ArticleBMC genomics2007
Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
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Who cites it
27 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled genome-wide analysis to identify novel risk loci for pediatric allergic asthma.PloS one · 2011Pooled it
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- A genome-wide association study identifies multiple loci associated with mathematics ability and disability.Genes, brain, and behavior · 2010Article
- A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.Behavior genetics · 2010Article
- Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction.BMC genetics · 2009Article
- Methodological Issues in Multistage Genome-wide Association Studies.Statistical science : a review journal of the Institute of Mathematical Statistics · 2009Article
- A genome-wide association study in 574 schizophrenia trios using DNA pooling.Molecular psychiatry · 2009Article
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Authors and funding
4 authors.
Funding
Abstract
backgroundGenetic 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.
resultsIn 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.
conclusionWe 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.
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