University of Newcastle upon Tyne

School of Mathematics and Statistics

Statistics Seminars 2005-2006

9 December 2005 M502 2:00pm

Ian Wilson

Approximate Likelihood Methods for modelling human genomic variation.

Abstract

The variation within and between human populations is being studied by the International HAPMAP project (www.hapmap.org), which has produced an extremely large database of human genetic variation. Shared ancestry causes complex correlations between chromosomes and between sites on the same chromosome making the analysis of such datasets extremely challenging. One of the more promising methods is the Product of Approximate Conditionals (PAC) (Li \& Stephens). This method models the shared ancestry by coalescence and its break-up by recombination as a sequence of hidden Markov models (HMMs). This method was developed for the estimation of recombination rates but can be used to make inferences about the block structure of data by sampling from the underlying HMMs using the forward-backwards algorithm, and can be used to make inferences for case-control association studies by looking at the properties of unseen genetic variants within these blocks. An extension of this method is developed to deal with data from multiple populations, or for Case-control data from disease studies.
 

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