Bayesian estimation of genetic regulatory effects in high-throughput reporter assays

William H. Majoros, Young Sook Kim, Alejandro Barrera, Fan Li, Xingyan Wang, Sarah J. Cunningham, Graham D. Johnson, Cong Guo, William L. Lowe, Denise M. Scholtens, M. Geoffrey Hayes, Timothy E. Reddy*, Andrew S. Allen, Bonnie Berger

*Corresponding author for this work

Research output: Contribution to journalArticle

Abstract

Motivation: High-throughput reporter assays dramatically improve our ability to assign function to noncoding genetic variants, by measuring allelic effects on gene expression in the controlled setting of a reporter gene. Unlike genetic association tests, such assays are not confounded by linkage disequilibrium when loci are independently assayed. These methods can thus improve the identification of causal disease mutations. While work continues on improving experimental aspects of these assays, less effort has gone into developing methods for assessing the statistical significance of assay results, particularly in the case of rare variants captured from patient DNA. Results: We describe a Bayesian hierarchical model, called Bayesian Inference of Regulatory Differences, which integrates prior information and explicitly accounts for variability between experimental replicates. The model produces substantially more accurate predictions than existing methods when allele frequencies are low, which is of clear advantage in the search for disease-causing variants in DNA captured from patient cohorts. Using the model, we demonstrate a clear tradeoff between variant sequencing coverage and numbers of biological replicates, and we show that the use of additional biological replicates decreases variance in estimates of effect size, due to the properties of the Poisson-binomial distribution. We also provide a power and sample size calculator, which facilitates decision making in experimental design parameters.

Original languageEnglish (US)
Pages (from-to)331-338
Number of pages8
JournalBioinformatics
Volume36
Issue number2
DOIs
StatePublished - Jan 15 2020

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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  • Cite this

    Majoros, W. H., Kim, Y. S., Barrera, A., Li, F., Wang, X., Cunningham, S. J., Johnson, G. D., Guo, C., Lowe, W. L., Scholtens, D. M., Hayes, M. G., Reddy, T. E., Allen, A. S., & Berger, B. (2020). Bayesian estimation of genetic regulatory effects in high-throughput reporter assays. Bioinformatics, 36(2), 331-338. https://doi.org/10.1093/bioinformatics/btz545