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Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies

Docherty, SJ; Butcher, LM; Schalkwyk, LC; Plomin, R; (2007) Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies. BMC Genomics , 8 , Article 214. 10.1186/1471-2164-8-214. Green open access

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Abstract

BACKGROUND: Genetic influences underpinning complex traits are thought to involve multiple quantitative trait loci (QTLs) of small effect size. Detection of such QTL associations requires systematic screening of large numbers of DNA markers within large sample populations. Using pooled DNA on SNP microarrays to screen for allelic frequency differences between groups such as cases and controls (called SNP Microarray and Pooling, or SNP-MaP) has been validated as an efficient solution on both 10 k and 100 k platforms. We demonstrate that this approach can be effectively applied to the truly genomewide Affymetrix GeneChip Mapping 500 K Array. RESULTS: In comparisons between five independent DNA pools (N ~200 per pool) on separate Affymetrix GeneChip Mapping 500 K Array sets, we show that, for SNPs with minor allele frequencies > 0.05, the reliability of the rank order of estimated allele frequencies, assessed as the average correlation between allele frequency estimates across the DNA pools, was 0.948 (average mean difference across the five pools = 0.069). Similarly, validity of the SNP-MaP approach was demonstrated by a rank-order correlation of 0.937 (average mean difference = 0.095) between the average DNA pool allele frequency estimates and the allele frequencies of an independent (CEPH) sample of 60 unrelated individually genotyped subjects. CONCLUSION: We conclude that SNP-MaP can be extended for use on the Affymetrix GeneChip Mapping 500 K Array, providing a cost-effective, reliable and valid initial screen of 500 K SNP microarrays in genomewide association scans

Type: Article
Title: Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/1471-2164-8-214
Publisher version: http://dx.doi.org/10.1186/1471-2164-8-214
Language: English
Additional information: © 2007 Docherty 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 - 20070720 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) LA - eng PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't RN - 9007-49-2 (DNA) SB - IM
Keywords: Alleles, Chromosome Mapping, methods, Cost-Benefit Analysis, Dna, genetics, Gene Frequency, Genetic Techniques, economics, Genome,Human, Genomics, Genotype, Humans, Oligonucleotide Array Sequence Analysis, Polymorphism,Single Nucleotide, Quantitative Trait Loci, Reproducibility of Results, Sequence Analysis,DNA
UCL classification: 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
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Cancer Bio
URI: https://discovery.ucl.ac.uk/id/eprint/1427990
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