Inconsistency in MON_SOFT_TISSUE cell line between DepMap and cbioportal

Q&A
1

Hi, I am checking the genetic profile of MON_SOFT_TISSUE and found troubles on interpreting the frameshift on the position H598 of NOTCH1:

In cbioportal citing CCLE as the source, it is reported that the cell lines has two frameshifts in this position H598Pfs34 and H598Qfs46. I assume that both alleles are frameshiifted in this position.

I checked DepMap and it is reported one single frameshift on H598 and a second frameshift on G597

Can you help me with this?

2

Hi, sorry for the late reply. I checked our WES data and don’t see any sign of this frameshift mutation in either the bam file or the mutation calls from Strelka, MuTect1, MuTect2. The mutation seems to be detected in our RNAseq. I wonder if cbioportal has used a different calling method on the RNAseq data.