A ‘gem’ of a partnership

Genoptix and Bionano to use Saphyr System to develop hematologic cancer diagnostics

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SAN DIEGO & CARLSBAD, Calif.—Diagnostics are the name of the game for a recently announced exclusive agreement between oncology diagnostics and informatics company Genoptix Inc. and Bionano Genomics Inc. The two companies shared news that they plan to co-develop “information-rich diagnostics” for certain hematologic oncology indications in the United States by leveraging Bionano’s Saphyr System.
The Saphyr System offers the ability to accurately visualize a genome’s structure with a DNA sample isolated directly from cancer cells, thereby eliminating the need for cell culture. It enables the detection of all major types of structural variants with greater sensitivity than sequencing-based methods, according to Bionano, and with much higher resolution than karyotyping or fluorescence in-situ hybridization.
Though no specific financial details were disclosed, Dr. Erik Holmlin, CEO of Bionano, tells DDNews that the company will support Genoptix in the development of novel tests, noting that “Bionano will supply Genoptix with the necessary instrumentation and consumables to support a commercial offering of these tests subject to all relevant regulatory factors.”
“We are excited about working with the leader in hematologic cancers. This alliance is a major milestone for Bionano, showing the potential of the Saphyr system for clinical analysis of cancer genomes. Bionano’s approach allows for the entire genome to be analyzed without the use of specific probes to detect variants of interest. Variants of clinical significance discovered in the future can easily be added to an assay without the need to develop additional detection tools,” he said in a press release.
Genoptix and Bionano will focus on cancer subtypes in hematology-oncology in which accurate diagnosis is dependent on detecting large structural variations in the genome. Cancer cells are known to present with an abundance of major rearrangements of the genome, and the presence or absence of these rearrangements can impact a tumor’s characteristics and response to treatment.
“There is an increased interest from different companies to offer specialized cancer panels that have been designed to detect single nucleotide variants responsible for cancer. Besides single nucleotide variants, structural variants—which are variations across large regions of DNA, that can include copy number variations, balanced translocations or inversions—play a significant role in the development of cancers,” Holmlin explains. “Bionano is the structural variation company and provides the technological advance to comprehensively and accurately detect this important class of variants. With Genoptix, we are focusing on improving the diagnosis for selected indications of hematologic cancers by detecting structural variations in cancer.”
He adds that while the companies have worked together informally for a while, “This announcement reflects the formalization of our relationship around a detail co-development plan,” noting that “Genoptix is one of the leading clinical labs providing testing for hematologic cancers. Their expertise in commercializing clinical tests in this space makes them an ideal partner.”
Genoptix offers comprehensive testing solutions in hematology, with a focus on cancers and diseases of the blood, bone marrow and lymph nodes, as well as solid tumor molecular profiling.
“We are pleased to be collaborating with Bionano to develop and validate robust clinical diagnostics for oncology applications utilizing Bionano’s promising technology. We look forward to commercializing these exciting technologies to empower physicians to more effectively diagnose and treat cancer,” commented Joseph M. Limber, CEO of Genoptix.
Back in March, Bionano shared news regarding the results its next-generation mapping (NGM) systems—Saphyr and Irys—generated in a first-of-its-kind study. NGM was found to accurately identify potentially clinically relevant oncogenes and pathogenic driver mutations that had not before been detected by next-generation sequencing. Specifically, in terms of large structural variations that play a role in the progression of prostate cancer, NGM with the Irys system at 35x genome coverage was capable of identifying 10 times more structural variations that were larger than 1,000 base pairs than the Illumina X10 platform at 60x genome coverage. As noted in the press release, “Importantly, of the large SVs detected on the Bionano system, half were in or near genes with oncogenic potential. Of the sequence variants detected with NGS, only 0.5 percent were in or near such genes.”

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