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  • Nucl. Acids Res.-2005-Simpson-e25

    Rights statement: © 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

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

Research output: Contribution to journalJournal article

Published
  • Claire L. Simpson
  • 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
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Article numbere25
<mark>Journal publication date</mark>2005
<mark>Journal</mark>Nucleic Acids Research
Issue number3
Volume33
Publication statusPublished
Early online date8/02/05
Original languageEnglish

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.

Bibliographic note

© 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