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.
![[thumbnail of 1471-2164-8-214.pdf]](https://discovery.ucl.ac.uk/style/images/fileicons/application_pdf.png) Preview |
PDF
1471-2164-8-214.pdf Download (290kB) |
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 |
Archive Staff Only
 |
View Item |
