CRISPR-FOCUS

CRISPR-FOCUS selects and prioritizes single-guide RNAs (sgRNAs) for CRISPR/Cas9 screening experiments to enable rational design of focused and high-throughput sgRNA libraries.

Key Features:

• Input identifiers: Accepts official gene symbols and RefSeq IDs as input for sgRNA selection.
• Comprehensive filtering and prioritization: Evaluates and ranks candidate sgRNAs using multiple criteria relevant to screening suitability.
• Efficiency: Prioritizes sgRNAs predicted to have high on-target activity.
• Specificity: Minimizes off-target effects by selecting sgRNAs with precise binding characteristics.
• Sequence Conservation: Prioritizes sgRNAs that target conserved genomic regions across species or cell types.
• Isoform Structure: Considers gene isoform structures to select sgRNAs that target relevant transcripts.
• Genomic Variations: Accounts for Single Nucleotide Polymorphisms (SNPs) and cancer somatic mutations that can affect sgRNA binding and efficacy.
• Controls and oligo components: Provides predefined positive and negative control sgRNAs and outputs U6 promoter sequences and CRISPR/Cas9 RNA scaffolds for direct oligonucleotide synthesis.
• High-throughput library design: Supports design of focused sgRNA libraries suitable for screening thousands of genes.

Scientific Applications:

• Focused CRISPR screens: Designs sgRNA libraries for focused screens targeting specific gene sets or pathways.
• High-throughput screening: Enables high-throughput screening experiments targeting thousands of genes.
• Genome-wide interrogation: Facilitates genome-wide interrogation of gene function through rational sgRNA selection.
• Cancer genomics: Improves targeting in cancer studies by accounting for somatic mutations during sgRNA selection.
• Validation controls: Provides positive and negative control sgRNAs for validating screening results.

Methodology:

Employs a comprehensive filtering and prioritization mechanism that evaluates sgRNAs based on efficiency, specificity, sequence conservation, isoform structure, and genomic variations (SNPs and cancer somatic mutations), and outputs predefined positive and negative control sgRNAs as well as U6 promoter sequences and CRISPR/Cas9 RNA scaffolds for oligonucleotide synthesis.