Dear DepMap,
I am using CCLE data to review RNA mutation data for BRAF. When there are missing AC values in RNA mutation data, should these be interpreted as missing data, or was the alternate allele was not detected? Is there a way I can differentiate? Also, there are a few cell lines for which there is no DNA allele count with any project except RNA, but the protein change is “V600E.” Are these protein change calls made directly from RNA only? Thank you.
Hi,
To your first question, I’d suggest looking at other mutations present in your cell line of interest. If this cell line has other mutations detected by RNA but not this particular variant, that suggests that the alternate allele was not detected by RNA. If it does not have any other mutations detected by RNA, that suggests we likely don’t have RNA calls for this line at all.
And to your second question, yes, if there’s no allele counts in any other modalities, that suggests that it is called from RNA only.
Thanks,
Simone
