The University of Southampton
University of Southampton Institutional Repository

Haplotype tagging for the identification of common disease genes

Record type: Article

Genome-wide linkage disequilibrium (LD) mapping of common disease genes could be more powerful than linkage analysis if the appropriate density of polymorphic markers were known and if the genotyping effort and cost of producing such an LD map could be reduced. Although different metrics that measure the extent of LD have been evaluated1, 2, 3, even the most recent studies2, 4 have not placed significant emphasis on the most informative and cost-effective method of LD mapping—that based on haplotypes. We have scanned 135 kb of DNA from nine genes, genotyped 122 single-nucleotide polymorphisms (SNPs; approximately 184,000 genotypes) and determined the common haplotypes in a minimum of 384 European individuals for each gene. Here we show how knowledge of the common haplotypes and the SNPs that tag them can be used to (i) explain the often complex patterns of LD between adjacent markers, (ii) reduce genotyping significantly (in this case from 122 to 34 SNPs), (iii) scan the common variation of a gene sensitively and comprehensively and (iv) provide key fine-mapping data within regions of strong LD. Our results also indicate that, at least for the genes studied here, the current version of dbSNP would have been of limited utility for LD mapping because many common haplotypes could not be defined. A directed re-sequencing effort of the approximately 10% of the genome in or near genes in the major ethnic groups would aid the systematic evaluation of the common variant model of common disease.

Full text not available from this repository.

Citation

Johnson, Gillian C.l., Esposito, Laura, Barratt, Bryan J., Smith, Annabel N., Heward, Joanne, Di Genova, Gianfranco, Ueda, Hironori, Cordell, Heather J., Eaves, Iain A., Dudbridge, Frank, Twells, Rebecca C.J., Payne, Felicity, Hughes, Wil, Nutland, Sarah, Stevens, Helen, Carr, Phillipa, Tuomilehto-Wolf, Eva, Tuomilehto, Jaakko, Gough, Stephen C.L., Clayton, David G. and Todd, John A. (2001) Haplotype tagging for the identification of common disease genes Nature Genetics, 29, (2), pp. 233-237. (doi:10.1038/ng1001-233).

More information

Published date: 2001

Identifiers

Local EPrints ID: 26409
URI: http://eprints.soton.ac.uk/id/eprint/26409
ISSN: 1061-4036
PURE UUID: 792b9ad7-8104-4459-ab91-b856a90f3b8c

Catalogue record

Date deposited: 24 Apr 2006
Last modified: 17 Jul 2017 16:07

Export record

Altmetrics

Contributors

Author: Gillian C.l. Johnson
Author: Laura Esposito
Author: Bryan J. Barratt
Author: Annabel N. Smith
Author: Joanne Heward
Author: Gianfranco Di Genova
Author: Hironori Ueda
Author: Heather J. Cordell
Author: Iain A. Eaves
Author: Frank Dudbridge
Author: Rebecca C.J. Twells
Author: Felicity Payne
Author: Wil Hughes
Author: Sarah Nutland
Author: Helen Stevens
Author: Phillipa Carr
Author: Eva Tuomilehto-Wolf
Author: Jaakko Tuomilehto
Author: Stephen C.L. Gough
Author: David G. Clayton
Author: John A. Todd

University divisions


Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×