mutation not in RNAseq read

Question

[Rob]

Hi guys how do you answer this:

You have first performed mutation calling from WGS in your tumor sample using blood as the normal control. Now looking at the RNAseq data from the same tumor sample, you notice that a heterozygous mutation in your gene of interest does not appear in the RNAseq reads even though there is plenty of coverage at this locus. Why might this be the case?

Answer 1

[Kevin Blighe]

Hmm, let me check with your course tutor... Hang on - I'll give them a call.

Or, just read my answer, here: Inferring genotype based on RNA sequences (RNA-seq variant calling)

Kevin

[Rob]

Hi Kevin Thanks you are always helpful. Please don't call my tutors they are crazy and overwhelmed us with too many questions for a short time and tomorrow morning is the deadline hahahha

Answer 2

[Jautis]

Two things I can think of off the top of my head: (i) a technical explanation would be that reads containing the mutation may not be mapping due to reference bias, but your WGS was mapped with different parameters which allowed the variant to be called; (ii) a biological explanation would be that there is a splicing variant, premature stop codon, etc. that prevents that allele from being on the sequenced transcripts. Also, if your WGS was from outside the tumor, it's also possible that there's a somatic mutation at the site which has risen to very high frequency within the cancer cell population.

[Rob]

thanks Jautis