Difference between revisions of "Biostatistics 666: Linkage Disequilibrium"

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== 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]]
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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  
  
 
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

Revision as of 20:23, 21 January 2010

Objective

Introduce the concept of linkage disequilibrium. Provide students with an understanding of D' and r^2, the most common measures of linkage disequilibrium, and the forces that shape them. Provide several illustrations of the extent of linkage disequilibrium in the genome. Introduce the concept of SNP-tagging.

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 [[ 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

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