Library Prep for FFPE Sample

[seq-ngs]

I posted this in a different forum but I think this one is more appropriate

I am designing several cancer panels to run on the MiSeq. Each panel consists of 600-800 amplicons - approximately 150 bp each. What I am pondering right now is the library prep method to use. There are 5 main options:

1. Illumina - TSCA
2. Life Tech - AmpliSeq
3. Agilent - Haloplex
4. NuGen
5. Qiagen

We deal with formalin-fixed, paraffin-embedded (FFPE) samples that are degraded and often of low DNA quantity/quality. I like Ampliseq better than TSCA because it is multiplex PCR rather than probe hybridization (like Illumina) but don't want to run Ampliseq on the MiSeq because the Life Tech people seem not to like that. Any thoughts on a good library prep method from the choices above for FFPE samples? Thanks so much for any input.

[jenserichsen]

Hello seq-ngs - my name is Jens Erichsen with Kapa Biosystems. Would you be interested in looking at Kapa's offering for library construction? Our Hyper Prep Kit has been demonstrated to work particularly well with FFPE DNA. Please send me an email - [email protected] - and we can talk further. I look foward to hearing from you. - Jens