Confirming OmicsCNGene.csv "NaN" Interpretations/Assumptions on the X and Y Chromosome

Q&A
1

Hi,
I have noticed in many of the updates that the OmicsCNGene.csv NaN are primarily for Y-chromosome genes. My assumptions are that these are a result of a lack of Y-chromosome mapped segments in XX individuals or cell-lines that have lost their Y-chromosome. If this assumption is true, would it be appropriate to replace these NaN with a zero in subsequent analysis?

I am a bit hesitant due to the existence of zero valued entries for other genes, so I was wondering if there are reasons NOT to assume these biases of NaN entries for Y-chromosome genes are due to the absence of a Y-chromosome in certain samples? Thank you!

2

Hi,

Thanks for reaching out! As part of our current QC process, if a sample has more than 150 chrY segments, all of its chrY segments are removed from segment- and gene-level copy number data because it’s likely noise.

Thanks,
Simone