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Archiver > GENEALOGY-DNA > 2005-06 > 1119908534


From: "Ken Nordtvedt" <>
Subject: Re: [DNA] Re: SNPs for Haplogroup I
Date: Mon, 27 Jun 2005 15:42:14 -0600
References: <062720050225.7018.42BF63A70009CC7600001B6A2200748184050B989A0E00@comcast.net>


David, How about P40? It presently is a non-redundant SNP for the most
robust subclade of I1a --- namely I1a1. Will that be in your inventory?
See my message on M227+ haplotypes and whether they are also P40+ or not?

Ken
----- Original Message -----
From: "David Faux" <>
To: <>
Sent: Sunday, June 26, 2005 8:25 PM
Subject: Re: [DNA] Re: SNPs for Haplogroup I


> Ken and all the "I folk" out there:
>
> Concerning the various SNP primers noted below; along with the standard
M170, M253, M223, P37, M26, M227 are "primed" and ready to go. Thanks to
your earlier request, M284 primers have been designed and are being "field
tested" to ensure that they are working satisfactorily. P38 is problematic
since for some reason, although used in a publication, the details of the
sequences are unavailable. This is very unusual and hopefully the requisite
information can be released to the public shortly but if a researcher wants
to sit on it there is nothing that can be done. P19 should not be a problem
so will get cracking on this. As to M307, if TG was able to find the
sequences, then all should be ok but if it is entirely redundant then it is
not worth the effort for the company and the cost for the customer. Will
have to do further checking on this matter. In general, my view is that all
this should be customer driven and it is a company's responsibility to do
everything they c!
> an to create each test or procedure that might shed light on a customer's
haplotype - although in many cases this may not be at all cost effective but
c'est la vie. What is important is to get a clear understanding of specific
subclades however deep one has to drill since this is the only way, along
with haplotype analysis, that we are going to be able to link a motif with a
geographic region. Will double check everything and make a formal
announcement in a few days.
>
> David F.
>
>
>
>
>
> -------------- Original message --------------
>
> > 1. I have now acquired from DNA Heritage the complete 43 marker extended
> > haplotype for the M284+ sample provided me by Peter Underhill. I
recently
> > put the whole haplotype out on the List. Although it looks to me
primarily
> > like "Isles I1c" variety, it is not that far from "Northern I1c", and it
> > would be useful to definitively determine that other varieties like
> > "Northern", "Southern" and even "Root I1c" are not M284+ (or maybe
are?).
> > So we can hopefully drum up some customers from each of the varieties of
I1c
> > for the M284 SNP. It will be valuable to pin down who in I1c is M284+
and
> > who is not. Of course if you could ever get your hands on the primers
for
> > P38 it would be sensible to have someone who is M223+ test for P38 to
see if
> > FTDNA did the correct thing in renaming it I2. Amazingly, FTDNA has not
> > apparently done this simple thing, or if they have they are not telling.
> >
> > 2. There is the new Ix clade with very unique properties such as modal
10
> > at DYS455, 12 at 454, and 19,19 at YCAIIa,b; yet it has the traditional
13
> > at DYS388 and modal 11,13 at DYS392,393 for haplogroup I1b. At least one
> > person has been found with a haplotype in this clade who indicates a
> > positive P19 test result for haplogroup I. We would like to get several
of
> > the folks in this Ix to test for P37 (for I1b), M223 (for I1c), and
perhaps
> > even M253 or P30 for I1a if the previous two go negative. My hunch is
that
> > Ix will be found to be negative for all three. It is too different.
> > Whether a brand new clade parallel to the three well known ones, or a
more
> > archaic root clade, we would have I* or I1* which could be distinquished
by
> > a P38 test if you can talk the necessary information out of Dr. Hammer's
> > lab? It beats me why he has not previously shared this SNP information
with
> > the rest of the community.
> >
> > Ix looks very much like the few SNP tested I* haplotypes in a Rootsi et
al
> > database. There are just a few markers, but they added YCAIIa,b. This
> > small collection shows diversity at YCAIIa,b which covers I1b, I1a, and
I1c;
> > and diversity at DYS388 covering the same. So the circumstantial
evidence
> > indicates to me that Ix will turn out to be an archaic clade of
haplogroup
> > I. Its haplotype pedigree geography suggests this also.
> >
> > 3. There is a haplotype which has been designated haplogroup F by FTDNA
and
> > said by them to have been SNPed P19-, among other things. But this short
> > haplotype looks very much like an I1c haplotype. It would be informative
to
> > have this haplotype tested for the alternative SNPs M258 and/or M170 for
I,
> > and M223 for I1c. Perhaps there is something not understood about the
triad
> > of "redundant" SNPs defining I --- P19, M170, and M258. Some have
suggested
> > that P19 sometimes has reversions to the ancestral state?
> >
> > 4. I acquired a sample of an Estonian I1a4 haplotype (M227+) while
recently
> > in Estonia. I am presently having a 43 marker extended haplotype
measured
> > for it by DNA Heritage. Hopefully I will find a few markers where its
> > values clearly distinquish it from more normal I1a or I1a1? If so, we
shall
> > be searching through Ysearch and Ybase for haplotypes which fit the I1a4
> > motif, contacting the owners and urging them to have a M227 test done in
> > order to improve our knowledge of this small but proven subclade of I1a.
> >
> > 5. Probably Mike Humphrey, and I for sure, would like an independent lab
to
> > test us for M307. We are reported M253+, P30+, P40+, but M307-. This
just
> > does not fit with what the journal articles have been reporting
concerning
> > these "redundant" SNPs.
> >
> > So there is a robust program of interesting things to do in haplogroup I
> > with some selected haplotypes and SNPs. Let us know what you can do.
> >
> > Ken
>
>
> ==============================
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