By Monica Heger
Illumina has slated a mid-year launch for a new instrument called the HiSeq 2500 that will have all the capabilities of a HiSeq 2000 as well as the option for a quicker, lower-throughput run that would enable users to sequence a "genome in a day," Omead Ostadan, Illumina's vice president of marketing, told In Sequence this week.
Additionally, the company said that it will be releasing improvements to its MiSeq desktop system by the middle of the year that will enable 2x250 base reads, increased data output to 7 gigabases per run, and faster run times.
The HiSeq 2500 will have a list price of $740,000 and existing HiSeq 2000 customers will have the option to upgrade for around $50,000 when it is launched. A full upgrade will be available for systems shipped in 2011, with upgrades at a lower performance level available for systems shipped prior to 2011.
New customers can purchase a HiSeq 2000 system now at a reduced price, then an upgrade to the 2500 when it becomes available, for a lower total cost than the $740,000 list price, officials said.
Discussing the new platform at the JP Morgan Healthcare Conference in San Francisco today, Illumina CEO Jay Flatley said that the company would first deploy this technology through its services business in the first quarter before launching the system commercially. In the second quarter, it plans to add "premium products" for the 2500 that would include enhanced sample prep and analysis to reduce turnaround time even more.
The HiSeq 2500 will leverage the existing architecture of the HiSeq 2000, but will incorporate a second option to sequence at lower throughout in less time. Users will simply press a button to choose either a 600 gigabase sequencing run or a 120 gigabase sequencing run.
The lower-throughput run will use a different flow cell and reagent kit than the higher-throughput run. Specifically, the 120-gigabase option has fewer channels on the flow cell and images fewer tiles, said Ostadan. The new system also borrowed some of the features of the MiSeq instrument, such as reduced chemistry cycles, he added.
One run on the lower-throughput option could generate 120 gigabases in 27 hours, or the equivalent of about one 30-fold human genome. Users can also use the option to multiplex and sequence 20 exomes in one day or 30 transcriptomes in less than eight hours, said Ostadan.
"It's an optimization of both the volume and composition of the reagents, as well as the configuration of the flow cell," he said.
Ostadan said the company chose to develop this platform because "over the course of the last year or so, we've started to see a faster-than-anticipated adoption … of sequencing into a clinical setting," but one major hurdle has been turnaround time for whole-genome sequencing.
While desktop instruments such as the MiSeq and Ion Torrent's PGM are good for rapid, targeted sequencing, neither are suited for whole-genome sequencing.
Ostadan expects that existing HiSeq customers looking to transition into clinical whole-genome sequencing will want to upgrade to the 2500. He said it could be particularly useful for translational medicine institutes that primarily perform discovery projects sequencing many samples, but occasionally want to rapidly sequence a single whole genome.
Sample-prep and analysis on the 2500 will be the same as on the 2000, and the same options for read lengths will be available, with paired-end reads of up to 100 base pairs available.
The accuracy profile will also be comparable. "One of our key requirements is no compromising on data accuracy," Ostadan said.
Running the 120-gigabase option will require a separate reagent kit, which Ostadan said would be less expensive overall than for the 600-gigabase run, though more expensive at a cost-per-gigabase level. The new kit will be cheaper than the current MiSeq reagent kit on a cost-per-gigabase level.
Illumina will also be rolling out upgrades to its MiSeq instrument by the middle of the year.
Flatley said that the company will first launch a less expensive, lower-throughput MiSeq kit for users who "don't require the full capability." This kit will be particularly suited for amplicon sequencing, small microbial sequencing, and targeted resequencing.
Additionally, the company plans to introduce a new kit and instrument upgrade to increase read lengths and throughput and reduce turnaround time.
Ostadan said that the company made improvements to the number of clusters that are imaged, which, in conjunction with the increased read lengths, leads to a three-fold jump in throughput.
Ostadan said that a new reagent kit and "minor modifications" to the instrument itself would allow for 2x250 base reads and a throughput of 7 gigabases.
Run times will depend on the type of sequencing experiment. A 2x150 base paired-end run will be 31 percent to 39 percent faster than current MiSeq run times and yield 28 percent to 35 percent more data. A 1x36 base single-end run will be 23 percent to 30 percent faster, generating between 28 percent and 35 percent more data.
Alternatively, for customers wanting more output, a 2x250 base paired-end run could generate 60 percent to 67 percent more data with an 11 percent to 20 percent faster run time over current MiSeq specs.
The company has not yet set a price for the new MiSeq reagent kit.
Have topics you'd like to see covered in In Sequence? Contact the editor at mheger [at] genomeweb [.] com.