An approach to incorporate linkage disequilibrium structure into genomic association analysis

Fengyu Zhang^,,
Diane Wagener

Statistics and Epidemiology Unit, Research Triangle Institute, NC 27709, USA

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Corresponding author: E-mail address: zhangf28@gmail.com (Fengyu Zhang)

摘要

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Abstract: In this study, we propose to use the principal component analysis (PCA) and regression model to incorporate linkage disequilibrium (LD) in genomic association data analysis. To accommodate LD in genomic data and reduce multiple testing, we suggest performing PCA and extracting the PCA score to capture the variation of genomic data, after which regression analysis is used to assess the association of the disease with the principal component score. An empirical analysis result shows that both genotype-based correlation matrix and haplotype-based LD matrix can produce similar results for PCA. Principal component score seems to be more powerful in detecting genetic association because the principal component score is quantitatively measured and may be able to capture the effect of multiple loci.
- genetic association analysis /
- principal component analysis /
- linkage disequilibrium

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参考文献(16)

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