The mystery of Chromosome 17

Number 17 happens to be my unlucky number, and once again it has proven to be just that.

When the DNA results of my father’s maternal half aunt Valentina have arrived not that long ago, I was all over the moon. As a half aunt, she shares quite a bit of DNA with her nieces and nephews (on 20 out of 23 chromosomes!) and her results are incredibly valuable, because they point directly to their maternal grandfather. That amounts to gold, if you are a fan of the Visual Phasing technique.

I downloaded the newest version of Steven Fox’s magical excel spreadsheet, and set out to do Visual Phasing for my father and his siblings all over again. Thanks to Valentina, I was basically flying through all chromosomes until I reached that unlucky chromosome 17. It made absolutely no sense!

Valentina’s results helped me to distinguish the segments my father and his siblings inherited from their maternal grandparents, Ivan Permyakov (MGF) and Raisa Zenkova (MGM).

As for the paternal side of my father and his siblings, I’ve worked with the DNA of two 1C from different lines – Galina and Andrey. 2C are much better for Visual Phasing than 1C since 1C have two grandparents in common, and thus, can’t help me to distinguish between my father’s paternal grandparents, Andrey Strelnikov (PGF) and Domna Pimshina (PGM). Nevertheless, they are still incredibly useful when it comes to finishing long chromosomes or assigning crossovers in those cases when siblings turn out to have very close recombination positions.

It isn’t the entire chromosome 17 that presents a problem, only the small region between 32 and 54Mbp. My father’s sister Liuba shares a half-identical region (HIR) with my father and their sister Galya there:

Sharing a half-identical region means that on one of her chromosome copies, either the maternal or the paternal, Liuba has inherited DNA from the same grandparent as my father and Galya. And that doesn’t seem to be the case here.

On their maternal side, Valentina shares a 32cM-segment with my father and Galya from 32 to 59Mbp and no DNA with Liuba. This means that from 32 to 59Mbp my father and Galya have inherited DNA from their maternal grandfather, Ivan Permyakov. Liuba, on the other hand, must have inherited DNA from their maternal grandmother at that region.

On their paternal side, Liuba shares a 60cM-segment with her paternal 1C Galina from 9 to 54Mbp. My father and Galya share no DNA with Galina there. I can’t say which paternal grandparent passed down his or her DNA to Liuba and 1C Galina, but I can say that it wasn’t the same paternal grandparent, who passed down his or her DNA to my father and Galya at that region.

The same is true when the siblings are compared to their other paternal 1C Andrey:

So, what is happening here?! If Liuba has received different DNA from different grandparents than her siblings on both chromosomes, then why is she reported to have a half-identical region with her siblings, instead of a non-identical region?

I’ve summarized the problem in the following image (and I’ve also included all their GEDmatch kit numbers in case you want to check it out for yourselves):

This seems to present a rather challenging situation and your thoughts and ideas are very welcome! Drop a comment or join the discussion in the Visual Phasing group on Facebook.

Please note that hidden or double crossovers aren’t the issue here. Neither would endogamy (there is none) or a pile up area explain the situation why Liuba is reported to share a half-identical region with her siblings when they are matching different people on both their maternal and paternal chromosome copies.

Could the 32cM-segment Valentina shares with my father and Galya be a false one? And if so, how could I prove it? So far, there aren’t any useful matches to compare to.

On very rare occasions, people can receive a small piece of a third chromosome during the recombination process. This seems a bit too crazy here, and besides, it is usually linked to a certain condition.

Well, I hope that publishing this article on the 16th of June, instead of the 17th, will somehow help shed light on this mystery… 😉 (717 words and 17 paragraphs though.)

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