OmicsSomaticMutations.csv, multiple mutation rows of the same cell-line and the same gene

[mw222]

Just want to reiterate how thankful I am for all the helpful and quick responses I have had about this dataset.

I had a question regarding the OmicsSomaticMutations dataset that is in MAF format. I am a bit naive when it comes to reporting mutation data, and had noticed the following situation:

I filtered out some columns that may be relevant to answering my question but I had noticed for KDM5D, and about ~3000 other genes, where there are multiple fixed mutations,1/1, for the same gene in the same cell-line. I am trying to draw out the model in which this is possible in a cancer cell-line, is there a reason why this occurs? I understand multiple fixed mutations due to chromosomal duplication, but I am not sure how to interpret situations like KDM5D where both mutants are a SNV with an allele-frequency above 90%.

Is this because there is no wild-type KDM5D in the cell-line, and these two mutants exist at a roughly 2:1 (25:13 count) ratio? I can check and see if this only occurs on chromosomes that have undergone aneuploidy.

[simz]

Hi,

Thanks for reaching out. Please correct me if I misunderstood the screenshot, but the mutations you highlighted are all located at different positions (see column Pos), and the allele frequency is calculated for each position individually according to the reads at that position. In this case, summing over the AF for these sites isn’t too meaningful because they don’t have the same denominator.

Hope this helps,
Simone

[mw222]

Oh I see, that was a silly oversight on my end. Thank you for clarifying!