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Bionano Genomics Outlines Strategy for Clinical Adoption of Optical Genome Mapping


NEW YORK – Bionano Genomics believes that 2021 will be transformative for getting its Saphyr optical genome mapping system in the hands of more users, seeing the approach adopted by cytogenetics laboratories for clinical diagnostics, and laying the foundation for reimbursement of Saphyr tests by health insurance.

"2021 is going to be critical to our long-term growth," said Erik Holmlin, Bionano's president and CEO, during a conference call this week to discuss the company's fourth quarter and full-year 2020 financial results. "We are squarely focused on driving the global development of Saphyr-based assays for use in clinical testing of patients with genetic diseases and hematologic malignancies, and on the adoption of Saphyr for larger clinical studies that will allow us to obtain a critical mass of data" for applications in prenatal and pediatric genetics, leukemias and lymphomas, and solid tumors.

Holmlin said there are about 2,500 cytogenetics labs in the world, which represent a market opportunity of $3 billion to $3.5 billion per year, including in research. "The total market opportunity for optical genome mapping goes well beyond that low single-digit billion dollar number and is substantially larger," he said. "It's harder for us to quantify it specifically, because some of the applications haven't even been developed."

Several studies have already been published that have compared optical genome mapping with traditional cytogenetic methods, he said, all showing that the Saphyr "is a superior alternative."

He mentioned as examples of clinical adoption a group at the University of Iowa, which has implemented optical genome mapping for the diagnosis of FSHD, a rare genetic muscle disease, and researchers at the University of California, San Francisco and Oakland Children's Hospital, who have used the technology to provide diagnoses to children with undiagnosed diseases.

"On the clinical side, specifically, we are seeing Saphyr bring value to cytogenetics analysis by reducing the total reagent cost, turnaround time, labor costs, and by simplifying the analysis of genomes in cancer patients and patients who are suspected of having a genetic disease, all compared to today's workflows in cytogenetics," he said.

Still, widespread adoption of the technology by clinical labs in the US will require additional studies that show concordance with the standard of care, he said, as well as the development and validation of clinical assays. "They need to be able to bill insurance providers and be reimbursed for their tests before they'll comfortably convert over from the standard of care," he added.

Obtaining reimbursement might be easier in Europe, where the company saw a lot of traction last year. Holmlin said Bionano signed reagent rental agreements with three large children's hospitals in Europe — in Spain, Italy, and France — in 2020 that are all conducting cytogenetic validation studies with the platform.

In addition, it signed agreements with cytogenetics labs and hospitals in Germany, Switzerland, Slovenia, Australia, and Canada. These countries are more likely to adopt new technologies for healthcare, Holmlin said, because they largely have single-payor systems that are quicker to grant reimbursement. "In the US, we've noted that the path to reimbursement from third-party payors is going to be a necessary step to gaining widespread adoption of optical genome mapping with the Saphyr system," he said, which can be a slow and challenging process.

Also last year, the Saphyr was accredited in Germany for the clinical detection of structural variations in genetic disorders. Beginning in the second quarter, the company expects the Saphyr to be accredited in other European countries, which Holmlin said "lower barriers for other labs in other markets to adopt [Saphyr] more broadly."

Labs in the US are also launching lab-developed tests, he said. Praxis, for example, has launched several such tests on the Saphyr, for which it has already obtained reimbursement codes. In addition, researchers at Augusta University in Georgia are developing LDTs for hematological cancers and solid tumors, he said.

Lineagen, a diagnostic services lab that Bionano acquired last year, will also play an important role in driving the adoption of Saphyr, he said, through its expertise in building assay menus. Bionano will continue to commercially launch assays this year, he noted, including, for the first time, prenatal tests.

In addition to working on clinical applications, Bionano has been further improving its technology. Last year, it implemented a major update to the Saphyr's software and introduced new DNA isolation kits that enable the isolation of ultra-long DNA fragments from smaller samples, including solid tumors, more quickly and easily. 

Later this year, the company plans to complete a prototype of a new version of Saphyr that will have higher throughput and expanded capabilities. By the time of its launch, which Holmlin did not specify, the new system will have a 14-times higher throughput than the current one, which can analyze about 5,000 human genomes per year. It will involve a "completely novel optical imaging system" but "no substantial invention," he said, as it will be using already-existing technologies.