This is an open access article.
European Journal of Human Genetics advance online publication 19 February 2014; doi: 10.1038/ejhg.2014.1
Using ancestry-informative markers to identify fine structure across 15 populations of European origin
Laura M Huckins et al.
The Wellcome Trust Case Control Consortium 3 anorexia nervosa genome-wide association scan includes 2907 cases from 15 different populations of European origin genotyped on the Illumina 670K chip. We compared methods for identifying population stratification, and suggest list of markers that may help to counter this problem. It is usual to identify population structure in such studies using only common variants with minor allele frequency (MAF) >5%; we find that this may result in highly informative SNPs being discarded, and suggest that instead all SNPs with MAF >1% may be used. We established informative axes of variation identified via principal component analysis and highlight important features of the genetic structure of diverse European-descent populations, some studied for the first time at this scale. Finally, we investigated the substructure within each of these 15 populations and identified SNPs that help capture hidden stratification. This work can provide information regarding the designing and interpretation of association results in the International Consortia.
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4 comments:
Wow, the 25% "Mediterranean" is the nearly same estimate I came up with based on Y-chromosomes in the US. I actually came with 23%. I suppose the US sample is of White "European" Americans. My estimate was based on all major populations in the US.
Pity Germany is considered one people. The north, which used to speak a different kind of German more akin to Dutch, is really different from the south. I would be very interested to see if these differences translate to genetic differences as well.
Bit disappointing that they didn't sample an Irish population, particularly given the know history of mass Irish migration to US, Canada and Britain during the 19th and 20th centuries.
"I would be very interested to see if these differences translate to genetic differences as well."
It does.
When Dodecad and Eurogenes Projects started I checked out what the German project members said about their backgrounds.
It was possible to spot 3 different regions (dont want to call em "clusters":
- Northwest (often overlapping with English, Dutch or Southern Scandinavia)
- Northeast (clearly moved eastwards, partly overlapping with GErman/Polish mixes)
HIstorical sources claim Eastgermans beeing Northwestgerman (Saxons to be exact) settlers mixed with Slavic natives.
-South+Austria (kind of seperate, not overlapping with anyone)
Historical sources claim Austrians beeing Southgerman (Bavarians to be exact) settlers mixed with Slavic natives)
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