The University of Southampton
University of Southampton Institutional Repository

MaGIC: a program to generate targeted marker sets for genome-wide association studies

Simpson, C.L., Hansen, V.K., Sham, P.C., Collins, A., Powell, J.F. and Al-Chalabi, A. (2004) MaGIC: a program to generate targeted marker sets for genome-wide association studies Biotechniques, 37, (6), pp. 996-999.

Record type: Article


High-throughput genotyping technologies such as DNA pooling and DNA microarrays mean that whole-genome screens are now practical for complex disease gene discovery using association studies. Because it is currently impractical to use all available markers, a subset is typically selected on the basis of required saturation density. Restricting markers to those within annotated genomic features of interest (e.g., genes or exons) or within feature-rich regions, reduces workload and cost while retaining much information. We have designed a program (MaGIC) that exploits genome assembly data to create lists of markers correlated with other genomic features. Marker lists are generated at a user-defined spacing and can target features with a user-defined density. Maps are in base pairs or linkage disequilibrium units (LDUs) as derived from the International HapMap data, which is useful for association studies and fine-mapping. Markers may be selected on the basis of heterozygosity and source database, and single nucleotide polymorphism (SNP) markers may additionally be selected on the basis of validation status. The import function means the method can be used for any genomic features such as housekeeping genes, long interspersed elements (LINES), or Alu repeats in humans, and is also functional for other species with equivalent data. The program and source code is freely available at

Full text not available from this repository.

More information

Published date: December 2004
Keywords: linkage disequilibrium, user-computer interface, exons, genes,'t, dna, psychiatry, p.h.s., software, methods, genetic markers, genetics, genome, sequence analysis, evaluation studies, chromosome mapping, disease, gene targeting, research support, single nucleotide, london, human, humans, polymorphism,'t, sequence alignment, algorithms


Local EPrints ID: 24956
ISSN: 0736-6205
PURE UUID: fa6cd6a1-e9d6-461c-8ed1-e871b8cc520f
ORCID for A. Collins: ORCID iD

Catalogue record

Date deposited: 06 Apr 2006
Last modified: 17 Jul 2017 16:12

Export record


Author: C.L. Simpson
Author: V.K. Hansen
Author: P.C. Sham
Author: A. Collins ORCID iD
Author: J.F. Powell
Author: A. Al-Chalabi

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 supports OAI 2.0 with a base URL of

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.