Admixture Question?

[mkdexter]

Nope, AncestrybyDNA, 176 ancestry informative SNP's. Reliable? Can't say, but a couple of aspects of my AbDNA results were not confirmed by 23andMe Relative Finder or FTDNA Family Finder.

thanks.. I was thinking it might be dnatribes or something... didn't take the time see which test..

[mkdexter]

STR tests can not provide a 10% admixture. STR tests are meaningless for admixture percentages.

Yes they can but why bother.. which speaks to your second point, I agree they are worthless.

[JTR]

If your family is Puerto Rican it is not at all unusual to have African ancestry, African ancestry on numerous lines, no family phenotypes that seem African in appearance, and no records identifying admixture events. The reasons for the effacement of that history are obvious.

BTW my AbDNA accorded me about 10% African ancestry that has never been confirmed by on four sibling genome-wide scans. AncestryDNA, 23andMe, FamilyTreeDNA Family Finder and Genographic2.0 all offer much more reliable ancestry admixture assays than AbDNA.

That's why I can't wait for my Geno 2.0 results. I only meant that my Granps looked Puerto Rican.

I wonder if some of the reason for these results is the quality of the marker/s they are using for African ancestry? How do they assign values to these things - do they have to occur 100% within that population or do they use them even if say they are found only 95% in that population. That still would mean that other populations have those markers at around 5%. I guess the more 'African SNP's' they use the more likely the chance that you got those from African ancestors rises.

Are there data where we can see SNP's that are used, for admixture tests, that show the % where they are found throughout the world?

[tomcat]

Although my fathers father did 'look' Puerto Rican -although nothing in the paper trail suggests any african ancestor. My mom's side did have a few ancestors that owned slaves but again the paper trail says nothing about any admixing.
...
I just find it harder to believe that there would be multiple African lines rather than just a more recent individual. I have pretty good paper records back to 5-6 generations so it must be before that.

If your family is Puerto Rican it is not at all unusual to have African ancestry, African ancestry on numerous lines, no family phenotypes that seem African in appearance, and no records identifying admixture events. The reasons for the effacement of that history are obvious.

BTW my AbDNA accorded me about 10% African ancestry that has never been confirmed by on four sibling genome-wide scans. AncestryDNA, 23andMe, FamilyTreeDNA Family Finder and Genographic2.0 all offer much more reliable ancestry admixture assays than AbDNA.

[JTR]

I skimmed through the study, which was published in 2008. The result of their study is that they used a 93 AIM SNP panel on various DNA samples, made up of subjects from various continents.

From the Results section:

"The 93 SNP AIM subset had substantially larger intercontinental paired Fst values than the random SNPs for any of the pairs of population groups from the sub-Saharan African, Amerindian, East Asian, Oceana and European (excluding the South Asian populations) continental groups (Table 1)."

Here is their conclusion:

"These data provide additional support for using the 93 AIM set to efficiently identify continental subject groups for genetic studies, to identify study population outliers, and to control for admixture in association studies."

By this they mean that the 93 AIM SNP panel was able to accurately separate the samples by continent - sub-Saharan African, Amerindian, East Asian, Oceana and European. They didn't claim to be able to differentiate ethnic/geographic populations within Europe.

I don't think this is the sort of resolution that most people expect when they take an admixture test, whether free third party tools like Dodecad or a paid for test like that of Ancestry's autosomal test or FTDNA's Population Finder. This is why the free third party tools and the commercial companies both use tens of thousands of AIM SNPs in their tests. That's what's state of the art today, not 93 or 176 AIM SNPs that were state of the art in 2008 and before.

Ok! Got it! But the AncestrybyDNA 176 SNP test only provided admixture according to 4 broad groups - Sub-Saharan Africa, European, East Asian, and Native American.

Anyway, like you pointed out the new tests will be better at this determination.

[MMaddi]

Just found this paper that seems to give some reliability to certain low number AIM's tests - still not sure how AncestrybyDNA (2006) falls in line with this - man I can't wait for my Geno 2.0 AHHH!

http://www.biomedcentral.com/1471-2156/10/39

I skimmed through the study, which was published in 2008. The result of their study is that they used a 93 AIM SNP panel on various DNA samples, made up of subjects from various continents.

