No somatic mutation in tumor sample
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5.8 years ago
umn_bist ▴ 390

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...

RNA-Seq STAR picard cutadapt prinseq • 1.4k views
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Not sure how long this link will last but click on the mutations tab when the page loads.

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

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5.8 years ago
umn_bist ▴ 390

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

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

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

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

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