Looking at the 22Q4 mutational data, I am realizing that some genes known to be mutated in CCLE cell lines are missing any mutation annotation (missing from the “overview” and the “characterization” tabs). An example is the ADAMTS2 gene for which no mutation information is listed. In the 22Q2 dataset (CCLE_mutations.csv), several SNPs were listed (223 to be precise) and I believe that they used to be visible in the 22Q2 portal characterization tab. SNPs for this gene are also listed in the 22Q4 “OmicsSomaticMutations.csv”. file, so it is not like the new mutation calling pipeline that is now being used has failed to “rediscover” these mutations.
The cell line “ACH-000943” is one of many listed in the OmicsSomaticMutations file as having a missense mutation to the ADAMTS2 gene, but this mutation is not listed in the mutation data for this cell line, on the portal “characterization” tab.
I am also finding that the 22Q4 “Damaging mutation” table contains data for “only” 16383 genes and ADAMTS2 gene is missing from the list. I thought that maybe now only “Damaging mutations” are shown on the portal, and perhaps the way to assess if a SNP is damaging or not has changed with the latest data release. However for other genes, silent mutations are listed (e.g. ADAMTS7 has mutation data listed in the overview tab and its silent mutations show up in the characterization tab, including one in the same “ACH-000943” cell line).
I would like to understand what is going on.
Thanks for your help.