Publication Reveals in Side-by-Side Comparison that Method Using PacBio Sequencing Detects Only 72% of the Large Structural Variants Detected by Optical Genome Mapping with Saphyr

Rhea-AI Summary

Bionano Genomics (Nasdaq: BNGO) announced a study showing its optical genome mapping (OGM) detected 72% more large structural variants (SVs) compared to PacBio's sequencing method across 32 human genomes. The OGM technology costs less than $500 per genome, while PacBio's method is estimated at $10,000 to $20,000. The study highlights the clinical relevance of OGM for detecting SVs linked to neurodevelopmental disorders and cancer. Bionano's Saphyr system can produce clinical quality SV calls efficiently, demonstrating superior performance in structural variation detection.

Positive

• OGM detected 72% more large SVs than PacBio sequencing, enhancing diagnostic potential.
• Saphyr system costs less than $500 per genome, significantly lower than PacBio's $10,000-$20,000.
• Faster clinical quality SV calls with the updated Saphyr software, generating results for 12 samples daily.

Negative

• Some large SVs uniquely detected by PacBio were misclassified, questioning data accuracy.
• Risks associated with competition and the need for continued funding in the genomic market.

SAN DIEGO, Dec. 23, 2020 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc. (Nasdaq: BNGO) announced the publication of a study by the Human Genome Structural Variation Consortium (HGSVC) revealing that their sequencing method based on PacBio HiFi reads detected only 72% of the large SVs that Bionano’s optical genome mapping (OGM) detected across 32 different human genomes. The consortium developed its custom sequencing method by combining sequencing with PacBio and the single-strand prep and sequencing method StrandSeq to establish a comprehensive catalog of human SVs with base-pair and haplotype resolution. The cost of this method is estimated, based on list pricing, to be between $10,000 and $20,000 per genome. OGM with Saphyr, which costs less than $500 per genome, was shown to be significantly more sensitive than the sequencing method.

Many of the SVs missed by the sequencing technologies overlapped with complex regions of the genome that cause microdeletion and microduplication syndromes, which are highly relevant clinically owing to their involvement in neurodevelopmental disorders. The analysis primarily focused on insertions and deletions, which are considered to be easier for sequencing to detect. Other studies have shown that OGM significantly outperforms sequencing for detection of other SVs, such as inversions and translocations, which are also highly clinically relevant, especially in cancer.

The publication did classify some large SVs as being uniquely detected by the sequencing-based method based on PacBio HiFi. Upon further analysis, however, most of these SVs were in fact identified by OGM, but classified differently. Overall, less than 2% of the large SVs detected by PacBio were missed by OGM.

Erik Holmlin, Ph.D., CEO of Bionano Genomics commented, “This publication outlines one of the most comprehensive side-by-side comparisons of PacBio sequencing and Bionano’s OGM for large SV detection. The unparalleled performance of Saphyr is remarkable because the Bionano data were generated on our commercially available Saphyr system and analyzed using its automated pipeline for a variable cost per genome of less than $500. With the latest update to Saphyr’s software released this week, the instrument can now generate clinical quality SV calls on 12 samples per day per instrument and up to 96 samples per week.

“Something else worth noting in these studies is that longer read lengths improve the accuracy of SV calls. With PacBio’s focus on matching Illumina-like read quality, their HiFi reads are significantly shorter than their traditional long-reads. By contrast, Saphyr images molecules that are consistently 20 to 30 times longer than PacBio reads. Sequencing reads are not getting longer, which we believe implies that Saphyr will remain the only effective and affordable technology currently capable of detecting the structural rearrangements in the genome that are involved in disease.”

The publication is available at https://www.biorxiv.org/content/10.1101/2020.12.16.423102v1

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, Saphyr’s continued position as the only effective and affordable technology capable of detecting structural variations in the genome that are involved in disease. 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 ability of medical and research institutions to obtain funding to support adoption or continued use of our technologies; 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:
Ashley R. Robinson
LifeSci Advisors, LLC
+1 (617) 430-7577
arr@lifesciadvisors.com

Media Contact:
Darren Opland, PhD
LifeSci Communications
+1 (617) 733-7668
darren@lifescicomms.com

FAQ

What did Bionano Genomics announce on December 23, 2020?

Bionano Genomics announced a study showing its optical genome mapping (OGM) technology outperformed PacBio sequencing in detecting large structural variants.

How does the cost of Bionano's OGM compare to PacBio's sequencing?

Bionano's optical genome mapping costs less than $500 per genome, while PacBio's method is estimated to be between $10,000 and $20,000.

What are the clinical implications of the study released by Bionano Genomics?

The study indicates that OGM is more effective in detecting structural variants linked to neurodevelopmental disorders and cancer.

What improvements were made to Bionano's Saphyr system?

The updated Saphyr software can now generate clinical quality SV calls for up to 12 samples per day.

How many large structural variants did OGM detect compared to PacBio's method?

OGM detected 72% more large structural variants compared to PacBio's sequencing method.