RegulationSpotter

RegulationSpotter annotates and interprets extratranscriptic DNA variants identified by Whole Genome Sequencing (WGS) to assess their regulatory potential.

Key Features:

• Extragenic variant annotation: Annotates extratranscriptic DNA variants (outside protein-coding regions) with over 100 genome-wide regulatory features.
• Regulatory potential scoring: Calculates a score reflecting the regulatory potential of each variant region and assigns dichotomous classifications 'functional' or 'non-functional'.
• Evidence presentation: Provides a human-readable presentation of the underlying evidence supporting score and classification.
• Input formats: Processes single variants and complete Variant Call Format (VCF) files.
• MutationTaster integration: Integrates MutationTaster assessments for variants within protein-coding transcripts to consider potential intragenic regulatory effects.
• Phenotype-based prioritization: Incorporates phenotypic data to focus on known disease genes and genomic elements that interact with them.

Scientific Applications:

• Non-coding variant impact assessment: Evaluates potential regulatory effects of non-coding variants identified by WGS for clinical and research interpretation.
• Variant prioritization in disease studies: Prioritizes candidate regulatory variants in known disease genes using integrated phenotypic data.
• Intragenic regulatory evaluation: Assesses potential intragenic regulatory effects by combining MutationTaster results with regulatory annotations.
• Evidence-supported interpretation: Generates evidence summaries to support biological interpretation of variant regulatory function.

Methodology:

Annotates variants with over 100 genome-wide regulatory features; computes a regulatory potential score with dichotomous 'functional'/'non-functional' classification and human-readable evidence; accepts single variants and VCF files; integrates MutationTaster for variants in protein-coding transcripts; incorporates phenotypic data to prioritize known disease genes and interacting genomic elements.