Question: No somatic mutation in tumor sample
0
gravatar for umn_bist
24 months ago by
umn_bist270
umn_bist270 wrote:

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...

ADD COMMENTlink modified 24 months ago • written 24 months ago by umn_bist270

Not sure how long this link will last but click on the mutations tab when the page loads: http://www.cbioportal.org/cross_cancer.do?cancer_study_list=&cancer_study_id=all&data_priority=1&case_ids=&patient_case_select=sample&gene_set_choice=user-defined-list&gene_list=TP53&clinical_param_selection=null&tab_index=tab_visualize&Action=Submit&Action=Submit#crosscancer/overview/1/TP53/hnsc_broad%2Chnsc_jhu%2Chnsc_tcga%2Chnsc_tcga_pub%2Cnpc_nusingapore%2Cacyc_mskcc

ADD REPLYlink written 24 months ago by GenoMax42k

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

ADD REPLYlink written 24 months ago by umn_bist270
0
gravatar for umn_bist
24 months ago by
umn_bist270
umn_bist270 wrote:

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

ADD COMMENTlink written 24 months ago by umn_bist270

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

ADD REPLYlink written 24 months ago by GenoMax42k

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

ADD REPLYlink modified 24 months ago • written 24 months ago by umn_bist270

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

ADD REPLYlink modified 24 months ago • written 24 months ago by GenoMax42k
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