Exploiting large scale computing to construct high resolution linkage disequilibrium maps of the human genome

Winston Lau; Tai-Yue Kuo; William Tapper; Simon Cox; Andrew Collins

doi:10.1093/bioinformatics/btl615

Exploiting large scale computing to construct high resolution linkage disequilibrium maps of the human genome

Bioinformatics. 2007 Feb 15;23(4):517-9. doi: 10.1093/bioinformatics/btl615. Epub 2006 Dec 1.

Authors

Winston Lau¹, Tai-Yue Kuo, William Tapper, Simon Cox, Andrew Collins

Affiliation

¹ Human Genetics Division, Duthie Building (Mailpoint 808), Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK.

PMID: 17142813
DOI: 10.1093/bioinformatics/btl615

Abstract

Linkage disequilibrium (LD) maps increase power and precision in association mapping, define optimal marker spacing and identify recombination hot-spots and regions influenced by natural selection. Phase II of HapMap provides approximately 2.8-fold more single nucleotide polymorphisms (SNPs) than phase I for constructing higher resolution maps. LDMAP-cluster, is a parallel program for rapid map construction in a Linux environment used here to construct genome-wide LD maps with >8.2 million SNPs from the phase II data.

Availability: The LD maps, LDMAP-cluster and documentation are available from: http://www.som.soton.ac.uk/research/geneticsdiv/epidemiology/LDMAP.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Chromosome Mapping / methods*
Cluster Analysis
Computing Methodologies*
Genetic Markers / genetics*
Genetics, Population
Genome, Human / genetics*
Humans
Linkage Disequilibrium / genetics*
Sensitivity and Specificity
Software

Substances

Genetic Markers