Abstract
The widespread availability of genome sequencing data has yielded different rare variant association methods in population-based or family-based designs. However, it is challenging to know which method is appropriate in practice. Our purpose of this paper is to provide a general review of the literature for rare variant association studies and suggestions on future research directions. This paper discusses methods for recent rare variant association studies in three categories. The first two categories are for population-based designs, with/without considering the direction of the effects of causal rare variants. In the third category, methods for family-based designs are concluded.
Highlights
Genome-wide association studies (GWAS) have successfully identified a large number of common variants underlying various complex diseases [1,2]
In the first two categories, we provide the summary on methods in population-based designs, with or without considering the direction of effects of causal rare variants
Li and Leal [10] extended the cohort allelic sums test (CAST) to come up with the combined multivariate and collapsing (CMC) method in which rare variants are collapsed within different subgroups and the information of both collapsed rare variants and common variants is used in the association test
Summary
Genome-wide association studies (GWAS) have successfully identified a large number of common variants underlying various complex diseases [1,2]. Several methods using the strategy of collapsing a group of rare variants in a gene or a pathway have been proposed recently. These methods include the cohort allelic sums test (CAST) method [11], the combined multivariate and collapsing (CMC) method [10], the weighted sum (WS) method [12], the variable minor allele frequency threshold (VT) method [13], and the cumulative minorallele test (CMAT) method [14], among others. In the first two categories, we provide the summary on methods in population-based designs, with or without considering the direction of effects of causal rare variants.
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