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From:
Subject: Re: [DNA] Finding new USEFUL SNPs?
Date: Fri, 18 Mar 2005 17:42:15 +0000


I do have communication with "SNP hunters" Ken, and I can tell you that your expectations are of the "perfect world" variety. Jim Wilson and Chris Tyler - Smith spent endless hours of their own time (since their employers have other expectations of what they should be doing with their time - as do the granting agencies who fund their research) in largely fruitless SNP searches. It is only now because of Perlegen that we may be able to make significant break throughs.

Potential SNP hunters have little incentive beyond their own curiosity to search for elusive single nucleotide polymorphism mutations that are "not private". The research money is pretty well dedicated to medical genetic screening and any other work must be "piggy backed" on this activity the granting agencies must give permission to use the samples in a way that is not directly tied to the intended use. I can assure you that Jim Wilson would love to be in a position to have free rein to go on a hunt for SNPs, but these days the analogy with police work may apply. The police generally do not have enough leads to locate a suspect so they must rely on the public to assist them and come forward with information that detectives can follow up. This is why we are pleased when someone on this list or elsewhere comes forward with information that could allow academic "SNP hunters" to spend their time (largely their own time) efficiently. We need the public's help unless you ca!
n convince funding agencies to shift priorities.

David F.


-------------- Original message --------------

> 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

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