2020-08-10 08:39:33 BNGO Bionano Genomics
08/10/20 08/1008:39 08/10/2008:39 | Bionano Genomics announces multiple data readouts at CGCBionano Genomics announced that the 2020 Cancer Genomics Consortium Annual Meeting held on August 4 and 5 featured several studies using Bionano genome imaging. Results of these studies underscore that Saphyr has the potential to modernize cytogenetics by consolidating analysis performed with each of the three standard cytogenetic methods into a single assay with performance that matches or exceeds that of these three methods combined. The Cancer Genomics Consortium is an organization comprised of leading cytogeneticists, molecular geneticists and molecular pathologists. Its annual meeting attracts the key opinion leaders and cytogenetics directors from North America's leading cancer centers and hospitals. In the last several years, the meeting has seen an increasing presence of studies and presentations featuring data generated using Bionano's Saphyr genome imaging system. At this year's virtual event, four speakers shared their results generated with Saphyr. Dr. Gordana Raca from the Children's Hospital of Los Angeles presented the case of a 2-year old boy with B-cell acute lymphoblastic leukemia who had been tested by the traditional methods of karyotyping, an extensive FISH panel and chromosomal microarray, as well as with an advanced custom sequencing panel for pediatric cancer, with no genetic driver of the disease found. CMA analysis called a duplication in the PAX5 gene, a known oncogene, but upon analysis with Saphyr, the two extra copies of the gene were shown to be four extra copies in tandem. In a second child with similar disease, Saphyr called five extra copies of the same oncogene, while CMA called only 2. The unambiguous resolution of these variants by Saphyr demonstrated the advantage of genome imaging of single molecules over hybridization-based methods like CMA. The extra copies of parts of the PAX5 gene are believed to be the primary driver of the disease in the patients, and to be correlated with a poor prognosis, including relapse and more severe progression of the disease. Dr. Nikhil Sahajpal from Augusta University presented results on 20 cancer patients, including leukemia patients with acute myeloid leukemia, chronic myeloid leukemia and myelodysplastic syndromes who were previously characterized by karyotyping and FISH analysis, and patients with solid tumors, previously characterized by OncoScan microarray. In all samples, Saphyr detected all previously found variants. Additionally, Saphyr identified variants that were not called by karyotyping and FISH, contributing to resolution of complex rearrangements with previously unclear structure, and the identification of precise breakpoints of pathogenic variants and many previously unknown translocation partners. In the solid tumor samples, Saphyr identified all previously identified events and also identified multiple translocations that are impossible to detect by microarray. These results form the basis for creating a Laboratory Developed Test for cancer by Dr. Ravindra Kolhe's team at Augusta University. The project aims to validate Saphyr as a first-tier diagnostic tool for solid tumors and hematological malignancies and to lay the groundwork for reimbursement codes for labs based in the United States. In addition to those new results, Dr. Alex Hoischen from Radboud Univeristy presented the previous reported validation studies by his team and an international consortium on 48 leukemia samples and 85 patients with constitutional disease, both showing 100% concordance between Saphyr and standard cytogenetics. Dr Hoischen also presented certain novel research findings, including new genetic variants that could form the basis of more refined testing algorithms in the future. Talks at CGC covering other technologies including long-read sequencing and nanopore sequencing provided additional support for Bionano genome imaging with Saphyr as a leading technology for modernizing cytogenetics. For example, Evan Eichler from the University of Washington discussed in his keynote talk on various long-read genome analysis technologies that the largest structural variants can be detected by Bionano genome imaging but not by long-read sequencing. Finally, in a presentation on nanopore sequencing, Dr. William Gleen from Medical University of South Carolina described the need to use 10 different bioinformatic algorithms to obtain a set of structural variation calls, yet this data included a high rate of wrong calls. |
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