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Open Access Highly Accessed Research article

Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition

Eleftheria Zeggini12*, Anne Barton3, Stephen Eyre3, Daniel Ward3, William Ollier3, Jane Worthington3 and Sally John1

Author Affiliations

1 Centre for Integrated Genomic Medical Research, University of Manchester, Manchester, UK

2 Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK

3 arc Epidemiology Unit, University of Manchester, Manchester, UK

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BMC Genetics 2005, 6:21  doi:10.1186/1471-2156-6-21

Published: 25 April 2005

Abstract

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.