW packing, but gave no specifics other than to suggest this is more "development" than "innovation" -- this was in response to a question asking if technical breakthroughs are required.   But we are left wondering on a timetable as well as what the next density might be; four-fold to 32M  wouldn’t be surprising on na├»ve geometry grounds. 

I suspect a huge area of joint effort with Invitae will be to automate HiFi library production. The current protocol is long, manual and labor intensive - not at all appealing for lease scale clinical use. How much of that will be retained as proprietary to Invitae will remain to be seen.  Henry claims that the Invitae effort will be separate but coordinated with existing development efforts; prior plans have not been shelved or diverted to support Invitae. A major software effort to support clinical operations is a given. PacBio has separate workflows for SNP and SV calling and those must be integrated and a clinician-friendly report generated. 

Henry believes that the new Sequel IIe will be the dominant product shipped going forward.  It will be interesting to see which of the older workflows PacBio updates and moves into the on-board compute.  For example, if you want to call methylation you must export BAM files with kinetics data, which are predicted to be five-fold fatter.  If the methylation calling happened on board, then that extra processing and extra data would be eliminated.  

Similarly, workflows such as microbial assembly are still based around Continuous Long Reads (CLR).  Henry didn't mention CLR once (I think).  While I doubt they would ever dump it altogether like they did Strobe Reads, it would seem likely that it won't get much attention.  Oxford Nanopore can beat them on very long reads and their single molecule accuracy is much higher; far better to focus on the CCS/HiFi reads where PacBio can deliver much higher accuracy.  It will be interesting to see if PacBio pushes the HiFi fragment read length longer.  On the one hand it will be more challenging to work with longer fragments and to routinely get enough circuits around them to deliver HiFi quality data.  Twenty five kilobases is a nice size for many applications, but there will always be incremental value for going to thirty or forty or beyond.

In response to a question about $1000 genomes, Henry described it as "just a number" around "where it makes sense" in high throughput applications.  He says the Invitae collaboration will be able to drive prices below $1000.  But he also pushed the idea that a PacBio genome is a truly clinical grade genome and has higher value than genomes produced on other platforms.  He argued that this higher value, in terms of higher diagnostic yield for rare diseases, will be more attractive to payers and that there will be a net benefit to the healthcare industry by ending diagnostic odysseys sooner.   He vowed to continue generating "diagnostic proof statements" to provide evidence to support the higher value claim.

Should be interesting to watch, particularly if you have a front row seat in front of a Sequel IIe,

Saturday, January 16, 2021

J.P. Morgan: 10X Genomics

As I attempt to collate various incomplete thoughts about the J.P. Morgan presentations I have read and listened to from genomics instrument shops, one thing stands out about 10X Genomics: they actually announced new gadgets and kits! I should thank the company for supplying the slides after I snarked on Twitter about how they weren't archived in the J.P. Morgan webcast -- but now it is there.  So either my eyes failed again or I had a personal IT failure (I think the website doesn't like iOS and I may have forgotten that).  The slides were presented by CEO Serge Saxonov

Thursday, January 14, 2021

JP Morgan: Illumina

Illumina presented at J.P. Morgan on Monday, reminding us that they aren't just a sequencing instrument company but an interlocking set of businesses focused on genomics. CEO Francis deSouza spent much of his time discussing the Grail acquisition and some of the other ways in which Illumina is pushing rapidly to become an essential part of clinical medicine, but there was one slide on future improvements to sequencing technology and a few on the lineup of existing sequencers.  Reminder: I'm working off public sources, as during the day we work closely with Illumina and they even sunk some serious cash into my employer last May.

Monday, January 11, 2021

J.P. Morgan 2021

The J.P. Morgan Healthcare Conference has started this morning in virtual form, so I'd really better get this draft cleaned up and out (indeed, Roche is presenting as I hurriedly type, though about pharma not diagnostics).  2021 already feels like a darker continuation of 2020, between the appalling putsch attempt in my nation's center of government last Wednesday and the still buggy roll-out of the coronavirus vaccine.  As I noted in my piece on the Oxford Nanopore Community Meeting, the many disruptions of 2020 make grading the progress of companies essentially impossible: many were disrupted by lockdowns, supply chain issues and the general distraction from the year of doomscrolling. 

Sunday, January 03, 2021

Advent of Code vs. FizzBuzz

A bunch of coding types at the Strain Factory participated in The Advent of Code, a clever 24-day set of programming challenges that runs each year before Christmas.  Each day a new two=part programming challenge was posted.  Technically it is a speed contest, but you won't find me on the public leaderboard as I'm not nearly quick enough to ever rate a point there.  One of my  major official activities last month was contributing towards screening candidates for three different computational positions, one of which we threw open to general data science experience.  As a result, I've been thinking far too much about the FizzBuzz problem and my prejudices towards it.

Saturday, January 02, 2021

Peri-New Year Nanopore Playing

Ever since the community meeting I've been toying with an idea,  then never quite trying to code it.
 So on New Year's Eve I started getting the dataset together and reducing it to a bunch of dataframes, and today I pushed that a bit further and started graphing some of it.  It's very much a rough project -- some of the dataframes have some issues I'm still chasing down with redundant data not being initially collapsed, but I think the data is accurate.  I also think I have my conventions consistent -- at one point confused myself into inverting the labels on the plots!  In other words, ApG would be labeled GpA -- not good! There's already some intriguing patterns, which are presumably the sort of signal tools like Medaka use to polish assemblies from FASTQ data aligned to draft references.

Friday, December 18, 2020

Nanopore Community Meeting: Progress Despite the Pandemic

I realized a few Oxford Nanopore announcements too late that I should have tried to log all their predictions with a date made so I could track carefully any delays or quiet disappearances from the new feature lineup.  If I had done that, this year would have presented an even worse conundrum: how do you score progress in a year of constant disruptions?  Like many companies in the sequencing field, at least some of that disruption has been a diversion of attention and resources to fighting the pandemic.  For ONT that is largely supporting the ARTIC viral genome sequencing and also developing LamPORE diagnostics.