ArticleBMC genomics2007
Allelotyping of pooled DNA with 250 K SNP microarrays.
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 9 papers.
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Who cites it
9 citing papers in PubMed.
- A novel candidate region for genetic adaptation to high altitude in Andean populations.PloS one · 2015Article
- Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.).BMC genomics · 2013Article
- Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays.BMC research notes · 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
- A genome-wide association study in 574 schizophrenia trios using DNA pooling.Molecular psychiatry · 2009Article
- The SNPMaP package for R: a framework for genome-wide association using DNA pooling on microarrays.Bioinformatics (Oxford, England) · 2009Article
- MPDA: microarray pooled DNA analyzer.BMC bioinformatics · 2008Article
- A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples.BMC genetics · 2008Article
- Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.BMC genomics · 2007Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenotyping technologies for whole genome association studies are now available. To perform such studies to an affordable price, pooled DNA can be used. Recent studies have shown that GeneChip Human Mapping 10 K and 50 K arrays are suitable for the estimation of the allele frequency in pooled DNA. In the present study, we tested the accuracy of the 250 K Nsp array, which is part of the 500 K array set representing 500,568 SNPs. Furthermore, we compared different algorithms to estimate allele frequencies of pooled DNA.
resultsWe could confirm that the polynomial based probe specific correction (PPC) was the most accurate method for allele frequency estimation. However, a simple k-correction, using the relative allele signal (RAS) of heterozygous individuals, performed only slightly worse and provided results for more SNPs. Using four replicates of the 250 K array and the k-correction using heterozygous RAS values, we obtained results for 104.141 SNPs. The correlation between estimated and real allele frequency was 0.983 and the average error was 0.046, which was comparable to the results obtained with the 10 K array. Furthermore, we could show how the estimation accuracy depended on the SNP type (average error for A/T SNPs: 0.043 and for G/C SNPs: 0.052).
conclusionThe combination of DNA pooling and analysis of single nucleotide polymorphisms (SNPs) on high density microarrays is a promising tool for whole genome association studies.
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