Greetings, and welcome to the Bionano Genomics, Inc. second quarter 2020 conference call. At this time, all participants are on a listen-only mode. A question and answer session will follow the formal presentation. If you would like to ask a question, please press star one on your telephone keypad. If anyone should require operator assistance during the conference, please press star zero on your telephone keypad. As a reminder, this conference is being recorded. It is now my pleasure to introduce your host, Ashley Robinson of LifeSci Advisors. Thank you. Please go ahead.
Thank you, Donna. Good afternoon, everyone. Welcome to the Bionano Genomics second quarter financial results conference call. Leading the call today will be Dr. Erik Holmlin, Chief Executive Officer of Bionano. After market close today, Bionano issued a press release announcing its financial results for the second quarter of 2020. A copy of the release can be found on the investor relations page of the company's website. Before we begin, I would like to remind everyone that certain statements made during this conference call may be forward-looking, including statements about our strategic and commercialization plans, 2020 sales pipeline, anticipated benefits or improvements to the Saphyr system, and the advantages of the Saphyr system over current technologies, our expectations regarding timing and content of study results, and anticipated benefits of these studies in driving adoption of the Saphyr system.
Such forward-looking statements are based upon current expectations, and there can be no assurances that these results contemplated in these statements will be realized. Actual results may differ materially from such statements due to a number of factors and risks, some of which are identified in our press release and our other reports filed with the SEC. These forward-looking statements are based on information available to Bionano today, and the company assumes no obligation to update statements as circumstances change. An audio recording and webcast replay for today's conference call will also be available online in the investor section of the company's website. For the benefit of those who may be listening to the replay or archived webcast, this call was held and recorded on August 13th, 2020. With that, I will turn the call over to Erik Holmlin. Erik?
Well, thank you, Ashley. Good afternoon, everyone. I want to thank you for joining us today for this review of our second quarter results. After my prepared remarks, we'll open the call for a Q&A session. I just want to say at the outset that we are really amazed and thrilled at the progress we see around the globe, in connection with the adoption of Saphyr and its use for really groundbreaking work across genomics. What we're seeing are papers published recently that are showing how Bionano can be a part of creating solutions such as potential treatments and vaccines for COVID-19, possibly even tests used to manage the disease of patients with COVID-19. All of this progress is happening amongst incredible advances that we're making in driving Saphyr to become the potential new standard in cytogenetic analysis for oncology and genetic diseases.
In the business, we are seeing an enthusiastic response to the new go-to-market strategy that we implemented earlier this year. Our goal has been to make it easier than ever for clinicians and researchers to access Bionano data in a way that's going to enhance their understanding and utility of our Saphyr technology. We see that we are gaining traction with significant increases in services projects, consumable sales, and reagent rental programs and system sales that, taken together, really grow the installed base of Saphyr systems around the world. We are seeing increasing interest in the academic community amongst researchers who are continuing to publish really groundbreaking research and findings that show using our system will advance their understanding of genomics.
We are also seeing publications now that illustrate the acceptance of Saphyr by clinical researchers who are developing assays for cytogenetics, including in areas such as genetic diseases and hematology oncology. In fact, two very powerful papers were published in "Nature" journals this quarter, and they highlight how Saphyr is important in cutting-edge research. One paper documented the largest study of a genetic disorder using our technology to date. In this study, researchers used Saphyr genome imaging technology to establish one of the largest and most structurally accurate data sets of genome analysis for a cohort of affected children and their parents in a study of DiGeorge syndrome, which is the most common disease amongst a class of genetic diseases called microdeletion syndrome. I can't emphasize enough how incredibly complex this region of the human genome is.
To be able to reach the level of resolution that the researchers did in their work is really groundbreaking, and that ability to resolve such complex regions of the human genome has implications across all areas of genome research and the clinical applications of genomics, including understanding the genome variants that drive diseases. These results can all potentially play central roles in the development of new medicines and diagnostic tests. The other paper that was noteworthy in Nature this quarter was one that was particularly topical. It highlights how Bionano data, combined with other analysis methods, can help find vaccines, treatments, and diagnostic tests for COVID-19. This work is related to how researchers use Bionano's genome imaging technology to build what we call a reference quality genome. In this case, the application of that work was on bat species, actually six different bat species.
