SNP and Haplotype Analysis – Algorithms and Applications
The recent release of the Haplotype Mapping project (Nature, Oct. 26, 2005 – see also, e.g., NY Times, Oct. 27), and the rapid reduction in genotyping costs open new directions and opportunities in the study of complex genetic disease such as cancer or Alzheimer’s disease. The datasets collected for these studies are DNA sequences, with some noise and ambiguous information.
In this talk I will discuss some of the algorithmic issues of disambiguating these DNA sequences, and the current and potential impact of these algorithms on genetics and medicine. In particular, I will discuss some of the problems in the field, such as genotype phasing, tag SNP selection (e.g. feature selection), and population stratification issues (e.g. clustering).
The talk will be self contained, although some introductory material for the biological terminology and the HapMap project can be found at http://www.hapmap.org/whatishapmap.html.