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aleferna 05-17-2011 09:36 AM

TruSeq Custom Enrichment Kits
Illumina was tuting these new kits in a seminar in Uppsalla, this is probably going to be very hot once the clinical sequencing wars (MiSeq vs PGM) get into full gear. Has anybody heard about these kits ? are they just hype? Is there anything better/cheaper/available? We are currently developing our own custom "kit" and I'm afraid that by the time we get it working there will be a cheaper and better way to do it.

james hadfield 05-24-2011 02:01 AM

These were also presented at AGBT.

The kits will be based on Illumina's GoldenGate technology so hopefully up to 1536 loci targeted by multiplex PCR producing barcoded libraries. The GG protocol required a 16 hour hyb then clean-up and extension & ligation. Assuming this is a 96well plate based kit a single person could probably process 4-8 plates a day allowing a whole flowcell to be prepped pretty quickly.

Illumina were going to release these kits at the same time as MiSeq. However a kit would need different numbers of barcodes to be run on MiSeq vs HiSeq. Perhaps running only 1 column on MiSeq and the hole plate on a lane of HiSeq might be possible? I guess we have to wait and see.

Illumina have been very successful with some Cancer projects so I'd expect to see Cancer gene panels on launch.

96well multiplex on miSeq at $400 a run could allow DNA fingerprinting using SNPs for only $5-10 per sample. A whole lot faster, cheaper and easier to analyse than STR profiles.

I am sure loads of applications will come out of this once the kits are released and we can access custom panels.

Comparison to other technologies suggests the GoldenGate kit wil be pretty competetive on many criteria. Whilst GG was used for genotyping I believe quite large regions could be targeted. Design is pretty easy, although I am not so sure about tiliing with multiplexed PCR primers. This wil use small amounts of DNA (perhaps les than 250ng), be in a standard 96well format and not require anything other than a bead cleanup. Assuming the PCR reaction is set to run to completion of primers then all samples should achieve the same yield and pooling will be straightforward.

razibus 05-24-2011 02:39 AM

Some information about TruSeq Custom Amplicon :
- 85% success rate
- 10% design failure
- 5% PCR failure
- 2 weeks from orders to shipment
- QC kit will be available

And if I'm not mistaken, you can note that Illumina's GoldenGate technology is already used in BeadXpress system.

GW_OK 08-04-2011 02:16 PM

Has anyone been playing around with this in the Design Studio?
Any thoughts on repeat masking?

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