NexteraXT sequencing primers sequences

[Laurence Game]

hi, I want to run NexteraXT libraries on the HiSeq and would like to order my own stocks of sequencing primers HP10, HP12 and HP11 rather than the Illumina dual index sequencing kit.

Has anyone worked out the sequences for these sequencing primers so that I can double check them with what I've worked out from the official Illumina Customer sequence letter from Sept 2012.

Thanks

[pmiguel]

I don't have an answer, but it is worth noting that it looks like Illumina uses different oligos, depending on the platform. I draw this conclusion because the specifications for custom oligos for the MiSeq emphasizes this point.

Also, let me toss in my obligatory denunciation of Illumina for obscuring this information. I think it would be helpful if granting agencies forbade using black-boxed methodologies of this sort. I double Illumina gets much (if anything) out of hiding this information from their customers. So any sort of regulatory nudge would be likely to move them from this absurd position.

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Phillip

[SeqR&D]

why would a company give up a secret that is making them money, so that you can buy it from someone else? they do give you a way to use your own sequencing primers...what more could you want? Can you just order the sequencing primers from them individually?

[james hadfield]

Yes you can buy the oligos from Illumina, but at a ludicrous cost compared to buying an oligo from most providers. Illumina's big loss would be for Agilent and Nimblegen to use the sequence information to produce blocking oligos for ther capture kits. This would allow them to offer Nextera based capture, an easy way to 50ng input capture preps. Something they are sorely lacking.

Of course any academic wanting to do the same could mess around or just buy TruSeq capture kits. I am sure illumina would prefer to keep these sequences locked down, but this is futile given the ease of sequencing a library to find out the base composition.

I agree with pmiguel's sentiments. Illumina have little to fear if their IP is good as commercial use would be in breach and they could litigate. Making sequence information hard to get hold of is a pain.

[pmiguel]

I agree with pmiguel's sentiments. Illumina have little to fear if their IP is good as commercial use would be in breach and they could litigate. Making sequence information hard to get hold of is a pain.

My guess is they are doing this as part of some agreement with someone they are licensing a technology from. At least that is an issue I have seen cause otherwise rational corporations act irrationally in the past.

That is why I think the answer is for the granting agencies to ban use of closed source technology of this type. Would make sense as it is questionable whether you are really doing science at all when relying on reagents of undisclosed composition from a 3rd party.

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Phillip