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Genotyping DNA pools on microarrays: Tackling the QTL problem of large samples and large numbers of SNPs

Meaburn, E and Butcher, LM and Liu, L and Fernandes, C and Hansen, V and Al-Chalabi, A and Plomin, R and Craig, I and Schalkwyk, LC (2005) 'Genotyping DNA pools on microarrays: Tackling the QTL problem of large samples and large numbers of SNPs.' BMC Genomics, 6. ISSN 1471-2164

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Abstract

Background: Quantitative trait locus (QTL) theory predicts that genetic influence on complex traits involves multiple genes of small effect size. To detect QTL associations of small effect size, large samples and systematic screens of thousands of DNA markers are required. An efficient solution is to genotype case and control DNA pools using SNP microarrays. We demonstrate that this is practical using DNA pools of 100 individuals. Results: Using standard microarray protocols for the Affymetrix GeneChip® Mapping 10 K Array Xba 131, we show that relative allele signal (RAS) values provide a quantitative index of allele frequencies in pooled DNA that correlate 0.986 with allele frequencies for 104 SNPs that were genotyped individually for 100 individuals. The sensitivity of the assay was demonstrated empirically in a spiking experiment in which 15% and 20% of one individual's DNA was added to a DNA pool. Conclusion: We conclude that this approach, which we call SNP-MaP (SNP microarrays and pooling), is rapid, cost effective and promises to be a valuable initial screening method in the hunt for QTLs. © 2005 Meaburn et al; licensee BioMed Central Ltd.

Item Type: Article
Subjects: Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science and Health > Biological Sciences, School of
Depositing User: Jim Jamieson
Date Deposited: 30 Jan 2015 12:23
Last Modified: 17 Aug 2017 17:46
URI: http://repository.essex.ac.uk/id/eprint/11069

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