SJSA-1 (ACH-000748)
This cell line is well characterised as being TP53 wild-type but in DepMap it is showing as having a hotspot mutation p.R273H. Can you clarify whether this could be a potential error in the data?
Sample overview for 909717 WT status
Thanks for reporting this. I checked the WGS bam file and the mutation was not there. This seems to be an error in our data. We will look into it.
Thanks much appreciated.
We looked more into this, and found that although this mutation is not present in our WGS bam file, it is present in Sanger’s WES bam file (there are 4 reads out of 39 that are mutated). This is a COSMIC and TCGA hotspot (and has been reported in dbSNP). Our pipelines tend to rescue hotspot mutations even if they originally get filtered in mutation calling. It is possible that we have rescued this mutation in our pipelines even though it has low allele frequency, whereas Sanger has not. If so this may be a case where DepMap and Sanger lines have diverged, or we do not have sufficient read depth to detect a rare cell line subclone.
Interesting, so it looks like a genuine difference in the recorded data. Thank you for investigating it further.