Of course, the bat is remarkably timely, and the work has been ongoing, but its implication is remarkably significant now because it can help explain the ability that bats have to tolerate viral infections. It may play a role in understanding how there can be a transmission of viral disease from bat species to humans, and even potentially lead to other areas of development of new vaccines and treatments. A significant shift in our go-to-market strategy has been toward a reagent rental program. The uptake of this model continues to increase in all geographies, and new sites which were previously inaccessible with our instrument sale-only model are now adopting Saphyr through this reagent rental program, and they are making large consumable commitments.
We have announced some of these key adoptions already with the National Health Service in the U.K., Medical College of Wisconsin, University of Iowa, South Korea, Yonsei University Hospital, among several others. These are all adopting and installing our Saphyr system for the digital cytogenetic applications. Turning to our second quarter commercial results, the revenues were $1.2 million for the quarter, which were weaker than the same period of last year of $2.2 million. That's mainly due to the impact of COVID, which has continued to impact many states and businesses, including our current and potential customers. Nevertheless, this level of performance was consistent with our expectations going into the quarter, we see that as a significant accomplishment under the circumstances.
While many regions of the U.S. remain nearly shut down or operating at a significantly lower pace than normal, we have seen a significant recovery of our business in Europe. During this third quarter, we believe that the worst of the impact of the pandemic may be behind us. Now, the number of Saphyr systems that were shipped to customers continues to be significant. Six Saphyr were shipped this quarter, one of which was a straight instrument sale, and five were reagent rental commitments. In the second quarter of last year, eight systems were sold. Considering the pressure of the pandemic, especially in the second quarter, where the effects were felt most dramatically, the expansion of the number of Saphyr adopted is extremely positive.
Since the commercial launch of Saphyr in February 2017 through the end of the second quarter of 2020, there were a total of 87 Saphyr systems that had been installed, and there are 19 that were awaiting installation as of the end of the second quarter. Now, as we discussed on our first quarter call, we have added a commercial services component to our product offering. We have done so as a way to serve customers who are either unable to operate Saphyr already in their lab or unable to adopt a Saphyr for any reason. In a favorable response from the market, we have seen tremendous uptake of our services program. We spoke about this quite a bit a few weeks ago when we were on discussing the first quarter results.
So far, on a year-to-date basis, we have run nearly 500 samples, 493 samples year-to-date. What's important about that is when we compare it to the same period last year, we had run just 212 samples. The response or increase in service projects and samples that we're processing really reflects an increasing awareness and acceptance of our data type and its benefits, and we believe that offering the community this services option will increase that data in the field even more and serve as a basis of continuous education of the market as to the power of Saphyr and Bionano data. Consumables sold on a per sample basis were up 189% in the second quarter of 2020 compared to the second quarter of 2019.
In this quarter, chip sales resulted in the sale of 1,421 flow cells, and that's a per sample equivalent, and that's compared to just 490 flow cells sold in the same period last year. Our focus on driving Saphyr adoption through sales of consumables in the form of reagent rental programs and our focus on driving utilization in the growing installed base is clearly working. The consumables business is expected to be more profitable over time, and it is anticipated to be the primary driver of our business. We believe that this large increase in data generated on Saphyr systems will yield wider and wider visibility of our capabilities and drive acceptance of our data type and its value. These are exciting results, and we're very pleased with them, and we believe that it reflects significant momentum even in a relatively tough quarter around the world.
As for the breakdown of these revenues, the $1.2 million were comprised of $229,000 in instrument sales, $711,000 in consumable sales, and $242,000 in services and other. The cost of revenues for the quarter was $603,000, which reflects a 49% gross margin for the second quarter of 2020. That can be compared to a cost of sales of $1.6 million or a 28% gross margin for the same period a year ago. This increase in gross margin is notable, and it really reflects a shift toward the increase in consumables as part of our overall product mix. That is really by design. More consumables brings in more gross margin for the company, and it brings more Bionano data into the field.
Our work in supporting COVID research has also deepened this quarter as the search for a solution to the virus continues on a global basis. Bionano's Saphyr system is capable of providing solutions that researchers are facing when a virus elicits different responses to patients who otherwise have similar risk profiles. We believe that analyzing the structural variation of the genome can help lead researchers and investigators to solve these challenges. We believe the Saphyr system, which is being utilized as a part of several major initiatives around the globe, will lead the way in structural variation analysis. Now, something I want to mention in particular, and it's something that we've announced to the field and we're very proud of and extremely excited to be a part of, and that is the COVID-19 Host Genome Structural Variation Consortium, which was started by Dr. Ravi Kolhe at Augusta University.
