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Bioinformatics Advance Access originally published online on December 1, 2006
Bioinformatics 2007 23(4):517-519; doi:10.1093/bioinformatics/btl615
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Winston Lau {dagger}, Tai-Yue Kuo {dagger}, William Tapper , Simon Cox 1 and Andrew Collins *

Human Genetics Division, Duthie Building (Mailpoint 808), Southampton General Hospital Tremona Road, Southampton SO16 6YD, UK
1 Southampton Regional e-Science Centre, School of Engineering Sciences, University of Southampton Southampton SO17 1BJ, UK

*To whom correspondence should be addressed.


  Abstract

Summary: 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 ~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

Contact: arc{at}soton.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Associate Editor: Keith A Crandall

Received on September 21, 2006; revised on November 14, 2006; accepted on November 28, 2006

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[Abstract] [Full Text] [PDF]


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