Archiver > GENEALOGY-DNA > 2009-04 > 1238894375

From: David Faux <>
Subject: [DNA] Upgrading 23andme Ancestry Painting;and Painting the X Chromosome
Date: Sat, 4 Apr 2009 18:19:35 -0700


I have begun to agitate for improvements to the Ancestry Painting feature at
23andme. Nothing has changed since day one, which also means that they have
yet to get around to painting the X chromosome. It is all static and will
remain so unless people step forward and express their opinions so that the
scientists can convince the resource allocators that it is imperative that
something be done to address this problem of they will lose business. I
have specifically not ordered testing of my uncle until I have direct
confirmation that 23andme understands that there are probably as many
customers interested in the ancestry component as the medical and trait
components (which are truly of no interest to me - the only thing I learned
that tweaked some curiosity was that I have a sprinter genotype).

When the present 23andme Ancestry Painting feature was designed only the
HapMap data was available to them - and to date there have been no
upgrades. Thus at the moment the Chinese and Japanese are proxies for all
East Asians, South Sea Islanders, and Native Americans. Their algorithm
appears to be quite good, such that there are unlikely to be many false
positives (a severe problem with decodeme data analysis). The problem is
that there are an unknown number of false negatives. My analysis (case
study) via Anders Palsen using the 52 worldwide populations via the
HGDP-CEPH database uses a much more robust approach to the search for
evidence of minority Native American. It succeeded in completely removing
any African on the X (decodeme had attributed 8% to this source) - there was
nothing there, only evidence of a number of blocks shared by Africans and
Europeans but not East Asians. Anders also found evidence of millions of bp
matches to East Asians but only from the northeast, and to Native
Americans. He usedthe PLINK phasing program, and validating it by a direct
inspection with Excel formula. Hence my 100% European seen in the 23andme
Ancestry Painting is incorrect, and according to the analysis by Anders is
almost exactly what is expected based on the paper trail which includes
multiple sources.

Anders found 6.5% Native American (via Yakut and Xibo proxies) on the X, and
a further 6.5% not found in any European sample and in the region flanking
the above. This is likely a founder effect comparable (perhaps) to mtDNA
haplogroup X2a found in the Great Lakes area.

The above brings up another point. At present there is not a representative
sample for the region where my ancestors lived, and so it is necessary to
employ the best proxies. Since I don't envision any change soon, at least
they could use northeastern Asian tribes instead of Chinese. I agree that
the approach they use will allow some percentage of the minority ancestry to
be caught in the net - but how much slips through?

I have started a thread at the 23andme community:

Please use this or write to 23andme directly if you feel as I do that it is
high time that the company address the needs of those of us interested in
autosomal and X ancestry. If they do not receive a flood of "constructive
criticism" they will come to the conclusion that we are all happy as clams
and put their efforts into beefing up other parts of their product. Only a
concerted effort by all of us will work. I know that the scientists are
willing and able, but the company needs to know that there is an interest or
"demand" out there for improving and upgrading the Ancestry Painting.

David K. Faux.

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