A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies
Abstract: The understanding of patterns of genetic variation within and among human populations is a prerequisite for successful genetic association mapping studies of complex diseases and traits. Some populations are more favorable for association mapping studies than others. The Saami from norther...
Published in: | European Journal of Human Genetics |
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Language: | English |
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2011
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ftunivantwerpen:c:irua:88991 2023-07-16T03:59:24+02:00 A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies Huyghe, Jeroen R. Fransen, Erik Hannula, Samuli Van Laer, Lut van Eyken, Els Maki-Torkko, Elina Aikio, Pekka Sorri, Martti Huentelman, Matthew J. Van Camp, Guy 2011 https://hdl.handle.net/10067/889910151162165141 eng eng info:eu-repo/semantics/altIdentifier/doi/10.1038/EJHG.2010.179 info:eu-repo/semantics/altIdentifier/isi/000287445600022 info:eu-repo/semantics/closedAccess 1018-4813 European journal of human genetics Biology Human medicine info:eu-repo/semantics/article 2011 ftunivantwerpen https://doi.org/10.1038/EJHG.2010.179 2023-06-26T22:15:05Z Abstract: The understanding of patterns of genetic variation within and among human populations is a prerequisite for successful genetic association mapping studies of complex diseases and traits. Some populations are more favorable for association mapping studies than others. The Saami from northern Scandinavia and the Kola Peninsula represent a population isolate that, among European populations, has been less extensively sampled, despite some early interest for association mapping studies. In this paper, we report the results of a first genome-wide SNP-based study of genetic population structure in the Finnish Saami. Using data from the HapMap and the human genome diversity project (HGDP-CEPH) and recently developed statistical methods, we studied individual genetic ancestry. We quantified genetic differentiation between the Saami population and the HGDP-CEPH populations by calculating pair-wise FST statistics and by characterizing identity-by-state sharing for pair-wise population comparisons. This study affirms an east Asian contribution to the predominantly European-derived Saami gene pool. Using model-based individual ancestry analysis, the median estimated percentage of the genome with east Asian ancestry was 6% (first and third quartiles: 5 and 8%, respectively). We found that genetic similarity between population pairs roughly correlated with geographic distance. Among the European HGDP-CEPH populations, FST was smallest for the comparison with the Russians (FST=0.0098), and estimates for the other population comparisons ranged from 0.0129 to 0.0263. Our analysis also revealed fine-scale substructure within the Finnish Saami and warns against the confounding effects of both hidden population structure and undocumented relatedness in genetic association studies of isolated populations. Article in Journal/Newspaper kola peninsula saami IRUA - Institutional Repository van de Universiteit Antwerpen Kola Peninsula European Journal of Human Genetics 19 3 347 352 |
institution |
Open Polar |
collection |
IRUA - Institutional Repository van de Universiteit Antwerpen |
op_collection_id |
ftunivantwerpen |
language |
English |
topic |
Biology Human medicine |
spellingShingle |
Biology Human medicine Huyghe, Jeroen R. Fransen, Erik Hannula, Samuli Van Laer, Lut van Eyken, Els Maki-Torkko, Elina Aikio, Pekka Sorri, Martti Huentelman, Matthew J. Van Camp, Guy A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies |
topic_facet |
Biology Human medicine |
description |
Abstract: The understanding of patterns of genetic variation within and among human populations is a prerequisite for successful genetic association mapping studies of complex diseases and traits. Some populations are more favorable for association mapping studies than others. The Saami from northern Scandinavia and the Kola Peninsula represent a population isolate that, among European populations, has been less extensively sampled, despite some early interest for association mapping studies. In this paper, we report the results of a first genome-wide SNP-based study of genetic population structure in the Finnish Saami. Using data from the HapMap and the human genome diversity project (HGDP-CEPH) and recently developed statistical methods, we studied individual genetic ancestry. We quantified genetic differentiation between the Saami population and the HGDP-CEPH populations by calculating pair-wise FST statistics and by characterizing identity-by-state sharing for pair-wise population comparisons. This study affirms an east Asian contribution to the predominantly European-derived Saami gene pool. Using model-based individual ancestry analysis, the median estimated percentage of the genome with east Asian ancestry was 6% (first and third quartiles: 5 and 8%, respectively). We found that genetic similarity between population pairs roughly correlated with geographic distance. Among the European HGDP-CEPH populations, FST was smallest for the comparison with the Russians (FST=0.0098), and estimates for the other population comparisons ranged from 0.0129 to 0.0263. Our analysis also revealed fine-scale substructure within the Finnish Saami and warns against the confounding effects of both hidden population structure and undocumented relatedness in genetic association studies of isolated populations. |
format |
Article in Journal/Newspaper |
author |
Huyghe, Jeroen R. Fransen, Erik Hannula, Samuli Van Laer, Lut van Eyken, Els Maki-Torkko, Elina Aikio, Pekka Sorri, Martti Huentelman, Matthew J. Van Camp, Guy |
author_facet |
Huyghe, Jeroen R. Fransen, Erik Hannula, Samuli Van Laer, Lut van Eyken, Els Maki-Torkko, Elina Aikio, Pekka Sorri, Martti Huentelman, Matthew J. Van Camp, Guy |
author_sort |
Huyghe, Jeroen R. |
title |
A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies |
title_short |
A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies |
title_full |
A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies |
title_fullStr |
A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies |
title_full_unstemmed |
A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies |
title_sort |
genome-wide analysis of population structure in the finnish saami with implications for genetic association studies |
publishDate |
2011 |
url |
https://hdl.handle.net/10067/889910151162165141 |
geographic |
Kola Peninsula |
geographic_facet |
Kola Peninsula |
genre |
kola peninsula saami |
genre_facet |
kola peninsula saami |
op_source |
1018-4813 European journal of human genetics |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1038/EJHG.2010.179 info:eu-repo/semantics/altIdentifier/isi/000287445600022 |
op_rights |
info:eu-repo/semantics/closedAccess |
op_doi |
https://doi.org/10.1038/EJHG.2010.179 |
container_title |
European Journal of Human Genetics |
container_volume |
19 |
container_issue |
3 |
container_start_page |
347 |
op_container_end_page |
352 |
_version_ |
1771547101058039808 |