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The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern

The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern
The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern
The extent and patterns of linkage disequilibrium (LD) determine the feasibility of association studies to map genes that underlie complex traits. Here we present a comparison of the patterns of LD across four major human populations (African-American, Caucasian, Chinese, and Japanese) with a high-resolution single-nucleotide polymorphism (SNP) map covering almost the entire length of chromosomes 6, 21, and 22. We constructed metric LD maps formulated such that the units measure the extent of useful LD for association mapping. LD reaches almost twice as far in chromosome 6 as in chromosomes 21 or 22, in agreement with their differences in recombination rates. By all measures used, out-of-Africa populations showed over a third more LD than African-Americans, highlighting the role of the population's demography in shaping the patterns of LD. Despite those differences, the long-range contour of the LD maps is remarkably similar across the four populations, presumably reflecting common localization of recombination hot spots. Our results have practical implications for the rational design and selection of SNPs for disease association studies.
pair 22, chromosomes, human, comparative study, genetic, demography, history, pair 6, pair 21, research support, population, polymorphism, recombination, genetics, linkage disequilibrium, single nucleotide, african americans, genes, disease, role, design, non-u.s.gov't, african continental ancestry group, asian continental ancestry group, european continental ancestry group, chromosome mapping, humans
1088-9051
454-462
De La Vega, Francisco M.
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Isaac, Hadar
cf76fee8-08da-4354-a4e5-f5fa49dc73cc
Collins, Andrew
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Scafe, Charles R.
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Halldórsson, Bjarni V.
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Su, Xiaoping
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Lippert, Ross A.
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Wang, Yu
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Laig-Webster, Marion
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Koehler, Ryan T.
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Ziegle, Janet S.
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Wogan, Lewis T.
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Stevens, Junko F.
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Leinen, Kyle M.
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Olson, Sheri J.
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Guegler, Karl J.
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You, Xiaoqing
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Xu, Lily H.
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Hemken, Heinz G.
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Kalush, Francis
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Itakura, Mitsuo
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Zheng, Yi
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de Thé, Guy
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O'Brien, Stephen J.
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Clark, Andrew G.
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Istrail, Sorin
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Hunkapiller, Michael W.
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Spier, Eugene G.
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Gilbert, Dennis A.
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De La Vega, Francisco M.
955932c6-f7b9-4581-98d5-ff97d0a6464a
Isaac, Hadar
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Collins, Andrew
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Scafe, Charles R.
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Halldórsson, Bjarni V.
0b2c87f6-d9bd-4d56-8ff8-4f1a611daadf
Su, Xiaoping
b067387d-d821-4d24-a98f-8f8670a25b68
Lippert, Ross A.
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Wang, Yu
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Laig-Webster, Marion
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Koehler, Ryan T.
85474eb0-0bdb-4aa6-a0a6-a9c717e49dc3
Ziegle, Janet S.
38f38944-df06-45e2-b045-617b4cfd8004
Wogan, Lewis T.
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Stevens, Junko F.
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Leinen, Kyle M.
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Olson, Sheri J.
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Guegler, Karl J.
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You, Xiaoqing
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Xu, Lily H.
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Hemken, Heinz G.
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Kalush, Francis
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Itakura, Mitsuo
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Zheng, Yi
dd7d8f35-8379-4c0a-83c3-52ceda9de570
de Thé, Guy
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O'Brien, Stephen J.
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Clark, Andrew G.
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Istrail, Sorin
4a43f5bf-eca5-42bd-b0ef-814c1cfd2071
Hunkapiller, Michael W.
a399bb42-0e27-460b-89f0-df1741d26cc6
Spier, Eugene G.
0ea6153d-7e83-4fca-8176-1ade5134b35f
Gilbert, Dennis A.
9f140d32-b465-48bf-b54b-143684fa4e70

De La Vega, Francisco M., Isaac, Hadar, Collins, Andrew, Scafe, Charles R., Halldórsson, Bjarni V., Su, Xiaoping, Lippert, Ross A., Wang, Yu, Laig-Webster, Marion, Koehler, Ryan T., Ziegle, Janet S., Wogan, Lewis T., Stevens, Junko F., Leinen, Kyle M., Olson, Sheri J., Guegler, Karl J., You, Xiaoqing, Xu, Lily H., Hemken, Heinz G., Kalush, Francis, Itakura, Mitsuo, Zheng, Yi, de Thé, Guy, O'Brien, Stephen J., Clark, Andrew G., Istrail, Sorin, Hunkapiller, Michael W., Spier, Eugene G. and Gilbert, Dennis A. (2005) The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern. Genome Research, 15 (4), 454-462. (doi:10.1101/gr.3241705).

Record type: Article

Abstract

The extent and patterns of linkage disequilibrium (LD) determine the feasibility of association studies to map genes that underlie complex traits. Here we present a comparison of the patterns of LD across four major human populations (African-American, Caucasian, Chinese, and Japanese) with a high-resolution single-nucleotide polymorphism (SNP) map covering almost the entire length of chromosomes 6, 21, and 22. We constructed metric LD maps formulated such that the units measure the extent of useful LD for association mapping. LD reaches almost twice as far in chromosome 6 as in chromosomes 21 or 22, in agreement with their differences in recombination rates. By all measures used, out-of-Africa populations showed over a third more LD than African-Americans, highlighting the role of the population's demography in shaping the patterns of LD. Despite those differences, the long-range contour of the LD maps is remarkably similar across the four populations, presumably reflecting common localization of recombination hot spots. Our results have practical implications for the rational design and selection of SNPs for disease association studies.

Full text not available from this repository.

More information

Published date: April 2005
Keywords: pair 22, chromosomes, human, comparative study, genetic, demography, history, pair 6, pair 21, research support, population, polymorphism, recombination, genetics, linkage disequilibrium, single nucleotide, african americans, genes, disease, role, design, non-u.s.gov't, african continental ancestry group, asian continental ancestry group, european continental ancestry group, chromosome mapping, humans

Identifiers

Local EPrints ID: 24679
URI: http://eprints.soton.ac.uk/id/eprint/24679
ISSN: 1088-9051
PURE UUID: eaa855ed-5879-45fb-b5ba-0e145f00e43f
ORCID for Andrew Collins: ORCID iD orcid.org/0000-0001-7108-0771

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Date deposited: 03 Apr 2006
Last modified: 10 Dec 2019 01:57

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Contributors

Author: Francisco M. De La Vega
Author: Hadar Isaac
Author: Andrew Collins ORCID iD
Author: Charles R. Scafe
Author: Bjarni V. Halldórsson
Author: Xiaoping Su
Author: Ross A. Lippert
Author: Yu Wang
Author: Marion Laig-Webster
Author: Ryan T. Koehler
Author: Janet S. Ziegle
Author: Lewis T. Wogan
Author: Junko F. Stevens
Author: Kyle M. Leinen
Author: Sheri J. Olson
Author: Karl J. Guegler
Author: Xiaoqing You
Author: Lily H. Xu
Author: Heinz G. Hemken
Author: Francis Kalush
Author: Mitsuo Itakura
Author: Yi Zheng
Author: Guy de Thé
Author: Stephen J. O'Brien
Author: Andrew G. Clark
Author: Sorin Istrail
Author: Michael W. Hunkapiller
Author: Eugene G. Spier
Author: Dennis A. Gilbert

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