By Aaron Krol 

February 3, 2014 | Last November saw the passage of a milestone in clinical sequencing, when the MiSeqDx became the first next-generation sequencing (NGS) instrument approved by the FDA for use in clinical diagnostics. The approval marked a new stage in genetic medicine, giving care providers their first on-site access to technology that has been driving down costs and accelerating testing in academic labs for years.

It was also a big win for Illumina, maker of the MiSeqDx, which will have the chance to plant a stake in the clinical markets before it’s joined by competitors like Life Technologies and QIAGEN. At the JP Morgan Healthcare Conference in San Francisco this January, Illumina CEO Jay Flatley told investors that the company had sold eight of the new MiSeqDx systems in the fourth quarter of 2013, citing this as part of a “continued evolution toward a fifty-fifty mix between academic and commercial customers” for a company that has traditionally leaned heavily on the research sector.

Flatley also announced a commitment to scaling up its clinical offerings. “We’ve made a strategic decision to submit the HiSeq 2500 for FDA clearance,” he said, referring to Illumina’s centerpiece production instrument, which boasts over 60 times the maximum data output of the MiSeq. Clearance of the HiSeq 2500 would enable high-volume sequencing in a clinical setting, as opposed to the targeted, individual tests for which the MiSeq is best suited.

Clinical Informatics News spoke to Greg Heath, Illumina’s Senior Vice President for In Vitro Diagnostics, about the company’s plans for clinical sequencing in 2014, and where he sees this technology moving in the future.

In terms of applications, “the low-hanging fruit for sequencing in its current performance is, first and foremost, genetic disease,” says Heath. “For genetic disease, sequencing has been done for quite some time, but it’s been done on a smaller scale… We think next-generation sequencing is a much more thorough and much more accurate approach.” Hundreds of rare genetic diseases have been linked to single-gene mutations that are easy to sequence, and clinicians already diagnose these conditions using PCR-based assays. “It’s just a technology substitution,” says Heath, to move from these assays to NGS.

The first two targeted kits cleared on the MiSeqDx are both for diagnosis of cystic fibrosis (CF), which is both a familiar application, and a test that can be done more powerfully on a sequencing instrument than by PCR alone. One of the CF kits screens for 139 possible variants on the CFTR gene involved in the disease, while the other sequences the entire gene, taking into account novel variants that have never been seen before. This will help clinicians to not just rapidly diagnose the disease, but also distinguish different subtypes of CF that present different treatment options.

The FDA also approved the more open-ended MiSeqDx Universal Kit. “What that enables is [for] people to build their assays as lab-developed tests on an approved platform,” says Heath. These lab-developed tests have traditionally been less subject to regulation than commercial kits, and should be major drivers of use in the early days of clinical NGS, when the number of targeted kits is still limited.

That said, Illumina sees a serious need for an expanded line of sequencing kits with explicit FDA clearance. “Most labs are more comfortable with using tests that are FDA-cleared, rather than homebrews,” says Heath, “because it comes with a higher level of quality assurance. It comes with an approved standard that they know they can replicate across their labs… With an IVD-cleared kit, they can just roll it out nationally, or even internationally, with that level of comfort.” Lab-developed tests, by contrast, are restricted to a specific laboratory with CLIA certification.

Looking a little further ahead, Heath sees three big diagnostic areas opening up as NGS moves into the clinic. “Oncology,” he says, “I think is a perfect match for the performance characteristics of next-gen sequencing, and I think you’ll see a lot of work both from us and others on those assays.” Because cancer is such a genetically heterogeneous disease, sequencing can help narrow down which therapies will be able to target an individual tumor, based on its mutation profile.

Illumina has already made a play in this area, announcing a partnership with Amgen on January 15 to develop its first NGS test in oncology. The kit will be a companion diagnostic for Vectibix, Amgen’s antibody therapy for colorectal cancer. It will be built for the MiSeqDx and will look for RAS mutations, which indicate that a tumor may be susceptible to Vectibix treatment. Highly personalized cancer diagnostics like this are already taking off in the CLIA-certified labs of companies like Foundation Medicine, but as specific test kits gain FDA approval, they will grow more accessible to hospitals and other points of care.

