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STA6178_2005(9) - (1 Schedule Mar 15 Linkage...

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(1) Schedule Mar 15 Linkage disequilibrium (LD) mapping Mar 17 LD mapping Mar 22 Guest speaker, Dr Yang Mar 24 Overview Attend ENAR Biometrical meeting in Austin from Mar 20 to 23 (2) Projects - Work on a problem learnt in the class - Select a problem from your own projects
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What I have learnt from my trip to Seattle -Fred Hutchinson Cancer Research Center -University of Washington Statistical Genetics of Complex Traits Single Nucleotide Polymorphisms (SNPs) Haplotype blocks HIV/AIDS dynamics Cancer progression
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Statistical Genetics of Complex Traits Rongling Wu, Chang-Xing Ma and George Casella Springer-Verlag New York Linkage, Disequilibrium and QTL
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Linkage Disequilibrium Linkage analysis – controlled crosses (backcross or F2) and structured pedigrees (grandparent- parent-children generation) Linkage disequilibrium analysis – Natural population Linkage mapping is used in plant and animal genetics, as well as human genetics of diseases like cancers. LD mapping is used for human genetics of diseases like HIV/AIDS and SARS.
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Mixture model-based likelihood without marker information L( y | ) = Π i=1 n [½f 1 (y i ) + ½f 0 (y i )] Height QTL genotype Sample (cm, y) Qq qq 1 184 ½ ½ 2 185 ½ ½ 3 180 ½ ½ 4 182 ½ ½ 5 167 ½ ½ 6 169 ½ ½ 7 165 ½ ½ 8 166 ½ ½ Linkage mapping - backcross
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Mixture model-based likelihood with marker information L( y ,M| ) = Π i=1 n [ π 1 |i f 1 (y i ) + π 0 |i f 0 (y i )] Sam- Height Marker genotype QTL ple (cm, y) M 1 M 2 Qq qq 1 184 Mm (1) Nn (1) 1 0 2 185 Mm (1) Nn (1) 1 0 3 180 Mm (1) Nn (1) 1 0 4 182 Mm (1) nn (0) 1- θ θ 5 167 mm (0) nn (1) θ 1- θ 6 169 mm (0) nn (0) 0 1 7 165 mm (0) nn (0) 0 1 8 166 mm (0) Nn (0) 0 1 Prior prob.
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