A comparison of principal component methods between multiple phenotype regression and multiple SNP regression in genetic association studies

DOI10.1214/19-AOAS1312MaRDI QIDQ2179976zbMATH OpenOpenAlexFDO

Authors Ian Barnett, Xihong Lin, Zhong-Hua Liu

Publication date 13 May 2020

Published in The Annals of Applied Statistics (Search for Journal in Brave)

Full work available at URL https://projecteuclid.org/euclid.aoas/1587002681

zbMATH Keywords

dimension reductioneigenvalueshypothesis testingminimum \(p\)-value testmultiple phenotypesprincipal component analysisSNP-setvariance-component test

Mathematics Subject Classification ID

Factor analysis and principal components; correspondence analysis (62H25) Classification and discrimination; cluster analysis (statistical aspects) (62H30) Applications of statistics to biology and medical sciences; meta analysis (62P10) Protein sequences, DNA sequences (92D20)

Review text

This paper focuses on application and justification of the principal component analysis, which is the widely used method for dimension reduction in unsupervised multivariate analysis. The authors have demonstrated that the lower order principal components (with large eigenvalues) are generally preferred and lead to a higher power in setting for the single nucleotide polymorphism (SNP-set). Simulation studies as well as two real data analyses were employed to validate the findings.

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Cites work

• A Geometric Perspective on the Power of Principal Component Association Tests in Multiple Phenotype Studies
• Multiple phenotype association tests using summary statistics in genome-wide association studies
• Variance component testing in generalised linear models with random effects

Cited in

(10)

• Analyzing multiple phenotypes based on principal component analysis
• Genetic association test based on principal component analysis
• Comparing the performance of linear and nonlinear principal components in the context of high-dimensional genomic data integration
• Visualizing genetic constraints
• A comparison of multifactor dimensionality reduction and \(L_{1}\)-penalized regression to identify gene-gene interactions in genetic association studies
• Data reduction prior to inference: are there consequences of comparing groups using a \(t\)-test based on principal component scores?
• Principal component analysis of canine hip dysplasia phenotypes and their statistical power for genome-wide association mapping
• A Geometric Perspective on the Power of Principal Component Association Tests in Multiple Phenotype Studies
• Estimating and correcting optimism bias in multivariate PLS regression: application to the study of the association between single nucleotide polymorphisms and multivariate traits in attention deficit hyperactivity disorder
• Principal component analysis (PCA) for high-dimensional data. PCA is dead. Long live PCA

Describes a project that uses

Uses Software

• MPAT
• PLINK
• Eigenstrat

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