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Archiver > GENEALOGY-DNA > 2007-07 > 1185643044


From: Thomas Krahn <>
Subject: Re: [DNA] A little note about haplogroup G Deep Clade tests
Date: Sat, 28 Jul 2007 12:17:34 -0500
References: <BAY111-DAV8A71CC1605D78920F5F3FB1EC0@phx.gbl>
In-Reply-To: <BAY111-DAV8A71CC1605D78920F5F3FB1EC0@phx.gbl>


Lawrence Mayka wrote:
> Thomas,
>
> It is not clear to me which customers you have re-tested (or are about to
> re-test). Only those customers who ordered a deepSNP-G recently? Or all
> customers who have ever ordered a deepSNP-G? Or all deepSNP-G customers who
> might possibly be affected by these adjustments? Or some select subset?
>
> For example, in my own Polish Project, 8 members already have deepSNP-G
> results, at least one of them highly suspicious: a G*, which both you and
> Garvey have not otherwise found. Another member has a deepSNP-G on order
> which is already almost 2 months beyond its due date. I assume that this
> last guy's results will be done "right." Will the putative G* be re-tested?
>
>
I know that there where a couple of re-tests in between my recent batch,
but as I only see the laboratory number I don't know the exact names
without looking them up. The difficulties in the external lab were the
reason why we
returned the deep clade G test back home and I had a closer look at it.
In case the new batch results are released and you still feel there is
an error in your deep clade G
results, then please contact Eileen Krause at Family Tree DNA so that
she can make a decision
if we re-test your case.

> 4 of these deepSNP-G members of my project have been classified as G2. On
> the one hand, you suggest we order DYF411 because it would indicate a
> recLOH, which in turn would "hide" a phylogenetic G2a; but I presume that
> this is really only a worthwhile investment if the haplotype suggests G2a
> membership. Otherwise, the recLOH is just a recLOH, and has no greater
> significance.
>
>
To be more precise:
If I was G2 (P15+, P16-) and my STR profile indicates a closer relatedness
to G2a than to most other G2 I would be interested in my DYF411 result.

> You say that P16, P18, and P20 should be deprecated. But you did not
> mention P17, which is supposed to be equivalent to P18. If it remains a
> valid SNP, then G2a1 remains a valid subhaplogroup, though perhaps under a
> different name. Controversially, Garvey did not find any G2a*--all G2a he
> encountered was G2a1. FTDNA deepSNP-G results, on the other hand, do indeed
> claim to have found G2a*, and one of them is in my project. Are you
> suggesting that he might be a "hidden" G2a1?
>
Garvey's finding seems to be true for my pre-testing phase of P18, too.
The problem with P18 is that there is usually only one out of three
alleles has the mutation.
So if the analyst isn't aware of the palindromic structure of P18, he
will consider it as negative.
P18 testing of this batch hasn't been finished. I will do it next week.

I didn't get a reply about P17 from the U of A yet, so the sequence
remains unknown to me.
I have reason to expect that this is also a palindromic marker, so I
wouldn't care until I know further details.
> And of course, you haven't mentioned the other SNPs examined by Garvey: U8,
> U16, U1, and U13. Especially if you want to deprecate P16 and P18, perhaps
> effort should be invested in Garvey's U series? Otherwise, customers may
> see the deepSNP-G product as offering little value for the money.
>
>
It is true that more efforts need to be invested in a finer and better
split of haplogroup G (esp. G2)
with more reliable markers. On the other hand we respect Dr. Garvey's
findings as his property and
we would never start offering his markers as a commercial product
without his permission.

> Please understand that I do not mean this to sound like either a gripe
> session or a want-list. Rather, I am simply trying to understand what you
> are about to do, and for whom. And, ideally, what your longer-term plans
> for the deepSNP-G product are.
>
>
I don't like to mention our newest plans on any product until I am very
sure that it works perfectly.
But as the lab in Houston is now finished with its construction phase we
are now able to
spend more time on developing new products.

Thomas


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