PrimeDesign

PrimeDesign designs prime editing guide RNAs (pegRNAs) and nicking sgRNAs (ngRNAs) for prime editing (PE) to enable computational planning of precise genome edits.

Key Features:

• pegRNA and ngRNA design: Computationally generates designs for prime editing guide RNAs (pegRNAs) and nicking sgRNAs (ngRNAs).
• End-to-end experiment design: Produces complete designs accommodating single and combination edits for prime editing experiments.
• Genome-wide and saturation mutagenesis support: Supports design workflows for genome-wide studies and saturation mutagenesis screens.
• PrimeVar database construction: Constructs PrimeVar, a searchable database of pegRNA and ngRNA combinations.
• ClinVar pathogenic variant solutions: Provides solutions for installing or correcting over 68,500 pathogenic human genetic variants cataloged in ClinVar.

Scientific Applications:

• Prime editing experiment planning: Design and selection of pegRNAs and ngRNAs for targeted prime editing.
• Combinatorial editing studies: Planning of multi-edit or combination edit strategies using pegRNA/ngRNA pairs.
• Genome-wide screens: Design support for large-scale genome-wide prime editing experiments.
• Saturation mutagenesis screens: Design support for saturation mutagenesis using prime editing.
• Therapeutic variant correction: Designing edits to install or correct pathogenic human genetic variants from ClinVar.

Methodology:

Computational design of pegRNAs and nicking sgRNAs (ngRNAs) and construction of a searchable PrimeVar database of pegRNA/ngRNA combinations, including mappings to ClinVar pathogenic variants.