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Article: A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays

TitleA central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays
Authors
Issue Date2005
Citation
Nucleic Acids Research, 2005, v. 33 n. 3, p. e25 How to Cite?
AbstractAnalysing pooled DNA on microarrays is an efficient way to genotype hundreds of individuals for thousands of markers for genome-wide association. Although direct comparison of case and control fluorescence scores is possible, correction for differential hybridization of alleles is important, particularly for rare single nucleotide polymorphisms. Such correction relies on heterozygous fluorescence scores and requires the genotyping of hundreds of individuals to obtain sufficient estimates of the correction factor, completely negating any benefit gained by pooling samples. We explore the effect of differential hybridization on test statistics and provide a solution to this problem in the form of a central resource for the accumulation of heterozygous fluorescence scores, allowing accurate allele frequency estimation at no extra cost.
Persistent Identifierhttp://hdl.handle.net/10722/175929
ISSN
2015 SCImago Journal Rankings: 7.458
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorSimpson, CLen_US
dc.contributor.authorKnight, Jen_US
dc.contributor.authorButcher, LMen_US
dc.contributor.authorHansen, VKen_US
dc.contributor.authorMeaburn, Een_US
dc.contributor.authorSchalkwyk, LCen_US
dc.contributor.authorCraig, IWen_US
dc.contributor.authorPowell, JFen_US
dc.contributor.authorSham, PCen_US
dc.contributor.authorAlChalabi, Aen_US
dc.date.accessioned2012-11-26T09:02:35Z-
dc.date.available2012-11-26T09:02:35Z-
dc.date.issued2005en_US
dc.identifier.citationNucleic Acids Research, 2005, v. 33 n. 3, p. e25en_US
dc.identifier.issn1362-4962en_US
dc.identifier.urihttp://hdl.handle.net/10722/175929-
dc.description.abstractAnalysing pooled DNA on microarrays is an efficient way to genotype hundreds of individuals for thousands of markers for genome-wide association. Although direct comparison of case and control fluorescence scores is possible, correction for differential hybridization of alleles is important, particularly for rare single nucleotide polymorphisms. Such correction relies on heterozygous fluorescence scores and requires the genotyping of hundreds of individuals to obtain sufficient estimates of the correction factor, completely negating any benefit gained by pooling samples. We explore the effect of differential hybridization on test statistics and provide a solution to this problem in the form of a central resource for the accumulation of heterozygous fluorescence scores, allowing accurate allele frequency estimation at no extra cost.en_US
dc.languageengen_US
dc.relation.ispartofNucleic acids researchen_US
dc.subject.meshDna - Analysisen_US
dc.subject.meshDatabases, Nucleic Aciden_US
dc.subject.meshFluorescenceen_US
dc.subject.meshGene Frequencyen_US
dc.subject.meshGenotypeen_US
dc.subject.meshHeterozygoteen_US
dc.subject.meshHumansen_US
dc.subject.meshInterneten_US
dc.subject.meshModels, Statisticalen_US
dc.subject.meshOligonucleotide Array Sequence Analysisen_US
dc.subject.meshPolymorphism, Single Nucleotideen_US
dc.subject.meshReproducibility Of Resultsen_US
dc.titleA central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarraysen_US
dc.typeArticleen_US
dc.identifier.emailSham, PC: pcsham@hku.hken_US
dc.identifier.authoritySham, PC=rp00459en_US
dc.description.naturelink_to_OA_fulltexten_US
dc.identifier.doi10.1093/nar/gni028-
dc.identifier.pmid15701753en_US
dc.identifier.pmcidPMC549427-
dc.identifier.scopuseid_2-s2.0-26444564724en_US
dc.identifier.volume33en_US
dc.identifier.issue3en_US
dc.identifier.spagee25en_US
dc.identifier.isiWOS:000227407300002-
dc.identifier.scopusauthoridSimpson, CL=12789397500en_US
dc.identifier.scopusauthoridKnight, J=13002769800en_US
dc.identifier.scopusauthoridButcher, LM=8901700200en_US
dc.identifier.scopusauthoridHansen, VK=7102356948en_US
dc.identifier.scopusauthoridMeaburn, E=7801402004en_US
dc.identifier.scopusauthoridSchalkwyk, LC=7003409002en_US
dc.identifier.scopusauthoridCraig, IW=7102548208en_US
dc.identifier.scopusauthoridPowell, JF=7403541196en_US
dc.identifier.scopusauthoridSham, PC=34573429300en_US
dc.identifier.scopusauthoridAlChalabi, A=7003751621en_US
dc.customcontrol.immutablesml 140917-

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