From the Results section:

"The 93 SNP AIM subset had substantially larger intercontinental paired Fst values than the random SNPs for any of the pairs of population groups from the sub-Saharan African, Amerindian, East Asian, Oceana and European (excluding the South Asian populations) continental groups (Table 1)."

Here is their conclusion:

"These data provide additional support for using the 93 AIM set to efficiently identify continental subject groups for genetic studies, to identify study population outliers, and to control for admixture in association studies."

By this they mean that the 93 AIM SNP panel was able to accurately separate the samples by continent - sub-Saharan African, Amerindian, East Asian, Oceana and European. They didn't claim to be able to differentiate ethnic/geographic populations within Europe.

I don't think this is the sort of resolution that most people expect when they take an admixture test, whether free third party tools like Dodecad or a paid for test like that of Ancestry's autosomal test or FTDNA's Population Finder. This is why the free third party tools and the commercial companies both use tens of thousands of AIM SNPs in their tests. That's what's state of the art today, not 93 or 176 AIM SNPs that were state of the art in 2008 and before.

[JTR]

Just found this paper that seems to give some reliability to certain low number AIM's tests - still not sure how AncestrybyDNA (2006) falls in line with this - man I can't wait for my Geno 2.0 AHHH!

http://www.biomedcentral.com/1471-2156/10/39

[thetick]

sorry this was a double post.

[thetick]

If that 10% came from an old 176 marker test I would not rely on it too much. It would be STR based.

STR tests can not provide a 10% admixture. STR tests are meaningless for admixture percentages.

[JTR]

If that 10% came from an old 176 marker test I would not rely on it too much. It would be STR based.

Geno 2 is the best bet for ethnicity at the moment. Can't wait to see how things turn out.

Think how I feel!

[JTR]

Nope, AncestrybyDNA, 176 ancestry informative SNP's. Reliable? Can't say, but a couple of aspects of my AbDNA results were not confirmed by 23andMe Relative Finder or FTDNA Family Finder.

Thanks tomcat! I would not be surprised then to find similar discrepancies - can't wait for the Geno 2.0 to come back. Man I took that test in 2006

Oh well I will just have to be satisfied with being a Euro Mutt

P.S. Would you mind sharing your discrepancies?

[tomcat]

If that 10% came from an old 176 marker test I would not rely on it too much. It would be STR based.

Nope, AncestrybyDNA, 176 ancestry informative SNP's. Reliable? Can't say, but a couple of aspects of my AbDNA results were not confirmed by 23andMe Relative Finder or FTDNA Family Finder.

[mkdexter]

If that 10% came from an old 176 marker test I would not rely on it too much. It would be STR based.

Geno 2 is the best bet for ethnicity at the moment. Can't wait to see how things turn out.

[JTR]

If you have 10% African ancestry, then your most probable African ancestor was one of your great grandparents--if you have only one African ancestral line. It appears that you understand that your African ancestry may lie farther back if there are more lines. You may discern whether or not you have multiple African lines or only one by examining the distribution of DNA from these lines on your chromosomes. If it is concentrated mostly in one or two large segments, then it is probably limited to a single line and is relatively close. If it is distributed across multiple smaller segments, then you probably have multiple African ancestral lines.

Understand that physical appearance can be very misleading about ancestral makeup. The place for you to start looking for your African ancestors is your grandparents. You have only four of them. Your recent African ancestor was the parent of one of your four grandparents.

Thanks for the response!

In regard to the above highlighted section - that would be chromosome painting or ancestry painting - correct? If so I understand that and would expect a more scattered distribution. Although my fathers father did 'look' Puerto Rican -although nothing in the paper trail suggests any african ancestor. My mom's side did have a few ancestors that owned slaves but again the paper trail says nothing about any admixing.

I just find it harder to believe that there would be multiple African lines rather than just a more recent individual. I have pretty good paper records back to 5-6 generations so it must be before that.

Question: I ordered the Geno 2.0 test to confirm this result (which was from a very early autosomal SNP test which tested for 176 markers in 2006 - do not know how reliable that is?). Would I be able to use the raw data from the Geno 2.0 to get a ancestry painting from a third party like FTDNA or someone else?

My strategy at this point is to conform this earlier result with my mom and me taking the Geno 2.0 and then getting both painted - hope that would go along way in helping.

[mkdexter]

The answer actually depends on which test gave you 10%. Was it Population Finder or a different test?