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Archiver > GENEALOGY-DNA > 2005-06 > 1119197810


From: Thomas Krahn <>
Subject: Re: [DNA] DYS459a/b
Date: Sun, 19 Jun 2005 18:21:54 +0200
References: <88.29073eb2.2fe6c1a4@aol.com>
In-Reply-To: <88.29073eb2.2fe6c1a4@aol.com>


wrote:

> Question for Thomas Krahn and anyone else who wishes to comment: In cases
> where DYS459 is reported as the same number of repeats at a and b (in my case 9
> and 9) are separate alleles seen, or a single that is called two same results
> by convention, as in the DYS464 called 15,15,16,16 by FTDNA and DNAH, but
> refined to two alleles 15C, 16C by BIOTIX?
>
> Decatur

Decatour:

We're just in an early stage of development in advanced typing of
DYS459. In this early stage I cannot guaranty that my ideas really work
in reality, but in theory this is the test that I want to prepare:

First I would type the DYS459 locus with conventional primers and I
would certainly observe a single peak in your case.

Then I would use a second primerset, that generates a larger PCR product
that also includes a poly-A sequence, which is located next to the
DYS459 repeats. I don't know, what's your exact lengt of the poly-A
sequence. The man from the human genome project, I call him HUGO, has 13
A's in a row next to one allele and 14 A's in a row next to the other
allele. So we have a good chance, that your poly-A sequences also differ
in one or more A's. If we're lucky, with this second PCR we will get two
peaks close next to each other in the electropherogram. The peaks are
spacet one or more bases appart from each other. If this is the case, we
would have proved, that there are really existing two distinct DYS459
alleles and there is certainly no deletion.

If we are unlucky and there is still just a single peak, then we really
can say nothing new. We still don't know if it is a deletion, or if
there are two alleles at DYS459.

Only practical experiments will show, if this might be a useful method.
It depends on the polymorphy of the mononucleotide stretch, in how many
cases we will be lucky or unlucky. Poly-A stretches are known to be
quite polymorphic, so I would expect that in many cases we might be
lucky. However, recombinational loss of heterocygosity would also
equalize the length of the poly-A stretch, of course. I hope that
experiments will tell us more.

Thomas


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