Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD

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Bosch E, Laayouni H, Morcillo-Suárez C, Casals F, Moreno-Estrada A, Ferrer-Admetlla A, Gardner M, Rosa A, Comas D, Graffelman J, Calafell F, Bertranpetit J. Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD. BMC Genomics. 2009; 10: 338. DOI 10.1186/1471-2164-10-338
http://hdl.handle.net/10230/16386
To cite or link this document: http://hdl.handle.net/10230/16386
dc.contributor.author Bosch Fusté, Elena
dc.contributor.author Laayouni, Hafid
dc.contributor.author Morcillo Suárez, Carlos
dc.contributor.author Casals, Ferran
dc.contributor.author Moreno Estrada, Andrés
dc.contributor.author Ferrer Admetlla, Anna
dc.contributor.author Gardner, Michelle
dc.contributor.author Rosa, Araceli
dc.contributor.author Comas, David
dc.contributor.author Graffelman, Jan
dc.contributor.author Calafell i Majó, Francesc
dc.contributor.author Bertranpetit, Jaume
dc.date.accessioned 2012-05-03T08:25:56Z
dc.date.available 2012-05-03T08:25:56Z
dc.date.issued 2009
dc.identifier.citation Bosch E, Laayouni H, Morcillo-Suárez C, Casals F, Moreno-Estrada A, Ferrer-Admetlla A, Gardner M, Rosa A, Comas D, Graffelman J, Calafell F, Bertranpetit J. Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD. BMC Genomics. 2009; 10: 338. DOI 10.1186/1471-2164-10-338
dc.identifier.issn 1471-2164
dc.identifier.uri http://hdl.handle.net/10230/16386
dc.description.abstract Background: It is well known that the pattern of linkage disequilibrium varies between human populations, with remarkable geographical stratification. Indirect association studies routinely exploit linkage disequilibrium around genes, particularly in isolated populations where it is assumed to be higher. Here, we explore both the amount and the decay of linkage disequilibrium with physical distance along 211 gene regions, most of them related to complex diseases, across 39 HGDP-CEPH population samples, focusing particularly on the populations defined as isolates. Within each gene region and population we use r2 between all possible single nucleotide polymorphism (SNP) pairs as a measure of linkage disequilibrium and focus on the proportion of SNP pairs with r2 greater than 0.8. Results: Although the average r2 was found to be significantly different both between and within continental regions, a much higher proportion of r2 variance could be attributed to differences between continental regions (2.8% vs. 0.5%, respectively). Similarly, while the proportion of SNP pairs with r2 > 0.8 was significantly different across continents for all distance classes, it was generally much more homogenous within continents, except in the case of Africa and the Americas. The only isolated populations with consistently higher LD in all distance classes with respect to their continent are the Kalash (Central South Asia) and the Surui (America). Moreover, isolated populations showed only slightly higher proportions of SNP pairs with r2 > 0.8 per gene region than non-isolated populations in the same continent. Thus, the number of SNPs in isolated populations that need to be genotyped may be only slightly less than in non-isolates. Conclusion: The "isolated population" label by itself does not guarantee a greater genotyping efficiency in association studies, and properties other than increased linkage disequilibrium may make these populations interesting in genetic epidemiology.
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartof BMC Genomics. 2009; 10: 338
dc.rights (c) 2009 Bosch et al. Creative Commons Attribution License
dc.rights.uri http://creativecommons.org/licenses/by/2.0/
dc.subject.other Genètica de poblacions
dc.subject.other Genètica humana -- Variació
dc.title Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/1471-2164-10-338
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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