COVID-19 Host Genome SV Consortium Identifies Structural Variants with Possible Roles in Pathogenesis and Outcomes in Severely Ill COVID-19 Patients Using Bionano’s Saphyr® System

First publication from international consortium highlights prowess of Saphyr in identifying large SVs with clinical significance and in COVID-19, an area with great public health implications

SAN DIEGO, Jan. 11, 2021 (GLOBE NEWSWIRE) — Bionano Genomics, Inc. (Nasdaq: BNGO), announced today the first publication from the COVID-19 Host Genome Structural Variant Consortium. The study found that optical genome mapping (OGM) with Bionano’s Saphyr System identified structural variants (SVs) that affect genes in pathways that control immune and inflammatory response, viral reproduction and mucosal function. The authors believe these SVs may provide key insights into the pathogenesis of COVID-19 and outcomes in patients who become severely ill.

The consortium was formed by Dr. Ravindra Kolhe from Augusta University with the goal of identifying large SVs that factor into the clinical course and outcomes of patients who contract COVID-19. Unlike other analyses of the host genome which are usually limited to genome-wide association studies or exome/genome sequencing and aim to detect single basepair changes, the consortium focuses on finding larger variants in patients’ genomes because they are believed to have a greater potential to impact genes. The consortium has selected OGM with the Saphyr System for genome analysis owing to Saphyr’s documented performance as the leading platform for detecting these large SVs. The current study received contributions from scientists at Augusta University, the University of California San Diego, Radboud University Medical Center, The Rockefeller University, University of Texas M.D. Anderson Cancer Center, Columbia University Medical Center, Virginia Commonwealth University, New York Genome Center, Harvard Medical School, and Bionano Genomics.

The study reports the analysis of the genomes of 37 patients who were admitted to the ICU at Augusta University with severe COVID-19 disease. 30 patients needed mechanical ventilation with a mean intubation duration of 12 days. Of the 37 patients, 25 recovered and 12 died. The SVs revealed by Saphyr were confirmed with other technologies such as quantitative PCR.

One of the most compelling findings among the SVs identified was the duplication of the STK26 gene, a key element of the Toll-Like Receptor signaling pathway which controls the cell’s response to viral infection. In the follow-on analysis of the expression of the STK26 gene in patients with the duplication, the study found significant upregulation of STK26 in all severely ill patients tested but not in asymptomatic COVID-19 patients, implying the duplication to be a potential novel, prognostic biomarker for the severe immune response seen in severely ill patients.

Ravindra Kolhe, MD, PhD, senior author of the study commented: “As director of a high-volume testing lab at Augusta University for COVID-19 I’ve seen first-hand the pain and devastation this virus can cause in those who get severely ill. The majority of the ICUs across the country are filled with patients fighting for their lives, yet we did not know why some become so severely ill while the same virus causes only mild symptoms in most. Our study shows clearly that many of the severely affected patients carry genetic variants that may cause or at least contribute to the severity of their disease by weakening the effectiveness of the immune response, increasing viral replication, or making it easier for the virus to spread between cells in the body. Importantly, the large genomic variants detected by optical genome mapping in this study are typically missed by the short-read sequencing or SNP-based methods used in other studies, which explains why previous studies haven’t made the same impact.”

Erik Holmlin, PhD, CEO of Bionano Genomics, commented: “The COVID-19 pandemic continues without signs of slowing down. This study demonstrates that the wide variation in symptoms exhibited by patients is likely not random for most of them, but instead, at least partially, the result of SVs affecting critical pathways in patients’ defenses against infection and immune responses to the disease. The results also demonstrate that even when a disease has already been studied extensively with sequencing, OGM with Saphyr has the potential to reveal significant insights not seen without it. While we are devastated by the loss of lives caused by this global pandemic, we are grateful that our genome analysis platform can contribute to a better understanding of the disease and possibly help save lives.”

These results will be presented by the authors at Bionano’s Next-Generation Cytogenomics Symposium on January 15, register here: http://bit.ly/3pLPT28

The publication is available at: https://www.medrxiv.org/content/10.1101/2021.01.05.21249190v1

About Bionano Genomics
Bionano is a genome analysis company providing tools and services based on its Saphyr system to scientists and clinicians conducting genetic research and patient testing, and providing diagnostic testing for those with autism spectrum disorder (ASD) and other neurodevelopmental disabilities through its Lineagen business. Bionano’s Saphyr system is a platform for ultra-sensitive and ultra-specific structural variation detection that enables researchers and clinicians to accelerate the search for new diagnostics and therapeutic targets and to streamline the study of changes in chromosomes, which is known as cytogenetics. The Saphyr system is comprised of an instrument, chip consumables, reagents and a suite of data analysis tools, and genome analysis services to provide access to data generated by the Saphyr system for researchers who prefer not to adopt the Saphyr system in their labs. Lineagen has been providing genetic testing services to families and their healthcare providers for over nine years and has performed over 65,000 tests for those with neurodevelopmental concerns. For more information, visit www.bionanogenomics.com or www.lineagen.com.

Forward-Looking Statements
This press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Words such as “may,” “will,” “expect,” “plan,” “anticipate,” “estimate,” “intend” and similar expressions (as well as other words or expressions referencing future events, conditions or circumstances) convey uncertainty of future events or outcomes and are intended to identify these forward-looking statements. Forward-looking statements include statements regarding our intentions, beliefs, projections, outlook, analyses or current expectations concerning, among other things: potential key insights into the pathogenesis of COVID-19 provided by SVs identified by Saphyr, including the potential of STK26 gene duplication to be a prognostic biomarker for severe immune response seen in severely ill COVID-19 patients; Saphyr’s ability to contribute to a better understanding of COVID-19 and help save lives; and timing of the study results to be presented. Each of these forward-looking statements involves risks and uncertainties. Actual results or developments may differ materially from those projected or implied in these forward-looking statements. Factors that may cause such a difference include the risks and uncertainties associated with: the impact of the COVID-19 pandemic on our business and the global economy; general market conditions; changes in the competitive landscape and the introduction of competitive products; changes in our strategic and commercial plans; our ability to obtain sufficient financing to fund our strategic plans and commercialization efforts; the loss of key members of management and our commercial team; and the risks and uncertainties associated with our business and financial condition in general, including the risks and uncertainties described in our filings with the Securities and Exchange Commission, including, without limitation, our Annual Report on Form 10-K for the year ended December 31, 2019 and in other filings subsequently made by us with the Securities and Exchange Commission. All forward-looking statements contained in this press release speak only as of the date on which they were made and are based on management’s assumptions and estimates as of such date. We do not undertake any obligation to publicly update any forward-looking statements, whether as a result of the receipt of new information, the occurrence of future events or otherwise.

CONTACTS
Company Contact:
Erik Holmlin, CEO
Bionano Genomics, Inc.
+1 (858) 888-7610
eholmlin@bionanogenomics.com

Investor Relations Contact:
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LifeSci Advisors, LLC
+1 (617) 430-7577
arr@lifesciadvisors.com

Media Contact:
Darren Opland, PhD
LifeSci Communications
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darren@lifescicomms.com