Modeling allele-specific expression at the gene and SNP levels simultaneously by a Bayesian logistic mixed regression model

• Main Authors: Jing Xie, Tieming Ji, Marco A. R. Ferreira, Yahan Li, Bhaumik N. Patel, Rocio M. Rivera
• Format: Article
• Language: English
• Published: BMC 2019-10-01
• Series: BMC Bioinformatics
• Subjects: Allelic imbalance; Hierarchical generalized linear mixed model; High-throughput sequencing experiments; Single nucleotide polymorphism
• Online Access: http://link.springer.com/article/10.1186/s12859-019-3141-6

Abstract Background High-throughput sequencing experiments, which can determine allele origins, have been used to assess genome-wide allele-specific expression. Despite the amount of data generated from high-throughput experiments, statistical methods are often too simplistic to understand the complexity of gene expression. Specifically, existing methods do not test allele-specific expression (ASE) of a gene as a whole and variation in ASE within a gene across exons separately and simultaneously. Results We propose a generalized linear mixed model to close these gaps, incorporating variations due to genes, single nucleotide polymorphisms (SNPs), and biological replicates. To improve reliability of statistical inferences, we assign priors on each effect in the model so that information is shared across genes in the entire genome. We utilize Bayesian model selection to test the hypothesis of ASE for each gene and variations across SNPs within a gene. We apply our method to four tissue types in a bovine study to de novo detect ASE genes in the bovine genome, and uncover intriguing predictions of regulatory ASEs across gene exons and across tissue types. We compared our method to competing approaches through simulation studies that mimicked the real datasets. The R package, BLMRM, that implements our proposed algorithm, is publicly available for download at https://github.com/JingXieMIZZOU/BLMRM. Conclusions We will show that the proposed method exhibits improved control of the false discovery rate and improved power over existing methods when SNP variation and biological variation are present. Besides, our method also maintains low computational requirements that allows for whole genome analysis.