The stated mission of this consortium is to look for the structural variations in or near genes that play a role in infection, as well as the genes connected to the immune response, among many other factors of the host response. The hope is to explain the variation we see in disease severity and progression. This project is getting underway. There have been about 30 samples run to date, but the goal is to map 1,000 genomes on Saphyr systems in sites around the world. Preliminary results have yielded some promising insights, but we all recognize there's still very much to be learned, and progress continues.
The consortium has been growing and includes more than 50 participating institutions, they have joined forces with the consortium in Germany at the University of Hannover, there's a truly global team coming together here in investigating structural variation's role in the host response to COVID-19. In addition to that important consortium, we have a significant research project underway in China, we've talked about that recently as well. While that was the first project that we had actually set up and established, access and ability to process samples was something that was tightly controlled in China, we have continued to work through the logistics. That study at GrandOmics, which is a Bionano Genomics service provider in Wuhan, has expanded.
It now includes another center in Shanghai, and we are now processing the initial samples there, and that research program continues to go at a much quicker pace than originally, after it was first formed. And know the urgency to find a solution has led to this incredible rise in testing and response globally. We feel honored to be a part of these programs, but I would also note that they are making contributions to the health of the business. While many researchers have seen their projects have to be put on hold as focuses on COVID-19 testing have taken over, COVID-19 research, especially in regard to the host response, is now something that is picking up, and so hopefully it can fill a gap that has formed there.
I want to turn the page and now begin to look at the various activities that are ongoing, designed to validate Saphyr as a replacement for traditional cytogenetic and genetic disease testing. Remember, Saphyr offers the opportunity to consolidate three and even four traditional methods into a single assay running on our platform. Those assays are karyotyping, fluorescence in situ hybridization, chromosomal microarrays, and Southern blot analysis. We have seen multiple presentations at scientific conferences over the course of this whole year, and it has continued even into the challenging second quarter. Those conferences include the European Society of Human Genetics, the Cancer Genomics Consortium, and others.
Those presentations that have been made, including the webinars and so forth, that have been out there, have been demonstrating that Saphyr is 100% concordant when it's compared to its ability to find the clinically relevant structural variations that standard cytogenetic methods find. This concordance is so important because it gives confidence to cytogenetics laboratories who are seeking to streamline their workflows and replace those traditional methods with a much more digital approach that Saphyr offers, and streamlined, and faster. This concordance gives them confidence to do that. A European consortium led by Laïla El Khattabi from the Cochin Hospital in Paris, France, and Alexander Hoischen, who we've spoken about in the past, who's at the Radboud University Medical Center in the Netherlands, published data from the first very extensive validation of Saphyr for constitutional genetic disorders.
They, too, along with studies that have been done and published in hematology oncology, this study was the first publication showing the 100% concordance with standard cytogenetics in constitutional genetic disorders. When you think of Saphyr adoption throughout the cytogenetic community, we're now seeing the validation in hematology oncology, which is a significant market, and that is being extended to constitutional genetic disorders. This progress is really remarkably significant, and these papers even describe the resolution of clinical cases of long-standing, otherwise undiagnosed diseases. This is really important because we all know that the standard of care of testing is fairly antiquated, relatively cumbersome to practice, so Saphyr streamlines that. It not only streamlines it, Saphyr is better because it allows for the resolution of diseases that would not typically be picked up and diagnosed using those traditional methods.
This is happening in leukemia, where we are finding novel fusion proteins, these novel fusion events that could lead to fusion protein expression, which could be druggable targets. We are seeing this in other areas of genetic diseases as well. The impact of these results on our business moving forward really should not be overlooked. Our own internal data has long convinced us that Saphyr cannot just replace, but it can improve upon the three major cytogenetic testing methods. These published and publicly presented results now show that we have an independent clinical validation of Saphyr, and it is beginning to build this critical mass of evidence in cytogenetic communities in Europe and in North America, where we are expecting a publication imminently following a great presentation from the Columbia team recently on their study.
We are really witnessing what we believe to be a pretty sudden change in the perception of Saphyr as a tool for cytogenetic analysis. What we're seeing is adoption by Saphyr in what we consider to be very short period of time relative to our typical sales cycle, and that's just a reflection of the increase in validation and increase in acceptance. The decisions are now being made based on more and more on the published results, and they don't require us to run demo studies as much internally. This is really a reflection of that increasing acceptance of the technology. What we're hopeful for is that translates into a ever improvement in the decrease and shortening of our sales cycle. I want to mention a few other key financial metrics.
