Sequencer vs. Library Prep Market Structures

Something I started pondering as I was prepping my JP Morgan items: the structure of the market for sequencing library prep is very different from that for sequencers.  Perhaps this is painfully obvious to many, but I hadn't turned it over before in my mind.   It also follows that the sequencer market was overweighted in who was invited to give talks at the banking conference - nearly every sequencer maker was there - Complete Genomics and Singular Genomics were the missing parties (and Singular is a bit of a quasi-sequencer company now).  Note that in this piece I will not claim a complete census of companies in this space - though please feel free to note exceptions in the comments

P2 Solo: ONT Extends Support But Not Sales

A brief update to the earlier P2 Solo piece - Oxford Nanopore has now announced they will extend their support for the device until 2030, but they are still ending sales this summer.  So a cosmetic victory for Solo fans, but not really much gain - and certainly disappointing for anyone saving their quid for a future purchase.  Solos may become very valuable, though it's hard to see ONT ever countenancing a healthy resale market.

ONT Axes P2 Solo, Roiling Community

Oxford Nanopore has a serious case of user community unrest, triggered by the announcement that the P2 Solo (aka P2s) will be phased out starting this summer.  P2 Solo is the two flowcell version of PromethION which required external GPU for basecalling; P2i is the sibling with onboard GPU. P2 Solo clearly has a very passionate constituency, one which feels betrayed by its discontinuation.  This ongoing episode - ONT could always change their mind and restore the P2 Solo - is a cautionary tale of the challenges of changing corporate strategy in the context of a brand which has built a near cult-like loyalty. 

JP Morgan 2026 Roundup

The J.P. Morgan conference last week was mostly small tidbits of info on the sequencing front, with Element delivering the one big teaser announcement. 

JPM 2026 Schedule Through A Molecular Tools & Testing Lens

The J.P. Morgan Healthcare Conference is this week in San Francisco.  As with every other one, I'm tracking any news remotely from Boston.  Some year I really should go to observe the sheer spectacle of it, but this isn't the year - and if I were in California now it probably would be more valuable to attend Plant & Animal Genomes down in San Diego.  If you do go, be sure to check out the 4 instrument autonomous laboratory Ginkgo will have running in the Marriott Marquis lobby.  But here are some notes to keep track of when different companies are presenting.  Public companies will make their presentations available shortly thereafter to comply with insider trading regulations.  Unfortunately, several years ago J.P. Morgan ended posting presentations from private companies - these companies could choose to post their decks but I'm not optimistic to see many.

Stalking the Elusive Product Market Fit

I had a wonderful breakfast conversation back in November with Arima Genomics Founder (and now President and Chief Operating Officer) Sid Selvaraj where he brought up the topic of product market fit.  I've often kibitzed on 'omics companies trials and tribulations trying to achieve product market fit, but now that I'm in an outward-facing product development role the concept is central to my daily work.  What is it and how does one achieve it - or fail to?

Scales of Instrumentation and Automation

Back in September I moved into a product role within the automation unit at Ginkgo, where we sell autonomous laboratories.  I'm going to end up posting a bunch on the topic, as I spend a lot of time thinking about it and this is an interesting place to expose my thinking to critique.  It's also a way to solicit feedback on semi-formed ideas.  I referenced autonomous laboratories in my previous post, which might have some wondering "what exactly is an autonomous laboratory?"  So this post will lay out a description of different levels of automation (or instrumentation) so I can refer back to it in future posts - and there will certainly be further posts focused on these different scales of automation. So here I will lay out four levels of laboratory instrumentation: Bench, Walkup, Workcell and Autonomous.  BTW, if you are in San Francisco next week during J.P. Morgan,  there will be a small autonomous lab running in the Marriott Marquis lobby - and it can be viewed regardless of whether you are registered for the conference

Sequencing Instrument Outlook 2026

The Joy of Rediscovery

A key goal of science is to discover new information, and it is one of the great joys of science to believe you have done so.  Sometimes it really does prove novel and interesting - an experience our genome explorations at Warp Drive Bio gave me often - and sometimes the joy is blunted by realizing what you thought was novel is already known.  When I was a graduate student I was on an immense high having found what seemed revolutionary while trawling through Genbank, but then a few days later I uncovered a Cell paper less than a year earlier which had shown that Archea possessed a Eukaryote-like transcription initiation system.  So close yet so far!  But there is also a special joy in certain rediscoveries, when without trying at all a fundamental fact about the universe just reveals itself in your data.  One of my New Year's resolutions is to rediscover the discipline to write frequently in this space, and so to kick that off early (and get the 2025 count to an even one quarter of a 96-well plate) I'm going to review my favorite rediscovery - one that that surprisingly few (in my opinion) who should know of this result are aware of it.

