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Bionano Genomics Acquiring BioDiscovery – The Perfect Alignment of the Stars

One of October’s headlines in the field of genomics and genetics  included the acquisition of BioDiscovery by Bionano Genomics. I spoke with Soheil Shams, President, Founder, and CSO of BioDiscovery and now Chief Informatics Officer (CIO) at Bionano Genomics (a 250 person company and growing), about this interesting marriage between a variant analysis company and a genome mapping provider, and the impact of this acquisition on the future of the genomics market and the clinical setting. BioDiscovery, a 30 person company headquartered in El Segundo, suburb of Los Angeles, was founded in 1997.

enlightenbio:  Congratulations on the acquisition of BioDiscovery by Bionano Genomics. This is an interesting marriage between a genome mapping and a clinical analysis solutions company. How do you envision the integration of your NxClinical and Nexus Copy Number solutions with the various capabilities offered within the Bionano Genomics platform?

EB: What can the end user expect from a combined solution?

Soheil Shams: I honestly believe the two companies are the best fit on multiple levels both from a product and strategic perspective. BioDiscovery has been in business for 24 years. It has been fabulously successful in the informatics space for some time, but I would say in the last 15 years our focus has been on structural variants, in particular CNV (Copy Number Variation) and LOH (Loss of Heterozygosity) detection via the means of  microarrays. Over the past six to seven years we heavily focused on our software technology, specifically in sequence data analysis which is our strength. Furthermore, Bionano’s optical genome mapping data does enable structural variant detection and other types of variants, including CNVs that are not easily detectable with the microarray technology or even by NGS.

So, this marriage is quite perfect because these different technologies – the BioDiscovery software NxClinical and the Bionano Genomics’ OGM (Optical Genome Mapping) technology – will get integrated into one platform, the NxClinical platform. No other platform/solution currently on the market which provides variant information based on short read sequencing or microarray data is capable of this deep dive level of variant information detection for difficult to detect variants.

I believe it will be phenomenal for the end user. It will extend the capabilities for our existing discovery researchers, which already use microarray- and NGS-type data, with variant information that is based on OGM data. Basically, they will get additional information from other parts of the genome, which conventional technologies don’t easily deliver.

“We’re going to enable our end users to have a full genomic view of the sample, which is something really unique and something that makes me super excited about this opportunity.”

EB: When you speak about the end user, are we talking discovery researcher, clinical researcher, or anybody in pharma, a clinical lab, or a research laboratory?

SS: We have two separate products that are tailored to specific areas and applications in different markets.

  • Discovery researcher/research organization: Uses our Nexus Copy Number product, which I refer to as the legacy product, for cohort type analyses and big population studies. Nexus Copy Number is a desktop software solution which derives copy number and BAF (B-allele frequency) from a variety of NGS data (WES, WGS, targeted panel, and shallow sequencing) as well as microarray data. We’ll continue to offer this product.
  • Clinical researcher/clinical research lab: Uses our NxClinical product, which has been our main focus over the most recent years. It’s a cytogenetics and molecular genetics solution within one system which provides analysis and interpretation of all genomic variants from microarray and NGS data.

Our initial focus with Bionano Genomics will be on the NxClinical product in support of clinical research and clinical reporting for the research labs. There are clinical labs that utilize our technology under the LDT (Laboratory Developed Test) guidance for research use only. Since clinical laboratories use our technology there is a focus on the clinical side.

EB: When do you envision an integrated product is going to be available?

SS: The interesting part is that we’ve been working with Bionano for the past few years already, and have had discussions and ongoing collaboration that led us to start integrating their data into our software a while back. As time progressed, we accelerated the implementation which eventually triggered us discussing a possible merger/acquisition. We have actually been working on this integration for a while now and made a lot of headway in laying the foundation. Since, as an entrepreneur I’m always optimistic, I expect some initial release will happen in the first quarter of 2022, while a more refined release can be expected sometimes later in 2022, or definitely by the end of 2022.

EB: How big is BioDiscovery and will most employees stay with the company after the acquisition? Will you stay in the same El Segundo site?

SS: BioDiscovery has about 30 employees – full time employees and contractors – of which all will stay with the company. In fact, everybody is super excited about the acquisition. I will take on the role of Chief Informatics Officer (CIO) and we are all staying at the BioDiscovery site in El Segundo for product multiple developments.

EB: So the BioDiscovery team will do the integration of the various solutions into NxClinical, correct?

SS: That’s right. The BioDiscovery team will continue with the integration of the OGM data, the actual genome mapping data, into NxClinical. Bionano, of course, has their own existing software that they’ve been developing and providing with their system. Now with the new relationship we are starting a tighter integration of the Bionano software. While NxClinical is a very platform-independent software tool, it can, of course, work with every genomic platform out there and we will keep it as such. The Bionano software is very specific and unique to the capabilities the Bionano platform is offering, and that is going to be kept by itself. The goal is to have people move effortlessly between the two software products.

