Question: Can I ignore somatic mutations that are also in dbSNP when analyzing cancer-related variants?
0
gravatar for mangfu100
3.5 years ago by
mangfu100610
Korea, Republic Of
mangfu100610 wrote:

Hi all.

I am having a bit of hard time analyzing somatic mutations for downstream analysis.

I found some somatic mutations and organized them into a group for my analysis. And then, I tried to see whether they are related to cancer or not using many sequencing filters and public databases. In this process, I have questions for you about the dbSNP.

I know that dbSNP have a list of mutations with population frequencies that are reported in only healthy-person. Suppose that I have mutation at chr1:1000 and I think this mutation is dominant and cancer-related by the fact that this mutation was also found at the sample position in other samples(all the samples have the same cancer-type. Therefore I regard the mutations detected across samples as recurrent mutations not as artifacts) and they passed all the filter I used. And then, I used the dbSNP databases to see if they have my detected mutation and ,finally, I identified the same mutations in dbSNP at the same positions with same base changes.

In this situations, my questions is as follows :
1) Can I ignore this mutations by the fact that they already existed in dbSNP?

2) Are there any other evidences that I am going check more in dbSNP such as allele frequencies, population levels before removing it?

3) What if my detected mutations are also both in COSMIC databases and dbSNP? How can I treat them for my downstream analysis? 
(Assumption is that cosmic reports the cancer mutations while dbSNP has variants that found in healthy-person.)

next-gen sequence genome • 2.1k views
ADD COMMENTlink modified 9 months ago by CY230 • written 3.5 years ago by mangfu100610
2
gravatar for Chirag Nepal
3.5 years ago by
Chirag Nepal2.1k
Copenhagen
Chirag Nepal2.1k wrote:

I doubt that the SNPs found in dbSNP are entirely from healthy people. Any reported (verified) SNPs are put in dbsnp, so which is likely to include somatic mutation as well. Many GWAS and exome-seq SNPs are updated in dbSNP.

 

ADD COMMENTlink written 3.5 years ago by Chirag Nepal2.1k
0
gravatar for CY
9 months ago by
CY230
United States
CY230 wrote:

Depending the one population frequency. Variants in dbSNP with high PF are highly unlikely to be driver mutation

ADD COMMENTlink written 9 months ago by CY230
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