I have an interesting history with BioNano. I visited their booth at AGBT early in the previous decade when they were a sponsor. We tried using their technology at Warp Drive Bio to solve a difficult assembly problem, but it didn't yield a useful (or correct) answer - nor did their then competitor OpGen. Luckily we soon had PacBio Continuous Long Reads solving that problem reliably.
But the real fireworks came around 2019. BioNano was hurting on the financial side, and I wrote a piece about it looking like curtains for it - a sort of pre-obituary. Now, I did screw up - I had missed a financing event, but they were still limping. What I didn't know at the time is that BioNano had acquired a "Robin Hood" group of stockholders, which had intense passion for the company and did not appreciate anyone suggesting the company was taking on water.
So when 2020 AGBT came around and BioNano was a sponsor, I was a bit thrown off balance by BioNano inviting me to some of their booth talks. Was I walking into an ambush? But the BioNano folks were absolutely wonderful - they truly just wanted me to see their scientific progress. They also lined me up for a late night chat with Alex Hoischen in one of the rooftop parties, and he has always been a strong advocate of the value of BioNano's optical mapping for rare disease work.
When Hastie left a year ago, I saw it as a suggestion that BioNano had hit a scientific plateau. They had successfully survived long enough to get reimbursement codes for both rare disease and oncology indications with their single-molecule DNA mapping to detect cytogenetic anomalies. Perhaps there were no more heights to climb.
I'll be upfront: I thought BioNano was going to get crunched by now. In my crystal ball, Oxford Nanopore was going to eat BioNano's lunch, providing far more data at similar prices. But that certainly hasn't happened - ONT hasn't pursued the same "molecular cytogenetics" market aggressively and BioNano probably still has a technical advantage for oncology due to obtaining much higher effective coverage with even longer molecules
But the space has gotten crowded. Nabsys, which I also once wrote an obituary which got a very passionate push-back comment - and Nabsys really did shut down! But then it rebooted and later had a majority interest purchased by Hitachi. Nabsys' method uses electronic detection rather than optical, but is a very analogous mapping process capable of detecting gross chromosomal abnormalities.
Also horning in on this space is a trio of Hi-C companies - Phase Genomics, Dovetail Genomics (part of Cantata) - and Arima Genomics. Yup, where Hastie had gone. So that definitely looked like a jump to try to catch the next wave. Hi-C can work on formalin-fixed, paraffin embedded (FFPE) material, which despite the headaches it gives for molecular analysis remains the standard for preserving clinical material. BioNano requires high quality, high molecular weight material - which is just not possible with FFPE. Hi-C also means leverage short read sequencers, which are proliferating in clinical pathology labs, rather then requiring a specialized instrument.
Wall Street isn't very keen on BioNano, with a current market cap of only $13M - another molecular tools company in the diagnostic space, Countable Labs, just raised twice that. BioNano has more cash than market cap, which can leave them open to the sort of reverse merger deal that took out Standard Biotools. Though it appears - this is definitely at the limit of my financial analysis skills - BioNano may have some loan obligations that basically account for the difference between market cap and cash-on-hand. These are unsecured loans - BioNano recently retired all their debt tied to assets. But their cash runway is apparently estimated to be only until sometime next year. They have gotten some more lucrative reimbursement codes, so perhaps the runway will be extended. BioNano also has the headache of a stock price just over $1; NASDAQ rules would require a reverse-split if it sinks below a buck.
But it is somewhat surprising that BioNano has remained independent. At $13M, they aren't a large acquisition for someone else in this space, even with a premium atop that. Illumina was sometimes floated in the past (probably not by serious analysts) as an acquirer, to enable BioNano to cover what short reads cannot. But now Illumina has TruPath (nee Constellation), and would hardly want to suggest that TruPath can't solve the same problem space as BioNano (TruPath would be expected to struggle equally with FFPE inputs). PacBio wouldn't make sense either - results increasingly suggest that HiFi genomes only fail to cover about one case - Robertsonian fusions - which BioNano would rescue.
And so that is another threat to BioNano - as long read genomes become more common in rare disease as a first line analysis those are cases that won't go for optical mapping - or maybe a fraction of the PacBio would reflex to optical mapping if no definitive result is detected from the genome.
BioNano also navigated some challenging bad luck - which I had missed since I hadn't been following closely. BioNano released their Stratys system in 2024, which offered superior workflow operations for clinical labs. The prior Saphyr system had relied on flowcell consumables which ran three samples at a time; Stratys replaced this with single sample flowcells. Furthermore, on Stratys there was a hotswap ability to remove finished flowcells and add new ones, and even let priority samples pass ones already loaded but not yet running.
But then they ran into a flowcell manufacturing hiccup. So a financially fragile company successfully launching a new instrument, but then losing potential sales due to supply chain issues outside their control. Early this year the issue was completely resolved, but it must have been a frustrating time for anyone inside the company.
Appointing a new CSO isn't the action of a company just waiting to be bought out or one resigned to just growing within current product bounds. Conversely, Hastie has had a close-up look at a competing technology and decided optical mapping still has legs. It will be interesting to see what new directions Hastie takes BioNano in, even if he must be very efficient in doing so given the financial restrictions of the company.
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