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  • Calling tumor CNVs without normal as control?



    I noticed that the recently IPOed Foundation Medicine only used tumor sample to find mutations, CNVs and rearrangements by sequencing 200+ genes panel.

    I think their approach is fine with mutations/indels but sequencing normal as well to differentiate the true somatic ones might be slightly better. For rearrangement/fusion genes, they are using some introns sequence for that. I think RNA-seq can cover more fusion cases than this approach, is that right?

    The only thing that bugs me a lot is their claim about CNVs. Isn't that without the normal control, GC bias can't be removed?

  • #2
    Also curious about this. Perhaps they are using pooled normals?
    If library prep & sequencer are the same, and the pooled samples are copy-number neutral, it should be possible to get decent results using ExomeCNV.

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    • #3
      Originally posted by bw. View Post
      Also curious about this. Perhaps they are using pooled normals?
      If library prep & sequencer are the same, and the pooled samples are copy-number neutral, it should be possible to get decent results using ExomeCNV.
      If I understand correctly, pooled normal only helps for calling CNVs on normal samples in the context of ExomeCNV.

      I presume they aren't very nosy about accuracy. As long as it works in their clinical trials, then it is ok. One error can bite their ass though....

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