Benzinga | Jan 19, 2021 08:07AM EST

Bionano Genomics Reports MD Anderson Cancer Center Publishes On Co.'s Saphyr System

Bionano Genomics, Inc. (NASDAQ:BNGO) announced the publication of a study in medRxiv by a team led by Dr. Rashmi Kanagal-Shamanna, Director of the Molecular Diagnostic Laboratory, the MD Anderson Cancer Center comparing the performance optical genome mapping (OGM) with Saphyr against standard of care methods for the analysis of cancer genomes in patients with Myelodysplastic Syndromes (MDS). MDS is a precursor to Acute Myeloid Leukemia and structural variation analysis is important for clinical management of patients with MDS. The study found that OGM detected all clinically important variants identified by the standard of care methods in a single assay plus several clinically relevant aberrations that were missed by such standard of care methods, that OGM eliminated the need for multiple confirmatory tests, and significantly reduced the turn-around time for results, potentially allowing for treatment decisions to happen sooner so patients can be treated more quickly.

For the clinical work-up of MDS, most well-characterized copy number variations (CNVs) and structural variations (SVs) are identified using a combination of the traditional cytogenetic techniques, including karyotyping for balanced events such as translocations and inversions, chromosomal microarray (CMA) for the detection of CNVs, and multiple fluorescent in-situ hybridization (FISH) tests for the detection of important gene or locus specific aberrations. Several tests are run sequentially after initial data analysis to confirm gene-specific variants, leading to a diagnostic process that can span several weeks.

In this study, Dr. Kanagal-Shamanna evaluated the performance of OGM in a series of 12 previously well-characterized MDS cases using clinical bone marrow samples. OGM successfully facilitated detection and detailed characterization of all 26 clonal chromosomal variants identified with karyotyping and CMA when present above the level of detection sensitivity. Further, OGM uncovered additional clinically relevant aberrations in one third of patients that were undetectable by standard of care technologies, all of which were subsequently confirmed by alternate platforms. OGM permitted precise gene-level mapping of clinically informative genes such as TP53, TET2 and KMT2A, which was not previously possible using conventional cytogenetic techniques, voiding the need for multiple confirmatory assays. Overall, OGM served as a single platform assay to identify different types of structural chromosomal alterations of clinical significance.

Rashmi Kanagal-Shamanna, MD, commented: "Currently, the first step of clinical management of MDS patients is prognostic risk-stratification using the R-IPSS scoring system, which is dependent on the number and type of structural variants, degree of cytopenia(s) and bone marrow blast percentage. In our study, OGM was able to comprehensively identify all SVs in a single assay, as well as detect additional SVs of potential clinical significance that were cryptic by standard of care technologies. Moving forward, I envision OGM to be a 'one-stop shop' for high-throughput chromosomal analysis and SV profiling for routine clinical evaluation of MDS and other hematological malignancies."

Erik Holmlin, PhD, CEO of Bionano Genomics, commented: "The MD Anderson Cancer Center is one of the world's most important cancer research and treatment centers. We are proud that several of our Saphyr systems are in use there, and grateful for Dr. Rashmi Kanagal-Shamanna's pioneering work in bringing OGM to patients with hematological malignancies. During our Next-Generation Cytogenomics Symposium, more than 30 speakers from around the world demonstrated Saphyr's ability to identify more actionable variants than standard of care methods in solid tumors and heme malignancies, and pathogenic variants in a variety of genetic disorders. Dr. Kanagal-Shamanna's work is an important demonstration of Saphyr's potential to revolutionize cytogenomic testing with a single assay that provides actionable results faster, with less hands-on time and for a lower cost than required by the current combination of several complex, traditional methods."

The study is available on medRxiv at https://www.medrxiv.org/content/10.1101/2021.01.13.21249611v1