A novel association test for rare variants based on algebraic statistics

DOI10.1016/J.JTBI.2020.110228MaRDI QIDQ2180778zbMATH OpenOpenAlexWikidataFDO

Authors Jingbo Meng, Wensheng Zhu, Canhui Li, Kyongson Jon

Publication date 14 May 2020

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jtbi.2020.110228

zbMATH Keywords

association analysiscontingency tablesMarkov basesMarkov chain Monte Carlo

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Algebraic statistics (62R01) Genetics and epigenetics (92D10)

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Cites work

• A survey of exact inference for contingency tables. With comments and a rejoinder by the author
• Algebraic algorithms for sampling from conditional distributions
• Algebraic Markov Bases and MCMC for Two‐Way Contingency Tables
• Algebraic Statistics for Computational Biology
• Inference from iterative simulation using multiple sequences
• Markov fields and log-linear interaction models for contingency tables
• Nonparametric covariate-adjusted association tests based on the generalized Kendall's tau
• One-Way Layout for Counts and the Exact Enumeration of the Kruskal-Wallis H Distribution with Ties
• The Diaconis-Sturmfels algorithm and rules of succession

Cited in

(10)

• A modified association test for rare and common variants based on affected sib-pair design
• Rare variant testing across methods and thresholds using the multi-kernel sequence kernel association test (MK-SKAT)
• Pooled association tests for rare genetic variants: a review and some new results
• Test for rare variants by environment interactions in sequencing association studies
• Logistic Bayesian LASSO for identifying association with rare haplotypes and application to age-related macular degeneration
• A Poisson approximation variable threshold method in rare variants association study
• Design and statistical analysis of pooled next generation sequencing for rare variants
• Association analysis of rare variants with quantitative trait based on minimum \(p\)-value
• Likelihood ratio and score burden tests for detecting disease-associated rare variants
• A Bayes factor approach with informative prior for rare genetic variant analysis from next generation sequencing data

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Uses Software

• GWAS Catalog

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