Biostatistics 666: Linkage Disequilibrium

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Objective

Introduce the concept of linkage disequilibrium. Provide students with an understanding of D' and r2, the two most common measures of linkage disequilibrium, and the forces that shape them. Provide several illustrations of the extent of linkage disequilibrium in the genome, including the idea that the extent of linkage disequilibrium will vary between populations and genomic regions.

Introduce the concept of SNP-tagging and its consequences for association studies, both positive (because it implies that powerful studies don't have to examine all variants) and negative (because it makes identification of causal variants more challenging).

Slides

Slides in PDF Format

Background Reading

Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Dibling T, Tinsley E, Kirby S, Carter D, Papaspyridonos M, Livingstone S, Ganske R, Lohmussaar E, Zernant J, Tonisson N, Remm M, Magi R, Puurand T, Vilo J, Kurg A, Rice K, Deloukas P, Mott R, Metspalu A, Bentley DR, Cardon LR and Dunham I (2002). A first-generation linkage disequilibrium map of human chromosome 22. Nature 418:544-548 Link

The International HapMap Consortium. (2005). A haplotype map of the human genome. Nature 437:1299-320 Link

Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA (2004). Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 74:106-120