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Old 02-10-2011, 11:38 AM   #1
upenn_ngs
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Default Illumina-compatible runs

Why hasn't ABI produced flow cells compatible with Illumina sample preparations? At our facility the SOLiD machine has yet to be turned on, while the HiSeqs constantly run.

I do not believe most people are adverse to using SOLiD sequencing technology, but the majority of users have settled into protocols for Illumina sample preparation.
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Old 02-10-2011, 03:48 PM   #2
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Bridge amplification is owned by Illumina. That's why SOLiD is ePCR.
The rest of the workflow is pretty much identical. I don't let people complain about the two protocols in my lab. It's a non issue these days.
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Old 02-11-2011, 07:37 AM   #3
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Right, I suppose the emulsion PCR could be done using microbeads with oligos homologous to the illumina adapters.

In addition, the blunt-end ligation scheme of SOLiD prep is not close to the efficiency of 3' adenylation followed by T overhang ligation for Illumina.

But it seems like a fair opportunity for ABI to gain some market share.
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Old 02-11-2011, 10:54 AM   #4
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Are you sure your lab is not being paid a subsidy by Illumina to allow your SOLiD to lay fallow?

I am doubting that Illumina owns bridge amplification. Seems very similar to the original polony amplification which is likely IP owned by George Church. I heard both Applied Biosystems and Illumina were licensing various Church patents initially.

SOLiD fragment libraries are easy to make. But if Illumina libraries are even easier, that is great news. We just got an Illumina.

Here is what I think happened. Illumina got a year lead on Applied Biosystems initially. From there they just needed not to mess up in any serious way. They have not so far.

Also, I think color space sequence is very much an acquired taste. The ECC that is being released in tandem with the 5500XL should have been released back with v2. Then you have the best of both worlds.

I actually like the idea of being able to run Illumina libraries on the SOLiD. Not sure it is feasible though. I think they have done a lot of optimization on the priming site they know.

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Old 02-11-2011, 03:24 PM   #5
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right. I'm pretty sure they don't own Bridge amp either, but it's most likely an exclusive license. Complete Genomics doesn't own RCAmp but i'm sure they tried to lock down nanoballs somehow.

the adenylation is more efficient, but it's not really needed. This is also not exclusive to Illumina ,and it actually adds another step to all library preps making illumina's take longer. If you can make nanogram libraries with both methods, then i don't see the clear advantage. You could probably make SOLiD libraries with sticky ends. Has anyone tried?
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Old 02-11-2011, 09:53 PM   #6
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From what I have read, Illumina does look like it actually owns some amount of bridge amp IP. Solexa and Lynx Therapeutics purchased solid phase amplification (bridge amplification) from Manteia SA which was a Swiss company. Where Manteia got it from (Turcatti?) I'm not sure, but all available information seems to indicate an outright purchase of the IP as opposed to licensing.
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Old 02-14-2011, 05:00 AM   #7
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Quote:
Originally Posted by SeqAA View Post
the adenylation is more efficient, but it's not really needed. This is also not exclusive to Illumina ,and it actually adds another step to all library preps making illumina's take longer. If you can make nanogram libraries with both methods, then i don't see the clear advantage. You could probably make SOLiD libraries with sticky ends. Has anyone tried?
In general one does not add anything to the insert, because that will get sequenced and waste that base. Sure it is only 2% of the total read, but the early bases have the highest quality.

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Old 02-14-2011, 05:05 AM   #8
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Looks like my doubt was misguided. Also, apparently "bridge amp" must be considered different enough from "polony" PCR that it was granted a patent. Anyone want to hazard a guess as to why that would be?

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Old 02-14-2011, 11:02 AM   #9
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Manteia got it from a failed Church-affiliated company (whose name escapes me). Anyone know how many years are left on the patent? It could be around a decade old by now.
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Old 02-14-2011, 01:50 PM   #10
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Mosaic Tech?
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Old 02-14-2011, 01:56 PM   #11
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Quote:
Originally Posted by pmiguel View Post
In general one does not add anything to the insert, because that will get sequenced and waste that base. Sure it is only 2% of the total read, but the early bases have the highest quality.

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If you're adding a defined sequence wouldn't you just put in the sequencing primer therefore wasting 0 bases?
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Old 02-15-2011, 05:47 AM   #12
pmiguel
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You don't pick your sequencing primers with the SOLiD. The methodology is based on annealing a group of 5 primers with different offsets. This is all bundled together in to the run chemistry kits.

In principle, Life Tech could create different run kits for "A-tailed" and blunt-end ligation methodologies. But, given the problems they have had keeping kits stocked, adding more complexity is not warranted.

All of this is really a non-issue. Ligation efficiency just doesn't seem to limit the protocol.

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