Non-zero chrY CpG sites in female samples
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2.8 years ago
lotus28 ▴ 70

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?

dnam illumina methylation sex gender • 530 views
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This probe is located inside this gene https://www.genecards.org/cgi-bin/carddisp.pl?gene=TGIF2LY

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Is this in the pseudoautosomal regions?

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Paralogous gene with the one from X chrom

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