Cargando…
Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition
BACKGROUND: The selection of markers in association studies can be informed through the use of haplotype blocks. Recent reports have determined the genomic architecture of chromosomal segments through different haplotype block definitions based on linkage disequilibrium (LD) measures or haplotype di...
Autores principales: | , , , , , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2005
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1090572/ https://www.ncbi.nlm.nih.gov/pubmed/15850495 http://dx.doi.org/10.1186/1471-2156-6-21 |
_version_ | 1782123888270901248 |
---|---|
author | Zeggini, Eleftheria Barton, Anne Eyre, Stephen Ward, Daniel Ollier, William Worthington, Jane John, Sally |
author_facet | Zeggini, Eleftheria Barton, Anne Eyre, Stephen Ward, Daniel Ollier, William Worthington, Jane John, Sally |
author_sort | Zeggini, Eleftheria |
collection | PubMed |
description | BACKGROUND: The selection of markers in association studies can be informed through the use of haplotype blocks. Recent reports have determined the genomic architecture of chromosomal segments through different haplotype block definitions based on linkage disequilibrium (LD) measures or haplotype diversity criteria. The relative applicability of distinct block definitions to association studies, however, remains unclear. We compared different block definitions in 6.1 Mb of chromosome 17q in 189 unrelated healthy individuals. Using 137 single nucleotide polymorphisms (SNPs), at a median spacing of 15.5 kb, we constructed haplotype block maps using published methods and additional methods we have developed. Haplotype tagging SNPs (htSNPs) were identified for each map. RESULTS: Blocks were found to be shorter and coverage of the region limited with methods based on LD measures, compared to the method based on haplotype diversity. Although the distribution of blocks was highly variable, the number of SNPs that needed to be typed in order to capture the maximum number of haplotypes was consistent. CONCLUSION: For the marker spacing used in this study, choice of block definition is not important when used as an initial screen of the region to identify htSNPs. However, choice of block definition has consequences for the downstream interpretation of association study results. |
format | Text |
id | pubmed-1090572 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2005 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-10905722005-05-07 Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition Zeggini, Eleftheria Barton, Anne Eyre, Stephen Ward, Daniel Ollier, William Worthington, Jane John, Sally BMC Genet Research Article BACKGROUND: The selection of markers in association studies can be informed through the use of haplotype blocks. Recent reports have determined the genomic architecture of chromosomal segments through different haplotype block definitions based on linkage disequilibrium (LD) measures or haplotype diversity criteria. The relative applicability of distinct block definitions to association studies, however, remains unclear. We compared different block definitions in 6.1 Mb of chromosome 17q in 189 unrelated healthy individuals. Using 137 single nucleotide polymorphisms (SNPs), at a median spacing of 15.5 kb, we constructed haplotype block maps using published methods and additional methods we have developed. Haplotype tagging SNPs (htSNPs) were identified for each map. RESULTS: Blocks were found to be shorter and coverage of the region limited with methods based on LD measures, compared to the method based on haplotype diversity. Although the distribution of blocks was highly variable, the number of SNPs that needed to be typed in order to capture the maximum number of haplotypes was consistent. CONCLUSION: For the marker spacing used in this study, choice of block definition is not important when used as an initial screen of the region to identify htSNPs. However, choice of block definition has consequences for the downstream interpretation of association study results. BioMed Central 2005-04-25 /pmc/articles/PMC1090572/ /pubmed/15850495 http://dx.doi.org/10.1186/1471-2156-6-21 Text en Copyright © 2005 Zeggini et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Zeggini, Eleftheria Barton, Anne Eyre, Stephen Ward, Daniel Ollier, William Worthington, Jane John, Sally Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition |
title | Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition |
title_full | Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition |
title_fullStr | Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition |
title_full_unstemmed | Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition |
title_short | Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition |
title_sort | characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1090572/ https://www.ncbi.nlm.nih.gov/pubmed/15850495 http://dx.doi.org/10.1186/1471-2156-6-21 |
work_keys_str_mv | AT zegginieleftheria characterisationofthegenomicarchitectureofhumanchromosome17qandevaluationofdifferentmethodsforhaplotypeblockdefinition AT bartonanne characterisationofthegenomicarchitectureofhumanchromosome17qandevaluationofdifferentmethodsforhaplotypeblockdefinition AT eyrestephen characterisationofthegenomicarchitectureofhumanchromosome17qandevaluationofdifferentmethodsforhaplotypeblockdefinition AT warddaniel characterisationofthegenomicarchitectureofhumanchromosome17qandevaluationofdifferentmethodsforhaplotypeblockdefinition AT ollierwilliam characterisationofthegenomicarchitectureofhumanchromosome17qandevaluationofdifferentmethodsforhaplotypeblockdefinition AT worthingtonjane characterisationofthegenomicarchitectureofhumanchromosome17qandevaluationofdifferentmethodsforhaplotypeblockdefinition AT johnsally characterisationofthegenomicarchitectureofhumanchromosome17qandevaluationofdifferentmethodsforhaplotypeblockdefinition |