EB: How will this integration – via the acquisition – impact the genomics field and specifically the clinical sector and possibly other companies in the space?

SS: We believe we are going to be the only company that’s going to be able to provide a fully integrated solution that takes in different modalities. NxClinical, up to now, has handled various sequence and structural variants including CNVs, LOH, SNVs (Single Nucleotide Variants) and other small variants. These are three modalities that are very important for clinical genomics, but other modalities that are still of importance are methylation as well as large SVs (Structural Variants), like translocations, inversions, and similar things like that. With the OGM technology, we can cover all these various additional structural variations. But we will also enable methylation analysis that comes with other platforms like the Illumina platform.

Back to the end user perspective, I believe the clinical market and the research sector want a single platform that can be used for different multi-omics data (e.g., patient data) that require integration to come up with the best possible answer. As a result of this integration, we will see the field moving forward – we’ve already had customers that took advantage of integrating CNV and sequence variant analysis to solve some unresolved cases. Clearly, combining these various modalities into one solution will enable the field to solve some of the most challenging structural variants.

Figure 1:  A screenshot of the NxClinical data analysis and visualization solution offered by BioDiscovery (Trio example: Dup 22q11.21 (highlighted blue region) inherited from a maternal allele (pink SNP probes in the BAF track).

EB: How would you describe the gain for Bionano Genomics with this acquisition, not just from a platform perspective, but perhaps from a market’s perspective or future vision perspective?

SS: I see two benefits.

  1. Both companies are established companies with extensive recognition in the market, and each with a global customer base, including clinical labs that perform CNV analyses. Our existing bases are very interested in the various types of variant analyses each of our company offers. For BioDiscovery, for example, this opens up the ability to easily provide our customer base access to Bionano data, and it will fit right into the software that they already use. This of course opens up a market for Bionano Genomics, as they will be able to provide their platform to the existing BioDiscovery customer base.
  2. More importantly, the Bionano Genomics platform is very complementary to the short-read sequencing (NGS) technology, like the one offered by Illumina and other vendors. This single fact alone will open up a huge potential market. The combination is, of course, very powerful for the end user, as it allows to cover all the large genomic aberrations that are otherwise not easily detectable.

EB: How do you envision that this union will impact and advance precision medicine?

SS: BioDiscovery over the years has developed a lot of new technology, but what has held us back was essentially access to resources. A lot of the technology we developed focused on cancer. Specifically, we have been focusing on classifying cancers based on CNV profiles. My personal hope is that with the integration of finance we will have a bigger team that will allow us to realize some of these new technologies to enhance precision medicine applications. My background is in AI/machine learning and data mining, going back 30 years. What we truly need to move the field of precision medicine forward are data solutions that help generate insights from large data from different data sources. Not wanting to repeat myself too often but integrating structural variant data from our two platforms will result in better disease classification and therefore better disease prognosis, particularly in cancer.

Figure 2: The Bionano Genomics Optical Genome Mapping workflow from mega-base size DNA to automatically detected, genome wide, structural variants using the Saphyr® Genome Imaging Instrument (Source is the Bionano Genomics website).

EB: How do you think the market/industry sector will change? Are there any speculations in terms of major collaborations or acquisitions we will see in the near or far future that may potentially compete with your new combined offering?

SS: We at BioDiscovery have had a great and close collaboration going on with Illumina  over the past year. We designed a new cytogenetic microarray with Illumina, which is just about to be marketed more actively. This is the first new cytogenetic microarray on the market in at least ten years. It has a lot of significant advantages over the legacy products. Bionano, is completely open and interested to continue expanding this market because the BioDiscovery/Illumina relationship is complementary to what they are doing and it expands both microarray and NGS applications. This, of course, will also result in a strong glue between Bionano and Illumina. This strong, collaborative partnership will be of benefit to the entire community.

“It will be interesting to see how long-read sequencing will evolve, as in my eyes that can be considered the competition to genome mapping Bionano Genomics is offering.”

EB: Any thoughts on how COVID-19 will shape the future of product development or impact advancements and adoption of these technologies in precision medicine? How will this impact healthcare in general, and how does it impact what you are doing?

SS: Many companies got active and developed a solution for COVID-19 as we were in dire need of a diagnostic solution. They pivoted and profited. We didn’t really change our focus. Our focus has always been on oncology and rare genetic diseases and this has not changed much. At this moment I can’t really speak to what Bionano Genomics’ vision is in this regard.

Unfortunately, COVID-19 moved a lot of resources away from genetic testing in the area of rare diseases and even cancer. A lot of the resources got shuffled around. As such it had a negative effect on healthcare in general. I’m hoping it’s transitory and it’ll get back if COVID really becomes what I think it probably will be, something like a flu that will come and go seasonally, can be managed via vaccination or therapeutically, and hopefully will not have a much bigger impact than that in a year or so from now.

