JSM 2011 Online Program

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Abstract Details

Activity Number: 418
Type: Contributed
Date/Time: Tuesday, August 2, 2011 : 2:00 PM to 3:50 PM
Sponsor: IMS
Abstract - #301670
Title: A New Method to Compare the Haplotype Distributions Between Populations
Author(s): Liping Tong*+
Companies: Loyola University Chicago
Address: 1032 W Sheridan Rd, Chicago, IL, 60660,
Keywords: haplotype distribution ; average mismatch score ; quadratic form of multinomial random variables ; association study ; fixation index
Abstract:

Accurate characterization of haplotype structure and diversity is a key challenge in statistical genetics. We propose a new statistic to assess and compare the haplotype variations among populations which is particularly suited to this emerging challenge. We first describe the properties and calculations of this method. Subsequently, using simulation studies, we show that the proposed method is more powerful than the chi-square test statistic when comparing haplotype distributions under the following two circumstances (1) when variations of haplotype distances are not balanced (2) when haplotypes are tainted by accumulated mutations or genotyping errors. We also performed simulations to show that the proposed method can be applied to case-control association study and can be much more efficient than the single locus association test by greatly decreasing number of multiple tests. Finally, we applied our method to the Human Genome Diversity Project (HGDP) and HapMap3 data for SNPs on chromosome 2 in the region surrounding the LCT gene. Our results showed that 726 pairs of populations (out of 780) can be distinguished (p-value < 0.05) using the 127 SNPs surrounding the LCT gene.


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