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

Meaburn, E; Butcher, LM; Liu, L; Fernandes, C; Hansen, V; Al-Chalabi, A; Plomin, R; ... Schalkwyk, LC; + view all (2005) Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs. BMC Genomics , 6 , Article 52. 10.1186/1471-2164-6-52. Green open access

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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

Type: Article
Title: Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/1471-2164-6-52
Publisher version: http://dx.doi.org/10.1186/1471-2164-6-52
Language: English
Additional information: © 2005 Meaburn et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. DA - 20050415 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't RN - 0 (DNA Primers) SB - IM
Keywords: Alleles, Chromosome Mapping, DNA Primers, chemistry, Gene Frequency, Genotype, Humans, Oligonucleotide Array Sequence Analysis, methods, Polymorphism,Single Nucleotide, Quantitative Trait Loci, Reproducibility of Results, Sensitivity and Specificity, Sequence Analysis,DNA, economics, Software
UCL classification: UCL
UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
URI: https://discovery.ucl.ac.uk/id/eprint/1427991
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