24Q2 - PureCN Integer Copy Number for Chr X and Y

Q&A
1

Hello,

I am looking through the data release in 24Q2 and notice that the PureCN copy number profiles for both genes and segments do not have data for chromosome X and Y.
Is there somewhere I can find this data? Is there a way to calculate allele specific copy number from the relative copy number files?

Thank you very much!

2

Hi,

Thanks for reaching out. We’re currently looking into this issue and evaluating other absolute copy number callers. In the meantime, for absolute copy number calls, there is one named
CCLE_ABSOLUTE_combined_20181227 from the CCLE (2019) project that’s available on the portal. However, it does contain less cell lines than the PureCN dataset.

Thanks,
Simone