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Mutect2 PoN for RNA-Seq

ivlachosivlachos AthensMember

We're analyzing a batch of RNA samples to identify mutations.
We don't have matched healthy tissue and we are wondering what would be the optimal panel of normals to use.

We are thinking of using RNA-Seq data from healthy subjects. However, the differences in expression (many genes and isoforms will be DE between healthy and patients) will result in numerous regions not having adequate coverage in the PoN.

Using WGS from e.g. 1000G would be a better option? Coverage will definitely be better, since expression is not a factor but we will not be capturing many technical artifacts from the process (reverse transcription, oligo-DT, spliced alignment, etc).

What do you recommend? We know it's an off-label use of the pipeline.

Thank you

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Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    @ivlachos

    It is best to use a pon that is most technically similar to your samples (same preparation methods, sequencing technology and so on). But if that is not available then maybe use 1000G. Some pon is better than no pon.

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