Cell line mutation data seems to have changed?

Q&A
1

Hi, I have been looking over cell line mutation data and noticed that some snvs for OCI-AML3 cells are no longer on the list, such as BAX and TP53. Is there a reason for this?

Thanks!

2

Hi,

Could you clarify which version of the mutation data you were previously using, so I can take a look at these variants specifically? DepMap’s mutation pipeline gets updated periodically, and the changes could be attributed to many factors, including updates of mutation caller, gnomAD version, internal QC filters, etc. For details on the current mutation calling and filtering pipeline, please see our documentation.

Thanks,

Simone

3

Hi Simone,

Thanks for getting back to me. I didn’t make a note of what version I was looking at previously. It would have been 1-2 years ago that I looked on DepMap to verify a Bax mutation in the OCIAML3 cell lines. When I was looking for other cell lines last week and checked AML3 for a different mutation I was interested in, I noticed the Bax mutation was gone. Sorry I don’t know what version it was except that it was 1-2 years ago.

Thanks!

Melissa

4
  • I know this has been awhile but I wanted to re-visit this issue of mutations that once were listed for OCI-AML3 cells now being absent from the DepMap mutation list. I do not know the version of the mutation data that I was previously using, but these were some mutations that were listed at the time I pulled the data. I am particularly interested in why the BAX and TP53 mutations are no longer listed for this cell line?? BAX mutation in AML3 cells has been published and I have also sanger sequenced my OCI-AML3 cells and verified the presence of the mutation listed in the previous DepMap mutation list that was also mentioned in the published article (linked above).
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5

Hi,

It appears that these two variants were detected in our WGS but excluded from DepMap because of high population frequency detected in gnomAD, with TP53 P72R being a common polymorphism. DepMap’s mutation pipeline gets updated periodically, and without knowing the version of the data you reference, I cannot confirm exactly in which release/pipeline change this was introduced. Please refer to our documentation linked above for more information on our filtering criteria.

Since this is a CCLE cell line, its raw sequencing data is also available if you’d like to confirm the variants upstream. Details can be found on our resources page.

Simone

6

DepMap’s pipeline updates periodically tighten germline filtering rules, so downloading raw CCLE alignment files directly from dbGaP or Terra lets you track specific loci regardless of portal filtering changes