CODIS & DNA Tribes

[Sonia]

I realized that the CODIS & DNA Tribes stuff might not belong in Articles & Interesting Links. I did receive a response from my 2nd email to DNA Tribes about Gram's results. They believe that it's a combination of the admixture and not having matching samples in their database at this time. It really pays to ask questions as they have offered me 2 free upgrades as their database grows

[GregKiroKH]

I ordered the CODIS test, and I am waiting for my results. I wonder if it will help me?

[GregKiroKH]

The big difference between my DNATribes score and AbDNA was with Mediterranean. I get the following:
European: 78.8%
African and Near Eastern: 21.7%
Native America: 1.0 %
Asian/Pacific: 0.5 %

High Resolution World Region Match
Northwest European 11.1 28.60824742
Eastern European 7.6 19.58762887
Finno-Ugrian 5.5 14.17525773
Mediterranean 4.9 12.62886598
Sub-Saharan African 3.2 8.24742268
Asia Minor 1.9 4.896907216
North African 1.9 4.896907216
North Indian 1.3 3.350515464
Basque 0.7 1.804123711
Mestizo 0.4 1.030927835
Southeast Asian 0.2 0.515463918
Arabian 0.1 0.257731959
South Indian 0 0
Chinese 0 0
Salishan 0 0
Japanese 0 0
Polynesian 0 0
Tibetan 0 0
Australian 0 0
Northeast Amerindian 0 0
Athabaskan 0 0
South Amerindian 0 0
Alaskan 0 0

Medium Resolution Global Population Match
Bucharest, Romania 68.1 5.448
Lodz, Poland 35.8 2.864
Czech 34.1 2.728
Strathclyde, Scotland 34.1 2.728
Estonia 31.4 2.512
Ireland 23.5 1.88
Glasgow, Scotland 22.8 1.824
Dundee, Scotland 20.5 1.64
Liguria, Italy 18.6 1.488
Podlasie (Northeast Poland) 17.7 1.416
Austrian 17.2 1.376
Lille, France 16.7 1.336
Northern Ireland 16.3 1.304
Vienna, Austria 16.1 1.288
Northeast Poland 14.4 1.152
Campania, Italy 13.8 1.104
Basque (Basque Country, Spain) 13.7 1.096
Toulouse, France 13.5 1.08
Polish 12.9 1.032
Russian Orthodox Old Believers (Suwalki, Poland) 12.5 1

Medium Resolution Global Population Match
Bucharest, Romania 68.1 4.729166667
Caucasian (Canada) 37.6 2.611111111
Caucasian 36.4 2.527777778
Lodz, Poland 35.8 2.486111111
Czech 34.1 2.368055556
Strathclyde, Scotland 34.1 2.368055556
Estonia 31.4 2.180555556
Ireland 23.5 1.631944444
Glasgow, Scotland 22.8 1.583333333
Dundee, Scotland 20.5 1.423611111
Liguria, Italy 18.6 1.291666667
Podlasie (Northeast Poland) 17.7 1.229166667
Austrian 17.2 1.194444444
Lille, France 16.7 1.159722222
Cantabrian (Spain) 16.4 1.138888889
Caucasian (Maine, U.S.A.) 16.4 1.138888889
Northern Ireland 16.3 1.131944444
Vienna, Austria 16.1 1.118055556
Hispanic (Michigan, U.S.A.) 15.4 1.069444444
Northeast Poland 14.4 1

[Sonia]

Tribes Results

Hi Greg,

If you check in the DNA & Genealogy Forum there are a few of us who are "playing" with putting markers into a few programs, Omnipop & the RCMP Database to see if we can learn anymore (a debatable, but fun process). By looking at the values of the alleles for Gram's results I think I figured out which was from each parent based on how she described her parents. The values of the markers on the one allele is really unusual (her mom). The other has a greater alignment toward African, mix them together and Gram's marker values come out with the East Indian results

[GregKiroKH]

I have seen your post, Sonia. I have tried to get individual frequencies from the RCMP site. However, the results are limited to racial groups and the matches are between 1 in 10^18 to 1 in 10^27.

[Sonia]

Allele Frequencies

Greg,
If you can download the Omnipop, the first sheet is the main page & you can put the alleles in individually. The second sheet is the data page & it shows frequencies of the alleles among the 179 populations the program has in its database. You still end up with outrageous numbers, but I guess that's what makes the CODIS markers so unique & useful for forensic work.

