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Archiver > GENEALOGY-DNA > 2010-03 > 1269778052


From: Doug McDonald <>
Subject: Re: [DNA] Need Help In Understanding and Using the Term "SNP"
Date: Sun, 28 Mar 2010 07:14:13 -0500
References: <201003281011.o2SABwiH008829@mail.rootsweb.com>
In-Reply-To: <201003281011.o2SABwiH008829@mail.rootsweb.com>


Harold Vannoy wrote:
>
> # Below is a text version of your data. Fields are
> TAB-separated
> '# Each line corresponds to a single SNP. For each SNP, we provide
> its identifier '
> '# (an rsid or an internal id), its location on the reference human
> genome, and the '
> # genotype call oriented with respect to the plus strand on the human
> reference
> # sequence. We are using reference human assembly build 36. ..."
>
> Should it, more correctly, say that each line corresponds to a
> "nucleotide" (or "base pair")?
>
> Also, shouldn't each result be better referred to as an "allele"
> instead of a "genotype" (wouldn't the "genotype" be made up of all of
> the individual "allele" values that were determined)?
>
> Can someone please help me with this??
>
> Also can anyone recommend a good "reference" that I can refer to in
> order to better understand "nomenclature" issues such as this?
>
> Thank you in advance.
>

Everything they say is correct jargon, as is what you say.

Yes, they are "genotypes" with two "allele values" for each location
(except mtDNA, Y, and X in males, which are haplotypes).

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).

Also there are locations with an RS number that are not technically
SNPS but rather insertions of deletions. 23andme has some of these but FamilyTreeDNA
does not. They are correctly called "Unique Event Polymorphisms";
real SNPs are also UEPs. OF course, some UEPs are known to have actually
happened more than once, for example, one called L176, first found in me
(on the Y).

Doug McDonald

Doug McDonald


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