No somatic mutation in tumor sample

Question

[umn_bist]

Just wondering if this is plausible...

I am working with head and neck squamous cell cancer samples from TCGA, and the tumors do not have any somatic mutations when I view it through IGV - specifically on TP53. Commonly there should be a high mutation rate for this cancer type.

I see common SNPs but no mutation. Could it be that part of the workflow removed them?

I simply trim adapters and poly-N and low quality (<10) reads. I then align it with STAR (assigning 60 MQ for unique mappers). I add RG info, mark duplicates, and split/trim N CIGAR (introns).

I've view the sample after alignment, after deduping, and after trimming N reads but in each case, there are no mutations...

[GenoMax]

Not sure how long this link will last but click on the mutations tab when the page loads.

[umn_bist]

Thanks for the link. I tried querying for head and neck cancer but weirdly nothing shows up.

Answer 1

[umn_bist]

Thanks for the link. I tried querying for head and neck cancer but weirdly nothing shows up.

[GenoMax]

Hmm. That link is for head and neck cancers. Are you not able to see the graphic under "mutations" tab?

[umn_bist]

No. I just see a blank in the results page. What does the results page look like for you?

[GenoMax]

I see this under the "mutations" tab for TP53 for Head/Neck Cancers: