The Mystery of Chromosome 17

Last updated on July 28th, 2022. The mystery has been solved by JD Cowell! All GEDmatch kits were deleted on August 2nd, 2022.

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

When the DNA results of my father’s maternal half aunt Valentina 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 32Mbp 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 30cM segment with my father and Galya from 32Mbp to 59Mbp and no DNA with Liuba. This means that from 32Mbp 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 9Mbp 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):

And as if this wasn’t complicated enough already, let’s throw in a fourth sibling into the picture – Pavel.

At first glance, there doesn’t seem to be any trouble with crossover assignment, and it is possible to complete the chromosome. The comparison with Valentina, however, throws everything off again!

Wait, there is more!

JD Cowell, a member of the Visual Phasing group on Facebook, has made a very valuable discovery! He checked the AYPR tool on GEDmatch and found Pavel showing a green segment from 32Mbp to 48Mbp on chromosome 17! Now, isn’t that interesting?!

That could mean two things:

  • my grandparents were very distantly related
  • Pavel has a partial trisomy 17 or a small uniparental segment

While the first explanation seems to be far more likely than the second, it doesn’t yet resolve the issue.

Valentina is the daughter of my great grandfather Ivan Permyakov and his second wife. Years ago, I’ve also tested her older half sister Lubov, Ivan’s daughter from his first marriage to my great grandmother Raisa. As a full aunt, Lubov can match her nieces and nephews on both of her chromosome copies – which isn’t very useful for Visual Phasing (full aunts/uncles are only occasionally helpful with crossover assignment). But in a strange case like this one, let’s have a look at how the Strelnikov siblings match her, too.

In a normal situation, you would expect Lubov to match either the Zenkova or the Permyakov segments. However, two things are off in this image!

First, she doesn’t match Liuba from 39Mbp to 59 Mbp as she does with Galya and my father – even though all three of them supposedly received their maternal grandmother’s (Zenkova’s) DNA segments in that region.

Second, Pavel switches to a different maternal grandparent at 48Mbp, while Galya and my father do not, but Lubov is reported to share the same segment from 39Mbp to 59Mbp with all three of them.

Situation 1: Is this a case of endogamy or pedigree collapse?

Valentina is not related to any of the three paternal 1C cousins, who have taken a DNA test, and their results have never contradicted themselves previously on any of the other chromosomes.

However, as I have mentioned earlier, group member JD Cowell has discovered that Pavel has one fully identical (homozygous) region on chromosome 17, which indicates that his parents were distantly related. (As for the other three siblings, there was no such indication.)

Following JD Cowell’s argumentation, maternal half aunt Valentina matches her half nieces and nephews on their paternal chromosome copy. As for Pavel, P1 and Permyakov segments are identical from 32Mbp-48Mbp.

Following the same argumentation, the comparison between Lubov and the Strelnikov siblings is very similar:

Is Pavel’s segment of 15cM enough to support this outcome? It’s true, everybody comes across pedigree collapse at some point in their genealogy. And of course, it doesn’t contradict the history of initially only a small number of Europeans in Siberia, where my Russian ancestors settled centuries ago.

Then why do I still have trouble accepting it, even though it makes everything fall so beautifully into place?

There are several reasons:

Remember, the AYPR tool results for the three other siblings said “This analysis indicates that your parents are probably not related within recent generations”. Pavel’s segment is likely much much older than recent generations. When I lower the thresholds for the comparison of Valentina and all three of my father’s paternal cousins, the results are the following:

  • 1 segment of 5cM shared with each Galina and Vera
  • 2 segments of 4cM shared with Andrey

That’s not how relatedness looks like. Even if all of these small segments were real, the pedigree collapse would be hundreds of years old.

That contradicts the size of the segment Valentina shares with the Strelnikov siblings – it’s a solid one of 30cM. How are the odds of it being several hundred years old? According to a very interesting article by Kevin Borland, there is a 96% chance that a common ancestor of a 20cM segment lived within the last 400 years. And we are talking about 30cM.

When you lower the threshold at GEDmatch for the comparison of Lubov and my father’s paternal cousins, the number of segments is higher, but they are all still small except for one:

  • 4 segments of less than 4cM shared with Galina
  • 9 segments between 3 and 5cM and one segment of 23cM
  • 11 segments between 3 and 5cM and one segment of 8cM

Again, even if some of them are real, the pedigree collapse is hundreds of years old.

(Even if I compare Lubov to Blaine Bettinger, I still get 7 segments between 3 and 6cM 🙂 )

Situation 2: Could it be a case of hidden or double crossovers?

When I first compared my father, Galya and Pavel to each other and then to Valentina, I tried different scenarios and could make the comparison work assuming several hidden close crossovers, as seen in this image:

However, everything is thrown off as soon as you take Liuba into the picture – nothing seems to 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.

Situation 3: Could the 30cM-segment Valentina shares with my father and Galya be a false one?

That is extremely unlikely given that it is a rather solid segment shared with both siblings.

Situation 4: Does Pavel have a partial trisomy 17 or a small uniparental segment?

This is the unlikeliest theory of all, but one that I would sell my soul for to be true 🙂

The AYPR tool can be used to find potential genetic abnormalities. On very rare occasions, people can receive a small piece of a third chromosome or two copies from the same parent during the recombination process and the tool can give you a hint.

There is a certain condition that runs on my paternal side of the family, which must be genetically linked. It’s neither a cognitive nor a physical disability, but has something to do with impaired social skills. More than 10 people on different lines are affected. Even unrelated people in my father’s village know that it runs in our family. People in my family know who has inherited “it”, even though not everybody was diagnosed with it. The question of what causes it, has been on my mind for decades. And it is reflected in the choice of which of my father’s siblings I’ve asked to take a DNA test and where. However, nothing meaningful so far.

The argument against situation 4 is that there was an issue with this chromosome even before Pavel was taken into the picture, remember? But Pavel has turned out to be crucial to the solution!

And that brings us back to JD Cowell. Has he solved the mystery of chromosome 17? Maybe. Probably. Most likely. Yes. Definitely.

Unless someone wants to challenge him? 😉 You can follow his arguments in the Visual Phasing group on Facebook.

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