How effective and reliable would "Ion AmpliSeq™ Cancer Hotspot Panel v2" be for identifying variants of oncogenes and tumor suppressors genes in xenograft tumor?
Expecting comments from users of this panel.
Hi
since it is an ampliseq design, it's easy to run at laboratory steps. this design works fine on low deep sequencers (as PGM or Proton) and analysis is fast and simple, but this panel has been designed mainly to sequence hotspots. if you have an account on the ampliseq designer web tool, download the files of this design and see (on UCSC or IGV) the targets. you'll then get enough informations to analyse if your favorite targets are covered. maybe you'll need to design your own panel.
fred
sure, the interest for such panels is to have a deep view on the samples (I mean with high coverage, for cellular clones for example). if you look the MET exon14 coverage, you'll see that only variants at 5' will be covered, forgetting 50% of the published variants in the 3' of this exon...this panel is a good base but you can adapt it to what you observed in your lab.
fred
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