UltraMarathonRT: When Your Reverse Transcription Must Go Long

The 1960s, 1970s and 1980s were both the early years and golden years for nucleic acid enzymology. Scientists unraveling the secrets of DNA replication and repair, RNA transcription, viral replication and other basic processes purified enzymes responsible for numerous processes.  Other scientists envisioned practical applications for these enzymes and put them to work in the recombinant DNA revolution that began just over 50 years ago.  Due in no small part to the great body of literature that has arisen around these pioneer enzymes, they tend to be important still today in biotechnology - sometimes retaining monopolies on a particular type of in vitro biochemistry.  But there are new entrants, and today I’m going to explore a new player in the reverse transcription space, UltraMarathonRT from a small Connecticut company, RNAConnect.  RNAConnect has launched two new products in the second half of this year, a kit for cDNA synthesis back in August and today a kit for generating long direct RNA reads on Oxford Nanopore platforms.

Two reverse transcriptases have dominated the field of cDNA generation for cloning, sequencing, RT-qPCR and other applications, both arising from early research on retroviruses.  Each is named for the retrovirus it was found in, Avian Myeloblastosis Virus (AMV) Reverse Transcriptase and  Moloney Murine Leukemia Virus (M-MuLV, MMLV).  Many of the reverse transcription kits on the market today are either formulations of one of these two retroviruses or made with versions carrying a small number of point mutations.   While these enzymes have served biotechnology well, they do have shortcomings, particularly in the lack of helicase activity which can cause them to stall on templates which have formed complex and strong secondary structures.

UltraMarathonRT is not from a eukaryotic retrovirus, but instead from a prokaryotic group II self-splicing intron. UltraMarathonRT is far more processive than the venerable eukaryotic RTs and able to reverse transcribe transcripts of 30 kilobases or longer.  A key difference from another group II retron RT on the market, Induro from NEB, is that UltraMarathonRT has a temperature optimum of 30C vs 55C for Induro; higher temperatures risk more damage to template RNA.  

Template switching is a property of reverse transcriptases in which the enzyme has a 3’ terminal transferase activity which adds a predictable set of untemplated nucleotides to the 3’ end of the first strand cDNA; for UltraMarathonRT this is three As.  By inclusion in the reaction of an oligo with the complementary sequence, second strand cDNA can be triggered in the same reaction.  Since the template switching oligo (TSO) can have barcode and unique molecular identifier sequences as well, this makes template switching particularly valuable for sequencing applications.  

RNAConnect today launched a kit for Oxford Nanopore direct RNA sequencing which uses UltraMarathonRT.  While direct RNA sequencing can work without any reverse transcription, having a first strand cDNA bound to the RNA improves performance, particularly since the helicase activity of UltraMarathonRT can unwind secondary structures which might not be unwound by the motor protein in ONT’s chemistry.  RNAConnect has run comparisons of their kit to a process using Induro and shown 67% more mapped reads which are in excess of 10Kb, with this dropping to 24% for mapped reads >5kb and only 11% for reads >2kb.  With increasing research interest in exploring long non-coding RNAs (lncRNAs) - the best known lncRNA, XIST responsible for driving X chromosome inactivation, is 17 kilobases long.  The kit also has the convenience of including all required components, other than those unique to ONT.

Higher processivity and greater ability to push through complex secondary structures - both highly desirable properties in a reverse transcriptase.  As the price/performance ratio of both PacBio and ONT improve for cDNA sequencing, continued improvement of metrics for ONT direct RNA and now meso-length reads from Roche’s SBX chemistry will all enable greater surveys of RNA at longer scales.  Such studies can be reasonably expected to sharpen our understanding of splicing.

When I was an undergraduate nearly 40 years ago, we were taught that alternative splicing existed but was a rare phenomenon that only rarely deserved attention. I think we were taught about the alternative splicing that drives soluble vs membrane-bound antibodies in B cells, but probably no other examples.  That view has changed radically over the last 40 years, with alternative splicing now recognized as a generator of both protein diversity and regulation.

As a graduate student, I discovered an overlooked set of alternative exons in a Drosophila visual protein gene which my labmate Carlos Alvarez demonstrated, by clever PCR assays, that while there are theoretically 8 different splice forms possible (which would all generate valid ORFs) only three of these are detectable in flies. Made a nice PNAS paper.  Nowadays we’d do that by sequencing.  Cataloging such coordinated splicing would be one clear use for long read direct RNA or long read cDNA sequencing.

