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. 2005 Feb 8;33(3):e25.
doi: 10.1093/nar/gni028.

A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays

Claire L Simpson  1 , Joanne Knight, Lee M Butcher, Valerie K Hansen, Emma Meaburn, Leonard C Schalkwyk, Ian W Craig, John F Powell, Pak C Sham, Ammar Al-Chalabi
Affiliations

A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays

Claire L Simpson et al. Nucleic Acids Res. .

Abstract

Analysing pooled DNA on microarrays is an efficient way to genotype hundreds of individuals for thousands of markers for genome-wide association. Although direct comparison of case and control fluorescence scores is possible, correction for differential hybridization of alleles is important, particularly for rare single nucleotide polymorphisms. Such correction relies on heterozygous fluorescence scores and requires the genotyping of hundreds of individuals to obtain sufficient estimates of the correction factor, completely negating any benefit gained by pooling samples. We explore the effect of differential hybridization on test statistics and provide a solution to this problem in the form of a central resource for the accumulation of heterozygous fluorescence scores, allowing accurate allele frequency estimation at no extra cost.

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Figures

Figure 1
Figure 1
The effect of differential hybridization and allele frequency on the test statistic. The control pool allele frequency was 0.05 greater than the case pool allele frequency shown on the x-axis.
Figure 2
Figure 2
Standard error of mean RASav for a random selection of SNPs showing that at least 20 estimates of RASav are needed for a standard error <0.01.
Figure 3
Figure 3
Correlation between real and predicted allele counts using data from 100 individually genotyped samples compared with allele frequency estimates from pooled data. (a) No correction; (b) corrected with RASav data from 10 to 14 heterozygotes.
See this image and copyright information in PMC

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