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Archiver > GENEALOGY-DNA > 2010-03 > 1269889009


From: Harold Vannoy <>
Subject: Re: [DNA] Need Help In Understanding and Using the Term "SNP"
Date: Mon, 29 Mar 2010 15:01:49 -0400
References: <201003281011.o2SABwiH008829@mail.rootsweb.com><4BAF4815.6040401@scs.uiuc.edu>
In-Reply-To: <4BAF4815.6040401@scs.uiuc.edu>


At 08:14 AM 3/28/2010, Doug McDonald wrote:

>However, they are using correct notation when referring to each
>as a "SNP" since it has an rs number. This means that that
>location is known to differ in different people, and the rs
>(or in a few cases "i") number is the "name" of the SNP. You
>may not "have that SNP" but somebody does. They are referring
>to POTENTIAL SNPs, in other words.
>
>If they had used locations that have never been known to mutate,
>it would be incorrect to call them SNPS. But they don't do that.
>(FanilytreeDNA does sell info for locations that are never
>known to have mutated, in the mtDNA full sequence and in the WTY).


Doug, thank you for your response. It is interesting about L176 first
being found in your Y-DNA!

I guess that I still must be missing something or that I don't
correctly understand your response. If, 23andMe is using correct
notation, when saying that "Each line corresponds to a single SNP,"
because "every line" relates to a position that has previously been
found to have been a SNP by someone at sometime in the past -
wouldn't this require the definition of a SNP to be: Any nucleotide
that has ever been found to have a mutation (for anyone at anytime in
the past) at a certain position is a SNP. This isn't correct, is it?

To determine if a SNP has occurred, doesn't the test result (allele)
have to be compared to a standard? 23andMe says that their
"reference" was "human assembly build 36". The current reference that
is being used by "NCBI" seems to be "build 37.1" and for mtDNA we use
"rCRS" as the reference It appears that up through position 304, all
three of these references are the same.

In this range of positions 1 through 304, both my 23andMe test
results and my FTDNA FGS results agree exactly with the reference
standards except for the following mutations: A73G, C150T, G185A,
A263G. Doesn't this mean that, in this range, I only have "SNPs" at
these four locations?

In my 23andMe test results a large number of the "lines" do not have
"rs" (refSNP) IDs listed (they have an "i" ,internal, ID listed). It
seems to me that an "rsid" would only be appropriate to be listed for
those cases where I have an actual SNP?? When I check at "NCBI" I
find that "rs" numbers have been assigned for SNPs at locations 73,
150, and 263 (no "rs" number is shown at location 185). In my
23andMe test results, only position 263 lists an "rs" number ("i"
numbers are given for the other three positions) - you figure!!

As I said earlier, I must still be missing something!!

Doug and others, I would appreciate any additional help that you can
give me in trying to understand this.

Thanks again,

Harold Vannoy





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