Journal Club Spring 2001

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• 21 February
  Alex Renwick
  Time Change to Wed. 3pm
  Room Change to DH 3092
  
  "Inferring Time to Most Recent Common Ancestor from Sequence Data: The Effect of Mutation Rate Variation "
  Abstract: Coalescent theory provides a probability distribution for the time to the most recent common ancestor (MRCA) of a set of chromosomes sampled randomly from a population. Conditional on this time, one can arrive at a distribution for the number of mutational differences between the sampled chromosomes. In this paper, the authors reverse the conditioning to arrive at the distribution of the time to MRCA conditional on the number of mutational differences observed. Further, they show that this distribution is sensitive to between-site variation in mutation rates. The authors present an MCMC method to arrive at the desired distibutions.
  
  Paper Title: The Effects of Rate Variation on Ancestral Inference in the Coalescent
  
  Authors: Lada Markovtsova, Paul Marjoram, and Simon Tavare
  
  Source: Genetics 2000 156: 1427-1436.
  
  
  
• 4 April
  Elise Eller
  Time Change to Wed. 1:30pm
  CANCELLED
  
  
• 4 May
  Mike Swartz
  1:30pm. DH 1044
  
  
  Title: Linkage Detection Adaptive to Linkage Disequilibrium: The Disequilibrium Maximum-Likelihood-Binomial Test for Affected-Sibship = Data
  
  
  Abstract: Huang and Jiang discuss a method that is adaptive to how much is known = about linkage disequilibrium in the population considered. They based their method on the Maximum Likelihood Binomial test, and simply added a parameter that considers linkage disequilibrium information. This form of the MLB, which they call the Disequilibrium =20 Maximum Likelihood Binomial, adaptively considers the identity by decent(IBD) sharing score, which is family based, and the contrast = between allele specific IBD sharing score, which is informative only when = linkage =20 disequilibrium is present. The authors compare the performance of their DMLB test to the mean test and the Transmission/Disequilibrium Test with theoretical power = calculations. They found that in most cases of strong and weak linkage = disequilibrium, the DMLB test is more powerful than that of either the = TDT, or the mean test. ONly in the absence of linkage is the Mean test = slightly more powerful than the DMLB.
  
  Authors: Jian Huang and Yanming Jiang
  

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