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Archiver > GENEALOGY-DNA > 2005-03 > 1111155303


From: "Ken Nordtvedt" <>
Subject: Re: [DNA] Finding new USEFUL SNPs?
Date: Fri, 18 Mar 2005 07:15:03 -0700
References: <81.23bcd22c.2f6c2320@aol.com>


Anne, I think you are suggesting what I've been hoping. When I find
objective varieties in I1a, I1b, and I1c that are not yet dignified with SNP
tags (or as we are now doing in R1b), I am hint, hint, hinting to the SNP
hunters that they specifically look for SNPs which would efficiently
identify these varieties as sub-clades of their parent haplogroup. Those
would be a useful SNPs!

I may be missing something about the procedure they go through, but my idea
was you take a bunch of haplotypes already identified as being of a variety
through their marker repeat structures, add a "control group" of haplotypes
definately not in the variety, and then hunt for SNP mutations appearing in
the one population but not the other.

There is this theory that SNPs are everywhere; that just about every male
has his own unique "private" and presently useless SNP. This would mean
that every objective variety found within a haplogroup has some useful SNPs
to be discovered which occured in the very early generations of the founding
of that variety and therefore now possessed by everyone descending from that
founder.

But I have no communication link with the SNP hunters so have to push these
views on others who may have such connections.

Ken
----- Original Message -----
From: <>
To: <>
Sent: Friday, March 18, 2005 5:27 AM
Subject: Re: [DNA] Finding new USEFUL SNPs?


> In a message dated 3/17/2005 11:48:57 AM Pacific Standard Time,
> writes:
>
> > Is there a strategy which could save the lab's time and money by
minimizing
> > the number of private SNPs they waste time and money on while maximizing
> > discovery of useful SNPs?
> >
>
> Another idea for which I will probably receive scorn and derision, but
here
> it is...SNP hunting strategy.
>
> Imagine for a moment that I have a fairly large group of WEBBs (n=9) that
are
> R1b, all but one of which have 25 or 37 markers tested. Now suppose that
> there are a substantial number of folks who match them at genetic distance
1 or 2
> on 25 markers and another group of folks who match them 0 -1 steps at 12
> markers (which is the case).
>
> And suppose that after examining the matches for each member of my group,
I
> have a list of say, 100 people with 11/12 or better matches. All of these
have
> been tested at the same lab (one was also tested at another lab, so we
have
> 48 markers for him).
>
> Why could that one lab not take a look at the larger group made up of
11/12
> and 12/12 marker or better matches to hunt for a SNP? Seems to me if they
> could spot some mutation, in whatever region of hte DNA SNP's turn up in,
shared
> by all (or even most) of a group of folks who match 11/12 (or maybe even
10/12
> since we have seen these turn into 23/25), wouldn't that indicate a
> non-private, useful SNP?
>
> OK take your best shots! I have my full body armor on today!
>
> Anne
>
>
> ==============================
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>
>


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