CHICAGO (GenomeWeb) – Genomic analytics startup Farsight Genome Systems has high ambitions, seeking to gain US Food and Drug Administration clearance of its software for use in labs conducting sequencing-based tests.
"We would like to be the first analytic pipeline that has won FDA clearance," CEO and Founder Glenda Anderson said.
Sunnyvale, California-based Farsight, founded in 2015, has submitted a first demonstration of its Farsight Correo platform to the FDA, according to Anderson, as it seeks 510(k) clearance for the technology.
Correo "enables pathology laboratories to deliver sequencing-based testing as routinely as they now do PCR and [fluorescence in situ hybridization]-based testing," according to Farsight's website. It is meant to fit into pathology workflows by running alongside existing pipelines and to adapt easily to growing panel sizes and testing needs. Anderson said the platform can, for example, pull FASTQ files from a data repository, run a test panel, then generate a report in HTML, PDF, or a machine-readable format to feed into an electronic health record or laboratory information system.
During development, Farsight tested Correo with more than 3,000 patient samples processed by 40 different labs running seven different types of sequencers and following nearly a dozen library preparation protocols, Anderson said.
"We saw at Farsight that we needed to create a platform that would enable not only ease of adoption — they needed to be able to snap it into their workflow with minimal disruption —  but it needed to be future-proof," Anderson told GenomeWeb earlier this month at the Healthcare Information and Management Systems Society (HIMSS) conference in Las Vegas. "That was our vision when we set out, and that's effectively what we've built today."
To Anderson, "future-proof" means three things. The technology must be scalable, from, say, a 20-gene panel to a 200-gene panel with minimal disruption. It has to be easy for researchers to add new panels to test menus, and users have to be able to migrate between wet-lab processes.
"They might start with very narrow Illumina enrichment, then move to a whole-exome enrichment from Agilent, all using the same basic analytic pipeline," Anderson said of the third criterion.
Going through the FDA review process would go a long way toward making the technology "future-proof" by taking some of the onus off of laboratory customers as they add new testing panels, Anderson said.
"Some would argue that [a genomic analytics platform] doesn't need FDA clearance, but without FDA clearance, every laboratory has to validate it from first principles," she said. "With FDA clearance, the validations are much lighter."
To date, though, genomic analysis software developers have stayed away from the FDA.
"What we're really describing here is an enabling technology, a platform that lets raw sequencing data from any Illumina sequencer be aligned, variant-detected, and a report generated in a high-reliability fashion," Anderson said. "We're really building a platform that's a component of a test." In her eyes, that makes it a diagnostic tool.
Correo features what Anderson called "panel-first" design.
"We start with a panel that's predefined," Anderson said. Typical interpretation software today spits out "a mountain of variants" that pathologists have to sift through in search of a variant to call, she said. That leads to labs taking shortcuts to speed up the process, perhaps by only looking at variants that have been linked to a specific disease, which raises the possibility of missing other illnesses.
Farsight offers its customers a menu of "starter" test panels for solid tumors and blood cancers. "Our customer laboratories typically start with these, then modify the content to suit their institution and treating physician preferences," Anderson said. The vendor has partnered with several medical specialty societies to push out new test panels as diagnosis and treatment guidelines evolve, she added.
"What we find is that our panel-first technology allows us to probe more deeply into genes and variants that are clearly actionable, that had treatments that are clearly associated with them. It strips the workload out of the tail end of the process because we've started with clear information about what we care about for a patient. We've really inverted the process," Anderson explained.
Anderson, who has been working in diagnostics and genomics since 2003, started Farsight in 2015 because she saw that genomic testing was different from other lab processes.
"Clinical laboratories are very good at bringing up an assay [for which] they can then deliver a patient report in a nice, stable way over years," Anderson said. But sequencing interpretation is different and far more complex than other lab workflows.
"What's happening in genomics, of course, is quite the opposite," Anderson noted. "You bring up a test panel, and two weeks later, it's out of date. You've got to add another variant, another genome. So, this notion of sort of creeping or evolving diagnostic medicine is quite novel to the clinical laboratory, although it's very commonly understood in the translational science world."
When it comes to genomics, pathology labs often struggle to determine which genes to put on a particular panel, and there are different ways to interpret results.
"Once I pick the genes and decided how to interpret them, how do I validate? Once I've validated, when treating physicians ask me for something new, how do I accommodate?" Anderson said. She likened it to being on a hamster wheel.
Farsight tightly controls updates to databases and test panels to help labs manage validation. The company provides updates semi-annually or annually to most customers, according to Andersen. Those labs conducting whole-exome and other large-panel sequencing can opt for more frequent updates, she said.
Correo — hosted on Amazon Web Services by ClearData, a healthcare-specific cloud services vendor based in Austin, Texas — is meant to help the labs at large, integrated health systems sort out those issues as they gear up to support the rapid shift to precision medicine. Anderson cited the work of one unnamed customer, which started with a 20-gene test panel for certain cancers.
"They had outgrown it earlier, but hadn't had the wherewithal to expand. They brought us in to help bring up a 40-gene panel. No sooner were we in place than their laboratory decided they really wanted to move to whole clinical exomes and report out 400 genes," Anderson said. She said it could take as long as 18 months to make such a move. "We did it with them in less than three months."
So far, the company has operated with seed funding, and Anderson said Farsight expects to conduct a Series A round of venture capital funding this fall.