ACH001956 removed from 22Q4 entirely

Issues and Bugs
1

Hi,

We have noticed ACH-001956 has been removed from the 22Q4 CCLE entirely.
The problem with WGS data for this cell line an others

  • ACH-001955, ACH-001956, ACH-001957 and ACH-000116 have been dropped from the Copy Number and Mutation data due to low quality.

We would like to know if there are any other issues with the datasets such as CRISPR, RNAseq etc and why the cell line would be completely removed?

Thank you!

2

Is your question, why was this line also removed from the CRISPR dataset?

If so, it’s a side effect of removing the copy number data. We require copy number data in order to correct for the copy-number-effect that occurs in CRISPR screens. As a result, we only ever report CRISPR results for those lines we have both screened in screen and have decent quality CN data.

Thanks,
Phil

3

Thanks for your quick reply.
It makes sense that would make CRISPR data unreliable.

My question was not only about the CRISPR data, but why this cell line can no longer be found via a portal search
here: DepMap: The Cancer Dependency Map Project at Broad Institute

4

That is most likely due to our policy of only showing lines on the portal for which we have some data.

Our model registry has a large number of models which we were unable to collect data (ie: lines which failed internally, lines that we could not obtain, etc). We don’t want to mislead people into thinking that some of these non-existent/ungrowable lines are real models that exist somewhere, so we only allow people to look up lines for which we have data. Only once we have a successful screen reported do we consider it a line worth sharing the metadata.

Since this line lost its mutation, CN and CRISPR screen data, I suspect this line now is falling into the bucket of lines that are filtered out for lack of data.

Thanks,
Phil