Saturday, November 14, 2020

Bionano Genomics: A Belated Update

Back before I can remember -- as in January of this year -- I wrote a piece on the challenging situation of BioNano Genomics.  I got an important detail wrong in that piece, missing some important fundraising, but in general from the point-of-view I took I thought it was a decent piece, meant to convey the challenge of a really amazing technology having its original market disappear.  Some commenters took strong exception to the piece and suggested I had not-so-pure motives for writing it.  They're wrong -- but at AGBT I got a chance to learn more about the company's new direction and how I hadn't been looking at things quite appropriately.  I should have written it up there, but working on a response to the pandemic started taking over my life and I let time slip away.  Preparing crow to be eaten also tends to be procrastinated.  But here, finally, is a re-look at the company (and, I drafted this over a month ago and never finished -- the procrastination drags on...)

I was a bit nervous strolling into the BioNano Genomics booth at Marco Island.  Maybe they were the ones so offended by the piece.  But no, they actually invited me to come to a morning talk and to chat afterwards, and were completely professional and cordial and made it clear they understood the angle I had taken as a sincere journalistic approach.  But not only did I hear the talk then, but I had gotten a preview the night before in the Twist Suite, which also illustrates a key card BioNano has: a collaboration with Alexander Hoischen

Alex is truly a triple threat as a collaborator.  First and foremost he is an accomplished genomics scientist who knows his way around cutting edge tools in the clinic; he's previously talked about work with Pacific Biosciences.  Second, he's practical: he has very real needs to be able to deliver clinical assays that can be used because they are actually reimbursed at an appropriate level.  No pie-in-the-sky from him, and it's clear that EU reimbursement rates can be quite tight.  Third, he's a really nice guy, truly someone enjoyable to chat with over drinks.  So the perfect ambassador for any company lucky enough to line him up.

What Alex told me over loud music at Twist's nighttime gala, and then told a crowd the next day in the BioNano suite, is the power and versatility of BioNano's Saphyr system for clinical cytogenetics and how it has real potential to take over from both traditional microscopy methods and the newer microarray methods.  New, very simple and relatively quick sample prep methods have replaced the old multi-day agarose embedding to extract the extremely high molecular weight material required.  The amount of data per chip has been trending upwards, which is important since that ultimately determines the resolution of the map.  

Microarrays have made great inroads into medical cytogenetics for measuring imbalances, but they can't read balanced translocations.  Several people told me that traditional microscopy based cytogenetics is a field viewed by too many students as undesirable, so it looks increasingly harder to fill positions.  BioNano potentially requires far less advanced skill -- and attention to difficult images.  Back at Infinity we were working with the EML4-ALK fusion, which is a balanced inversion -- so not seen by microarrays and worse the split-FISH assay for it was dealing with two things that are not much different in linear separation with or without the inversion -- 12 megabases on linear space and of course the chromosomes are never perfectly stretched out.

It sounds like medical cytogenetics is a promising space for BioNano to expand into, particularly since my prediction that it would be crowded out of the research de novo genomics space is proving true: the recent astounding announcements from the Telomere-to-Telomere (T2T) Consortium of nearly truly finishing the human genome relied on PacBio HiFi and Oxford Nanopore.  Of course, success by BioNano is likely to encourage other entrants, either HiC companies or quite likely Oxford Nanopore or someone using that technology -- indeed, Phase Genomics is already moving this direction.  To hold a lead, BioNano must concentrate on the entire user experience so that their first mover advantage really sticks .

In my last piece, on 10X Genomics, I commented how their rocketing stock price gave them capital for an aggressive acquisition strategy.  BioNano unfortunately remains at the other end of the stock spectrum, trading for about fifty cents a share and a total market cap around $70M.  So BioNano must fight for their market position without having a lot of resources to do so.  That doesn't mean they can't do it, just that execution must be very focused and some luck needs to break their way.  So my best wishes to them, as they appear to be delivering real value for medical providers and patients.

1 comment:

Steve Huang said...

As someone who recently looked into Bionano data for a clinical research sample, I think one feature is that while the format is open, the pipeline is quite opaque (trying to set up the visualization software itself was already a hassle). In fact the only pipeline I know that is not from the vendor is OMTools. Hopefully the T2T consortium helps people become more interested in this promising tech.