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In an online presentation hosted by the Cancer Genomics Consortium (CGC) on May 12, 2020, Dr. Brynn Levy from Columbia University and Dr. Rashmi Kanagal-Shamanna from the MD Anderson Cancer Center each presented updates on their work showing 100% concordance between Bionano Genomics’ optical mapping technology and current gold standard cytogenetic methods.

In his presentation, Dr. Levy reported on a blinded, prospective study comparing the results generated by Bionano’s Saphyr instrument to results from routine clinical testing in CLIA laboratories using current gold standard cytogenetic techniques. On 91 samples from patients with Acute Myeloid Leukemia (AML) and Acute Lymphoblastic Leukemia (ALL) that passed inclusion criteria, Bionano was 100% concordant with karyotyping results. Additionally, Dr. Levy illustrated concordance with chromosomal microarray (CMA) for both the size and the breakpoints of identified aberrations in several cases of ALL and AML. Overall, Dr. Levy noted that Saphyr provided “Tremendous and remarkable concordance with traditional cytogenomic analyses for karyotype, FISH and CMA.”

Dr. Levy described how the current gold standard of leukemia testing requires karyotyping on all samples. When requested by the physician, multiple rounds of FISH with different FISH probes, and/or chromosomal microarray are run in addition. CMA provides a genome-wide scan for copy number variants (CNVs) but cannot detect balanced structural rearrangements or map chromosome structure of large imbalances.

The study run by Dr. Levy is part of the Cancer Genomics Research Network and its members lead cytogenetics departments from Harvard Medical School, PathGroup, Columbia University, Penn State College of Medicine, Mayo Clinic, Seattle Cancer Care Alliance, MD Anderson Cancer Center, Augusta University and Legacy Laboratory Services.

In a second presentation, Dr. Rashmi Kanagal-Shamanna from the MD Anderson Cancer Center gave an update on her study involving 100 samples of patients suffering from Myelodysplastic Syndrome (MDS), a precursor to AML. The clinical management of patients with MDS is largely determined by the number of structural aberrations detected, and therefore a single technology, like Saphyr, that is able to detect all CNVs and balanced rearrangements is desirable. Before the closure of Dr. Shamanna’s lab due to the COVID-19 crisis, she analyzed 13 samples using Saphyr. A combined 39 aberrations that passed inclusion criteria were detected by karyotyping, and all of those variants were detected by Saphyr. Additionally, there was 100% concordance between Saphyr and calls made with CMA. Importantly, Bionano identified critical rearrangements important for prognostication of the disease and identified many novel aberrations that change the R-IPSS risk score, which would alter therapeutic management.

Both aforementioned studies are expected to be submitted for publication this quarter. The online presentation from the CGC is available for viewing at https://bionanogenomics.com/library/webinars/.


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