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Distinguish tumor or normal type from WES data

I have a set of paired tumor and normal WES next generation sequencing data. I would like to ask if there is a way I can make accurate judgments when I don't know the type of data?

I would like to find a way to know whether a sample is tumor or normal without knowing their types.

Can anyone help me with some information? Thanks!

wes
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updated by Kevin Blighe Kevin Blighe • written by Nich • Nich

1 answer

Was there a labelling mix-up? - how can it be that you do not know which sample is which?

Different cues can help:

  • in the tumour sample, assuming that it's a bulk biopsy, you would expect to find variants (somatic mutations) against the standard reference genome at frequencies ranging from ~1 to 100%; whereas, in the normal sample, they should be either 50% or 100%, that is, in the normal sample, they should be germline.
  • the tumour sample should contain most or all of those variants identified in the normal sample, plus extra, with these extra representing the somatic mutations.
  • one would expect more structural variants in the tumour sample depending on the level of genomic instability

Kevin

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written by Kevin Blighe Kevin Blighe

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