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tirsdag 15. oktober 2013

Digging deeper in Fennoscandian ancestry II

This is a continuation of the previous analysis (not a new analysis run!) and this time we look at the analysis possibilities of differentiating Scandinavians (Swedes, Norwegians, Danes). This time all individuals who shows considerable Saami (both North-Saami like or South-Saami like) or Finnish admixture in the previous analysis was removed from further analysis to keep any outside influence reduced to a minimum and lumped into the "other" group containing the rest of the world.

The data was run through Finestructures clustering processing but it was unable to differentiate the remaining Scandinavians meaning it appeared by the software to be one population. However in the PCA plot it was possible to infer structure. As we so in the previous analysis the first two dimensions of the PCA plot appears to reflect level of external influences in Scandinavians. In both dimensions the Norwegians clustered in the upper left corner closest to the "others" while Swedes clustered in much of the lower right corner but with a huge spread over large part of the plot. The single Danish individual appear to cluster with the Norwegians.

PCA dimension 1(horizontal) and 2 (vertical)

Dimension 3 on the other hand appears to be internal between Norwegians and Swedes, below together with dimension 2 and seem to give a better clustering. The Danish individual still in the Norwegian cluster but closer to the Swedes.

PCA dimension 2(H) and 3 (V)

So the Chromopainter-Finestructure pipeline appears to be able to differentiate Norwegian and Swedish ancestry even only using 289k SNP's. The division isnt entirely clear cut but there have been populations movement between these countries for many centuries so the classification labels may not be entirely correct and some individuals also have mixed backgrounds.

lørdag 5. oktober 2013

Digging deeper in Fennoscandian ancestry I

I have been the last few months become more aware by the authors of Chromopainter-Finestructure that I have not been doing the analysis completely "according to book" even the software manuals have not being saying it explicitly.

I have from the start had this practice of running the Chromopainter-Finestructure analysis with the whole world panel and then later extracted from the output file the subdata from each run into a European panel and into a Fennoscandian panel for more detailed local analysis. However actually you should use the "superindividual" and "continent" functionality in Finestructure to get the analysis right and no file editing necessary and you also need to do a new ChromoCombine run with the forcefiles with these superindividuals.

I have been testing the difference using my earlier practice in the last standard run (this is NOT a new run!) data with these new settings to compare the results. It appears that after the advice from the authors its possible to extract even more information from the run with the current resolution than I was aware of even at Fennoscandiia level. I have in this reanalysis grouped all others than Fennoscandia into the superindividual "Others".

First the heatmaps. As we can see as before the heatmap identify a range of main clusters as before, some may notice that the numbers of identified clusters seem to be lower than from previous runs.

CC Fennoscandia 289k Aggregated

CC Fennoscandia 289k Raw

We then turn the attention to the PCA plots to see if we can infer more resolution than the standard heatmaps. As the superindividual "Others" contain much of the rest of the world it appears quite distant in both heatmap tree and the PCA. The "Other" group dominate the first 3 PCA dimensions as it appears far away from the Fennoscandia group in sum. The direction of "Others" are indicated on the plot.

PCA D1-D2 Fenno vs Others

PCA D1-D3 Fenno vs Others 

As I understand it these PCA D1-D3 reflect level of external influences on Fennoscandinans possibly from continental Europe as DK1 is closest "Others" in both dimensions. Scandinavians are closest to "others" on both dimension 1 and 2 while Finns and Saamis are closest "others" in dimension 3 especially FI18. In any way all these 3 dimensions can be used to differentiate Scandinavians vs Finns and Saamis. We had a similar dimension in the earlier local Fennoscandia analysis.

In dimension 4 we get a dimension that is able to differentiate Saamis from Finns and Scandinavians. We see North-Saami individuals at the extreme. If we combine this dimension with any other two dimensions we would get a plot differentiating Scandinavians, Finns and Saamis. Notice that we now also get a better grouping of the Finns.

PCA D1-D4 Fenno vs Others

At this point from previous analysis we would not get any more information using my earlier method, however using these new setting we can dig even deeper in the PCA plot. This can be shown below as we move to dimension 5.

As we can see below SWE7 a South-Saami individual clearly stand out in a own dimension separately from dimension 4 peaking in North-Saami. What this mean that using this new method the project can explicit differentiate South-Saami ancestry from North-Saami ancestry.

In earlier analysis the South-Saami ancestry appear to blend in somewhere between North-Saami and Scandinavians but as this show they are in a dimension of their own even they do share ancestry with North-Saami in dimension 4. However the North-Saami share very little of this South-Saami specific component but it appears far more common among other Fennoscandians both Scandinavians and even some Finns than the North-Saami specific component.

PCA D1-D5 Fenno vs Others 

This means that we can combine dimension 4 and 5 to map further explicit for Saami ancestry both North and South in Finns and Scandinavians.

PCA D4-D5 Fenno vs Others

There are more dimensions after dimension 5 but they appear to become more unclear and increasingly reflect individual variation. However dimension 6 (vertical axis) may be something worth looking at in the future as it appears populated with what seem to be western Finns, central Swedes and two Saamis depending on where you set the borderline.

 PCA D1-D6 Fenno vs Others 

CONCLUSION: This study shows that using superindividuals one can extract even more detailed ancestry information from autosomal genetic data within Fennoscandia. This new knowledge will be used in future project updates.