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LDMAP: the construction of high-resolution linkage disequilibrium maps of the human genome

LDMAP: the construction of high-resolution linkage disequilibrium maps of the human genome
LDMAP: the construction of high-resolution linkage disequilibrium maps of the human genome
The precise characterization of the linkage disequilibrium (LD) landscape from highdensity single-nucleotide polymorphism (SNP) data underpins the association mapping of diseases and other studies. We describe the algorithm and implementation of a powerful approach for constructing LD genetic maps with meaningful map distances. The computational problems posed by the enormous number of SNPs typed in the HapMap data are addressed by developing segmental map construction with the potential for parallelization, which we are developing. There is remarkably little loss of information (1-2%) through this approach, but the computation times are dramatically reduced (more than fourfold for sequential map assembly). These developments enable the construction of very highdensity genome-wide LD maps using data from more than 3 million SNPs in HapMap. We anticipate that a whole-genome LD map will be useful for disease gene mapping, genomic research, and population genetics.
linkage disequilibrium maps, human genome, computational load, relative efficiency, segmental assembly
9781588296696
47-57
Humana
Kuo, Tai-Yue
862be417-73e0-4d28-9bd5-bc83242a9192
Lau, Winston
2ae746d0-c61c-449f-b447-a95e9f3f7503
Collins, Andrew R.
7daa83eb-0b21-43b2-af1a-e38fb36e2a64
Collins, Andrew R.
Kuo, Tai-Yue
862be417-73e0-4d28-9bd5-bc83242a9192
Lau, Winston
2ae746d0-c61c-449f-b447-a95e9f3f7503
Collins, Andrew R.
7daa83eb-0b21-43b2-af1a-e38fb36e2a64
Collins, Andrew R.

Kuo, Tai-Yue, Lau, Winston and Collins, Andrew R. (2008) LDMAP: the construction of high-resolution linkage disequilibrium maps of the human genome. In, Collins, Andrew R. (ed.) Linkage Disequilibrium and Association Mapping: Analysis and Applications. (Methods in Molecular Biology, 376) Totowa, USA. Humana, pp. 47-57. (doi:10.1007/978-1-59745-389-9_4).

Record type: Book Section

Abstract

The precise characterization of the linkage disequilibrium (LD) landscape from highdensity single-nucleotide polymorphism (SNP) data underpins the association mapping of diseases and other studies. We describe the algorithm and implementation of a powerful approach for constructing LD genetic maps with meaningful map distances. The computational problems posed by the enormous number of SNPs typed in the HapMap data are addressed by developing segmental map construction with the potential for parallelization, which we are developing. There is remarkably little loss of information (1-2%) through this approach, but the computation times are dramatically reduced (more than fourfold for sequential map assembly). These developments enable the construction of very highdensity genome-wide LD maps using data from more than 3 million SNPs in HapMap. We anticipate that a whole-genome LD map will be useful for disease gene mapping, genomic research, and population genetics.

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More information

Published date: 5 February 2008
Additional Information: ISSN 1064-3745
Keywords: linkage disequilibrium maps, human genome, computational load, relative efficiency, segmental assembly

Identifiers

Local EPrints ID: 59954
URI: http://eprints.soton.ac.uk/id/eprint/59954
ISBN: 9781588296696
PURE UUID: 908e24e4-71b0-41d4-b822-c2d1298c64db
ORCID for Andrew R. Collins: ORCID iD orcid.org/0000-0001-7108-0771

Catalogue record

Date deposited: 28 Oct 2008
Last modified: 16 Mar 2024 02:42

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Contributors

Author: Tai-Yue Kuo
Author: Winston Lau
Editor: Andrew R. Collins

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