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  • Any program reports somatic CNVs with tumor fraction?

    I noticed Mutect reports somatic mutations with tumor fraction (ie the percentage of tumor cells that has said mutation). I think this makes sense because it reflects tumor heterogeneity.

    But when I tried ExomeCNV for somatic CNV. It doesn't report tumor fraction. (or maybe it does but how to do that?) Do you know any somatic CNV program that reports tumor fraction?

    Thanks

  • #2
    It is probably extra difficult to identify a 3-fold duplication in 10% of the tumor cells, since it will look like normal diploid levels + a small increase over the whole sample. And you wouldn't be able to distinguish a 3-fold duplication in 10% of the tumor cells from a 30-fold duplication in 1% of the tumor cells.

    Some programs may report it anyway, but I do not know of any.
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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    • #3
      Originally posted by SNPsaurus View Post
      It is probably extra difficult to identify a 3-fold duplication in 10% of the tumor cells, since it will look like normal diploid levels + a small increase over the whole sample. And you wouldn't be able to distinguish a 3-fold duplication in 10% of the tumor cells from a 30-fold duplication in 1% of the tumor cells.

      Some programs may report it anyway, but I do not know of any.
      Thanks for your reply. Presumably, I suppose the prevailing FISH/IHC method to detect HER2 amplification/overexpression also suffer from the same problem?

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