Mutation counts corrected by number of samples
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21 days ago
garcesj ▴ 50

Hi,

I have performed whole-genome sequencing (WGS) in two different conditions: condA (n = 15) and condB (n = 23). I want to compare the number of mutations, but obviously, the different numbers of samples in each condition bias this number.

Is there a way of "correcting" by the number of samples? Note I don't want to take just the average (ie, total mutations/total samples condX) but "correct" the number of mutations in each different sample.

I tried just doing number of mutations in each sample/total samples condX, but something doesn't make sense to me.

Thanks a lot!

mutations WES genomics WGS • 340 views
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I want to compare the number of mutations

This comparison will give you literally no useful information.

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How come? If I have a pro-tumorigenic product, for example, wouldn't this comparison be valid?

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Something with 4 mutations need not be worse than something with 1. It depends on the effects of those mutations as well as other mitigating factors. Mut vs WT is a valid comparison, comparing number of mutations is not.

Or maybe you're on to something and I'm missing a critical component of your analysis.

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I see your point, especially depending on affected genes, totally agree. However, differential values in the number of aberrations (in the broad sense, eg TMB, chromothripsis, etc.) seem to have a relevant value... or maybe I'm misunderstanding something?

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