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Archiver > GENEALOGY-DNA > 2010-04 > 1272216464


From:
Subject: Re: [DNA] 23andMe X-SNPs compared to FF
Date: Sun, 25 Apr 2010 13:51:59 EDT


In a message dated 4/25/2010 9:44:34 AM Pacific Daylight Time,
writes:

> It is great to hear that FTDNA and 23andMe use (all?) the same
> versions. It is confusing when deCODEme uses a different version (Plus
> versus Minus) and it takes hours to convert.

Going from deCODEme to the plus orientation used by 23andMe and FTDNA can
be done reasonably quickly with Excel formulas, although it's faster to do it
with some program code. Going from all plus to dbSNP orientation (a mixture
of plus and minus) isn't practical, so it's best to standardize on the plus
orientation.

I was just thinking about the best way to standardize the DIP
(deletion/insertion polymorphism) notation. 23andMe and deCODEme reports genotypes as DD,
DI, or II, while FTDNA reports a double dash -- for DD and a single dash
with a base (e.g. "-C") would be like DI. The double dash represents a no-call
at 23andMe, and FTDNA uses a triple dash for no-calls. The single dash
makes things complicated in Excel, since it thinks you are starting a formula
for subtraction. I'd be in favor of standardizing on the DI method, but there
will still be some cases where alleles might be GG at FTDNA and II at
23andMe. Maybe we need a master list for DIPS?

> I am wondering if FTDNA really left out the genes and just lists the
> intergenic areas?

No, the claim was that they scrubbed medically significant SNPs. They still
include over 1600 SNPs with entries in SNPedia, which would have some
phenotype implications, according to an analysis posted at DNA-Forums:

http://tinyurl.com/27slbj8

Ann Turner


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