GENEALOGY-DNA-L Archives

Archiver > GENEALOGY-DNA > 2008-10 > 1225302906


From: Al Aburto <>
Subject: Re: [DNA] 23andMe: rs34534058
Date: Wed, 29 Oct 2008 10:54:39 -0800
References: <49078C0E.1030005@san.rr.com> <a623541e0810281918k3308e3d6ncafbcbe9cdf4c79@mail.gmail.com> <4907F348.1070200@san.rr.com> <4907EF32.30902@familytreedna.com> <4908740D.8060400@san.rr.com><49089022.80504@familytreedna.com>
In-Reply-To: <49089022.80504@familytreedna.com>


Thomas,
Ah! I have forgotten about DYS459 and CDY and many other palindromic
markers where I have more than the normal alleles! Two years now
probably and no one else has showed up with similar results. Maybe
someday FTDNA will display all these palindromic markers (all the
advanced markers) properly in the projects and in Ysearch?

Yes, I should have CCC at rs4081948. I zoomed out around that region
too and it just didn't dawn on me :-( ...

I think Chia indicated that at some later date 23andMe would consider
presenting data for the heterozygous Y calls and the Y calls for females.
Al


> Thomas Krahn wrote:
> Hi Al,
>
> I just wanted to point you to the problem of palindromic SNPs (as you
> already found out).
>
> 23andMe has simply striped off all heterozygote alleles from their raw
> results. This was an easy fix for them, but unfortunately this was still
> not correct.
> Like rs4081948 there are some more SNPs on their chip that are located
> in palindromic regions. This means that they actually show up more than
> once on the Y chromosome. At least for some people we would definitely
> expect to see heterozygotes at some palindromic SNPs which may have a
> phylogenetic meaning.
>
> rs4081948 is in the yellow segments of the P1 palindromic arms. This is
> the same segment that contains DYS459 and CDY(DYS724) and the other
> yellow markers on my palindromic map. Most males will have two copies of
> each STR marker, but of course they will also have two copies of
> rs4081948. So we would expect either a signal with double intensity on
> the chip or a heterozygote. The possible results for the regular man
> would be CC, CA or AA.
>
> But from our STR tests on your DNA we know already that you're not one
> of these regular men. We know that you have a P1/P2 duplication and you
> have 3 alleles at CDY, 3 alleles at DYS459 and of course we'd expect
> also 3 alleles at rs4081948. So the signal for this SNP should have
> triple intensity and should be properly reported as CCC.
>
> I must admit that rs4081948 doesn't seem very relevant because everybody
> has a C (on each palindromic arm), but I notice many missing results on
> other palindromic markers which seem to have disappeared during the
> "heterozygote cleanup". This is an unfortunate loss of valuable
> information which might have helped us to understand recombination
> processes better, in my opinion.
>
> Thomas
>
>
> Al Aburto wrote:
>
>> Hi Thomas,
>> I just checked rs4081948 (in the new downloaded file) and it has just
>> one "C" base. I see this SNP is in the palindromic region. If it is
>> supposed to be a 3 base deletion or insertion then perhaps 23andMe only
>> displays the first base? I noticed this in other multibase UEPs that
>> have an rsID ...
>> Al
>>
>> > Thomas Krahn wrote:
>>
>>
>>> Al,
>>>
>>> I would be very interested what your rs4081948 allele looks like now?
>>> It should be CCC, shouldn't it? If your other alleles have only one
>>> letter now this would be the correct display :)


This thread: