Linkage disequilibrium (LD) maps for human populations

Project overview

We have developed metric linkage disequilibrium maps which have additive distances analogous to linkage maps. Using data both publicly available and in collaborative projects we will apply and extend these methods to develop and integrate standard maps and scaling factors to represent LD in a range of human populations. Construction of maps for whole chromosomes requires GRID technology, database and web development and other bioinformatics applications. Analysis of the maps combines statistical and mathematical genetics and will enable the study of evolutionary aspects of human origins, recombination hot spots and their relationship to sequence and haplotype extension associated with selective sweeps and re-arrangements.

Research outputs

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, 2007, BMC Bioinformatics, 23(4), 517-519

DOI: 10.1093/bioinformatics/btl615

Type: article

Effects of single SNPs, haplotypes, and whole-genome LD maps on accuracy of association mapping

Nikolas Maniatis, Andrew Collins & Newton E. Morton, 2007, Genetic Epidemiology, 31(3), 179-188

DOI: 10.1002/gepi.20199

Type: article

A first-generation metric linkage disequilibrium map of bovine chromosome

Mehar S. Khatkar, Andrew Collins, Julie A.L. Cavanagh, Rachel J. Hawken, Matthew Hobbs, Kyall R. Zenger, Wes Barris, Alexander E. McClintock, Peter C. Thomson, Frank W. Nicholas & Herman W. Raadsma, 2006, Genetics, 174(1), 79-85

DOI: 10.1534/genetics.106.060418

Type: article

Letter. Magnitude and distribution of linkage disequilibrium in population isolates and implications for genome-wide association studies

Susan Service, Joseph DeYoung, Maria Karayiorgou, J. Louw Roos, Herman Pretorious, Gabriel Bedoya, Jorge Ospina, Andres Ruiz-Linares, António Macedo, Joana Almeida Palha, Peter Heutink, Yurii Aulchenko, Ben Oostra, Cornelia van Duijn, Marjo-Riitta Jarvelin, Teppo Varilo, Lynette Peddle, Proton Rahman, Giovanna Piras, Maria Monne, Sarah Murray, Luana Galver, Leena Peltonen, Chiara Sabatti, Andrew Collins & Nelson Freimer, 2006, Nature Genetics, 38(5), 556-560

DOI: 10.1038/ng1770

Type: article

Extended tracts of homozygosity in outbred human populations

Jane Gibson, Newton E. Morton & Andrew Collins, 2006, Human Molecular Genetics, 15(5), 789-795

DOI: 10.1093/hmg/ddi493

Type: article

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

Francisco M. De La Vega, Hadar Isaac, Andrew Collins, Charles R. Scafe, Bjarni V. Halldórsson, Xiaoping Su, Ross A. Lippert, Yu Wang, Marion Laig-Webster, Ryan T. Koehler, Janet S. Ziegle, Lewis T. Wogan, Junko F. Stevens, Kyle M. Leinen, Sheri J. Olson, Karl J. Guegler, Xiaoqing You, Lily H. Xu, Heinz G. Hemken, Francis Kalush, Mitsuo Itakura, Yi Zheng, Guy de Thé, Stephen J. O'Brien, Andrew G. Clark, Sorin Istrail, Michael W. Hunkapiller, Eugene G. Spier & Dennis A. Gilbert, 2005, Genome Research, 15(4), 454-462

DOI: 10.1101/gr.3241705

Type: article

Cosmopolitan linkage disequilibrium maps

Jane Gibson, William Tapper, Weihua Zhang, Newton Morton & Andrew Collins, 2005, Human Genomics, 2(1), 20-27

DOI: 10.1186/1479-7364-2-1-20

Type: article