Entering edit mode
6.8 years ago
liannesimon
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0
My karyotype is 46,XY,22qs+/45,X,22qs+. My VCF file has some X chomosome variants that are homozygous and some that are heterozygous. All of my Y chromosome variants are homozygous except for the intergenic ones, which are heterozygous. I'm trying to make sense of it all. The lab insists that the allele counts are legit. There's a really high incidence of twins in the family, so I suppose chimerism's a possibility. But I was wondering if it wasn't just because of the way they built the VCF file. Is there something I can look at in the file that might tell me?
I have not seen that notation before. Can you explain what it means? I found this but I don't know what you mean by 22qs+; it seems pretty rare, so it would be helpful if you could provide a link.
I don't understand why that would be the case. Typically, females should have no variants called on Y (though in practice there will be a few), males should have lots, and mosaic individuals would tend more toward the male outcome, but with lower allele frequency of variants. I see no reason why intergenic regions should be different from exonic regions.
Actually, I don't see how those are related in any way... typically, modern twin births have more to do with fertility treatment than anything else. It appears that fertility treatments might be related to mosaicism, but if you are not a twin of another person with different sex... it's hard for me to see how that relates.
There are lots of things you can look into. You can remap the entire dataset and call variants yourself. You might do a better job than the sequence provider... or, maybe not. It depends on how much effort you want to invest.
I can think of one: merged data from exome sequencing with genome sequencing data...
Oh, yep. I was assuming WGS data.
The 22qs+ is exceedingly rare. At the time my karyotype was run, LabCorp said they'd seem 14 similar cases out of more than 400 million karyotypes. Half were stillborn. Half familial. Mine's familial. It's an improperly-satellited autosome. The Chromosome 22 Project says it's attached by a second NOR, and 22qter appears to be intact.
The lab seemed to think I might have two different X chromosomes out there somewhere. Since my heterozygous to homozygous ratio is low, I'm wondering if it isn't just an artifact. I have more than 500 X chromosome variants. Less than 100 are heterozygous. I have four Y chromosome variants, not counting the intergenic ones.