gms | German Medical Science

MAINZ//2011: 56. GMDS-Jahrestagung und 6. DGEpi-Jahrestagung

Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e. V.
Deutsche Gesellschaft für Epidemiologie e. V.

26. - 29.09.2011 in Mainz

Population-genetic comparison of a German isolated population with a German mixed population on the basis of genome-wide SNP markers

Meeting Abstract

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  • Arnd Groß - Institut für Medizinische Informatik, Statistik und Epidemiologie, Universität Leipzig, Leipzig
  • Markus Scholz - Institut für Medizinische Informatik, Statistik und Epidemiologie, Universität Leipzig, Leipzig

Mainz//2011. 56. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (gmds), 6. Jahrestagung der Deutschen Gesellschaft für Epidemiologie (DGEpi). Mainz, 26.-29.09.2011. Düsseldorf: German Medical Science GMS Publishing House; 2011. Doc11gmds061

DOI: 10.3205/11gmds061, URN: urn:nbn:de:0183-11gmds0612

Published: September 20, 2011

© 2011 Groß et al.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc-nd/3.0/deed.en). You are free: to Share – to copy, distribute and transmit the work, provided the original author and source are credited.


Outline

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Background: Isolated populations are assumed to be interesting for disease mapping. A population of about 15,000 individuals resident in the region of Lusatia, Saxony is considered as genetically isolated (Sorbs). A sample of about 1,000 individuals is currently analyzed in several genome-wide meta-analyses. We compare this population with the German outbred population of the KORA F3 cohort (N=1644) and other publically available European HapMap populations by population genetic means. We also aim to separate effects of over-sampling of families in the Sorbs from effects of genetic isolation and to compare the power of genetic association studies between the samples.

Methods: We estimated pair-wise relatedness, performed principal component analysis (PCA), compared the number of monomorphic SNPs, calculated F-statistics, counted runs of homozygosity (ROHs) and analyzed linkage disequilibrium (LD) for samples with and without related individuals. We also assessed the power to detect causal SNPs by proxies in high LD.

Results: As expected, the degree of relatedness was significantly higher in the Sorbs sample. PCA revealed a west to east clustering of KORA individuals born in Germany, KORA individuals born in Poland or Czech Republic, Half-Sorbs (less than four grandparents from within the population) and Full-Sorbs. The number of monomorphic SNPs is significantly higher in the isolated population. FST between KORA and Sorbs is an order of magnitude higher than between different regions in Germany. Compared to the other populations, Sorbs show a higher proportion of individuals with ROHs between 2.5 Mb and 5 Mb. LD at longer range is also slightly increased, but this has no effect on the power of potential association studies. Oversampling of families in the Sorbs sample causes detectable bias regarding higher FST values and higher LD, but the effect is an order of magnitude smaller than the observed differences between unrelated KORA and unrelated Sorbs.

Conclusions: The Sorbs show signs of genetic isolation which cannot be explained by over-sampling of relatives, but the effects are moderate in size. The Slavonic origin of the Sorbs is still genetically detectable. Regarding LD structure, a clear advantage for genome-wide association studies cannot be deduced. The significant amount of relatedness in the Sorbs requires appropriate statistical methods for bias correction in genome-wide association studies.