Illumina Launches NovaSeq Sequencers, Aiming To Replace 1900 Sequencers

January 9, 2017

By Allison Proffitt

January 9, 2017 | Speaking at the J.P. Morgan Healthcare Conference this afternoon, Francis deSouza, President and CEO of Illumina, unveiled the NovaSeq series, a new and scalable sequencing architecture, comprised of two instruments: the NovaSeq 5000 and NovaSeq 6000.

The announcement must have gone over fairly well. In after hours trading, Illumina jumped 10.2%, and during the announcement deSouza said that all six customers Illumina presented the new platform to are in the process of buying one.  

The NovaSeq instruments offer ease of use features similar to those found in Illumina's desktop sequencing portfolio, the company said in a statement, including automated onboard cluster generation, cartridge-based reagents, and streamlined workflows. With scalable throughput, users will have the flexibility to perform sequencing applications requiring different levels of output by simultaneously running one or two flow cells from up to four different flow cell types. Illumina’s public stats sheet is available, and there are some nice blogger breakdowns on specifics (and weaknesses) around. Mick Watson at Opiniomics has his assessment up. Keith Robison at Omics! Omics! has his take live as well. (Robison also Storified his source tweets and articles.) 

The NovaSeq 5000 and 6000 Systems are priced at $850,000 and $985,000 respectively. The NovaSeq 5000 can be upgraded to a 6000 in situ. The difference between the two are the new flow cells each system can run. The 6000 can run four flow cell formats. The S2 format flow cell will be the first available. S1, S3, and S4 flow cells will be available over the course of 2017. 

Compared with other Illumina sequencing systems, both have lower per-sample consumable costs for most sequencing applications.

The NovaSeq instruments are the most deeply cloud-integrated instruments Illumina has produced, deSouza said. Users can monitor the health of the instruments via cloud, getting log files to do proactive monitoring and maintenance; or they can store output on the cloud. “BaseSpace is tuned to be able to get the data at the throughputs that NovaSeq runs, and do that in a seamless way,” deSouza said. Though, of course, customers aren’t compelled to use the cloud.

New Year, New Life

deSouza spent a fair amount of his time talking about the market. “We intend to really push the envelope beyond where we were with the HiSeq line, which is now entering its 8th year of operations and even upgrade the HiSeq X customers.”

The business structure of the NovaSeq launch is different in almost every way from how Illumina chose to launch the HiSeq X instruments at J.P Morgan two years ago. NovaSeq is an instrument Illumina’s high throughput customers can all buy, deSouza emphasized. There’s no minimum order as with the HiSeq X5 and X10. There’s no restriction on coverage, species, or application.

On Twitter, commentary bemoaned the future of the HiSeq X series—a $10m fleet—but deSouza has his sights set on all the HiSeq instruments.

“The focus will be to work on our HiSeq install base, and we have about 800 customers representing about 1,900 instruments that are out in the field that we’ll be looking to catalyze and upgrade. 

NovaSeq will create a “multiyear replacement cycle over a HiSeq install base,” de Souza said.

deSouza ran quickly through the comparisons. For a HiSeq 2500 customer, NovaSeq delivers 50% price reduction per Gb; 100% more output per run on the S2 flow cell. For HiSeq 4000 customers, NovaSeq delivers 45% price reduction and 2.5x the output based on the S3 flow cell. For X customers, “NovaSeq will be 20% more economical while delivering three times the throughput.”

For customers who have bought a HiSeq or an X in the past two quarters, deSouza says Illumina will exchange that instrument for partial value applied to a NovaSeq. For customers with X instruments on order that they haven’t received, they can change that order to a NovaSeq and keep all of their investment.

Of course there will be a backlog of NovaSeqs as well. deSouza listed early customers: the Broad Institute, Novogene, HLI, Regeneron, Baylor, and the Chan Zuckerberg Biohub. These earliest customers have already committed to 49 instruments, deSouza said, “which is close to double what we can manufacture and ship in Q1.” The NovaSeq 6000 will ship, “in limited quantities” later this quarter, deSouza said; the NovaSeq 5000 will ship over the summer.

$100 Genome of the Future

Every new Illumina high throughput platform, deSouza said, has enabled new applications. He has the same hopes for the NovaSeq. He expects the new architecture to drive sequencing focus from exomes to genomes. He expects to see more population sequencing, tumor/normal analyses, and liquid biopsies become broadly accessible. He sees opportunities for much deeper sequencing and single-cell sequencing. (Together with BioRad, Illumina also today announced the launch of the Illumina Bio-Rad Single-Cell Sequencing Solution, the first next-generation sequencing (NGS) workflow for single-cell analysis.)

Although the instrument won’t, now, achieve a $100 genome, deSouza believes a new era has been launched. “For the first time, as we look at all the different components, we feel that every component we have in the system has enough head room that we can see a path to get there. Now we have to do the work to get there, and that will take time.”