Mutation doesn't exist in LS180 and LS513 by testing by ourselves

[hyjforesight]

Hello DepMap,
Thanks for developing this amazing project.

We’re doing research on CRACD. Based on Mutation 21Q4 Public data, we found LS180 and LS513 have p.PK165fs mutations on CRACD. (BTW, is this annotation wrong? Should it be p.P165Kfs?)

Then, we bought LS180 and LS513 from ATCC. We isolated their genomic DNAs, PCR the exon 6, and did sanger sequencing of PCR product to check whether they have the p.PK165fs mutations. The reference sequence of exon 6 was determined by ensembl (https://useast.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000109265;r=4:56049098-56330609;t=ENST00000504228). We matched the transcript version ENST00000504228.
However, we found no base is inserted at 165aa. Please see our Sanger results below.

Could you please help us to check this issue?
Thanks!
Best,
YJ

[jkobject]

Hello YJ,

As you can see, for LS180, the mutation is only supported by RNAseq and no other sequencing methods. It hasn’t been found in WES nor WGS. I would treat this mutation with caution and it might be a FP.

I checked and it is the same for LS513.

Hope it helps,
Best,