FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases

The majority of disease-associated variants identified through genome-wide association studies are located outside of protein-coding regions. Prioritizing candidate regulatory variants and gene targets to identify potential biological mechanisms for further functional experiments can be challenging. To address this challenge, we developed FORGEdb ( https://forgedb.cancer.gov/ ; https://forge2.altiusinstitute.org/files/forgedb.html ; and https://doi.org/10.5281/zenodo.10067458 ), a standalone and web-based tool that integrates multiple datasets, delivering information on associated regulatory elements, transcription factor binding sites, and target genes for over 37 million variants. FORGEdb scores provide researchers with a quantitative assessment of the relative importance of each variant for targeted functional experiments.

High-Throughput Analysis of Retinal Cis-Regulatory Networks by Massively Parallel Reporter Assays

Inherited retinal degenerations are diverse and debilitating blinding diseases. Genetic tests and exome sequencing have identified mutations in many protein-coding genes associated with such diseases, but causal sequence variants remain to be found in many retinopathy cases. Since 99% of our genome does not code for protein but contains cis-regulatory elements (CREs) that regulate the expression of essential genes, CRE variants might hold the answer for some of these cases. However, identifying functional CREs within the noncoding genome and predicting the pathogenicity of CRE variants pose a significant challenge. Here, we review the development of massively parallel reporter assays in the mouse retina, its use in dissecting retinal cis-regulatory networks, and its potential application for developing therapies.

Optimized PCR conditions minimizing the formation of chimeric DNA molecules from MPRA plasmid libraries

Background

Massively parallel reporter assays (MPRAs) enable high-throughput functional evaluation of various DNA regulatory elements and their mutant variants. The assays are based on construction of highly diverse plasmid libraries containing two variable fragments, a region of interest (a sequence under study; ROI) and a barcode (BC) used to uniquely tag each ROI, which are separated by a constant spacer sequence. The sequences of BC–ROI combinations present in the libraries may be either known a priori or not. In the latter case, it is necessary to identify these combinations before performing functional experiments. Typically, this is done by PCR amplification of the BC–ROI regions with flanking primers, followed by next-generation sequencing (NGS) of the products. However, chimeric DNA molecules formed on templates with identical spacer fragment during the amplification process may substantially hamper the identification of genuine BC–ROI combinations, and as a result lower the performance of the assays.

Results

To identify settings that minimize formation of chimeric products we tested a number of PCR amplification parameters, such as conventional and emulsion types of PCR, one- or two-round amplification strategies, amount of DNA template, number of PCR cycles, and the duration of the extension step. Using specific MPRA libraries as templates, we found that the two-round amplification of the BC–ROI regions with a very low initial template amount, an elongated extension step, and a specific number of PCR cycles result in as low as 0.30 and 0.32% of chimeric products for emulsion and conventional PCR approaches, respectively.

Conclusions

We have identified PCR parameters that ensure synthesis of specific (non-chimeric) products from highly diverse MPRA plasmid libraries. In addition, we found that there is a negligible difference in performance of emulsion and conventional PCR approaches performed with the identified settings.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5847-2) contains supplementary material, which is available to authorized users.