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View Full Version : Sub Saharan African Segment, can anyone please advise?



Boudicca
01-27-2013, 03:58 PM
Hi,
I did start a thread about SSA in Europeans over at 23andme but it has been taken over by the Ancestry Composition bug debate so I'm hoping someone here might be able to help!
Basically my mother has a segment of SSA on Chr11 on Ancestry Composition. It is not near the centromere or telomeres. I never bothered to check for African DNA before until this appeared. In the same location there is also a segment of African that shows up with Doug, Gedmatch chromosome paintings and at deCODEme. Someone suggested I look at SNP map to find SNPs exclusive to African populations. I couldn't get onto that site, but I did look on the SNSmart website that Davidski had mentioned a while back. Many of the SNPs were shared by all populations so it was difficult to ascertain anything other than my mother being human (!), however I have found 2 SNPs that were quite interesting (I have not gone through all of them in the region of the segment).
One is made up of C/C, C/T or T/T. My mother is C/T.
0.987 of all populations get C with 0.013 getting T. Broken down into groups:
C/C=100% of Europeans and Asians.
C/T=Africans, African Americans, a few Mexicans from Los Angeles.
T/T=Only Africans (Yoruba).
The other is made up of G/G, A/G, A/A. My mother is A/G.
0.98 of all populations get G with 0.02 getting A. Broken down into groups:
G/G=100% Europeans and Asians.
A/G=Africans, African Americans.
A/A=Only Africans.

My question is, does the fact that a variety of tests plus the rare SNPs indicate that this is actually a real African segment? Doug seems to think is it real when AC and his test pick it up in Europeans. This segment is under the 1% noise threshold used in many analyses hence my query. My mother is half UK half unknown American.

AJL
01-27-2013, 04:23 PM
I'd say there's a very good chance it's real if it's being picked up with multiple tests. How old it is, though, is harder to guess at.

A related question is, do you have any overlap with genetic cousins via Ancestry Finder/Relative Finder at that spot? If so, how many of those cousins are identifying as either African, or African American?

Boudicca
01-27-2013, 04:28 PM
Hi,
Thanks for your reply. I don't think there are any cousin matches in that location that are African American and certainly none from Africa. The US matches in that spot are anonymous so no way to check :\ still it's interesting but as you say finding a timeframe is difficult.

Veridicus
01-27-2013, 05:47 PM
Boudicca, could you list the 2 SNP's you are talking about - I would like to look them up on my raw data since I have a small segment of SSA. Also, how long is this segment you are talking about?

Thanks!

Boudicca
02-02-2013, 10:39 AM
I have another question:
Which is better at detecting African ancestry in Europeans, Ancestry Composition or Dodecad Africa 9 chromosome painting at Gedmatch and why?