Comparison of haplotype-based statistical tests for disease association with rare and common variants

Briefings in Bioinformatics
Ananda S Datta, Swati Biswas

Abstract

Recent literature has highlighted the advantages of haplotype association methods for detecting rare variants associated with common diseases. As several new haplotype association methods have been proposed in the past few years, a comparison of new and standard methods is important and timely for guidance to the practitioners. We consider nine methods-Haplo.score, Haplo.glm, Hapassoc, Bayesian hierarchical Generalized Linear Model (BhGLM), Logistic Bayesian LASSO (LBL), regularized GLM (rGLM), Haplotype Kernel Association Test, wei-SIMc-matching and Weighted Haplotype and Imputation-based Tests. These can be divided into two types-individual haplotype-specific tests and global tests depending on whether there is just one overall test for a haplotype region (global) or there is an individual test for each haplotype in the region. Haplo.score is the only method that tests for both; Haplo.glm, Hapassoc, BhGLM and LBL are individual haplotype-specific, while the rest are global tests. For comparison, we also apply a popular collapsing method-Sequence Kernel Association Test (SKAT) and its two variants-SKAT-O (Optimal) and SKAT-C (Combined). We carry out an extensive comparison on our simulated data sets as well as on the Genetic A...Continue Reading

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Dec 17, 2016·BMC Proceedings·Ananda S DattaSwati Biswas

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Citations

Apr 27, 2018·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·J MiaoH Gao
Jul 23, 2019·Briefings in Bioinformatics·Charalampos Papachristou, Swati Biswas
Feb 26, 2019·Human Heredity·Ananda S DattaSwati Biswas

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