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Old 10-23-2014, 08:32 AM   #1
Junior Member
Location: GA

Join Date: Sep 2014
Posts: 3
Default Library Prep for Cancer NGS

Hi all,

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 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.
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