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Genomic Informatics

Linkage disequilibrium

Linkage disequilibrium (LD) research has underpinned the past decade of medical genetics research. The Genetic Epidemiology group started work to develop and apply approaches for the investigation of LD patterns, and have applied these to many populations, human and otherwise.

Diagram showing association between alleles
Diagram showing association between alleles

The Genetic Epidemiology group was instrumental in the early days of developing gene mapping and GWAS studies, being the first to show cost-effective GWAS can be achieved using a small panel of tag SNPs (just ~1% of all SNPs) because of extensive linkage disequilibrium. The group also developed the Malécot-Morton model of LD, drawing on the population genetics and geographical isolation work of Gustave Malécot to apply his models to loci in the genome. This work is now ongoing alongside the Genomic Informatics group.

The group have written the software LDMAP to apply the Malécot-Morton model to genetic data. This software has been applied to varied populations, initially with small scale and GWAS datasets. More recently, in collaboration with Complete Genomics, the group have shown the greatly improved utility of WGS data for LD mapping. The increase resolution greatly improves our ability to investigate the motifs underlying recombination and other features of the genome.

In addition to work looking at the LD patterns of human populations, the application of this approach to agriculturally important (namely bovine and galline genomes), in collaboration with researchers including Dr Mehar Khatkar (University of Sydney) and Prof Dave Burt (Roslin Institute, University of Edinburgh).

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Some key publications from the group relating to LD are listed below.

Articles

Book Chapter

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