EB: The integration of clinical genomics data with other clinical patient data has been notoriously slow. How do you tackle that issue, if at all, and when can we expect full integration and adoption of genomics in the clinic? Where do you think these leading developments will take place?

SS: As a software company, we don’t generate data. Customers that use the Bionano Saphyr System, or any Illumina sequencing system do generate that kind of data. We help process the data, but for the data to be of maximum utility, you want to have additional patient information. You want to be able to study the data for research and translational research purposes. To achieve this, we need the integration of unique data, for example data generated via the Saphyr system or genetic testing data within a healthcare system. So far this has not been a focus of ours, because our interest is mostly on the genomic side. And I know there are other companies that are focusing more on the data side. This includes companies like Philips Precision Medicine or IBM (IBM Watson). However, these systems are still pretty early in the development process. Certainly, companies like Roche and Philips will be able to bring various data components together, including genomic data with patient management health records data. I believe we are probably about a decade away to really fully benefit from such a system.

EB: Do I see this right: for now you focus on the workflow component that produces data and insights? You are not going beyond that which includes the integration of the generated data into an EHR system?

SS: Right, that’s not a focus of ours. Our solutions focus on interrogating genomics data, e.g., genomics data of postnatal, childhood data with a certain phenotype. We help identify pathogenic genomic variants that are communicated via a generated report to the clinician. But that’s a single data point. Some of these will be unresolved and what really needs to happen is that information should stay in the patient’s medical record for future reference or future population type data aggregation and analysis.

EB: NxClinical’s output is a report, correct? A report used for clinical-decision purpose?

SS: Well, yes and no. The report that is generated via the software is a clinical report, but usually the end user takes that report and integrates it into a LIMS system that is part of a laboratory/healthcare system. One of the benefits for us: no privacy information is ever in our systems – something we don’t really want to deal with. Our report gets integrated into their internal system which integrates it into the “final report” used by the clinician and potentially shared with the patient. Different organizations have slightly different approaches, but in general this is the process. 

EB: When you think about the biggest challenges to overcome for genomics applications to be a routine in the clinic and to make them broadly accepted across medical organizations, what are they?

SS: We had a very close family member diagnosed with stage two colorectal cancer. The practicing oncologist was great but did not utilize all the genomic resources for decision-making to provide potentially better care, and this in a metropolitan city like Los Angeles. I am a strong believer that we need to educate healthcare providers and medical professionals of the advantages and the possibilities that genomics can bring to the table. Unfortunately, most clinicians are too busy doing their daily work to really be keeping up with all of the possibilities available to them. So, number one would be to just better educate our medical professionals on capabilities and continuous improvements of the guidelines, because most practitioners of course follow established guidelines. Some of these guidelines need to be frequently updated as we better understand the value of genomics and RWE (Real-World Evidence) for decision-making. That’s my personal opinion. In this particular family member case, I took it on myself to educate the physician on the possibilities available to apply genomics as part of the diagnosis and treatment decision.

Though unfortunately, it’s been even more frustrating to identify labs that could perform the types of clinical testing required. For example, from a cancer perspective, most of the common tests are looking only at a subset of genes. Most of them don’t look at CNVs because they don’t know what to do with that kind of information. Clearly, we still need to do a lot in the clinical sector.

It’s also important to move this process forward faster. We are dealing with real patients that don’t have a lot of time. We got to do more at a much faster rate. And that’s what I’m dedicated to do. I want to get this technology to the point that you can help people faster. There’s a lot of useful information that’s not being used right now.

EB: How about the challenges in the whole reimbursement sector? Especially with this new technology that you have, you have to present value and value in general is hard to show or being accepted by some of these providers.

SS: Absolutely right! Reimbursement is a very important area and getting these bodies to recognize that these new technologies are of value is a huge challenge. While it’s important to me, I’m not actively involved in this area. I know other people are doing a good job pushing it forward, though it does need to move faster.

EB: Let’s talk a minute or two about your new role as CIO (Chief Informatics Officer) at Bionano Genomics. What are some of the exciting aspects of this new role and what will your focus be?

SS: It’s a unique position. For the past 24 years I’ve been the CEO, President, and CSO of BioDiscovery. So, I’ve been wearing many different hats, being responsible and overseeing sales and marketing activity development, and all this while running the company. The exciting part with this new role is to focus on one area, which I really enjoy much more. I will be focusing on the informatics part with the goal of creating novel and useful products.  That’s what really excites me about this new position. I will spend my time focusing on and creating great new products.

“I’m so happy about this marriage with Bionano because I feel like it’s this perfect alignment of the stars. It couldn’t have been a better fit as far as what our capabilities are and what they do. I think it will have a very substantial impact on pushing forward the genomic medicine field, which is ultimately why I started down this path 25 years ago.”

Brigitte Ganter


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