PINCER

PINCER optimizes CRISPR/Cas9 guide design for genome-wide functional screens to improve gene knockout efficacy and support drug target discovery.

Key Features:

• Enzymatic Efficiency Optimization: Optimizes Cas9 cleavage efficiency to enhance the likelihood of effective gene disruption.
• Conserved Protein Region Targeting: Prioritizes targeting conserved regions within proteins to increase the probability of functional knockout.
• Comprehensive Feature Database: Utilizes a feature database derived from a large reanalysis of CRISPR tiling data identifying predictive features including domains, coding sequence position, U6 termination sequences (TTT), restriction sites, polymorphisms, and specificity.
• Integrated Guide Design Algorithm: Combines enzymatic efficiency, conserved-region prioritization, and predictive genomic features into a unified algorithm for guide selection.

Scientific Applications:

• Genome-wide CRISPR/Cas9 screening (human and mouse): Applied to genome-wide screens in human and mouse genomes to improve guide selection and knockout sensitivity.
• Functional genomics and drug target discovery: Supports functional genomics studies and drug target discovery by increasing the rate of effective gene knockout.
• Benchmarking and validation of CRISPR libraries: Validated in head-to-head comparisons with alternative CRISPR libraries to demonstrate improved capability to disrupt gene function.

Methodology:

PINCER reanalyzes CRISPR tiling data to build an extensive feature database, identifies features predictive of guide activity (domains, coding sequence position, U6 termination sequences (TTT), restriction sites, polymorphisms, specificity), optimizes Cas9 cleavage efficiency metrics, prioritizes conserved protein regions, and integrates these criteria into a guide design algorithm.