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

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

9 pages, 2 figures, 4 additional files.

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Main Authors: Bosch, Elena, Laayouni, Hafid, Morcillo-Suárez, Carlos, Casals, Ferran, Moreno Estrada, Andrés, Ferrer Admetlla, Anna, Gardner, Michelle, Rosa, Araceli, Navarro, Arcadi, Comas, David, Graffelman, Jan, Calafell, Francesc, Bertranpetit, Jaume
Format: artículo biblioteca
Language:English
Published: BioMed Central 2009-07-28
Online Access:http://hdl.handle.net/10261/22524
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spelling dig-ibe-es-10261-225242021-12-28T16:07:52Z Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD Bosch, Elena Laayouni, Hafid Morcillo-Suárez, Carlos Casals, Ferran Moreno Estrada, Andrés Ferrer Admetlla, Anna Gardner, Michelle Rosa, Araceli Navarro, Arcadi Comas, David Graffelman, Jan Calafell, Francesc Bertranpetit, Jaume 9 pages, 2 figures, 4 additional files. [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. This research was supported by "Fundación Genoma España" (proyectos piloto CEGEN 2004–2005), Dirección General de Investigación, Ministerio de Educación y Ciencia of Spain (grants BFU2005-00243, BFU2006-01235, BFU2006-15413-CO2-01, SEJ2006-13537) and Direcció General de Recerca, Generalitat de Catalunya (2005SGR00608). SNP genotyping services were provided by the Spanish "Centro Nacional de Genotipado" Peer reviewed 2010-03-18T14:04:12Z 2010-03-18T14:04:12Z 2009-07-28 artículo http://purl.org/coar/resource_type/c_6501 BMC Genomics 10:338 (2009) 1471-2164 http://hdl.handle.net/10261/22524 10.1186/1471-2164-10-338 19638193 en Publisher’s version http://dx.doi.org/10.1186/1471-2164-10-338 open 362477 bytes application/pdf BioMed Central
institution IBE ES
collection DSpace
country España
countrycode ES
component Bibliográfico
access En linea
databasecode dig-ibe-es
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region Europa del Sur
libraryname Biblioteca del IBE España
language English
description 9 pages, 2 figures, 4 additional files.
format artículo
author Bosch, Elena
Laayouni, Hafid
Morcillo-Suárez, Carlos
Casals, Ferran
Moreno Estrada, Andrés
Ferrer Admetlla, Anna
Gardner, Michelle
Rosa, Araceli
Navarro, Arcadi
Comas, David
Graffelman, Jan
Calafell, Francesc
Bertranpetit, Jaume
spellingShingle Bosch, Elena
Laayouni, Hafid
Morcillo-Suárez, Carlos
Casals, Ferran
Moreno Estrada, Andrés
Ferrer Admetlla, Anna
Gardner, Michelle
Rosa, Araceli
Navarro, Arcadi
Comas, David
Graffelman, Jan
Calafell, Francesc
Bertranpetit, Jaume
Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD
author_facet Bosch, Elena
Laayouni, Hafid
Morcillo-Suárez, Carlos
Casals, Ferran
Moreno Estrada, Andrés
Ferrer Admetlla, Anna
Gardner, Michelle
Rosa, Araceli
Navarro, Arcadi
Comas, David
Graffelman, Jan
Calafell, Francesc
Bertranpetit, Jaume
author_sort Bosch, Elena
title Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD
title_short Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD
title_full Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD
title_fullStr Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD
title_full_unstemmed Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD
title_sort decay of linkage disequilibrium within genes across hgdp-ceph human samples: most population isolates do not show increased ld
publisher BioMed Central
publishDate 2009-07-28
url http://hdl.handle.net/10261/22524
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