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Illumina's New HiScanSQ Lets Users Perform Array, Sequencing Applications


By Julia Karow

This article, originally published March 19, has been updated to correct the number of lanes per flow cell, and to include additional information from Illumina.

Illumina's newly launched HiScanSQ platform, which combines a microarray scanner with a sequencing module, is targeted at existing Illumina array users who want to start sequencing, as well as new users interested in both Illumina's array and sequencing technologies, according to the firm.

The system, which the company debuted last week and will begin shipping early in the second quarter, has three main components: the HiScan Reader, a high-performance array scanner with sub-micron resolution that can also image sequencing flow cells; the SQ Module, an add-on fluidics device that delivers the SBS sequencing reagents; and the cBot clonal amplification system that grows the DNA clusters.

Originally slated to launch last year, the complete platform will have a list price "in the low $400,000" range, according to Tristan Orpin, senior vice president for commercial operations at Illumina. That price includes the $125,000 SQ Module, the $55,000 cBot station, and the HiScan Reader. All components can also be purchased separately.

The HiScanSQ further expands Illumina's offering of sequencing instrumentation, which also includes the recently launched high-throughput HiSeq 2000; its original Genome Analyzer IIx; and its recently launched scaled-down version of the GAIIx, the GAIIe.

The company was demonstrating the HiScanSQ at the Association of Biomolecular Resource Facilities annual meeting in Sacramento, Calif., this week. Jasmine Pritchard, a product manager at Illumina, told In Sequence at the conference that the system is expected to appeal to a number of different customers, including small core labs that might not want to purchase separate platforms to run sequencing and microarray experiments; groups that primarily run arrays but are looking to move into sequencing for the first time; and facilities that run both arrays and capillary electrophoresis sequencing and are shopping for their first high-throughput sequencer.

She added that the falling cost of sequencing has made arrays and sequencing "convergent," so many core labs are looking for a system that will allow them to perform some initial discovery with arrays, and then use sequencing to further characterize or validate the results in-house.

"The whole idea of the SQ platform was to give people ultimate flexibility," Orpin said. "It was not to draw people away from arrays and towards sequencing."

The new platform "isn't like a compromise between sequencing and arrays," he said, but rather combines "the best" of both technologies. The HiScanSQ system shares a number of design features with the high-throughput HiSeq 2000, for example, including larger flow cells than the Genome Analyzer, pre-packaged reagents, and reduced hands-on time.

Orpin also pointed out that the HiScanSQ has a software interface that allows users to visually integrate sequencing data with array data.

Pritchard noted that the company's sequencing portfolio now addresses the full "breadth" of the market, with the GAIIe, which has a list price of $250,000 and is targeted at "capital expenditure-sensitive" labs that are focused primarily on sequencing; the higher-priced GAIIx for larger sequencing facilities; and the $690,000 HiSeq 2000 for groups that are looking to "push the boundaries" of the technology.

Originally, Illumina had planned to launch the SQ module last year (see In Sequence 5/5/2009) but decided last fall to delay its release until early 2010 in order to be able to improve the platform's performance.

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The current iScan Reader for array applications will not work with the SQ Module, but existing iScan users who purchase the SQ Module by the end of the year will receive a free upgrade to the HiScan Reader, Illumina said.

Illumina had initially intended to make the existing iScan Reader compatible with the sequencing module, but decided later to make sequencing-specific improvements to the reader, now part of the HiScan Reader.

Orpin said the company will sell the iScan and HiScan readers as separate products, the latter at a slightly higher — but yet unannounced — list price.

One apparent difference between the HiScan and the iScan reader is the HiScan's larger size. The module — about the size of a dishwasher — offers the same capabilities as the iScan for array applications, but it also packs in sequencing features developed for the HiSeq 2000. Alex Treiner, associate director of engineering at Illumina, told In Sequence at the ABRF conference that while the HiSeq 2000 offers two flow cells along with a dual-surface imaging method to provide a total of four surfaces for analysis, the HiScan only uses one flow cell and a single surface for imaging, effectively giving it one-quarter of the throughput of the HiSeq 2000.

For sequencing, the HiScanSQ offers an output-per-run that places it between the high-throughput HiSeq 2000 and the lower-throughput GAIIe. For instance, the system can generate more than 50 gigabases of high-quality data per run, with run times ranging from 1.5 days for a 36-base single-end run to 8 days for a 2x100-base paired-end run. Each flow cell has 8 lanes and generates approximately 250 million filtered reads.

By comparison, the HiSeq 2000 generates up to 200 gigabases of quality-filtered data per run, the GAIIx currently delivers up to 50 gigabases per run, and the GAIIe provides up to 20 gigabases per run initially.

In terms of data generation speed — at least 6 gigabases of high-quality filtered bases per day — the HiScanSQ is faster than both the GAIIx and the GAIIe, Orpin noted, and is only topped by the HiSeq 2000.

Orpin said Illumina is in the process of signing up beta-test sites for the platform. According to Pritchard, the company will begin shipping the system to early-access customers over the next month.

Bernadette Toner contributed reporting for this article from the Association of Biomolecular Resource Facilities annual meeting in Sacramento.

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