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Linkage disequilibrium and diversity for three genomic regions in Azoreans and mainland Portuguese

Studies on linkage disequilibrium (LD) across the genome and populations have been used in recent years with the main objective of improving gene mapping of complex traits. Here, we characterize the patterns of genetic diversity of HLA loci and evaluate LD (D') extent in three genomic regions:...

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Autores principales: Branco, Claudia C., Pacheco, Paula R., Cabrol, Ester, Cabral, Rita, Vicente, Astrid M., Mota-Vieira, Luisa
Formato: Texto
Lenguaje:English
Publicado: Sociedade Brasileira de Genética 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3036928/
https://www.ncbi.nlm.nih.gov/pubmed/21637671
http://dx.doi.org/10.1590/S1415-47572009000200003
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author Branco, Claudia C.
Pacheco, Paula R.
Cabrol, Ester
Cabral, Rita
Vicente, Astrid M.
Mota-Vieira, Luisa
author_facet Branco, Claudia C.
Pacheco, Paula R.
Cabrol, Ester
Cabral, Rita
Vicente, Astrid M.
Mota-Vieira, Luisa
author_sort Branco, Claudia C.
collection PubMed
description Studies on linkage disequilibrium (LD) across the genome and populations have been used in recent years with the main objective of improving gene mapping of complex traits. Here, we characterize the patterns of genetic diversity of HLA loci and evaluate LD (D') extent in three genomic regions: Xq13.3, NRY and HLA. In addition, we examine the distribution of DXS1225-DXS8082 haplotype diversity in Azoreans and mainland Portuguese. Allele distribution has demonstrated that the São Miguel population is genetically very diverse; haplotype analysis revealed 100% discriminatory power for X- and Y-markers and 94.3% for HLA markers. Standardized multiallelic D' in these three genomic regions shows values lower than 0.33, thereby suggesting there is no extensive LD in the São Miguel population. Data regarding the distribution of DXS1225-DXS8082 haplotypes indicate that there are no significant differences among all the populations studied, (Azorean geographical groups, the Azores archipelago and mainland Portugal). Moreover, in these as well as in other European populations, the most frequent DXS1225-DXS8082 haplotype is 210-219. Even though São Miguel islanders and Azoreans do not constitute isolated populations and show LD for only very short physical distances, certain characteristics, such as the absence of genetic structure, the same environment and the possibility of constructing extensive pedigrees through church and civil records, offer an opportunity for dissecting the genetic background of complex diseases in these populations.
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spelling pubmed-30369282011-06-02 Linkage disequilibrium and diversity for three genomic regions in Azoreans and mainland Portuguese Branco, Claudia C. Pacheco, Paula R. Cabrol, Ester Cabral, Rita Vicente, Astrid M. Mota-Vieira, Luisa Genet Mol Biol Human and Medical Genetics Studies on linkage disequilibrium (LD) across the genome and populations have been used in recent years with the main objective of improving gene mapping of complex traits. Here, we characterize the patterns of genetic diversity of HLA loci and evaluate LD (D') extent in three genomic regions: Xq13.3, NRY and HLA. In addition, we examine the distribution of DXS1225-DXS8082 haplotype diversity in Azoreans and mainland Portuguese. Allele distribution has demonstrated that the São Miguel population is genetically very diverse; haplotype analysis revealed 100% discriminatory power for X- and Y-markers and 94.3% for HLA markers. Standardized multiallelic D' in these three genomic regions shows values lower than 0.33, thereby suggesting there is no extensive LD in the São Miguel population. Data regarding the distribution of DXS1225-DXS8082 haplotypes indicate that there are no significant differences among all the populations studied, (Azorean geographical groups, the Azores archipelago and mainland Portugal). Moreover, in these as well as in other European populations, the most frequent DXS1225-DXS8082 haplotype is 210-219. Even though São Miguel islanders and Azoreans do not constitute isolated populations and show LD for only very short physical distances, certain characteristics, such as the absence of genetic structure, the same environment and the possibility of constructing extensive pedigrees through church and civil records, offer an opportunity for dissecting the genetic background of complex diseases in these populations. Sociedade Brasileira de Genética 2009 2009-06-01 /pmc/articles/PMC3036928/ /pubmed/21637671 http://dx.doi.org/10.1590/S1415-47572009000200003 Text en Copyright © 2009, Sociedade Brasileira de Genética. http://creativecommons.org/licenses/by/2.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Human and Medical Genetics
Branco, Claudia C.
Pacheco, Paula R.
Cabrol, Ester
Cabral, Rita
Vicente, Astrid M.
Mota-Vieira, Luisa
Linkage disequilibrium and diversity for three genomic regions in Azoreans and mainland Portuguese
title Linkage disequilibrium and diversity for three genomic regions in Azoreans and mainland Portuguese
title_full Linkage disequilibrium and diversity for three genomic regions in Azoreans and mainland Portuguese
title_fullStr Linkage disequilibrium and diversity for three genomic regions in Azoreans and mainland Portuguese
title_full_unstemmed Linkage disequilibrium and diversity for three genomic regions in Azoreans and mainland Portuguese
title_short Linkage disequilibrium and diversity for three genomic regions in Azoreans and mainland Portuguese
title_sort linkage disequilibrium and diversity for three genomic regions in azoreans and mainland portuguese
topic Human and Medical Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3036928/
https://www.ncbi.nlm.nih.gov/pubmed/21637671
http://dx.doi.org/10.1590/S1415-47572009000200003
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