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BMC Genetics

, 6:21

First Online: 25 April 2005Received: 17 November 2004Accepted: 25 April 2005

Abstract

BackgroundThe 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.

ResultsBlocks 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.

ConclusionFor 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.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2156-6-21 contains supplementary material, which is available to authorized users.

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Autor: Eleftheria Zeggini - Anne Barton - Stephen Eyre - Daniel Ward - William Ollier - Jane Worthington - Sally John

Fuente: https://link.springer.com/article/10.1186/1471-2156-6-21



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