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With Upcoming iScan Module, Illumina Looks to 'Transition' Array Users to Sequencing

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Illumina is developing a new sequencing module for its iScan array scanner that it expects to launch later this year, according to company officials.

The firm recently disclosed details about the new product, called the iScan sequencing module, on its website. It will allow existing array customers to perform sequencing experiments at a lower instrument cost and throughput than the Genome Analyzer.

The company is targeting the module toward core labs that are "looking to increase the breadth of [their] offering to include small next-generation sequencing projects," as well as individual academic labs wanting to perform both array and sequencing experiments, an Illumina spokesperson told In Sequence.

The list price for the module is $130,000, considerably cheaper than the GA, which has a price tag on the order of $400,000 to $500,000. Not included in this price are an iScan-compatible cluster station and data processing and analysis tools, both necessary to run the sequencing module, according to the website.

Illumina CEO Jay Flatley said during the company's first-quarter earnings call last month that the development of the system is "on track" and that the company expects to make it commercially available toward the end of the year.

He said company engineers need to build a fluidics module that interfaces with the existing iScan imaging platform and to make changes to the iScan system and software that will allow it to be used for sequencing.

Flatley said the module will be a "great transition product" for customers already using Illumina arrays who want to do targeted resequencing, for example to follow up on results from genome-wide association studies. It should also appeal to customers interested in performing sequencing-based expression and methylation studies, he added.

Conversely, researchers can use the system to generate sequencing data to design custom genotyping arrays, according to Illumina's website.

Applications for the iScan sequencing module include sequencing of bacterial genomes; targeted resequencing of genome regions; mRNA sequencing; ChIP sequencing; and small RNA sequencing.

The sequencing module uses the same cluster station, flow cells, and sequencing chemistry as the GA, but the image acquisition happens inside the iScan Reader, the array scanner that is part of the iScan system.

The system's sequencing throughput is expected to be one-fifth to one-eighth of that of the Genome Analyzer, according to the spokesperson. Product literature states that the module will be able to generate up to 300 megabases of sequence data per day, and up to 3 gigabases and more than 32 million reads per run. Each eight-channel flow cell will be able to run up to 96 samples.

Runs generating paired-end reads of at least 50 base pairs will take less than 10 days, and runs resulting in single reads at least 25 base pairs in length will take less than 2.5 days.

For comparison, according to the most recent available specification sheet for the GA, that instrument produces up to 1.8 gigabases of data per day, or up to 10 gigabases and 100 million reads per run, based on 50-base paired-end reads. By the end of the year, Illumina expects the instrument to be capable of producing up to 100 gigabases per run.

Illumina is currently accepting pre-orders for the iScan sequencing module. The company spokesperson said the firm has received "a lot of interest" in the new product from current and potential customers.

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