Search for Risk Haplotype Segments with GWAS Data by Use of Finite Mixture Models

Ali, Fadhaa and Zhang, Jian (2015) Search for Risk Haplotype Segments with GWAS Data by Use of Finite Mixture Models. Statistics and its interface, 9 (3). pp. 267-280. ISSN 1938-7989. E-ISSN 1938-7997. (doi:https://doi.org/10.4310/SII.2016.v9.n3.a2) (Full text available)

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Abstract

The region-based association analysis has been proposed to capture the collective behavior of sets of variants by testing the association of each set instead of individual variants with the disease. Such an analysis typically involves a list of unphased multiple-locus genotypes with potentially sparse frequencies in cases and controls. To tackle the problem of the sparse distribution, a two-stage approach was proposed in literature: In the first stage, haplotypes are computationally inferred from genotypes, followed by a haplotype co-classification. In the second stage, the association analysis is performed on the inferred haplotype groups. If a haplotype is unevenly distributed between the case and control samples, this haplotype is labeled as a risk haplotype. Unfortunately, the in-silico reconstruction of haplotypes might produce a proportion of false haplotypes which hamper the detection of rare but true haplotypes. Here, to address the issue, we propose an alternative approach: In Stage 1, we cluster genotypes instead of inferred haplotypes and estimate the risk genotypes based on a finite mixture model. In Stage 2, we infer risk haplotypes from risk genotypes inferred from the previous stage. To estimate the finite mixture model, we propose an EM algorithm with a novel data partition-based initialization. The performance of the proposed procedure is assessed by simulation studies and a real data analysis. Compared to the existing multiple Z-test procedure, we find that the power of genome-wide association studies can be increased by using the proposed procedure.

Item Type: Article
Subjects: Q Science > QA Mathematics (inc Computing science) > QA276 Mathematical statistics
Divisions: Faculties > Sciences > School of Mathematics Statistics and Actuarial Science > Statistics
Depositing User: Jian Zhang
Date Deposited: 16 Jun 2015 13:47 UTC
Last Modified: 13 Mar 2016 17:26 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/49031 (The current URI for this page, for reference purposes)
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