KM12 RKO mutation on CBR3

Issues and Bugs
1

Hi
I have a question about KM12 and RKO cell line mutation data on CBR3 gene.
Using data reported in “CCLE_mutations.csv” in 21Q2 version I noted that this cell lines are not mutated.
Using bam files (from RNASeq) reported on GDC data portal
RKO: https://portal.gdc.cancer.gov/legacy-archive/files/c88b8503-73ce-4c8e-89a9-498b614037ae
KM12: https://portal.gdc.cancer.gov/legacy-archive/files/02b56f2a-6813-4afe-88be-50c00ed9db55
I inspect gene by IGV and I find a mutation on CBR3 p.L84V that I validated also with Sanger

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So my question is why this mutation is not reported in KM12 and RKO in CCLE_mutations.csv?

Thanks

2

Hi. This seems to be a common germline variant:
https://www.ncbi.nlm.nih.gov/snp/rs9282628?horizontal_tab=true

We filter out common variants in our pipelines. For the CCLE subset which has bam files publicly available we are considering releasing the germline data in the near future, but unfortunately this data is not available on the portal yet.