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Linkage mapping by variance components analysis

Linkage mapping by variance components analysis. Uppsala 5-7 April 2011 Dario Beraldi. Variance components mapping. A strategy to map QTLs in general pedigrees by testing the significance of the variance explained by specific chromosomal regions. What is needed (from the field & lab).

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Linkage mapping by variance components analysis

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  1. Linkage mapping by variance components analysis Uppsala 5-7 April 2011 Dario Beraldi

  2. Variance components mapping A strategy to map QTLs in general pedigrees by testing the significance of the variance explained by specific chromosomal regions. What is needed (from the field & lab) • Phenotypic records for the phenotype(s) of interest and possible co-variates (phenotype file) • A pedigree of individuals (pedigree file) • Genotypes for these individuals (genotype file) • Map of the markers used (map file) In this tutorial we start with these data and we are not worried how they were obtained

  3. Outline of the method/tutorial After having loaded the data: • Produce IBD matrices (chromosomal regions to test) – lokisuite • Parse the matrices • Estimated the likelihood of the null polygenic model – ASreml • Estimated the likelihood of the QTL model (polygenic + IBD matrix) – ASreml • Compare the null vs QTL likelihoods to identify QTL regions

  4. These steps are implemented here:

  5. Variance components - Power 0.1 0.5

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