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Question: Distinguish tumor or normal type from WES data
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gravatar for Nich
11 days ago by
Nich • 10
Nich • 10 wrote:

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 • 116 views
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modified 9 days ago by Kevin Blighe ♦ 69k • written 11 days ago by Nich • 10
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gravatar for Kevin Blighe
9 days ago by
Kevin Blighe ♦ 69k
Republic of Ireland
Kevin Blighe ♦ 69k wrote:

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
ADD COMMENT • link modified 9 days ago • written 9 days ago by Kevin Blighe ♦ 69k
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