[GregKiroKH]

Hi Sonia,

I have downloaded Omnipop from the following:

http://www.uni-duesseldorf.de/WWW/M...y/database.html

http://www.dna-fingerprint.com/modules.php?op=modload&name=Downloads&file=index&req=viewdownload&cid=2

The results from DNAtrobes seem to be better. However, Omnipop is more flexible. I can look at the data that I want to with Omnipop. The only way that I can get new results from DNAtribes is to order an update for about $30. I am going to look at Omnipop in detail when I have time. Examining the maps given by DNAtribes. I find good agreement with my surname research. I live in Northeastern United States. They put me in the northern part of that region while I live in the southern part. This maybe due to the ancient Native American markers which are often put in Canada or Mexico depending on which markers are left out. My Old World tribal affiliation on my father's side and surname has always suggested a connection between Silesia and Perth. Historically, this is associated with the Volkerwanderwung.

By the 3rd century AD various German tribal confederations, all of whom will leave a lasting mark on European history, are ranged along the natural borders of the Roman empire. They have settled in the territories east of the Rhine and north of the Danube and Black Sea. From here, in the great upheavals of the 4th and 5th century (known as the Völkerwanderung, 'migration of the peoples'), they will move throughout [Western] Europe.

The large values for Romanian and Mediterranean regions seem to match the 16224 value in my mtDNA, and the presence of Sub-Saharan African autosomes matches with my L1c mtDNA. I guess I will find out more later.

[Sonia]

The big difference between my DNATribes score and AbDNA was with Mediterranean. I get the following:
European: 78.8%
African and Near Eastern: 21.7%
Native America: 1.0 %
Asian/Pacific: 0.5 %

High Resolution World Region Match
Northwest European 11.1 28.60824742
Eastern European 7.6 19.58762887
Finno-Ugrian 5.5 14.17525773
Mediterranean 4.9 12.62886598
Sub-Saharan African 3.2 8.24742268
Asia Minor 1.9 4.896907216
North African 1.9 4.896907216
North Indian 1.3 3.350515464
Basque 0.7 1.804123711
Mestizo 0.4 1.030927835
Southeast Asian 0.2 0.515463918
Arabian 0.1 0.257731959
South Indian 0 0
Chinese 0 0
Salishan 0 0
Japanese 0 0
Polynesian 0 0
Tibetan 0 0
Australian 0 0
Northeast Amerindian 0 0
Athabaskan 0 0
South Amerindian 0 0
Alaskan 0 0

Hi Greg,
I snipped off part of your post. Tribes changed the way they report results a little bit since my August results. You have 2 values listed next to each area, what do they signify? Gram's results only showed one value, but I haven't noticed that they added any additional data for their African and Near Eastern Region so I'm holding off on an upgrade. Gram's ABD2.5 was 82% Sub-Saharan African & 18% European. While her DNA Tribes scores for World Region listed Sub-Saharan Africa first, the value was less than 0.45.

It's great you have the genealogical and historical paper trails to compare to your results!

[GregKiroKH]

Hi Greg,
I snipped off part of your post. Tribes changed the way they report results a little bit since my August results. You have 2 values listed next to each area, what do they signify? Gram's results only showed one value, but I haven't noticed that they added any additional data for their African and Near Eastern Region so I'm holding off on an upgrade. Gram's ABD2.5 was 82% Sub-Saharan African & 18% European. While her DNA Tribes scores for World Region listed Sub-Saharan Africa first, the value was less than 0.45.

It's great you have the genealogical and historical paper trails to compare to your results!

I normalized my results so that the numbers add up to 100%.

I work with Omnipop, and it is clear that there is some racial profiling done. There results are more like ABDNA 2.5. Also, my most likely groups were different than DNA tribes.

Omnipop CODIS -
7 CAUCASIAN (Virginia, Swiss, Alabama, other types)
PORTUGESE
SCOTTISH
3 BRAZILIAN (non black, other types, black)
3 HISPANIC (American, Michigan. Other types)
4 N AFR (TUNISIAN, MOROCCAN ARAB, MAGHREB, CANARY ISLAND)
10 AFRO AMERICAN (Florida, Alabama, Canada, Connecticut, Virginia, other types)
Michigan Native American

D8S- INDIA//AFR/BASQUE
D21- CAUCASIAN//WEST MEDIT/SE ASIA
D7S- PUNA/SPAN/NW AFR.//NAT AMERICAN
CSF- TUNISIAN/CAUCASIAN/INDIA/NAT AMER
D3S - CAUCASIAN
TH0-CAUCASIAN//AFRO AMER
D13- ALSAKA/INDIA//N&W AFR/AFRO AMER/INDIA
D16- CAUCASIAN/ADMIX AMER//NW AFR/SE EURO/NAT AM
VWA - S ASIAN//AFRO AMER
TPO- CAUCASIAN VARIOUS REGIONS
D18- N&E AFR/AFR SPAN/APACHE//NAT AMER/HISPAN
D5S- N&E AFR/INDIA/POLISH//AFRO AMER/ANGOLAN
FGA - N. AFR/SPAN//INDIA/YEMEN/ALASKA


Did you try to add up and group all of the regions?