For example, in the second quarter, operating expenses had increased by about $550,000- $8 million, compared to $7.5 million last year. Folks should remember that we have had a fairly significant increase in sales and marketing as we have really increased our focus on driving the adoption of Saphyr, as well as the support teams that are required to assist them in this growth. This is a relatively modest increase in expenses because it has been offset by salary reductions that we implemented temporarily starting in April of 2020, as well as a decrease in discretionary spending and other costs. As of June 30th, our cash was $17.2 million, and as noted in our save the date press release, since the end of the second quarter through August 12th, we have received about $14 million in cash pursuant to warrant exercises.
We believe that our current cash and cash equivalents are sufficient to fund the company's operations well into the first quarter of 2021. If you're following our filings today, you will see that we have filed a universal shelf registration statement on Form S-3, and that it includes an at-the-market sales prospectus. These filings should not be interpreted as a reflection of any imminent financing. We believe that it's prudent and good corporate practice to have our house in order and to be in a position to raise financing when the need arises. In closing, I would say that we are extremely encouraged by the results that we are seeing. Q2 has been a difficult quarter around the globe in our business, in another business, and despite those challenges, our teams have been incredibly focused on driving the company forward.
Our customers have been very responsive to our focus on getting the message out about Bionano and have supported us in a number of online venues to create awareness and understanding of our data type. These events have been attended by record numbers of participants, and these are all in connection to our efforts to establish Saphyr as a potential new standard in cytogenetic testing. We believe that this will lead to Saphyr replacing traditional genome analysis methods and ushering in really a new era of broad, accessible, reliable structural variation analysis that can create new drug targets leading to new medicines, new diagnostic biomarker signatures, leading to new pathways for patient management, as well as a complete understanding, throughout nature, including such important projects like the Bat Genome Assembly Project, as well as the first telomere to telomere assembly of the X chromosome.
With that, I would like to open up the call for Q&A. Operator?
Thank you. The floor is now open for questions. If you would like to ask a question, please press star one on your telephone keypad at this time. A confirmation tone will indicate your line is in the question queue. You may press star two if you would like to remove your question from the queue. For participants using speaker equipment, it may be necessary to pick up your handset before pressing star keys. Once again, that's star one to register questions at this time. Our first question is coming from Kevin DeGeeter of Oppenheimer. Please go ahead.
Hey, guys. Thanks. Just had a question. Erik, appreciate the really thorough update. A few things. Appreciate the disclosure with regard to flow cells. I think you said about 1,200 in the quarter. Is that still overwhelmingly research, or are you beginning to see some pull-through from cytogenetics customers? I suppose a related question is, do you always have kind of visibility as to whether or not a customer is using this for sort of a research project versus cytogenetics at this point?
Yeah. We have pretty good visibility because we're engaged in the selling process, and so there's a pretty deep discussion as to the applications. I would underscore for everybody following along, and for you, that the Saphyr is for research use only and not for diagnostic purposes. Labs will develop it and develop clinical diagnostic assays on it, which they offer as laboratory-developed tests, or in accordance with whatever their regional regulatory requirements are, such as throughout Europe. When a customer intends to develop clinical assays on the system, we're generally aware of that. What I will tell you is that at least half of the flow cells, and I think it was about 1,400 or so flow cells that were sold in the quarter, at least half of those are going to sites that are developing assays that they intend to apply in a clinical setting.
Many of those assay development projects and adoptions are through the reagent rental program, which is sort of predicated on a volume of chips up front. At least half are going towards these assay development projects.
No, that's very positive. It's good to hear. If you were to kind of characterize uptake for some of this use potentially in a clinical setting, in Europe versus U.S., are you seeing any geographic variation in terms of uptake for applications, outside of the traditional research market?
Well, we do, and it would be difficult to disentangle the remarkably complex sort of macro environment that we're in right now. The facts are that Europe is really accelerated in its adoption of Saphyr for these types of cytogenetic-oriented applications. One would need to disentangle whether that's a reflection only of Europe's relatively progressive state regarding an exit from pandemic shutdown versus that here in the United States, or is it something structural about the European health economic system? I think both of those things are playing a role here, and it will take some time for it to play out. The facts are that Europe is really doing incredibly well and showing really leadership, at least in our company, around adopting this cutting-edge technology.
