Question: Distribution of mutations in different parts of the genome
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gravatar for banerjeeshayantan
25 days ago by
banerjeeshayantan140 wrote:

I have obtained exome sequencing data from 10 normal-tumor samples from patients suffering from pancreatic cancer (PDAC). I am interested in finding the distribution of mutations (single base substitutions specifically) in different parts of the genome (both coding and non-coding). Is there a computational approach to do that?

genome • 77 views
ADD COMMENTlink modified 25 days ago by venu6.3k • written 25 days ago by banerjeeshayantan140
1
gravatar for venu
25 days ago by
venu6.3k
Germany
venu6.3k wrote:

This is called topography of mutations. There are not many papers on this aspect of the mutations. One way is to follow this paper. You will get more insights if you do mutational signature analysis first and do genome distribution of these signatures.

You can download matching cell-type epigenomic data from ENCODE and create genome features for yourself such as open/closed chromatin (or from ENCODE chromHMM results) and check if mutations are skewed to any of these genomic areas or do mutational processes have any effect on genome structure (or vice versa; both are interdependent in cancer).

PS: As you say it's whole exome data, I doubt there will be many non-coding mutations unless there is some off-target capturing.

Good luck.

ADD COMMENTlink modified 25 days ago • written 25 days ago by venu6.3k
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