A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays.
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.
Simpson
Claire L
CL
Department of Neurology, PO43, Institute of Psychiatry London SE5 8AF, UK.
Knight
Joanne
J
Butcher
Lee M
LM
Hansen
Valerie K
VK
Meaburn
Emma
E
Schalkwyk
Leonard C
LC
Craig
Ian W
IW
Powell
John F
JF
Sham
Pak C
PC
Al-Chalabi
Ammar
A
D004247:DNA / Q000032:analysis; D030561:Databases, Nucleic Acid; D005453:Fluorescence; D005787:Gene Frequency; D005838:Genotype; D006579:Heterozygote; D006801:Humans; D020407:Internet; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results
D004247:DNA