Another emerging class of splicing events of great interest are “poison exons” and “detained introns”.  Detained introns are introns that are normally spliced out, but are systematically retained in certain contexts.  If these cause the translation of a premature stop codon which leads to nonsense-mediated decay of that mRNA, then it is a poison exon.  A number of labs have reported on poison exons that appear to be very carefully regulated, providing yet another opportunity for cells to regulate production of a particular gene product.  Inadvertent retention of poison exons is yet another way that mutations can negatively affect mRNAs and trigger rare genetic disorders.  

Clearly for a complete survey of alternative splicing, poison exon usage, and other types of retained/detained introns it is important to have an unbiased view of a transcript, not degraded by secondary structure or biased to the 3’ end.  UltraMarathonRT shows approximately 2X higher detection of retained introns than other RTs when applied to the Universal Human Reference RNA (UHRR) sample.  

 

RNAConnect the company is sited in Branford CT, not far from Yale University where founder Dr. Anna Marie Pyle teaches.  For this piece I spoke with Andrew Bond, previously at gene synthesis company Gen9, and Jason Underwood, ex-PacBio,

UltraMarathonRT appears to be a useful new tool in the molecular biology toolbox, enhancing the ability to sequence long and difficult RNA templates.  It shows promise for advancing the understanding  of splicing as well as the medical consequences of inappropriate splicing.  UltraMarathonRT citations in PubMed are currently only from Dr. Pyle’s lab; it will be interesting to see what new discoveries are made as kits with this enzyme enter widespread use in RNA sequencing laboratories.

Countable Labs: New Approach to Enumerating DNA

Countable Labs, formerly Enumerix, was founded by serial entrepreneur Stephen Fodor, who originally stormed on the molecular tools scene with Affymetrix.  I caught up with their new CEO, Giovanna Prout, at ASHG the other week and got a rundown on their new approach to counting molecules with PCR.

Prout recently found herself out of the CEO job at Scale Biosciences after its acquisition by 10X Genomics.  She says she resolved to become the best stay-at-home mother ever and her kids loved having her home - but soon urged her to find a new gig as they recognized it was what made her happiest.  So she quickly landed the CEO role at Countable Labs.  Formerly Enumerix, the company is yet another molecular tools company from prolific scientific entrepreneur Stephen Fodor, best known for Affymetrix.

Countable’s standard workflow is simple.  A 50 microliter reaction of sample DNA, probes, primers, PCR mastermix, and Countable’s proprietary matrix consumable are placed in a spin column.  Centrifuging the columns generates a matrix, with approximately 30M individual picoliter-scale compartments capturing individual DNA molecules.  After a brief (60 minute) PCR amplification in a conventional thermocycler (Countable has a list of preferred instruments), the tubes are placed in Countable’s benchtop instrument for light sheet microscopy imaging of the compartments, requiring 5 minutes of imaging per tube.  There’s no dead volume - every picoliter scale chamber in the tube will be imaged.  Because there are so many compartments, the system has a dynamic range of 6 logs!  Countable’s instrument holds 96 tubes in the form of 24 strips of 4 tubes each.  The instrument is priced at $150K with consumables adding up to $16 per sample. A full set of 96 samples can be processed in half a workday.

Assays can be designed using Countable’s universal multiplexing kit or conventional TaqMan hydrolysis probes can be included.  The universal multiplexing kit has the advantage of enabling the use of inexpensive, fast arriving ordinary oligos which simply require a 5’ tail sequence on the forward primer to enable linking (via primer extension) the universal multiplexing codes to the user primers.  Countable provides a software tool to streamline converting existing assays into universal multiplexing assays and analyze the resulting multiplex primer designs for undesirable cross-reactivity. Assays based on the universal multiplexing kit can be designed and tested in under a week

Countable is developing a high degree of multiplexing by managing the optical system so that it is capable of distinguishing 10 different fluorescent dyes.  By imaging in 9 different channels, each channel a different pairing of excitation wavelength and emission wavelength, each dye can be distinguished by the unique fingerprint of intensities in each channel.  This yields 10 clearly separable labeling schemes. Theoretically 48 different labeling schemes can be distinguished in this way.  One ASHG poster from Countable demonstrated 8-fold multiplexing

So what can you do with so many colors? And with 6 logs of dynamic range?

