Design tools for MPRA experiments

Abstract

Motivation: Genetic reporter assays are a convenient, relatively inexpensive method for studying the regulation of gene expression. Massively Parallel Reporter Assays (MPRA) are high-throughput functionalization assays that interrogate the transcriptional activity of many genetic variants at once using a library of synthetic barcoded constructs. Despite growing interest in this area, there are few computational tools to design and execute MPRA studies.

Results: We designed an online web-tool and R package that allows for interactive MPRA experimental design encompassing both power analysis and design of constructs. Our tool is tuned using data from real MPRA studies. Users can adjust experimental parameters to examine the predicted effect on assay power as well as upload VCFs for automated construct sequence generation.

Availability and implementation: The MPRA Design Tools web application is available here: https://andrewghazi.shinyapps.io/designmpra/, https://github.com/andrewGhazi/designMPRA and https://github.com/andrewGhazi/mpradesigntools.

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

(a) Two synthetic example MPRA outputs for hypothetical variants (see Supplementary Data S2) in scenarios A and B with transcriptional shifts of 1.5. Variant A uses 40 barcodes per allele and exhibits a standard deviation of 2 while B uses 100 barcodes per allele and exhibits a standard deviation of .5. Variances are based on observed data from Ulirsch et al. (2016) and Tewhey et al. (2016). (b) Line plots showing power to detect changes using the given multiplicities of barcodes and standard deviations in a MPRA assay with 1000 variants. In scenario A the statistical power to detect the shift is less than 20% while in scenario B the power is effectively 1. This example shows the necessity of selecting design parameters that maximize experimental efficiency