Statistics and Data Science Seminar
Prof. Liping Tong
Loyola University Chicago
A New Method to Compare the Haplotype Distributions between Populations
Abstract: Accurate characterization of haplotype structure and diversity is a key challenge in statistical genetics. Attempts to apply findings from genome wide association studies to populations not included in the discovery phase present unique challenges in terms of the statistical methods. In this talk, I propose a new statistic to assess and compare the haplotype variations among populations which is particularly suited to this emerging challenge. Subsequently I show that this statistic follow a weighted chi-square distribution and how to use a chi-square distribution to approximate it. This approximation is very important since no other haplotype similarity tests have (correctly) used approximate theoretical distributions. In stead, the computational intensive permutation tests are generally performed, which limit the application of haplotype-based comparisons to the whole genome wide studies. In the simulation studies, I first discuss the performance of the approximate distribution under different definitions of similarity matrix, and then compare the power of my new method with the ones proposed by others. At last, this method is applied to the HapMap data to test population differences based on haplotypes on chromosome 2 in the region surrounding the LCT gene (135.3-136.9 Mb).
Wednesday March 4, 2009 at 3:00 PM in SEO 636