Does TruSeq Amplicon work on FFPE ?!

[HedleyC]

Hi all,
Several people have posted questions on this forum about TruSeq Custom Amplicon (TSCA) or the TruSeq Amplicon - Cancer Panel (same tech?) but nobody seems to have the answers (or are not willing to share them).

Illumina's website states their TruSeq Amplicon - Cancer Panel works on FFPE (well, if your FFPE DNA samples pass their QPCR test, and then only "around" 80% will work). Separately, Illumina Tech Support stated to me they did not recommend using FFPE DNA with TSCA (though that was in March, perhaps things have changed).

My question is - has anyone used TruSeq Custom Amplicon or the TruSeq Amplicon Cancer Panel on DNA from FFPE samples, and if so - how did it perform? The lack of information may be telling in itself, but someone must be willing/able to share...

Regards,
HedleyC

[Bukowski]

I was told FFPE was not a supported application for TruSeq from someone who spoke to Illumina directly (recently), as you say, despite claiming it is optimised for that on their website. They were keen to help us to get it to work however after we tried it with very limited success - i.e. about 80% of samples *failed* - these are samples that we have happily used SureSelect on. I'm not claiming they were great quality samples, but it wasn't a great experience.

[HedleyC]

Thanks Bukowski,
Illumina Tech Support state FFPE is now supported - though all I can see is that they've added the rather stringent QPCR test so you can vet out most of your FFPE samples before you waste your time and money on them! That's one way to support FFPE I suppose...not very useful though. Hopefully they'll come out with a better solution in the next few months. Right now I would select a LifeTech or Qiagen panel.