Fabric Genomics: New Identity, Partnerships, Products for Omicia

By Allison Proffitt 

March 29, 2017 | Omicia rebranded last week, relaunching itself as Fabric Genomics with new products and new partnerships.

In the past two years, the company has changed, CEO Matt Tindall told Bio-IT World. “Revenue has grown by hundreds of percentages,” and headcount has doubled in the past 18 months.

“We looked at moving from what was a world-class genomic data analysis company that was focused on hereditary disease… [to] launching a somatic cancer capability, acquiring a company named Spiral Genetics in Seattle… and integrating with EMR systems to bring our important insights into the workflows of lab directors and physicians,” Tindall explained. “We looked back and said, we should probably reimagine where we want to go with this incredible technology we have in this burgeoning market.” 

Looking Back: Omicia

Omicia has been around since 2002, when co-founder Martin Reese started exploring clinical genome annotation. Early on, the company offered its services through partnerships: with Applied Biosystems (Reese was a co-author on the first NGS human genome paper using the SOLiD platform in 2009); the Genome Cancer Care Alliance; and the University of Utah. The partnership with the University of Utah on VAAST—the Variant Annotation, Analysis and Selection Tool—won the company a Bio-IT World Best Practices award in 2012.

In January 2014, the company raised $6.8 million in a Series A funding round. “We made a transition at that point, from 2014-2016, from the research market to the clinical market,” said Tindall, who has been with the company since March 2016. 

In June 2016, the company added $23 million more in a Series B round, and in January of this year, Omicia acquired Spiral Genetics, whose graph-based technology enables accurate detection of structural variants and provides population-scale data mining capabilities for clinical laboratories, life science companies and country sequencing programs.

Around the same time, Tindall says, the company expanded its customer base, welcoming customers that “were not typical for us”. Omicia had traditionally served commercial clinical labs, but now began welcoming health systems and pharma companies—Tindall mentions UPMC and Roche Venture Funds—groups with a strong interest in precision medicine.

Looking Ahead: Warp and Weft

The name change—to Fabric Genomics—is a “reimagination of where we want to play in the fabric of healthcare and the systems of healthcare, delivering this incredibly valuable information to the stakeholders who ultimately use it to make better clinical decisions with their patients,” Tindall explains.

Fabric Enterprise—the new product launched with the rebranding—gives a hint of how Tindall sees that playing out. The software platform performs secondary and tertiary genomic analysis: taking data directly from a sequencer (FASTQ or BAM files) and delivering a clinical report. The clinical report is fed into the workflow of the lab director, who signs off on the report and delivers it to a physician.

“That whole process, for most partners, is one or two or three different vendors,” Tindall said. “We’ve combined all of those tools and capabilities, all of the software behind the sequencers, into an end-to-end precision medicine platform.”

Once users open the box of a new sequencer—any platform, Tindall insisted—Fabric Enterprise can be appended to the “back of the sequencer”, and start delivering clinical reports.

“There aren’t many private companies, if any, that can do that for panels, exomes, and genomes as well as hereditary and genetic cancer,” Tindall said. “Anyone can get started right now performing this kind of advanced analysis.”

Product Suite Development

If that sounds too easy (or too hands off), Fabric is still offering the components of the pipeline a la carte.

Fabric Standard is the company’s secondary analysis pipeline, combining BioGraph technology from Omicia’s January 2017 acquisition of Spiral Genetics, and algorithms from a newly-announced partnership with Sentieon. The Fabric Standard pipeline is now 10x faster than BWA-GATK tools, the company says, and unlike BWA-GATK, Fabric Standard has no down-sampling of reads and is deterministic, even when run on multiple threads. Moving forward, Fabric Genomics and Sentieon plan to co-develop new variant calling capabilities for hereditary disease and oncology; and structural variant and copy number variant capabilities for genomic analysis built upon Sentieon’s award-winning tools and the BioGraph technology.

Fabric Annotation connects to the company’s 90 annotation sources and uses ACMG guidelines to classify variants, and lets customers deliver annotation in their own report. “This is for very high throughput labs that almost want to annotate within their LIMS system,” Tindall explained.

Offering just annotation is new, but it gives customers more flexibility to customize their own reports. “We don’t need to own the white labeled reports!”

As a prime example, last week the company launched a technology partnership with Veritas Genetics to accelerate Veritas’ myGenome product for personal whole genome sequencing using Fabric Annotation. Veritas’ $999 myGenome product provides sequencing, interpretation, and a call with a genetic counselor, when appropriate. Veritas now uses Fabric Annotation to help automate variant interpretation, the companies said in a joint statement. The automation assists in production scaling, cost reduction, and 24-7 processing availability.

Finally, Opal Clinical is the company’s historic product, an interpretation and reporting platform that will still be available as a standalone product.

Partner Guarantees

“We need to be able to provide industrial-scale genomic data analytics and reporting,” Tindall said. “We’re starting to weave our data into the systems of healthcare in really interesting ways: in EMR systems with EPIC and Cerner integration, LIMS system integration.”

And he’s willing to make bold promises to his customers.

“We can annotate a full genome in less than ten minutes, and annotate a whole exome in less than ten seconds. I don’t think anybody else in the world does that as efficiently as we do,” Tindall said. “We’ve guaranteed [Rady Children's Institute for Genomic Medicine in San Diego, Calif.] a one hour turnaround time from the time we receive the VCF file to the time we generate the report.”

Stephen Kingsmore, president and CEO of the Rady Children’s Institute for Genomic Medicine, knows fast. He set a world record for diagnostic whole genome sequencing in 2015, and has proven willing to explore new technologies to move even faster. “They are providing the world’s fastest clinical genome evaluation or assessment,” Tindall said.

Though fast isn’t the only metric; actually arriving at answers helps. Tindall reports diagnostic rates of 54% in pediatric odyssey cases at Rady. (In the Genomics England project, Fabric has diagnostic rates of 44.7%, Tindall said. At LabCorp the rate is 54.4% in exome tests.) 

“In all three cases we’re well ahead of the industry’s averages for pediatric diagnostic rates,” Tindall says. The clinicians are doing the actual diagnosing. Fabric Genomics is, “just providing the insights,” Tindall emphasized. “But we are extraordinarily proud of those kinds of results. We think that’s super differentiating for our platform. That’s three different, major centers around the world where we’re delivering the best possible insights.”