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

Simpson, Claire L. and Knight, Joanne and Butcher, Lee M. and Hansen, Valerie K. and Meaburn, Emma and Schalkwyk, Leonard C. and Craig, Ian W. and Powell, John F. and Sham, Pak C. and Al-Chalabi, Ammar (2005) A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays. Nucleic Acids Research, 33 (3). ISSN 0305-1048

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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.

Item Type:
Journal Article
Journal or Publication Title:
Nucleic Acids Research
Additional Information:
© The Author 2005. Published by Oxford University Press. All rights reserved The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oupjournals.org
Uncontrolled Keywords:
/dk/atira/pure/subjectarea/asjc/1300/1311
Subjects:
ID Code:
79916
Deposited By:
Deposited On:
07 Jun 2016 13:54
Refereed?:
Yes
Published?:
Published
Last Modified:
29 Nov 2020 03:41