A novel association test for rare variants based on algebraic statistics

Rare variants: data types and analysis strategies

“…It automatically controls the type I error rates and can produce individual effect estimates for rare variants. Association test for rare variants based on algebraic statistics (ASRV) is a novel method to test association when the causal variants has effects in different directions (13). Single variant association tests such as Transmission Disequilibrium Tests (TDTs) (14) or Family-based Association Tests (FBATs) (15) that are robust against genetic confounding can be applied in family-based association studies.…”

Nonparametric Bayes multiresolution testing for high-dimensional rare events

“…Rare variants, defined as 'alternative forms of a gene that are present with a minor allele frequency (MAF) of less than 1%', play a critical role in explaining the genetic contribution to complex diseases by accounting for disease risk and trait variability, previously unexplained by large genome-wide association studies focused on common variants (Pritchard 2001). In spite of the advent of low-cost parallel sequencing approaches and the resultant development of statistical and machine learning methods for rare variants (see Nicolae (2016), Meng et al (2020) and references therein), very few previous works fully characterize the spatial nature of the rare mutations while retaining robustness, power, and scalability to massive dimensions. In this paper, we develop a flexible, multi-scale method for assessing differences in rare mutation rates between groups by probabilistically modeling them as rare events across the whole genome.…”