Heath also sees infectious disease, which can be diagnosed by sequencing the DNA of viruses and other pathogens, and transplantation and transfusion, whose success is tightly tied to genetic similarities between the host and donor genomes, as promising areas for rapid adoption of clinical NGS.

In the longer term, he adds, “people are coming up with very creative applications of the technology. We’re fortunate that we’ve got such a large footprint on the research side that we see kind of what’s coming… We’re seeing things like microbiome, we’re seeing things in CNS [the central nervous system]. So I think there is both an immediate application for a technology substitution, but [also] a longer-term play for some of these novel applications.”

Scaling Up 

Approval of the HiSeq 2500 may also open up new potential for clinical sequencing. “There will probably be different users,” says Heath. “It’s targeted at a higher-throughput segment, and so for some of the centralized labs I think it may be a better choice if they’re doing lots and lots of the same assay.”

As an example, Heath brings up the verifi test, a non-invasive prenatal test (NIPT) for fetal aneuploidies like Trisomy 21 (Down syndrome) and Monosomy X (Turner syndrome). The verifi test is produced by Verinata, a wholly-owned subsidiary of Illumina, and will be the first test submitted to the FDA alongside the HiSeq 2500 for approval as a diagnostic. At present, the verifi NIPT is a very popular screen for mothers at heightened risk of having a child with an aneuploidy, because it relies on a simple blood draw rather than invasive amniocentesis. The verifi test can’t yet be legally considered diagnostic, but there is suggestive evidence that it is highly accurate even in mothers with average risk for aneuploidies.

“Right now there are a number of labs that are running non-invasive prenatal testing,” says Heath, “and that’s targeted for high-risk populations. But we anticipate that will move to the average-risk population, and as it does, of course then that would cover all pregnancies. So to achieve those volumes, you’d probably want a higher-throughput instrument.”

These are the kinds of routine tests that a production instrument like the HiSeq could enable. Today, genetic testing in the clinic is too expensive, and too time-consuming, for routine use without some indication of risk. But if the FDA finds that the HiSeq meets the same high standards of clinical validity as the MiSeqDx, these applications will become much more realistic.

Of course, that’s no minor bar to clear. “We have to do clinical trial work, we have to do reproducibility studies,” says Heath. “Some of that work, like shipping studies and analytical claims, of course we do already for the RUO [Research Use Only] product, but it’s a much higher level of rigor.” In some cases, Illumina actually has more validation work ahead of it than behind. “The FDA classifies things based on risk, and so for things like NIPT or some of the cancer tests, or even HIV tests, those are considered a riskier application, so to do that you have to do much more rigorous prospective clinical trials.”

“Our relationship with the FDA is very positive,” he adds. “We’ve built that over time by going to them early and often, and having a very collaborative approach with them. We have the same standards that they do. We want our products to be safe and effective, they want our products to be safe and effective.” Heath predicts the odds of the HiSeq 2500 making it through the FDA process over the next year or two are “quite good,” pointing out that the precedent of the MiSeqDx, which uses the same chemistry as the HiSeq, gives the agency a basic level of comfort with the technology.

In the meantime, Life Technologies is in talks with the FDA over its Ion PGM instrument – which the agency itself has agreed to use in screening food for contamination by E. coli and Salmonella – and QIAGEN is building its GeneReader instrument specifically for clinical use. “We will see competition, because the opportunities are so great,” says Heath. But he sees good reason to believe Illumina will maintain its edge in clinical NGS. “Illumina has really been solid on the innovation front. We don’t stand still and wait for a competitor to challenge us – we continue to challenge ourselves.”

Whether or not Illumina stays on top in the years to come, its early success with the FDA has finally made it possible to bring state-of-the-art sequencing instruments directly into clinical labs. Having an approved platform also empowers third parties to build assays on the MiSeqDx and partner with Illumina to shepherd them through the FDA process, expanding the universe of applications. While only a relatively small number of early adopters are likely to bring NGS into the clinic this year, 2014 will be the start of a long-anticipated shift in how care centers view genetic testing, and which areas of medicine the technology can be applied to.