Can RNA-Seq be used for TMB calculation?
2
0
Entering edit mode
18 months ago
rotemkat ▴ 10

Hi, I have RNA-seq data of cancer patients and their matched normal as well. I'd like to calculate for each patient the TMB, but I mostly find information about such calculations for Whole Genome/Whole Exome. Can you advice me what would be the best way to do such calculations? Thanks

RNA-Seq tmb • 889 views
ADD COMMENT
0
Entering edit mode
18 months ago

You could first call variants using the RNA-seq reads, but this is not ideal - see here: A: Inferring genotype based on RNA sequnces

Kevin

ADD COMMENT
0
Entering edit mode
9 months ago
Michael • 0

You could check out this approach which seems reasonable (https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-021-00898-y). It would be great to do this in a case where you have TMB from WES for most samples and want to estimate it for the portion that are missing it. You could verify it's accuracy in your data before applying to your missing data. You could use the TMB data you have to tune the results of your missing data. Good luck.

ADD COMMENT
0
Entering edit mode

Curiously, their GitHub page (https://github.com/Jessen-Erik/RNA.TOMS) is empty.

ADD REPLY
0
Entering edit mode

Patent? It's always about the money and never about the patient in biotech, but we'll try to convince them otherwise.

ADD REPLY

Login before adding your answer.

Traffic: 1394 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