SAN FRANCISCO (GenomeWeb) – Following its acquisition of Edico Genome last month, Illumina plans to focus initial development work on applications related to rare and undiagnosed diseases. Edico Genome is a data analysis firm that markets the platform DRAGEN, which uses field programmable gate array technology in combination with software algorithms to analyze genomic data.
The Edico team has moved into Illumina's R&D building in San Diego, California and is working with Illumina on developing the next generation of technologies, said Susan Tousi, senior vice president of product development at Illumina.
Tousi said the main reason for acquiring Edico is that "data analysis is still a bottleneck for our customers. We want to get to where [the secondary analysis] is standardized and of the highest clinical utility."
Edico has developed its DRAGEN platform to do rapid genomic sequencing data analysis. Notably, Rady Children's Institute for Genomic Medicine has been using DRAGEN in its rapid diagnostic whole-genome sequencing protocol, working to reduce the time to diagnosis for babies in the neonatal intensive care unit. Earlier this year, the Australian Genome Center also partnered with Edico to bring rapid genomic testing to 12 NICUs and six pediatric ICUs.
Going forward, one major focus of development will be in the area of rare and undiagnosed diseases. It's "an important beachhead for our technology and for driving clinical utility," Tousi said.
Initially, two main goals will be reducing turnaround time and improving the ability to detect variants typically considered difficult to address with short-read sequencing technology, such as structural variants and repeat expansions.
Ryan Taft, senior director of scientific research at Illumina, who leads Illumina's efforts in clinical whole-genome sequencing for rare and undiagnosed diseases, said that researchers at Illumina's proof-of-concept clinical sequencing lab have started testing various methods for calling copy number variants and mitochondrial variants. In addition, he said, the firm is working on a "new bespoke piece of the pipeline for spinal muscular atrophy" and has a "clear roadmap" for better detecting structural variants and repeat expansions.
Currently, exome and whole-genome tests have diagnostic rates between 25 percent and 40 percent for rare genetic diseases. One way of improving that is to be able to detect alterations other than SNVs. "It's low hanging fruit for increasing diagnostic yield," Taft said.
Aside from the rare and undiagnosed diseases market, the DRAGEN pipeline will ultimately be applicable to "all areas of our portfolio," Tousi said. Edico already has a pipeline for somatic variant calling in cancer and the ongoing work to improve structural variant calling would be relevant in oncology as well.
In addition, the acquisition will support Illumina's other efforts in the clinical market. Although Tousi declined to disclose specific plans for bringing tests, such as a whole-genome sequencing diagnostic, through regulatory clearance, she said that Illumina is "developing every technology with clinical grade in mind" and the acquisition of Edico fits into that picture. "The ultimate goal is the clinic," she said, "but it's too early to say what specifically we're taking through the regulatory process."
Illumina is also considering different ways of bundling the Edico software and its sequencing instruments. Tousi declined to disclose specifics on such plans but noted that there would likely be a range of options in future products, including having the software integrated on the instrument, available on-site but separate from the instrument, or in the cloud.