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Archiver > GENEALOGY-DNA > 2010-11 > 1288796100


From: Kathy Johnston <>
Subject: Re: [DNA] WTY Update slides
Date: Wed, 03 Nov 2010 10:55:00 -0400


Thomas Krahn really does need to publish his material. There are plenty of genealogists who could add information to this discovery. When he first talked about the X to Y transfer, he said: "The C allele at rs12859783 is coming from a different X-haploblock than the G observed in the ChrX HUGO sequence." He was talking about the L88 region. That was a clue to me that there could be a phased pattern that we should be looking for that is different from HUGO. Whit Athey taught us some phasing techniques at the FTDNA conference for those who don't know what I am talking about. Maybe now people will also understand what I was talking about several months ago. The X chromosome has very ancient blocks that seem to hold together over thousands of years and there are only rare crossovers in some of the regions. So, it is easy to phase these.


Neither 23andMe nor FTDNA shows the results at rs12859783. The question I was asking way back then was, can we predict our own SNPs at rs12859783 (position 7133305 at HapMap) based on our own phased pattern? Yes I think we can. If so, then we know which "haplogroup" on the X chromosome carried the SNP that got passed from the X to the Y.


By letting us download raw data, I really like the way these testing companies have permitted us mere mortals to play with the data and make some of the discoveries ourselves. We can collect contributions from FTDNA and 23andMe data then get redacted SNPs from HapMap to add to the predicted sequences.


When Thomas found the X to Y SNP in Bonnie Shrack's father, I remember I was playing around with HapMap and 23andMe X raw data over a year ago, phasing different haplotypes and there were three phased haplotypes on the X chromosome that emerged in the mostly European populations for this tiny haploblock. There was only one of these three haplotypes (which I would call a haplogroup, but I have no academic authority to do so) that could have made that crossover or maybe I should call it a contribution. I am learning that not all exchanges are crossovers. I started adding Family Tree DNA data to the chart as soon as it became available. So I assume Bonnie's father would have been heterozygous in the L88 Region because one SNP was on the Y and the other was on the X but may have looked like it was a Y SNP.


Anyway, the data that a group of us genealogists collected is shown here in this Google Doc sheet if anybody is interested in adding to it. Its kind of a free-for-all approach to scientific discovery. I hope this web site does not suddenly self destruct since too many cooks tend to spoil the broth.


https://spreadsheets.google.com/ccc?key=0Ah3qUyFYAhKudDhWVXJyMkN3eXJoMUlGNi1IS08zZVE&hl=en#gid=0


I have not kept it updated (last update in April) but the darker blue is the predicted haplotype that probably transfered the X to the Y chromosome based on HapMap combined with 23andMe and FTDNA data. If you phase a larger region from HapMap, you will see that the two blue groups are more closely related to each other on the (still to be constructed) X phylogenetic tree than the red group.


I called the Y SNP "transgametic" and I hope that is the appropriate terminology. I hope a geneticist will critique the methodology and tell me if I am on the right track here. Are these conclusions reasonable? In addition, why is there a transfer from one end of the X to the middle of the Y? Is that to be expected? I hope we got the correct SNP ID numbers here.


Kathy J.
--------
> Thanks for sharing this very informative
> set of slides with us, Thomas.
>
> Are you working on a technical paper about
> the obsolescence of NRY? This kind of discovery
> should spread beyond the genetic genealogy community.
>
> Ann Turner
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