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Fine-scale human genetic structure in Western France. (Articolo in rivista)

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Fine-scale human genetic structure in Western France. (Articolo in rivista) (literal)

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Karakachoff M, Duforet-Frebourg N, Simonet F, Le Scouarnec S, Pellen N, Lecointe S, Charpentier E, Gros F, Cauchi S, Froguel P, Copin N, Le Tourneau T, Probst V, Le Marec H, Molinaro S, Balkau B, Redon R, Schott JJ, Blum MG, Dina C, the D E S I R Study Group (2014)
Fine-scale human genetic structure in Western France.
in European journal of human genetics (Online); Macmillan Publisher Ltd, London (Regno Unito)
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Karakachoff M, Duforet-Frebourg N, Simonet F, Le Scouarnec S, Pellen N, Lecointe S, Charpentier E, Gros F, Cauchi S, Froguel P, Copin N, Le Tourneau T, Probst V, Le Marec H, Molinaro S, Balkau B, Redon R, Schott JJ, Blum MG, Dina C, the D E S I R Study Group (literal)

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INSERM UMR 1087, Nantes, France, Laboratoire TIMC-IMAG UMR 5525, Centre National de la Recherche Scientifique, Universite´Joseph Fourier, Grenoble, France; INSERM UMR 1087, Nantes, France, INSERM UMR 1087, Nantes, France, Universite´ de Bretagne Occidentale, Brest, France, INSERM UMR 1087, Nantes, France, INSERM UMR 1087, Nantes, France, INSERM UMR 1087, Nantes, France, European Genomic Institute for Diabetes (EGID), Lille, France, IRSA, Institut inter-Regional pour la Sante , La Riche, France, IRSA, Institut inter-Regional pour la Sante' , La Riche, France, INSERM UMR 1087, Nantes, France, INSERM UMR 1087, Nantes, France, INSERM UMR 1087, Nantes, France, Institute of Clinical Physiology, CNR, Pisa, Italy, INSERM, CESP Center for Research in Epidemiology and Population Health, U1018, Villejuif, France, INSERM UMR 1087, Nantes, France, INSERM UMR 1087, Nantes, France, 5Laboratoire TIMC-IMAG UMR 5525, Centre National de la Recherche Scientifique, Universite´ Joseph Fourier, Grenoble, France, INSERM UMR 1087, Nantes, France (literal)

Titolo

Abstract

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 Vende´e 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. (literal)

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