Bionano says data confirms Saphyr's potential to replace cytogenetics methods
Bionano Genomics announced a summary of results from two key studies presented this week at the 2019 Cancer Genomics Consortium Annual Meeting in Nashville, Tennessee. In a preliminary read-out of a multi-center clinical validation study using blinded samples, Professor Brynn Levy, Director of Cytogenetics at Columbia University, presented outcomes on the first 11 patient samples analyzed and unblinded. This study compares Saphyr to technologies used in traditional cytogenetics workflows for patient testing in oncology and is being run by a consortium of leading cytogenetics teams at institutions in the United States, including Columbia University, the MD Anderson Cancer Center of the University of Texas, the Mayo Clinic, the University of Washington, Penn State University, Augusta University and the PathGroup. In each of the 11 samples, Saphyr detected all known clinical variants identified by various combinations of karyotype, Fluorescent In-Situ Hybridization, and Chromosomal MicroArray, which define the current standard of care in cytogenetics. Some of the variants identified include: in Acute Myeloid Leukemia samples, a large inversion on chromosome 16, which creates a CBFB MYH11 fusion; in one B-Cell Acute Lymphoblastic Leukemia (B-ALL) sample, a BCR-ABL1 translocation, and deletions of tumor suppressor genes IKZF1 and CDK6; and in a separate B-ALL sample, a NF1 deletion, which is a well-known risk factor for childhood leukemia. This detailed characterization of variants allows for a precise treatment tailored to the specific patient's tumor. During his presentation, Dr. Levy discussed the strong concordance of the size of the deletions and the breakpoints identified by Saphyr with those determined by microarray results. Based on the preliminary results, Dr. Levy concluded that Saphyr has the potential to be a powerful new tool in cytogenomics for assessing chromosome structure and copy number. Upon completion of the clinical validation phase, Dr. Levy's team plans to evaluate the benefits of using the Saphyr system for discovery of novel variants by analyzing samples previously deemed "normal" by karyotype, FISH, and CMA to identify the existence of any recurring abnormalities with prognostic and therapeutic value that may have been missed by traditional methods. In a second study, Associate Professor Rashmi Kanagal-Shamanna, Microarray Director in the Molecular Diagnostics Lab of the University of Texas MD Anderson Cancer Center, presented results from the analysis of seven patient samples with Myelodysplastic Syndrome, a precursor to leukemia characterized by the presence of large structural variants. In addition to identifying all clinically relevant variants previously detected by karyotyping and CMA, Saphyr revealed additional structural variants of research interest that were missed by these methods, including deletions of the TP53 and TET2 genes, which have prognostic and therapeutic implications. Use of the Saphyr system further enabled elucidation of a complex rearrangement involving three chromosomes, with deletions and duplications at the breakpoints, all of which were not captured by other cytogenetic methods. Additionally, Saphyr facilitated precise mapping of variants within genomic co-ordinates, especially in cases involving complex rearrangements. Dr. Kanagal-Shamanna stated that the high concordance between Bionano optical mapping and conventional techniques provides proof-of-concept for potential use of Saphyr as a single-platform for comprehensive assessment of all structural variants, including copy number variants and balanced rearrangements. In hematological malignancies, this eliminates need for cell culture and provides higher resolution than standard of care assays.