Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome.

Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome. Research Abstract Details 

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Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome. Abstract Text:

Michael A Eberle,Mark J Rieder,Leonid Kruglyak,Deborah A Nickerson,

Significant interest has emerged in mapping genetic susceptibility for complex traits through whole-genome association studies. These studies rely on the extent of association, i.e., linkage disequilibrium (LD), between single nucleotide polymorphisms (SNPs) across the human genome. LD describes the nonrandom association between SNP pairs and can be used as a metric when designing maximally informative panels of SNPs for association studies in human populations. Using data from the 1.58 million SNPs genotyped by Perlegen, we explored the allele frequency dependence of the LD statistic r(2) both empirically and theoretically. We show that average r(2) values between SNPs unmatched for allele frequency are always limited to much less than 1 (theoretical approximately 0.46 to 0.57 for this dataset). Frequency matching of SNP pairs provides a more sensitive measure for assessing the average decay of LD and generates average r(2) values across nearly the entire informative range (from 0 to 0.89 through 0.95). Additionally, we analyzed the extent of perfect LD (r(2) = 1.0) using frequency-matched SNPs and found significant differences in the extent of LD in genic regions versus intergenic regions. The SNP pairs exhibiting perfect LD showed a significant bias for derived, nonancestral alleles, providing evidence for positive natural selection in the human genome.

Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome. Publishing Authors By Initials

MA Eberle,MJ Rieder,L Kruglyak,DA Nickerson,

For similar investigative techniques: genetic techniques: sequence alignment research abstracts see: investigative techniques: genetic techniques: sequence alignment research

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Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: PLoS genetics

VOLUME: 2

Page Numbers: e142

Journal Abbreviation: PLoS Genet.

ISSN: 1553-7404

DAY: 25

MONTH: 07

YEAR: 2006

Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome. Information

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LANGUAGE: eng

NlmUniqueID: 101239074

Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome. Keywords Mesh Terms:

KEYWORDS: Sequence Alignment

MESH TERMS: methods

Chemical & Substance for Abstract: Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome. Information

Substance Name: Genetic Markers

Registry Number: 0

Grant and Affiliation Information for Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome.

AFFILIATION: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America. eberle@u.washington.edu

Country: United States

AGENCY: United States NHLBI

GRANT: U01 HL66642

ACRONYM: HL

MEDLINETA: PLoS Genet

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