Illumina at EmTech

By Aaron Krol

September 25, 2014 | Francis de Souza, president of gene sequencing company Illumina, spoke about the future of practical genomics at the EmTech emerging technologies conference in Cambridge this week, as reported by Antonio Regalado for conference host MIT Technology Review. One figure from De Souza's address has been getting particular attention from observers: Illumina surmises that 2014 alone will see the sequencing of 228,000 whole human genomes.

Estimates for the total number of human genomes being sequenced around the world are hard to come by, but if anyone should know, it's Illumina. The company's instruments represent at least two-thirds of the total gene sequencing market, and because Illumina machines can sequence samples in greater bulk than competitors, they yield an even greater portion of the total genetic data being produced. The estimate of 228,000 whole genomes for 2014 is certainly in the same league as, and may even exceed, the entire volume of human genomes sequenced in every previous year combined. De Souza also suggested that whole genome sequencing will cross the threshold of one million per year by 2017.

To this reporter, however, other observations from De Souza are even more noteworthy. One is the notion that his company has already pushed the price of gene sequencing about as low as it's likely to go. While Illumina made waves earlier this year with the announcement that its new HiSeq X device could sequence nearly 2,000 genomes a year for $1,000 apiece (a figure that is disputed, but certainly not wildly off base), it seems the company will now focus less on its relentless drive for higher throughput, and more on bottlenecks like the slow and expensive process of genome interpretation. Meanwhile, companies like Oxford Nanopore are gambling that it's still possible to drive the cost of sequencing down even further with a new technological approach.

Second, De Souza spoke about a company-wide "pivot" to clinical use. This is not unexpected, as Illumina has already secured the first FDA clearance for a next generation sequencer and has been hard at work designing new gene panels for routine medical use. The same path is being pursued by competitor Thermo Fisher, whose Ion PGM Dx instrument seems to be inching steadily toward clearance, and by QIAGEN, which intends to skip the research market and go directly to clinical use with the as-yet-unseen GeneReader instrument.

But what may be surprising is Illumina's commitment to moving forward by releasing traditional, FDA-approved diagnostic tests for specific use cases, even as De Souza cites cancer diagnostics, a regulatory minefield, as accounting for fully half of a predicted $20 billion sequencing market. Illumina already dominates this field, thanks to companies like Foundation Medicine and MolecularHealth that use its sequencers for in-house genetic cancer tests while positioning their services as "laboratory developed tests," exempt from scrutiny by the FDA. Yet Regalado quotes Illumina's CMO, Rick Klausner, as saying this model "is not serving patients well... We think these tests need to be regulated."

While deemphasizing third-party test providers may be a short-term obstacle to growing the clinical sequencing market, in the long term, it's likely to bring Illumina and companies like it more directly into patient care. Illumina recently announced that it is developing its own broad cancer panel, to be used in clinical trials for new cancer drugs. At the same time, the FDA has signaled that it's ready to end the laboratory developed test exemption, lending new urgency to efforts to create reproducible panels that can win agency clearance.

Read Regalado's entire article for more on De Souza's EmTech address.