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Original Paper

Patterns of Linkage Disequilibrium between SNPs in a Sardinian Population Isolate and the Selection of Markers for Association Studies

Angius A.a, b · Hyland F.C.L.c · Persico I.a · Pirastu N.a · Woodage T.c · Pirastu M.a, b · De La Vega F.M.c

Author affiliations

aShardna Life Sciences, Cagliari, and bIstituto di Genetica delle Popolazioni, CNR, Alghero, Italy, and cApplied Biosystems, Foster City, Calif., USA

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Hum Hered 2008;65:9–22

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Article / Publication Details

First-Page Preview
Abstract of Original Paper

Received: September 27, 2006
Accepted: April 30, 2007
Published online: July 25, 2007
Issue release date: October 2007

Number of Print Pages: 14
Number of Figures: 4
Number of Tables: 3

ISSN: 0001-5652 (Print)
eISSN: 1423-0062 (Online)

For additional information: https://www.karger.com/HHE

Abstract

Objective: In isolated populations, ‘background’ linkage disequilibrium (LD) has been shown to extend over large genetic distances. This and their reduced environmental and genetic heterogeneity has stimulated interest in their potential for association mapping. We compared LD unit map distances with pair-wise measurements of LD in a dense single nucleotide polymorphism (SNP) set. Methods: We genotyped 771 SNPs in an 8 Mb segment of chromosome 22 on 101 individuals from the isolated village of Talana, Sardinia, and compared with outbred European populations. Results: Heterozygosity was remarkably similar in both populations. In contrast, the extent of LD observed was quite different. The decay of LD with distance is slower in the isolate. The differences in LD map lengths suggest that useful LD extends up to three times farther in the Sardinian population; smaller differences are seen with pairwise LD metrics. While LD map length slightly decreases with average relatedness, cryptic relatedness does not explain the decrease in LD map length. Haplotypes, block boundaries, and patterns of LD are similar in both populations, suggesting a shared distribution of recombination hotspots. Conclusions: About 15% fewer haplotype tagging SNPs need to be genotyped in the isolate, and possibly 70% fewer if selecting SNPs evenly spaced on the metric LD map.

© 2008 S. Karger AG, Basel


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Article / Publication Details

First-Page Preview
Abstract of Original Paper

Received: September 27, 2006
Accepted: April 30, 2007
Published online: July 25, 2007
Issue release date: October 2007

Number of Print Pages: 14
Number of Figures: 4
Number of Tables: 3

ISSN: 0001-5652 (Print)
eISSN: 1423-0062 (Online)

For additional information: https://www.karger.com/HHE


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