Fine-scale human genetic structure in Western France

The difficulties arising from association analysis with rare variants underline the importance of suitable reference population cohorts, which integrate detailed spatial information. We analyzed a sample of 1684 individuals from Western France, who were genotyped at genome-wide level, from two cohor...

Full description

Saved in:
Bibliographic Details
Published in:European journal of human genetics : EJHG 2015-06, Vol.23 (6), p.831-836
Main Authors: Karakachoff, Matilde, Duforet-Frebourg, Nicolas, Simonet, Floriane, Le Scouarnec, Solena, Pellen, Nadine, Lecointe, Simon, Charpentier, Eric, Gros, Françoise, Cauchi, Stéphane, Froguel, Philippe, Copin, Nane, Le Tourneau, Thierry, Probst, Vincent, Le Marec, Hervé, Molinaro, Sabrina, Balkau, Beverley, Redon, Richard, Schott, Jean-Jacques, Blum, Michael Gb, Dina, Christian
Format: Article
Language:English
Subjects:
Association analysis
Diabetes
Disease
France
Genetic structure
Genetics
Genome, Human
Genomes
Genomics
Histocompatibility antigen HLA
HLA Antigens - genetics
Humanities and Social Sciences
Humans
Information processing
Lactase
Lactase - genetics
Life Sciences
Linkage disequilibrium
Polymorphism, Genetic
Population
Population - genetics
Population structure
Sociology
Spatial discrimination
Studies
Thorax
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:The difficulties arising from association analysis with rare variants underline the importance of suitable reference population cohorts, which integrate detailed spatial information. We analyzed a sample of 1684 individuals from Western France, who were genotyped at genome-wide level, from two cohorts D.E.S.I.R and CavsGen. We found that fine-scale population structure occurs at the scale of Western France, with distinct admixture proportions for individuals originating from the Brittany Region and the Vendée Department. Genetic differentiation increases with distance at a high rate in these two parts of Northwestern France and linkage disequilibrium is higher in Brittany suggesting a lower effective population size. When looking for genomic regions informative about Breton origin, we found two prominent associated regions that include the lactase region and the HLA complex. For both the lactase and the HLA regions, there is a low differentiation between Bretons and Irish, and this is also found at the genome-wide level. At a more refined scale, and within the Pays de la Loire Region, we also found evidence of fine-scale population structure, although principal component analysis showed that individuals from different departments cannot be confidently discriminated. Because of the evidence for fine-scale genetic structure in Western France, we anticipate that rare and geographically localized variants will be identified in future full-sequence analyses.
ISSN:1018-4813
1476-5438
DOI:10.1038/ejhg.2014.175