Benzinga | Jan 14, 2021 08:08AM EST

Bionano Genomics Highlights Day 3 Of Its 5-Day Next-Gen Cytogenomics Symposium Featured 6 Saphyr Users Presenting Results, Experiences With Saphyr

Bionano Genomics, Inc. (NASDAQ:BNGO) announced that day three of its five-day Next-Generation Cytogenomics Symposium featured six Saphyr users presenting their results and experiences using the Saphyr(r) system for optical genome mapping (OGM) to analyze solid tumor genomes. The presentations by scientists and clinicians from leading hospitals and medical research institutions in Europe and the US discussed results on a variety of solid tumors such as cancers of the head and neck, brain, breast, liver, and the eye. All six studies showed that Saphyr enables for the first time a complete and clear picture of structural variation in the genome and provides opportunity for the discovery of novel cancer drivers, therapeutic targets, and prognostic markers, something which has not been possible to date with next-generation sequencing (NGS) and array platforms.

Dr. Jim Broach, Director of the Penn State Institute for Personalized Medicine presented on HPV-induced head and neck cancer, one of the few cancers on the rise in the US while most other cancers continue to decline. OGM allowed his team to reconstruct complicated genomic changes that next-generation sequencing hasn't been able to identify. He concluded that Saphyr is a powerful tool to identify and characterize viral integration in tumors and that it can detect the genome instability associated with HPV integration.

Dr. Adrian Lee, Director of the Institute for Precision Medicine at the University of Pittsburgh presented on his use of OGM to study invasive lobular breast cancer, the sixth most common cancer in women. Using Saphyr, he was able to reconstruct extremely complex chromosome-wide rearrangements as well as clinically important single gene deletions. He stated that cancer genomics has long focused on small point mutations simply because the structural variants (SVs) were not accessible with next-generation sequencing tools, and he believes that OGM will allow for the discovery of therapeutic targets and diagnostic markers from SV data. He concluded that large structural variants are common in breast cancer and have important clinical value, that Saphyr can detect copy number changes as well as the standard single nucleotide polymorphism (SNP) arrays and that additionally it can detect all other SV types genome-wide as well.

Dr. Justin Balko, Vanderbilt University Medical Center presented his work on inflammatory breast cancer, a form of breast cancer that has a poor prognosis and responds poorly to treatment. Using Saphyr, he was able to identify recurring structural variants in a gene that was never before associated with breast cancer and may be a critical factor that defines this aggressive disease. He concluded that in cases like inflammatory breast cancer where sequencing and other techniques have been exhausted, OGM offers a unique opportunity to find critical variants.

Dr. Eric Letouz?, Cordeliers Research Center, Paris presented on his use of OGM to determine the exact structure of complex genomic rearrangements in liver cancer, which he was unable to do with whole genome sequencing. He concluded that Saphyr revealed 50% more structural rearrangements than NGS, was able to unravel complex rearrangements and may be used to identify replication stress in clinical samples, which may determine if patients can be treated with the highly effective PARP inhibitor drugs.

David Gentien, Manager of the Genomics Platform, Curie Institute, Paris presented his study with OGM of uveal melanoma, a cancer of the eye that can be very aggressive once it metastasizes. Using Saphyr, he identified different types of structural variants that created several gene fusions believed to define this tumor type and that were missed by whole genome sequence and other molecular methods.

Dr. Ravindra Kolhe, Vice-Chairman of Pathology at the Medical College of Georgia at Augusta University described his progress in developing a laboratory developed test (LDT) for solid tumor with Saphyr. Preliminary results from his study on the first five glioblastoma samples showed 100% concordance between OGM and the current workflow for solid tumor testing in his laboratory, the Oncoscan SNP array platform combined with five locus specific tests using several different techniques. Dr. Kolhe concluded that Saphyr outperformed the Oncoscan array by detecting 100% of the variants found by the array platform and many more clinically actionable events it missed, and that Saphyr better characterized complex events. In addition to the higher performance, Saphyr has reduced hands-on time, faster turn-around time, and is cost effective compared to this current combination of methods. He believes that tests developed on Saphyr may help in making a more accurate prognosis and could measure therapy response.

The symposium continues Thursday and Friday. The full schedule of speakers and registration access is available at http://bit.ly/3pLPT28