LS180 (ACH-000957) mutations are different between 20Q1 and 23Q4

Issues and Bugs
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1

Dear DepMap team,

Two frameshift mutations in KMT2D (g.chr12:49444973_49444974insG and g.chr12:49444978_49444979insTCAAG) were reported in version 20Q1 and are missing in version 23Q4.

Any ideas why?

2

Hi,

The DepMap mutation calling and annotation pipeline has gone through multiple updates over the years, and there could be various reasons for discrepancies between two versions. For the examples you gave specifically, it appears that these two mutations were only caught by legacy RNAseq mutations calls, not WGS or WES. We dropped all such legacy mutation calls in 2022, which is why you are not seeing them on the portal.

I’d recommend always referring to the latest version of our data, as we continue to update and improve our pipelines. For details on our latest mutation calling pipeline, please refer to our documentation.

Thanks,
Simone