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Archiver > GENEALOGY-DNA > 2005-06 > 1118913115


From: Thomas Krahn <>
Subject: Re: [DNA] Questions about Biotix conventions
Date: Thu, 16 Jun 2005 11:13:07 +0200
References: <REME20050615212016@alum.mit.edu>
In-Reply-To: <REME20050615212016@alum.mit.edu>


Dear John:

John Chandler wrote:
> Among the offerings of the Biotix lab are a number of markers that
> "fill in" the gaps of other labs. For example, there are three
> (DYS570, DYS576, and DYS607) that are part of FTDNA panel 3, but
> aren't available from RelGen or DNAH. Also, they have Y-GATA-C4 and
> DYS463 that are part of the RelGen/DNAH 43-marker test, but aren't
> available from FTDNA. It seems that the Biotix convention differs by
> two steps from RelGen and DNAH on DYS463, but agrees on C4. My
> question is about 570, 576, and 607 -- do the Biotix results follow
> the same conventions as FTDNA on these three?
Yes, all markers except DYS461, DYS463 and Y-GATA-H4 should be
synchronized with FTDNA. We use NIST / ISFG nomenclature.
The conversion formula are:

DYS461 (NIST) + 1 = DYS461 (DNA-H, FT-DNA, RelGen)
DYS463 (NIST) - 2 = DYS463 (DNA-H, RelGen) ; FTDNA unknown.
Y-GATA-H4 (NIST, DNA-H, RelGen) - 1 = Y-GATA-H4 (FT-DNA)

We had only one single exception at one person's DYS458, which seems to
be an insertion/deletion issue in the flanking sequence next to the
repeat. We're working on that.

>
> I have another question that may not have a simple answer, this one
> regarding DYS464. In the new DYS464 test, where the standard backward
> primer is replaced by two slightly longer primers ending with C and G,
> respectively, what are the chances that different alleles exist for
> the other three bases between the standard primer and the C or G on
> the end? In other words, if a test shows, say, only two copies of
> DYS464 in this new system, could that be simply because the two other
> copies are "invisible" to the extra-length primers?
It is very, very unlikely that we will have a T or an A at this
position. Most SNPs are only biallelic. The singlenucleotide mutation
must have happened quite recently, because only R1b persons have the
C-type at all.
However, if there was an A or T, the primers wouldn't match and no
amplification would result. In the case below, this could be
demonstrated if we'd also include a DYS447 reference peak in the DYS464X
primermix and compare peak heights with the short DYS464 primer against
the two elongated DYS464 primers.

>
> A participant in one of my groups has received a report showing
> DYS464=15c,16c (he is R1b, of course). I'm guessing that the usual
> doubts about single-vs-double are eliminated in this case purely
> because the R1b configuration is "always" 3 C's and 1 G: the lack of a
> G implies at least one copy is missing, and the parity between the 15c
> and 16c peaks implies the total number is even, and therefore two. I
> have to balance this report against the reports from FTDNA and DNAH
> for this person, which *both* say DYS464=15,15,16,16.
No. In this particular case the peak heights in comparison to an
independent DYS447 allele in the same fluorescence color also suggest
that each of the two peaks only represents one genome equivalent. This
means, that if all the other persons in the batch have 4 DYS464 alleles,
then this particular case has only 2 of them. If he would have 4
alleles, the others must have 8.

I hope this helps.

Thomas Krahn

--
Dipl.-Ing. Thomas Krahn biotix GmbH
Tel.: +49-331 / 2300 452 Hermannswerder Haus 14
Fax: +49-331 / 2300 450 D-14473 Potsdam / Germany
http://www.biotix.de


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