Non-zero chrY CpG sites in female samples

Question

[lotus28]

Hi all,

I am inspecting DNAm data in GEO, and I have come across one peculiar detail and I don't know what to make of it.

Shortly, various samples marked as female contain non-zero values for Y-chromosome specific CpG sites. Let me illustrate:

1. Here is an entry for a female sample (GSM1401202)
2. Let's check CpG site cg03515901. In the platform data table, column 9, line 3657 we find that this CpG is located on Y chromosome;
3. And now let's see what the female sample has at this site LINK
   0.4526316
   

That could be a one-off mistake, but from what I've seen that happens quite frequently in female data. Has anyone encountered this issue? Why? How? What do?

[German.M.Demidov]

This probe is located inside this gene https://www.genecards.org/cgi-bin/carddisp.pl?gene=TGIF2LY

[WouterDeCoster]

Is this in the pseudoautosomal regions?

[German.M.Demidov]

Paralogous gene with the one from X chrom