Is it possible to detect somatic SNVs from C57BL/6 tumor samples WXS without normal tissue control?

Question

[tarekzakaria.badr]

Hi everyone,

i am a little bit new to whole exome seq analysis and did it only once before for human samples using bwa and Gatk pipeline and now I have whole exome sequencing data from tumor samples for C57BL/6 mice ( Gut tumor samples 3 wild type vs 3 KO). Unfortunately the mice aren't avialabe anymore and they didn't sequence parallel normal tissue. In Humans i would have compared it to 1000 genomes or something but what be the best way here to detect somatic SNVs in inbred mice. as most of the Pipeline i found like GATK MuTect2 run normal tissue parallel to the tumor samples?

My PI would like at the end to reach similar to the approach mentioned in this paper:- https://www.sciencedirect.com/science/article/pii/S153561081730507X?via%3Dihub).

Thanks in advance.

Answer 1

[igor]

Ideally, you certainly want a matched normal sample. You may want to use the WT samples as the normals.

You can get previously reported SNPs from something like dbSNP. It's not a perfect resource, but it's better than nothing. These previous discussions may be helpful:

• Bundle file for mouse
• Using GATK4 Mutect2 on mouse data, need a genome snp reference