Archiver > GENEALOGY-DNA > 2010-03 > 1269921485

From: Nelda Percival <>
Subject: [DNA] US judge strikes down patent on cancer genes
Date: Mon, 29 Mar 2010 23:01:56 -0500
References: <>
In-Reply-To: <>

I don't know if this is supposed to be good or bad.. But I found it interesting..


My websites :

> From:
> Date: Mon, 29 Mar 2010 16:48:25 -0400
> To:
> Subject: Re: [DNA] Need Help In Understanding and Using the Term "SNP"
> 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,
> writes:
>> 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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