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Old 03-21-2010, 12:49 AM   #1
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Default HiScanSQ and iScan with SQ module

Hi all,

I find that genomeweb has a news article saying there will be an SQ module for iScan. But the last time I talked to an Illumina sales rep, she said that plan was scrapped. Anyone knows the truth?

Also, I want to know if I understand the difference between HiScanSQ and iScan with SQ module. Based on what I know, HiScan and iScan both scan BeadChips at the same speed (e.g. 50min for one Omni1 chip). But HiScanSQ can sequence 50G per run whereas iScan with SQ can only do 20G per run which is on par with GAIIe. Is that right?

Thanks a lot!

Illumina Launches HiScanSQ, Hoping to Lure Microarray Users to Sequencing
March 19, 2010
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+EmailPrinter-friendly versionRSS FeedBy Julia Karow

This article has been updated to correct the number of lanes per flow cell.

Illumina today launched HiScanSQ, which combines a microarray scanner with a sequencing module that is primarily targeted at existing Illumina array users who want to start sequencing, as well as new users interested in both Illumina's array and sequencing technology.

The instrument, which the company said will begin shipping "early" in the second quarter, consists of two components: the HiScan Reader, a high-performance array scanner with sub-micron resolution that is an update to the firm's existing iScan Reader for its BeadArray productsp; and the SQ Module, an add-on fluidics device for sequencing that uses the same SBS chemistry as Illumina's other sequencing platforms. For sequencing, it also requires the cBot clonal amplification system to grow DNA clusters.

Illumina is not disclosing the price for the system.

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

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 its performance (see In Sequence 9/22/2009).

The HiScanSQ offers performance that places it between the high-throughput HiSeq 2000 and the lower-throughput GAIIe: 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.

The system shares a number of design features with the HiSeq 2000, including larger flow cells, pre-packaged reagents, and reduced hands-on time.

For 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.

Illumina said that existing users of its iScan reader for array scanning will be able to perform sequencing with the purchase of the SQ module.
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Old 03-22-2010, 03:17 AM   #2
james hadfield
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I believe HiScanSQ is the model Illumina are launching in place of iScan sequencing module.

It has the output of GAIIx so this is probably the last kiss goodnoght for our old Solexa based systems...
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Old 09-01-2010, 08:21 AM   #3
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Default HiScanSQ

Does anyone have experience with the HiScanSQ? I am looking for a lower throughput sequencer to support R&D efforts. A HiSeq would be overkill and I like the ability to run arrays if needed. I also like that the HiScanSQ will have the new vacuum flow cell holder and easier reagent loading. Not sure it is worth the price versus a refurb GAII though.
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