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

San Diego, California, UNITED STATES

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

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 or

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Company Contact:
Erik Holmlin, CEO
Bionano Genomics, Inc.
+1 (858) 888-7610

Investor Relations Contact:
Ashley R. Robinson
LifeSci Advisors, LLC
+1 (617) 430-7577

Media Contact:
Darren Opland, PhD
LifeSci Communications
+1 (617) 733-7668