MaGIC

A program to generate targeted marker sets for genome-wide association studies

Claire Simpson, Valerie K. Hansen, Pak C. Sham, Andrew Collins, John F. Powell, Ammar Al-Chalabi

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

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 http://cogent.iop.kcl.ac.uk/MaGIC.cogx.

Original languageEnglish (US)
Pages (from-to)996-999
Number of pages4
JournalBioTechniques
Volume37
Issue number6
StatePublished - Dec 1 2004
Externally publishedYes

Fingerprint

Genome-Wide Association Study
Genes
Association reactions
Alu Elements
Genome
HapMap Project
Essential Genes
Linkage Disequilibrium
Genetic Association Studies
Oligonucleotide Array Sequence Analysis
Workload
Base Pairing
Single Nucleotide Polymorphism
Exons
Databases
Technology
Costs and Cost Analysis
DNA
Microarrays
Polymorphism

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

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

MaGIC : A program to generate targeted marker sets for genome-wide association studies. / Simpson, Claire; Hansen, Valerie K.; Sham, Pak C.; Collins, Andrew; Powell, John F.; Al-Chalabi, Ammar.

In: BioTechniques, Vol. 37, No. 6, 01.12.2004, p. 996-999.

Research output: Contribution to journalArticle

Simpson, C, Hansen, VK, Sham, PC, Collins, A, Powell, JF & Al-Chalabi, A 2004, 'MaGIC: A program to generate targeted marker sets for genome-wide association studies', BioTechniques, vol. 37, no. 6, pp. 996-999.
Simpson C, Hansen VK, Sham PC, Collins A, Powell JF, Al-Chalabi A. MaGIC: A program to generate targeted marker sets for genome-wide association studies. BioTechniques. 2004 Dec 1;37(6):996-999.
Simpson, Claire ; Hansen, Valerie K. ; Sham, Pak C. ; Collins, Andrew ; Powell, John F. ; Al-Chalabi, Ammar. / MaGIC : A program to generate targeted marker sets for genome-wide association studies. In: BioTechniques. 2004 ; Vol. 37, No. 6. pp. 996-999.
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