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

Claire 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

Research output: Contribution to journalArticle

32 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1-5
Number of pages5
JournalNucleic acids research
Volume33
Issue number3
DOIs
StatePublished - Oct 18 2005

Fingerprint

Oligonucleotide Array Sequence Analysis
Gene Frequency
Fluorescence
DNA
Single Nucleotide Polymorphism
Alleles
Genotype
Genome
Costs and Cost Analysis

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Simpson, C., Knight, J., Butcher, L. M., Hansen, V. K., Meaburn, E., Schalkwyk, L. C., ... Al-Chalabi, A. (2005). A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays. Nucleic acids research, 33(3), 1-5. https://doi.org/10.1093/nar/gni028

A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays. / Simpson, Claire; Knight, Joanne; Butcher, Lee M.; Hansen, Valerie K.; Meaburn, Emma; Schalkwyk, Leonard C.; Craig, Ian W.; Powell, John F.; Sham, Pak C.; Al-Chalabi, Ammar.

In: Nucleic acids research, Vol. 33, No. 3, 18.10.2005, p. 1-5.

Research output: Contribution to journalArticle

Simpson, C, Knight, J, Butcher, LM, Hansen, VK, Meaburn, E, Schalkwyk, LC, Craig, IW, Powell, JF, Sham, PC & Al-Chalabi, A 2005, 'A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays', Nucleic acids research, vol. 33, no. 3, pp. 1-5. https://doi.org/10.1093/nar/gni028
Simpson, Claire ; Knight, Joanne ; Butcher, Lee M. ; Hansen, Valerie K. ; Meaburn, Emma ; Schalkwyk, Leonard C. ; Craig, Ian W. ; Powell, John F. ; Sham, Pak C. ; Al-Chalabi, Ammar. / A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays. In: Nucleic acids research. 2005 ; Vol. 33, No. 3. pp. 1-5.
@article{70fad37649a646a9bde0898d74b39ad5,
title = "A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays",
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.",
author = "Claire Simpson and Joanne Knight and Butcher, {Lee M.} and Hansen, {Valerie K.} and Emma Meaburn and Schalkwyk, {Leonard C.} and Craig, {Ian W.} and Powell, {John F.} and Sham, {Pak C.} and Ammar Al-Chalabi",
year = "2005",
month = "10",
day = "18",
doi = "10.1093/nar/gni028",
language = "English (US)",
volume = "33",
pages = "1--5",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "3",

}

TY - JOUR

T1 - A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays

AU - Simpson, Claire

AU - Knight, Joanne

AU - Butcher, Lee M.

AU - Hansen, Valerie K.

AU - Meaburn, Emma

AU - Schalkwyk, Leonard C.

AU - Craig, Ian W.

AU - Powell, John F.

AU - Sham, Pak C.

AU - Al-Chalabi, Ammar

PY - 2005/10/18

Y1 - 2005/10/18

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=26444564724&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=26444564724&partnerID=8YFLogxK

U2 - 10.1093/nar/gni028

DO - 10.1093/nar/gni028

M3 - Article

VL - 33

SP - 1

EP - 5

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 3

ER -