Archiver > GENEALOGY-DNA > 2010-03 > 1269895401

Subject: Re: [DNA] Need Help In Understanding and Using the Term "SNP"
Date: Mon, 29 Mar 2010 16:48:25 EDT

Harold, mtDNA is sort of in a world of its own. The two reference
sequences, Yoruba and the Cambridge Reference Sequence, are not related to build
numbers, but to two specific sequences that were selected for comparison years
ago. The CRS was the very first mtDNA molecule to be sequenced, and it is
used by most people. For some unknown reason, the Yoruba sequence was selected
for the RefSeq database, the source for protein structure used in medical
studies. It differs from the CRS by having a few insertions / deletions, so
the numbering gets out of alignment.

The chip companies use the medically oriented reference, although the CRS
finally became the official RefSeq sequence just last year.

FTDNA's full sequence results list YOUR differences according to the
revised CRS (see above). Since they are looking at every single base, they don't
need an rs number. In fact, very few variations in the CRS have been given an
rs number -- they're simply listed by position in the mtDNA molecule.
23andMe probes for the existence of ~2000 common variations, many of which are
used for haplogroup assignments. If these don't have an rs number, they get an
"i" (internal) number from 23andMe. The probes are keyed to bases
surrounding the variant, not the absolute position. If you browse your raw data,
you'll see both the Yoruba and the CRS position listed.

Maybe I'm just muddying the waters more!

Ann Turner

In a message dated 3/29/2010 12:02:28 PM Pacific Daylight Time,

> 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!!

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