JSM 2011 Online Program

The views expressed here are those of the individual authors and not necessarily those of the JSM sponsors, their officers, or their staff.

Abstract Details

Activity Number: 515
Type: Contributed
Date/Time: Wednesday, August 3, 2011 : 10:30 AM to 12:20 PM
Sponsor: Section on Nonparametric Statistics
Abstract - #302689
Title: A Hierarchical Dirichlet Process Mixture Model for Genotype Calling: Combining SNP Calling Algorithm (Within Sample) with Sample Genotyping Strategy (Each SNP)
Author(s): Gengxin Li*+ and Hongyu Zhao
Companies: Yale University and Yale University
Address: STE 503, New Haven, CT, 06511-6660, USA
Keywords: Dirichlet Process ; Genotype Calling ; mixture model
Abstract:

Large scale genotyping is a crucial process to assign genotype to hybridization data through calling algorithms. With the development of the illumine chip technique, a number of genotyping methods have been developed recently. The classical genotyping calls for a SNP are made by GenCall with GenTrain clustering algorithm that requires a large number of samples to make sure the calling accuracy. When rare SNPs are commonly observed in the large scale genotyping, it is extremely difficult to perform the genotype calling. GenoSNP based on within-sample SNP genotyping was explored to address this challenge. Because of the richness of DNA information within sample, its calling result greatly reduces the missing rate, especially for some rare SNPs and samples. However, GenoSNP fails the Hardy-Weinberg equilibrium tests for a great many SNPs due to the assumption that SNPs within-sample is hard to satisfy. In this paper, we propose an efficient Hierarchical Dirichlet Process Mixture Model to combine the superiorities of both calling methods. While comparing with GenCall and GenoSNP, the better performance of our discussed method is demonstrated in the simulation study and real case.


The address information is for the authors that have a + after their name.
Authors who are presenting talks have a * after their name.

Back to the full JSM 2011 program




2011 JSM Online Program Home

For information, contact jsm@amstat.org or phone (888) 231-3473.

If you have questions about the Continuing Education program, please contact the Education Department.