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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.
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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. -
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.Comment
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Has anyone been playing around with this in the Design Studio?
Any thoughts on repeat masking?Comment
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Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.
There is no single reason why many patients don’t respond to treatment as expected. Cancer is...Today, 05:17 AM -
Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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