Was the silent mutation removed from the OmicsSomaticMutations.csv in 24Q2?

Q&A
1

Hi, Sorry for the frequent question.
While checking the 24Q2 dataset, I found that there were no silent mutation labels in the OmicsSomaticMutation.csv file.
Although I filtered out the silent mutations from the previous version of the dataset (i.e., 23Q2), were they removed automatically from the current version?

+) The number of genes in the OmicsCNGene.csv file was slightly reduced from 25368 to 24383 compared to the 23Q2 version of the same file. Can anyone explain about this?

2

Hi,

To your first question, yes, we had a major pipeline update in 23Q4 and removed all of the silent mutations, among others. Please refer to our documentation on the mutation pipeline for more details.

To your second question, in 23Q4 we started masking genes that fall in segmentally duplicated/short repeat regions in our copy number matrix. This section of our 23Q4 release announcement describes this change.

Thanks,
Simone