Saami ancestry and the MDLP Oracle-x Population Fitting

Update 08.10.2014: The MDLP calculators have been updated and now do not give the results as shown below. This post is then considered outdated and should not be used as guide vs the MDLP calculators.

This is a short test of MDLP Oracle-x Population Fitting at Gedmatch ability to catch Saami ancestry. Only MDLP calculators have been tested as these are the only one with Saami population reference.

As the test shows finding Saami ancestry using these calculators may give very different and even erroneous results (no Saami ancestry or minor Saami ancestry when there is actually major Saami ancestry) but one stand clearly out as the preferred choice. The "test subject" (with consent) is a North-Saami individual participating in the project with mostly Saami ancestry.


Absent = Saami ancestry not detected.
Minor = Saami ancestry detected but as minority ancestry.
Top but minor = Saami ancestry detected as top population but with less than 50%.
Top majority = Saami ancestry detected as top population with more than 50%.

As the result shows using MDLP K=5 Oracle X "Pct. Calc. Option 1" appears to be the preferred choice to detect Saami ancestry.

EDIT 20/9-13

Please note that all the other functionalities of the different versions of the MDLP calculators like Oracle and Oracle-4 was neither able to find that the Saami individual had majority Saami ancestry. Some where able to infer Saami minority ancestry and some didnt detect anything at all. The exception again is the MDLP K=5 that managed in Oracle to get a Saami population as number two and 3 of 4 in Oracle-4. Thie MDLP 27 calculator (not in Gedmatch) managed using Gaussian method 1 population mode to infer the correct population but failed in the 2,3 and 4 approximations.

La Braña 2 and modern European variation

This is a reanalysis of the La Braña's but this time separately. The La Braña 2 matched the 1000 genome reference panel with 56k SNP's. These SNP's was used together with the 288k SNP's from the standard population that match the 1000 genome reference SNP's to impute the missing 56k SNP's from the La Braña as described earlier. These SNP's was then further LD pruned in PLINK to 26k SNP's and then run through the Chromopainter-Finestructure unlinked pipeline using the world panel. The European panel was then later extracted from the Chromopainter output files and run through Finestructure using 21k SNP's.

The heatmap, tree structure and PCA plot below shows somewhat different result than for the La Braña 1 as La Braña 2 appears to have a position that cluster around with the Scandinavian-Saamis (individuals with both Scandinavian and Saami background).

This means that the original analysis of the composite La Braña need to be adjusted after the findings here. La Braña 2 appears most similar to individuals of mixed Scandinavian and Saami ancestry..

CC Euro unlinked 21k

 CC Euro unlinked 21k detailed 

 CC Euro unlinked 21k D1-D2

  CC Euro unlinked 21k D1-D3

EDIT: 20/9-13

Download BRA2 individual results

La Braña 1 and modern European variation.

This is a reanalysis of the La Braña's but this time separately. The La Braña 1 matched the 1000 genome reference panel with 129k SNP's. These SNP's was used together with the 288k SNP's from the standard population that match the 1000 genome reference SNP's to impute the missing 129k SNP's from the La Braña as described earlier. These SNP's was then further LD pruned in PLINK to 47k SNP's and then run through the Chromopainter-Finestructure unlinked pipeline using the world panel. The European panel was then later extracted from the Chromopainter output files and run through Finestructure using 38k SNP's.

The heatmap and tree structure below shows somewhat different result than for the composite La Braña individual consisting of both La Braña 1 and La Braña 2. As we can see the La Braña 1 do not completely cluster witht the Finns and Saamis anymore but appears to have a more intermediate position between the Saami-Finnish cluster and the Eastern European cluster.

CC Euro 47k unlinked La Braña 1

This is also reflected in the PCA D1-D2 (horisontal and vertical) where La Braña 1 appears to appear in the middle between the Finnish-Saami cluster and Eastern Europeans.

 CC Euro 47k unlinked La Braña 1 detailed 

CC Euro 47k PCA unlinked D1-D2

CC Euro 47k PCA unlinked D1-D3

The analysis of La Braña 2 will follow later

EDIT 23/9-13

Download individual results