Abstract
RegulationSpotter is a web-based tool for the user-friendly annotation and interpretation of DNA variants located outside of protein-coding transcripts (extratranscriptic variants). It is designed for clinicians and researchers who wish to assess the potential impact of the considerable number of non-coding variants found in Whole Genome Sequencing runs. It annotates individual variants with underlying regulatory features in an intuitive way by assessing over 100 genome-wide annotations. Additionally, it calculates a score, which reflects the regulatory potential of the variant region. Its dichotomous classifications, ‘functional’ or ‘non-functional’, and a human-readable presentation of the underlying evidence allow a biologically meaningful interpretation of the score. The output shows key aspects of every variant and allows rapid access to more detailed information about its possible role in gene regulation. RegulationSpotter can either analyse single variants or complete VCF files. Variants located within protein-coding transcripts are automatically assessed by MutationTaster as well as by RegulationSpotter to account for possible intragenic regulatory effects. RegulationSpotter offers the possibility of using phenotypic data to focus on known disease genes or genomic elements interacting with them. RegulationSpotter is freely available at https://www.regulationspotter.org.
Highlights
In the general search for disease mutations, Whole Genome Sequencing (WGS) is steadily gaining ground
In a novel approach to analysing regulatory variants, we focus on the human-readable presentation of the underlying biological data combined with an annotation-based score, thereby rendering RegulationSpotter usable to those clinicians and researchers who lack bioinformatics skills but who still strive to make sense of large sequencing data on their own
RegulationSpotter is aimed at clinicians and life scientists
Summary
In the general search for disease mutations, Whole Genome Sequencing (WGS) is steadily gaining ground. One major drawback of these programs is that they provide results in the form of scores instead of biologically meaningful annotations that are critical for our target audience, clinicians and life scientists This is inherently problematic since the expertise of the latter groups is indispensable for the determination of the molecular cause of inherited diseases [7,8]. A recent study by Shyr et al [9] concluded that the ‘successful adoption of a clinical WES/WGS system is heavily dependent on its ability to address the diverse requirements of specialists in distinct healthcare domains’. They propose software interfaces tailored to the needs of different professional groups.
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