The genome-wide patterns of variation expose significant substructure in a founder population. Jakkula, E., Rehnström, K., Varilo, T., Pietiläinen, O., P., H., Paunio, T., Pedersen, N., L., deFaire, U., Järvelin, M., Saharinen, J., Freimer, N., Ripatti, S., Purcell, S., Collins, A., Daly, M., J., Palotie, A., & Peltonen, L. American journal of human genetics, 83(6):787-94, 12, 2008.
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Paper Website abstract bibtex Although high-density SNP genotyping platforms generate a momentum for detailed genome-wide association (GWA) studies, an offshoot is a new insight into population genetics. Here, we present an example in one of the best-known founder populations by scrutinizing ten distinct Finnish early- and late-settlement subpopulations. By determining genetic distances, homozygosity, and patterns of linkage disequilibrium, we demonstrate that population substructure, and even individual ancestry, is detectable at a very high resolution and supports the concept of multiple historical bottlenecks resulting from consecutive founder effects. Given that genetic studies are currently aiming at identifying smaller and smaller genetic effects, recognizing and controlling for population substructure even at this fine level becomes imperative to avoid confounding and spurious associations. This study provides an example of the power of GWA data sets to demonstrate stratification caused by population history even within a seemingly homogeneous population, like the Finns. Further, the results provide interesting lessons concerning the impact of population history on the genome landscape of humans, as well as approaches to identify rare variants enriched in these subpopulations.
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abstract = {Although high-density SNP genotyping platforms generate a momentum for detailed genome-wide association (GWA) studies, an offshoot is a new insight into population genetics. Here, we present an example in one of the best-known founder populations by scrutinizing ten distinct Finnish early- and late-settlement subpopulations. By determining genetic distances, homozygosity, and patterns of linkage disequilibrium, we demonstrate that population substructure, and even individual ancestry, is detectable at a very high resolution and supports the concept of multiple historical bottlenecks resulting from consecutive founder effects. Given that genetic studies are currently aiming at identifying smaller and smaller genetic effects, recognizing and controlling for population substructure even at this fine level becomes imperative to avoid confounding and spurious associations. This study provides an example of the power of GWA data sets to demonstrate stratification caused by population history even within a seemingly homogeneous population, like the Finns. Further, the results provide interesting lessons concerning the impact of population history on the genome landscape of humans, as well as approaches to identify rare variants enriched in these subpopulations.},
bibtype = {article},
author = {Jakkula, Eveliina and Rehnström, Karola and Varilo, Teppo and Pietiläinen, Olli P H and Paunio, Tiina and Pedersen, Nancy L and deFaire, Ulf and Järvelin, Marjo-Riitta and Saharinen, Juha and Freimer, Nelson and Ripatti, Samuli and Purcell, Shaun and Collins, Andrew and Daly, Mark J and Palotie, Aarno and Peltonen, Leena},
journal = {American journal of human genetics},
number = {6}
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