Great. Maybe one last one for me, then I'll get back in the queue. That is, the service revenue, you did see what looks like a nice sequential uptick, which I think is consistent with what some of us hoped we would see with the new commercial model. If we think about that $240,000, give or take, revenue, is that a base that we should think about as continuing to grow through the balance of the year? Were there specific service contracts, perhaps large, more one-off contracts in 2Q that may not make that representative of a trend in service revenue?
No, I believe that this is a reflection of what to expect overall. Within that services and other revenue, I would note that there are some other things, such as revenues tied to warranty, and service warranty, service contract. I do believe that that's not dominated by any single event.
Great. Listen, thanks for taking my questions. It was actually a pretty nice quarter. Thank you.
Thank you.
Ladies and gentlemen, that is star one if you have additional questions. Kevin, we are coming back to you for any additional questions that you have.
Okay. I actually just had maybe one more, and it's sort of largely a housekeeping item, and that's, as you think about, you've really cleaned up the capital structure here. It looks like, in fact, you've converted over half of the warrants that were outstanding. With a little bit more balance sheet flexibility, are there certain COVID-related spending cuts that you mentioned, salary reductions, other items that may look to reverse here in the nearer term? Should we think about the operating expense structure as reported in 2Q as being the baseline for the balance of the year?
Well, we have reversed out the salary reductions. That's certainly a portion of the relative benefit. Even though we were up on a YoY basis, we might've been up more if the salary reductions weren't in place. We have reversed those out, but fairly limited travel and expense costs overall, and laboratory work and headquarters is focused primarily on those services projects. We're able to do some product development, but it's not as much as we would have been doing a year ago. Some discretionary spending remains relatively down on a YoY basis. It's probably somewhere in between.
Just lastly from me, you did mention upcoming publication from a very visible consortium that I think many folks, particularly in the U.S., view as thought leaders in the cytogenetics space. My question is for potential U.S. cytogenetics-related business. Do you think that publication is important to drive potential customer engagement, or is there a sense from the data that's been presented at a number of meetings, actually, over the last 6-12 months that Saphyr works and that for cytogenetics and publication sort of validating that it works may not be as important in driving uptake or use decisions?
Well, I would say that we are certainly buoyed by the results that are coming from these studies and publications in Europe. We have had, for example, the Columbia-led study has been presented, and we've been able to share those results. They were phenomenal results, 100% concordance in that study. The publication is proximal, and as you know, with publications, they get on timelines that are fairly unpredictable, but there's no reason for the delay other than publications are on a unpredictable timeline. The results are very positive. We're buoyed by the study that are in Europe. I will say that because of overall differences in just the structure of approaching clinical testing workflows, studies conducted in and published out of U.S.-based laboratories are also going to be needed and very important and play a significant role. It won't be just one.
There are several that are ongoing, and one is great, but there needs to be a critical mass, and so that's really something that we're deeply focused on.
Very well. Thanks for taking all my questions.
Yeah, you're welcome.
Thank you. Our next question is coming from Jason McCarthy of Maxim Group. Please go ahead.
Hey, everyone, thanks for taking my question. It's Dave on the line for Jason. Just looking beyond COVID-19, given the fact that tumor heterogeneity plays a substantial impediment to therapy in many cancer indications, do you see the Saphyr platform playing more of an increasingly central role in drug research? Do you see this becoming an increasingly larger revenue stream?
Yes, I believe that our ability to see adoption by drug-developing firms such as pharmaceutical companies, biotech companies, and the partners that serve them, CROs, for example, we expect that to improve. There have been improvements and enhancements in our product portfolio that will help drive that, including the release of a solid tissue DNA isolation kit, because that can be directed to solid tumor research. Our product portfolio is rounding out there. When you couple that with Saphyr's remarkable ability to see the pathogenic events, even if they're present in extremely low abundance, it means we have a very powerful system and data type to uncover novel events that may be druggable targets.
It is our expectation that pharma research, initially in a basic research setting, but eventually as part of clinical trial enrollment and other forms of patient testing, will continue to be something that is a significant opportunity for us.
Great. Thanks for the additional clarity.
Thank you. This brings us to the end of our question-and-answer session. I would like to turn the floor back over to Mr. Holmlin for closing comments.
Thank you very much, operator. I want to thank everybody who has joined the call, and I wish you all the very best. We're excited about the future of Saphyr and our progress within Bionano. Thank you very much.
Ladies and gentlemen, thank you for your participation. This does conclude today's teleconference. You may disconnect your lines or log off the webcast at this time, and have a wonderful day.