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Allelic association with SNPs: metrics, populations, and the linkage disequilibrium map. [In Special Issue: SNP 2000: Third International Meeting on Single Nucleotide Polymorphism and Complex Genome Analysis]

Allelic association with SNPs: metrics, populations, and the linkage disequilibrium map. [In Special Issue: SNP 2000: Third International Meeting on Single Nucleotide Polymorphism and Complex Genome Analysis]
Allelic association with SNPs: metrics, populations, and the linkage disequilibrium map. [In Special Issue: SNP 2000: Third International Meeting on Single Nucleotide Polymorphism and Complex Genome Analysis]
Comparison of different metrics, using three large samples of haplotypes from different populations, demonstrates that is the most efficient measure of association between pairs of single nucleotide polymorphisms (SNPs). Pairwise data can be modeled, using composite likelihood, to describe the decline in linkage disequilibrium with distance (the Malecot model). The evidence from more isolated populations (Finland, Sardinia) suggests that linkage disequilibrium extends to 427-893 kb but, even in samples representative of large heterogeneous populations, such as CEPH, the extent is 385 kb or greater. This suggests that isolated populations are not essential for linkage disequilibrium mapping of common diseases with SNPs. The ? parameter of the Malecot model (recombination and time), evaluated at each SNP, indicates regions of the genome with extensive and less extensive disequilibrium (low and high values of ? respectively). When plotted against the physical map, the regions with extensive and less extensive linkage disequilibrium may correspond to recombination cold and hot spots. This is discussed in relation to the Xq25 cytogenetic band and the HFE gene region.
snp, linkage disequilibrium mapping, ld, malecot model, association metrics, hfe, fmr1, disease, single nucleotide, research, x chromosome, population, alleles, histocompatibility antigens class i, molecular sequence data, recombination, hla antigens, finland, genome, human, genetics, genetic, membrane proteins, gene frequency, protein, cold, antigens, polymorphism, proteins, time, linkage disequilibrium, likelihood functions, chromosome mapping, humans, haplotypes, models
1059-7794
255-262
Collins, A.
7daa83eb-0b21-43b2-af1a-e38fb36e2a64
Ennis, S.
7b57f188-9d91-4beb-b217-09856146f1e9
Taillon-Miller, P.
6f72eea0-063f-4cfd-98aa-969cea2a3566
Kwok, P-Y.
e61c8895-4bbb-4169-bf14-ef3cb83a635f
Morton, N.E.
c668e2be-074a-4a0a-a2ca-e8f51830ebb7
Collins, A.
7daa83eb-0b21-43b2-af1a-e38fb36e2a64
Ennis, S.
7b57f188-9d91-4beb-b217-09856146f1e9
Taillon-Miller, P.
6f72eea0-063f-4cfd-98aa-969cea2a3566
Kwok, P-Y.
e61c8895-4bbb-4169-bf14-ef3cb83a635f
Morton, N.E.
c668e2be-074a-4a0a-a2ca-e8f51830ebb7

Collins, A., Ennis, S., Taillon-Miller, P., Kwok, P-Y. and Morton, N.E. (2001) Allelic association with SNPs: metrics, populations, and the linkage disequilibrium map. [In Special Issue: SNP 2000: Third International Meeting on Single Nucleotide Polymorphism and Complex Genome Analysis]. Human Mutation, 17 (4), 255-262. (doi:10.1002/humu.21).

Record type: Article

Abstract

Comparison of different metrics, using three large samples of haplotypes from different populations, demonstrates that is the most efficient measure of association between pairs of single nucleotide polymorphisms (SNPs). Pairwise data can be modeled, using composite likelihood, to describe the decline in linkage disequilibrium with distance (the Malecot model). The evidence from more isolated populations (Finland, Sardinia) suggests that linkage disequilibrium extends to 427-893 kb but, even in samples representative of large heterogeneous populations, such as CEPH, the extent is 385 kb or greater. This suggests that isolated populations are not essential for linkage disequilibrium mapping of common diseases with SNPs. The ? parameter of the Malecot model (recombination and time), evaluated at each SNP, indicates regions of the genome with extensive and less extensive disequilibrium (low and high values of ? respectively). When plotted against the physical map, the regions with extensive and less extensive linkage disequilibrium may correspond to recombination cold and hot spots. This is discussed in relation to the Xq25 cytogenetic band and the HFE gene region.

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More information

Published date: April 2001
Keywords: snp, linkage disequilibrium mapping, ld, malecot model, association metrics, hfe, fmr1, disease, single nucleotide, research, x chromosome, population, alleles, histocompatibility antigens class i, molecular sequence data, recombination, hla antigens, finland, genome, human, genetics, genetic, membrane proteins, gene frequency, protein, cold, antigens, polymorphism, proteins, time, linkage disequilibrium, likelihood functions, chromosome mapping, humans, haplotypes, models

Identifiers

Local EPrints ID: 24660
URI: https://eprints.soton.ac.uk/id/eprint/24660
ISSN: 1059-7794
PURE UUID: 4e3a491c-5ab6-4739-8202-f1884c6def8d
ORCID for A. Collins: ORCID iD orcid.org/0000-0001-7108-0771
ORCID for S. Ennis: ORCID iD orcid.org/0000-0003-2648-0869

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Date deposited: 04 Apr 2006
Last modified: 20 Jul 2019 01:23

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Author: A. Collins ORCID iD
Author: S. Ennis ORCID iD
Author: P. Taillon-Miller
Author: P-Y. Kwok
Author: N.E. Morton

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