Difference between revisions of "Biostatistics 666: Linkage Disequilibrium"
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== Objective == | == Objective == | ||
| − | Introduce the concept of linkage disequilibrium. Provide students with an understanding of D' and r | + | Introduce the concept of linkage disequilibrium. Provide students with an understanding of D' and r<sup>2</sup>, 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 == | ||
| − | [[Media:666.03.pdf|Slides in PDF Format]] | + | [[Media:666.2017.03 - Linkage Disequilibrium.pdf|Slides in PDF Format]] |
== Background Reading == | == 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 [http://www.nature.com/nature/journal/v418/n6897/full/nature00864.html Link ] | + | 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 [http://www.nature.com/nature/journal/v418/n6897/full/nature00864.html Link] |
| − | The International HapMap Consortium. (2005). A haplotype map of the human genome. Nature 437:1299-320 | + | The International HapMap Consortium. (2005). A haplotype map of the human genome. Nature 437:1299-320 [http://www.nature.com/nature/journal/v437/n7063/full/nature04226.html 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 | 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 | ||
Latest revision as of 07:53, 13 September 2017
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
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