One poster presented by ASHG focused on BRAF oncogenic mutation detection.  Three clinically relevant mutations are seen at position 600 of the protein: V600E, V600K, and V600R.  By first using 18 cycles of a PCR design agnostic to the status of codon 600 as a pre-amplification and then using allele-specific primers covering the four alleles (three oncogenic variants plus wildtype) and each primer a different color, Countable was able to demonstrate detection of the variants when present in a sample at a frequency of 0.08% - much better than the 1-5% achievable with qPCR and 0.1% for digital PCR.   That’s also not a trivial detection limit to achieve with a sequencing assay - but at about $16 per sample the Countable assay will be far less expensive than any NGS assay unless you can batch to a very high degree.  These results also leverage the high dynamic range of Countable’s assay - detecting between 400 and 700K molecules with a single assay system.  

In another poster, Countable demonstrates measuring mitochondrial genome copy number, using multiple distinguishable probes targeting the mitochondria plus an additional one to get the nuclear genome as a reference.

Countable is also touting that they have built the system for GMP workflows, with the built-in software providing audit trails and other required security features for 21 CFR Part II compliance.  

Another interesting feature of Countable PCR is the ability to recover samples post-amplification - a protocol is provided to extract DNA out of the matrix. So you can count from a precious sample and then potentially fully sequence it as well.

Bell Labs Wasn't Built in a Day. Or Two Years.

Rome is famous for persisting for centuries - and having not been built in a day. If you go there, then one of the most magnificent sites is the most famous sporting arena in the world, the Flavian Amphitheater - better known as the Coliseum. Last week there was colossal news in the biotech world that Arena Bioworks was shutting down, after only two years and $100M spent of its "committed' half billion in funding.  What went wrong?

Nineteen

If I had been more atop things, I would have written this just under a week ago, on the nineteenth anniversary of my starting to write in this space.  That's a milestone, and actually writing something is the way to try to push back towards some regular frequency in posting here.  But the real reason for the title is something I've mused on a small bit for many of those years: can we shave one amino acid out of the proteome?

ASHG Posters: The Agony and The Ecstasy

ASHG is a huge meeting, probably the second largest I've ever attended after ASCO.  ASBMB is similar in size perhaps, though I think a hair smaller and definitely a bigger than ESHG.  And certainly multiple AGBTs in scale.  And that is crashing in on me now.

PacBio: $300 Genome Via Chemistry Update

ASHG is here in Boston, just down the street from Ginkgo's HQ.  I'm in a new role in Ginkgo Automation, trying to convince the NGS world that our automation platform is the bee's knees.  So excellent timing.  In advance of the meeting I was able to grab 30 minutes of PacBio CEO Christian Henry's time - last time I saw him he was fresh out of the legendary midnight AGBT  ILMN vs. PACB doubles beer pong match.  Christian gave me a heads up on some of the product news that hit the wires a bit earlier this morning. At the top of that is a new version of the core chemistry, SPRQ-Nx, which boosts yields 10-15% as well as the official launch of flowcell reuse.

Ship of ThesION

10X Scoops Scale

News broke this afternoon that microfluidics single cell genomics leader 10X Genomics has bought out split-pool single cell company Scale Biosciences for $30 million up front in cash and stock, with additional payments of undisclosed amounts if certain milestones are reached.  

Could It Have Been Found With Short Reads?

Initially, the ESHG program was overwhelming.  With the exception of the official opening and closing sessions, every timeslot had multiple parallel sessions - and sometimes those also had competing corporate sessions.  Everything would be recorded and available for playback through November.  That took some pressure off "did I pick the wrong session?", but also is a double-edged sword - I might be attending ESHG for half a year! So I decided that my focus would be rare diseases, and if competing sessions on rare diseases then the one that most focused on genomics technology.  And that led to hearing what amounted to a refrain in the questions at the end of each long read talk: could this causative variant have been found by short reads?

Food For Thought On ONT's Proteomics Push

This year, instead of touring London after the Nanopore confab I headed to Italy for the European Society of Human Genetics meeting.  Upon hearing Lakmal Jayasinghe describe ONT's proteomics plans, I was debating what to do with my pre-LC piece on the peptide sequencing. Perhaps I could ask a restaurant owner in the shadow of the Duomo whether it would go better with risotto Milanese or perhaps as an addition to a minestrone.  But with more thought, while I remain intrigued by ONT's concept, I still think many parts of what I wrote still stand up.

Roche Gives SBX Updates - and a Name!

Last week I double-dipped on conferences, going from London Calling to European Society for Human Genetics (ESHG) in Milan.  I have a raft of notes and ideas from these, which I'll try to spool out over the next week or two before jumping to a long list of more whimsical ideas I've jotted down.   First up are some updates on Roche's SBX sequencing technology, which has now been christened Axelios - which Nava Whiteford reported in his ASeq newsletter.