Illumina this week made further inroads into the clinical market with the launch of disease-specific targeted sequencing products, diagnostic whole-genome sequencing on the HiSeq 2500, and a new collaboration with Partners HealthCare for clinical interpretation of sequencing data.
The company's disease-specific content sets, dubbed TruSight, are specific for autism, cardiomyopathy, inherited cancer, inherited diseases, and exome sequencing.
These products are the latest step in Illumina's ongoing strategy to capture a share of the nascent clinical sequencing market and shed some light on the direction that its Translational and Consumer Genomics business unit is taking.
Earlier this year, Matt Posard, general manager of the Translational and Consumer Genomics business unit at Illumina, told Clinical Sequencing News that the group was focused on enabling genomics-based healthcare and would seek to develop a physician's report as well as disease-focused panels that could be customized by clinical labs that wanted to launch them as laboratory-developed tests (CSN 3/14/2012).
The new products are "the realization of that plan," Posard said this week.
Illumina's other clinically focused unit, its Diagnostics business, has also been moving forward as it seeks to increase hires within its clinical and medical affairs group (CSN 9/5/2012).
The TruSight products are designed to be run on the MiSeq and to be interpreted using Partners Healthcare's GeneInsight Suite, a genome interpretation software package that is already registered with the US Food and Drug Administration as a Class I exempt medical device, Posard said.
"We identified very early on that an individual customer's ability to analyze and interpret sequencing data was a bottleneck in adoption with clinical research customers," Posard said. To address that bottleneck, Illumina considered various options, including building an interpretation tool itself, buying one, or partnering.
Posard said that after evaluating the landscape, the GeneInsight Suite by Partners HealthCare quickly "rose to the top." The software has been in the field for over seven years and a number of clinical labs already use it. The tool can also scale to evaluate both targeted panels and whole genomes.
It is compliant with CLIA and HIPAA and the fact that it is registered with the FDA could potentially be helpful as Illumina looks to bring its MiSeq system through FDA 510(k) clearance along with one or several of the TruSight assays, Posard said
"The company's intention is to take any or all of these products through the FDA based on clinical trial design and market interest in this research phase of the product's usage," he said.
Posard said that the company would be looking to get market feedback about the products before deciding which or when to take them through the FDA.
Because the TruSight assays are being sold as research-use-only products, Posard said that labs interested in using them for diagnostic purposes would have to validate them in a CLIA-approved setting.
Additionally, he said, the TruSight products have been designed so that "individual customers can augment the design, or content of the oligos, and create additional content if they wish, and therefore create a customized product that would satisfy the [laboratory-developed test] requirement" under CLIA.
The TruSight products are based on the Nextera "tagmentation" chemistry. Tim McDaniel, Illumina's director of scientific research, told CSN that the company chose to use the Nextera chemistry versus the TruSeq chemistry because it was much simpler and fast — requiring 90 minutes for library preparation. By comparison, the TruSeq kits require eight hours for library prep.
Illumina partnered with experts in the field to develop each of the TruSight assays.
The TruSight Autism assay was developed with Jonathan Pezsner at the Kennedy Krieger Institute and targets around 100 genes. TruSight Cancer targets germline mutations in around 94 genes associated with inherited forms of cancer and was developed with Nazneen Rahman at the Institute of Cancer Research in London. The assay includes the BRCA 1 and 2 genes.
TruSight Cardiomyopathy focuses on 46 genes and was developed with Heidi Rehm's group at Partners HealthCare's Laboratory for Molecular Medicine. Rehm's team had already been developing a cardiomyopathy test that originally used both next-gen and Sanger sequencing (CSN 2/22/2012).
The TruSight Inherited Disease assay was developed with Stephen Kingsmore at Children's Mercy Hospital. His team had been working on its own inherited disease panel — comprising the same 552 genes that are now in the TruSight assay — originally as part of the National Center for Genome Resources, but moved the test to Children's Mercy Hospital for the clinical launch.
Last year, Kingsmore's team began a validation study of the assay in a clinical trial of 1,000 known patient samples using the HiSeq 2000 and Agilent's SureSelect enrichment kit (CSN 8/9/2011)
And finally, Illumina's TruSight Exome assay targets 2,761 genes — all the genes that are known to be associated with clinical ailments or conditions as reported by the Human Genome Mutation Database.
Additionally, Illumina has expanded its diagnostic sequencing services and now offers whole-genome sequencing on the HiSeq 2500 in its CLIA-certified laboratory. The service will require a physician's prescription and will initially be available on a limited basis. Illumina will evaluate cases submitted for sequencing on the 2500 to prioritize which patients will most benefit from a faster turnaround.
Posard said that Illumina does not intend to offer its TruSight assays as a diagnostic service, because that would compete directly with its customers.