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Hoppo
01-17-2021, 06:38 PM
Some of my yDNA SNPs test as heterozygous or indeterminate, with around 50% of multiple counts testing as positive and 50% testing as negative.
A paternal line relative of mine has the same results for the same SNPs.
E.g. For R1b-Z39589, half of our counts show the ancestral positions, half show the deletion of all 18 base pairs indicative of the Z39589 mutation.
How is this possible when the y chromosome passes intact from a single parent?

rms2
01-19-2021, 12:58 AM
The answer to this should be really interesting.

Seems really strange, since a SNP is just a change at a single nucleotide, and we don't have a pair of y chromosomes.

Unless the problem is a pair of y chromosomes?

Hoppo
01-19-2021, 07:29 PM
I hope not, as I don't know what the health implications are??? Would a pair of y chromosomes be passed down?
DF13 is certain for both of us - 100% on multiple counts, including for its equivalent. All downstream branches of Z39589 and all other downstream branches of DF13 are definitely negative.
I'm inclined to believe the derived readings for Z39589, as it seems less likely for 18 deletions to be mis-read on multiple counts, but I don't know.

rms2
01-19-2021, 07:50 PM
XYY is rare, but it does occur.

I'm not saying that is what is happening here, but I was just wondering at the use of the term "heterozygous" when applied to the Y chromosome, since we only get a single Y chromosome, not a pair of them.

Probably I'm just revealing my ignorance here, and someone else will pop up with the right explanation.

DMXX
01-19-2021, 08:31 PM
... and someone else will pop up with the right explanation.


*Poof*

Check that the heterozygous calls in question aren't in any of the two PAR regions located at the poles of the Y chromosome, which are subject to recombination during meiosis (unlike the rest of Y-DNA, a.k.a. NRY region) (link (https://www.researchgate.net/publication/5455178_The_human_pseudoautosomal_regions_A_review _for_genetic_epidemiologists)):

https://en.wikipedia.org/wiki/Pseudoautosomal_region

Also, depending on the technology used to analyse your DNA samples, they may (or may not be) exposed to some sort of artifact of the processing technique (i.e. "mismapping reads").

According to this study (https://arxiv.org/pdf/1404.0929.pdf), areas of the genome consisting of "low-complexity regions" (which include the human Y chromosome (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814889/)) assessed with techniques like WGS.

So, there's two plausible explanations as to why you're seeing heterozygous calls at those sites.

If you're seeing a substantial number of those calls in the NRY region and any other portion of your genome doesn't exhibit other quality control-dependent issues, then, the XYY scenario's worth entertaining (in which case, you'd best see a medical geneticist and get karyotype testing organised).

*Poof*

Hoppo
01-19-2021, 11:18 PM
*Poof*

Check that the heterozygous calls in question aren't in any of the two PAR regions located at the poles of the Y chromosome, which are subject to recombination during meiosis (unlike the rest of Y-DNA, a.k.a. NRY region) (link (https://www.researchgate.net/publication/5455178_The_human_pseudoautosomal_regions_A_review _for_genetic_epidemiologists)):

https://en.wikipedia.org/wiki/Pseudoautosomal_region

Also, depending on the technology used to analyse your DNA samples, they may (or may not be) exposed to some sort of artifact of the processing technique (i.e. "mismapping reads").

According to this study (https://arxiv.org/pdf/1404.0929.pdf), areas of the genome consisting of "low-complexity regions" (which include the human Y chromosome (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814889/)) assessed with techniques like WGS.

So, there's two plausible explanations as to why you're seeing heterozygous calls at those sites.

If you're seeing a substantial number of those calls in the NRY region and any other portion of your genome doesn't exhibit other quality control-dependent issues, then, the XYY scenario's worth entertaining (in which case, you'd best see a medical geneticist and get karyotype testing organised).

*Poof*
The heterozygous calls aren't in the PAR regions and I've discovered that they're mainly on SNPs considered "lower quality", so I guess "mismapping reads" is a better explanation. YFull doesn't include Z39589 on its tree, so maybe this too is a lower quality SNP, and I will just conclude we are indeterminate for it