calculate mutation burden per gene
1
0
Entering edit mode
2.1 years ago
shubhrab • 0

Dear all,

I have a list of genes for which I want to calculate the mutations per MB.

How do I do this since every gene has a different gene size and the data is exome sequencing data.

Should I normalize it with respect to exome size or gene size. Also the coverage of the samples vary so that is a added variable.

Is there any existing utility that can do this?

--Thanks

mutations snps • 587 views
ADD COMMENT
0
Entering edit mode
2.1 years ago
Brice Sarver ★ 3.7k

This may not be the most helpful answer, but mutational burden can be calculated any of these ways. It's difficult to compare apples-to-apples among studies unless you say explicitly how you're doing it. You may be interested in the number of mutations per coding MB or per exon, which you'll be able to get from your annotation. If you have a large variability in coverage/depth among samples, you'll want to make sure that you take this into account so you don't bias the calculations due to false positives or false negatives.

This paper is a decent starting place outlining some of the different challenges and ways of estimating tumor mutational burden in a clinical setting.

ADD COMMENT

Login before adding your answer.

Traffic: 1768 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6