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

TitleMaGIC: A program to generate targeted marker sets for genome-wide association studies
Authors
Issue Date2004
PublisherEaton Publishing Co. The Journal's web site is located at http://www.biotechniques.com
Citation
Biotechniques, 2004, v. 37 n. 6, p. 996-999 How to Cite?
AbstractHigh-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.
Persistent Identifierhttp://hdl.handle.net/10722/175898
ISSN
2015 Impact Factor: 2.298
2015 SCImago Journal Rankings: 1.132
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorSimpson, CLen_US
dc.contributor.authorHansen, VKen_US
dc.contributor.authorSham, PCen_US
dc.contributor.authorCollins, Aen_US
dc.contributor.authorPowell, JFen_US
dc.contributor.authorAlChalabi, Aen_US
dc.date.accessioned2012-11-26T09:02:16Z-
dc.date.available2012-11-26T09:02:16Z-
dc.date.issued2004en_US
dc.identifier.citationBiotechniques, 2004, v. 37 n. 6, p. 996-999en_US
dc.identifier.issn0736-6205en_US
dc.identifier.urihttp://hdl.handle.net/10722/175898-
dc.description.abstractHigh-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.en_US
dc.languageengen_US
dc.publisherEaton Publishing Co. The Journal's web site is located at http://www.biotechniques.comen_US
dc.relation.ispartofBioTechniquesen_US
dc.subject.meshAlgorithmsen_US
dc.subject.meshChromosome Mapping - Methodsen_US
dc.subject.meshGene Targeting - Methodsen_US
dc.subject.meshGenetic Markers - Geneticsen_US
dc.subject.meshGenome, Humanen_US
dc.subject.meshHumansen_US
dc.subject.meshLinkage Disequilibrium - Geneticsen_US
dc.subject.meshPolymorphism, Single Nucleotide - Geneticsen_US
dc.subject.meshSequence Alignment - Methodsen_US
dc.subject.meshSequence Analysis, Dna - Methodsen_US
dc.subject.meshSoftwareen_US
dc.subject.meshUser-Computer Interfaceen_US
dc.titleMaGIC: A program to generate targeted marker sets for genome-wide association studiesen_US
dc.typeArticleen_US
dc.identifier.emailSham, PC: pcsham@hku.hken_US
dc.identifier.authoritySham, PC=rp00459en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.pmid15597550-
dc.identifier.scopuseid_2-s2.0-10044275309en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-10044275309&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume37en_US
dc.identifier.issue6en_US
dc.identifier.spage996en_US
dc.identifier.epage999en_US
dc.identifier.isiWOS:000225696500020-
dc.publisher.placeUnited Statesen_US
dc.identifier.scopusauthoridSimpson, CL=12789397500en_US
dc.identifier.scopusauthoridHansen, VK=7102356948en_US
dc.identifier.scopusauthoridSham, PC=34573429300en_US
dc.identifier.scopusauthoridCollins, A=7403183390en_US
dc.identifier.scopusauthoridPowell, JF=7403541196en_US
dc.identifier.scopusauthoridAlChalabi, A=7003751621en_US

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