[GregKiroKH]

Updates are funny, maybe I should have summarized one locus as

D21- CAUCASIAN//EAST MEDIT/MACAU

I wonder when they use geographic location or region?

[GregKiroKH]

There are many programs you can use for your mtDNA and Y-DNA. To use Omnipop, you use your CODIS markers.

http://www.cstl.nist.gov/div831/strbase/fbicore.htm

You get your CODIS markers from your DNATribes results. First put in all of your markers and record the top 30 populations. They are the lowest non-zero numbers. Then test each allele for each Locus. Each allele comes from either your mother or your father. For each locus, one will come from your mother and one will come from your father. The US data was basically for police work. And race is separated into several groups. For example, they do not look at Afro-American or Asian American as an admixture. All Afro-Americans are not from a recent African Diaspora. Each allele will give a result. If both alleles for a locus are the same, then the results you get for the pair will be the same as the results for the single allele. Remember that you are obtaining population data when you do this. It is not your data. Some allele values are constant for a population while others represent a migration from point A to Point B or a wandering. While others might be random . . . As you might have read in the paper, the CODIS was carefully chosen to represent population data which could be used to identify individuals just like AMEL will tell if the person is a male, XY or a female, XX. The total CODIS profile is typical of a population also.

example. Father AB Mother CD
Child AC or AD or BC or BD

Just think why there is a 50% of boy or girl
XY XX

XX
XX
YX
YX

There are 13 CODIS autosomes and different populations mix just like boy and girl

[casadecoqui]

Pretty darn good explanation, Greg!

There are many programs you can use for your mtDNA and Y-DNA. To use Omnipop, you use your CODIS markers.

http://www.cstl.nist.gov/div831/strbase/fbicore.htm

You get your CODIS markers from your DNATribes results. First put in all of your markers and record the top 30 populations. They are the lowest non-zero numbers. Then test each allele for each Locus. Each allele comes from either your mother or your father. For each locus, one will come from your mother and one will come from your father. The US data was basically for police work. And race is separated into several groups. For example, they do not look at Afro-American or Asian American as an admixture. All Afro-Americans are not from a recent African Diaspora. Each allele will give a result. If both alleles for a locus are the same, then the results you get for the pair will be the same as the results for the single allele. Remember that you are obtaining population data when you do this. It is not your data. Some allele values are constant for a population while others represent a migration from point A to Point B or a wandering. While others might be random . . . As you might have read in the paper, the CODIS was carefully chosen to represent population data which could be used to identify individuals just like AMEL will tell if the person is a male, XY or a female, XX. The total CODIS profile is typical of a population also.

example. Father AB Mother CD
Child AC or AD or BC or BD

Just think why there is a 50% of boy or girl
XY XX

XX
XX
YX
YX

There are 13 CODIS autosomes and different populations mix just like boy and girl

[GregKiroKH]

Thanks, Ana . . .

[clarkedenise]

Deep Clade E Test

Dear Dra. Ana and Greg,
I received an email indicating there is a Deep Clade E test now available which I ordered this weekend. IHopefully, a sub-clade will be discovered. I will let you know when the results are available. Hope all is well with everyone in the group. We out here in California survived last year's fires and we replaced our avocado grove with a vineyard. Our vines are growing very rapidly. Our fingers are crossed for a successful crop.
Denise

[GregKiroKHR1bL1]

That is interesting Denise . . . not only has some interesting research been done with hg E, there has been some exciting results for mt hg A. So, I ordered my father's full mtDNA to be done. It is mt hg A so far without the 16111 mutatation for the HVR-I region. One match so far is A2a. His family is from Virgina. I cannot wait to find out the results. I am still a little puzzled about my mt-DNA full scan I did two years ago. We now know all the mutations happen in some other mt DNA. Neverthelesss, no exact matches yet. I did my deep Y-DNA test, and it came back, R-U106. Well, My grandfather's name was Egbert Adolph Haynes which matches his DNA. There is still a lot more work which needs to be done, and another sub-clade to be founded.

I hope the crops come out ok for you.

Dear Dra. Ana and Greg,
I received an email indicating there is a Deep Clade E test now available which I ordered this weekend. IHopefully, a sub-clade will be discovered. I will let you know when the results are available. Hope all is well with everyone in the group. We out here in California survived last year's fires and we replaced our avocado grove with a vineyard. Our vines are growing very rapidly. Our fingers are crossed for a successful crop.
Denise