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Archiver > GENEALOGY-DNA > 2008-10 > 1225243241


From: Al Aburto <>
Subject: Re: [DNA] 23andMe: rs34534058
Date: Tue, 28 Oct 2008 17:22:26 -0800
References: <49078C0E.1030005@san.rr.com> <490799E7.7050909@san.rr.com><4907B71A.5030306@familytreedna.com>
In-Reply-To: <4907B71A.5030306@familytreedna.com>


Thomas,
This helps a lot! I will check the other IJ SNPs. Thank you!,
Al


> Thomas Krahn wrote:
> Dear Al,
>
> This isn't strange at all:
>
> Go to http://ymap.ftdna.com
> Search for rs34534058
> Zoom out to 100 bp
> Download decorated FASTA file
> Copy the DNA sequence into the clipboard
> Open a new browser window at http://genome.ucsc.edu
> Click Blat
> Paste the sequence from the clipboard and submit
>
> Ah! there's a match at the X chromosome as well...
> Guess what? There's a C exactly at the position that corresponds to the
> position of the SNP on the X chromosome.
>
> I haven't tried, but I expect that this will be the same with the other
> SNPs that you mentioned.
>
> The probe on the chip has simply picked up a remaining bad hybridization
> with the X chromosome DNA because there was no better Y chromosome
> sequence available.
>
> What do we learn from this?
> Most of the SNPs that we use can be traced back to some kind of
> recombination events. In this case we have likely observed a X-Y
> recombination that has happened a very long time ago. Only a very small
> share are real de novo mutations. Still those recombination events
> happen rare enough so that they can be considered phylogenetically as UEPs.
>
> The biggest challenge for us primer designers is to make sure that we
> really just pick up the Y chromosome sequence and not homologue
> sequences from the X or any other chromosome because they're so similar.
>
> I have mentioned earlier on this list that understanding recombination
> processes will play a key role when we want to learn about human evolution.
> This is also (almost always) the process that is involved when a SNP
> shows up at two different positions of the tree.
>
> I hope this helps,
>
> Thomas
>
>
> Al Aburto wrote:
>
>> Good grief, I found some more of my SNPs also present in the female X.
>> They are coming in on my unique SNPs for J1*, J2a1* and I1 or the IJ
>> SNPs. These are the IJ SNPs that are labeled as female in Adriano's list:
>> rs17250887 == P130 (IJ)
>> rs17306671 == P125/M429 (IJ)
>> rs17306699 == P129 (IJ)
>> rs17315772 == P124 (IJ)
>> These have to be ancient SNPs!! What happened back then??
>> Al
>>
>>
>> > Al Aburto wrote:
>>
>>
>>> Hi list,
>>> I just realized that I have a strange SNP in my 23andMe results :-) ...
>>> It is rs34534058 (you can see it in Ann's and Adriano's spreadsheets).
>>> Adriano's spreadsheet though has the interesting information that
>>> rs34534058 is also found in testing the XX person (Mrs Lishner)! Mrs.
>>> Lishner & I (fully male :-)) have the same SNP! What does this mean?
>>> How can it happen? Is this a true SNP that can be used in the Y-DNA
>>> Tree? Chia are you there? Mainly I want to know if it is a valid SNP
>>> for me? Could it be very ancient and unique in me?
>>> Al
>>>
>>>

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