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Tuesday, October 4, 2011

MDLP modification of DIYDodecad calculator: additional instructions/ideas

I have come up with another idea of how to use the estimated frequencies of my project for inferring the origin of shared HIR segments. Suppose, for example, that a Lithuanian/Belorussian and a Norwegian share some HIR segment. This could be:

1)Balto-Slavic-like ancestry in the Norwegian individual
2)Scandinavian-like ancestry in the Lithuanian individual
3)third party ancestry in both individuals

Using byseg 500 50 mode in DIYDodecad, AncestryFinder file, and MDLP allele frequencies, i was able to predict the origin of the HIR segment by picking one of three scenarios:

1) if the Lithuanian sees an excess of Scandinavian, then he should pick the second scenario
2) if he sees nothing unremarkable, the first one
3) if an excess of some component (relatively) low in both Lithuanian and Norwegian (e.g., Caucassian-Anatolian), the third.


After analyzing my "Scandinavian" "matches" from AF's file, i can conclude that DIYDodecad analysis (in byseg mode) reveals the presence of all three possible scenarios:

Scenario nr.2 (Balto-Slavic-like ancestry in the Scandinavian individual)
X Sweden Sweden United States United States 1 156.4 160 3.6 5.6
60%-Scenario nr.1 (Scandinavian-like ancestry in the Balto-Slavic individual)
X Denmark Denmark Denmark Denmark 1 87.9 94.3 6.4 6.3
Scenario nr.1 (Scandinavian-like ancestry in the Balto-Slavic individual)
X Norway Norway Norway Norway 1 62.1 65.4 3.3 5
Scenario nr.1 (Scandinavian-like ancestry in the Balto-Slavic individual)
Anonymous0454 Finland Finland Finland Finland 1 104.8 110.3 5.5 6.4
Scenario nr.2 (Balto-Slavic-like ancestry in the Scandinavian individual)
X Sweden Not Provided Not Provided Not Provided 2 82.2 88.1 5.9 5
60%-Scenario nr.2 (Balto-Slavic-like ancestry in the Scandinavian individual)
X Sweden Sweden United States United States 3 174.9 178.1 3.2 5
80%-Scenario nr.2 (Balto-Slavic-like ancestry in the Scandinavian individual)
Anonymous0353 Denmark Denmark Denmark Denmark 3 68.4 73.3 4.9 8.1
50%-Scenario nr.2 (Balto-Slavic-like ancestry in the Scandinavian individual)
Anonymous0245 Denmark Denmark Denmark Denmark 4 70.5 77.3 6.8 5.3


HLA-MHC group
-Scenario III - third party (Celto-Germanic) ancestry in both individuals

X Sweden Sweden United States United States 6 25.8 34.2 8.4 5.4
X Sweden Denmark United States United States 6 27.6 34.5 6.9 5.1
Anonymous0207 Sweden Sweden Not Provided Not Provided 6 25.6 34.1 8.5 5.3
X Norway Not Provided Belgium Not Provided 6 29.7 36.1 6.4 5.3
Anonymous0370 Sweden Sweden Not Provided Sweden 6 30.7 36.6 5.9 5.4
X Denmark Denmark Denmark Denmark 6 25.6 35.5 9.9 5.9
Anonymous0439 Denmark Not Provided United States Hungary 6 26.3 36 9.7 6
X Denmark Denmark Denmark Denmark 6 26 34 8 5.1
X Norway Norway Norway Norway 6 25.6 34.2 8.6 5.6

Chr14. group - 70%-Scenario nr.2 (Balto-Slavic-like ancestry in the Scandinavian individual)
Anonymous0001 Norway Norway Norway Norway 14 38 48.8 10.8 6.5
Anonymous0037 Sweden Norway United States United States 14 39.2 48 8.8 5.1

Scenario nr.1 (Scandinavian ancestry in the Balto-Slavic individual)
Anonymous0002 Denmark Denmark United States United States 15 43.9 51.3 7.4 6














2 comments:

  1. I have mapped the MDLP components onto Dodecad v3 and vice versa

    http://dodecad.blogspot.com/2011/10/comparing-different-admixture-runs.html

    ReplyDelete
  2. Dienekes,

    Thank you for using our modification as a proof of concept )

    ReplyDelete