Day Three of Bionano’s Next-Generation Cytogenomics Symposium

Saphyr Provides Complete Structural Variation Analysis in Solid Tumors, Enables Discovery of Novel Diagnostic Markers and Drug Targets - Seite 2

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 Letouzé, 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.