Distinguish tumor or normal type from WES data

Question

[Nich]

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!

Answer 1

[Kevin Blighe]

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