How to Design High-Quality Gene Editing Tools for a Whole Genome

This patent describes a computer system and method for creating a comprehensive library of gene-editing guides (sgRNAs) by carefully designing and filtering them to be accurate and avoid unintended genetic changes.

What it covers

The patent details a system for building a "genome-wide sgRNA library," which are small RNA molecules used to guide gene-editing tools like CRISPR. The system has three main parts. First, an "input module" downloads genetic information, like DNA sequences and gene descriptions, from a database and picks specific gene regions (such as commonly deleted segments or CDS for protein-coding genes, per claim 2) to target. Second, an "sgRNA design module" creates many potential sgRNAs, checking them against the entire genome (claim 1). It looks for how well they match and assigns a risk score based on how likely they are to hit unintended spots (off-target sites), using rules like allowing 3 to 6 mismatches (claim 4). Finally, an "sgRNA filtering module" cleans up this list, removing problematic sgRNAs (like those with four or more consecutive identical bases, per claim 1) and ensuring the remaining ones are spread out evenly across the target genes (claim 1). For example, if a scientist wanted to study every gene in a human cell, this system could generate a precise set of sgRNAs, each designed to target a specific gene without accidentally editing other genes.

What it doesn't cover

• —Does not cover systems that design sgRNAs without evaluating off-target rates or grading them by risk (claim 1, 4).
• —Does not cover systems that do not filter sgRNAs based on consecutive base repeats, overlap, or even distribution on a CDS (claim 1).
• —Does not cover methods of constructing sgRNA libraries that do not use a 20 nucleotide guide sequence combined with a specific PAM sequence (NGG or GGN) (claim 1).
• —Does not cover systems that only target non-coding regions and do not extract CDS sequences for protein-encoding genes (claim 1, 2).
• —Does not cover the actual chemical synthesis or biological delivery of the sgRNA molecules themselves into a cell.

The clever bit

The patent's novelty lies in its systematic, multi-stage approach to designing and filtering sgRNAs, combining specific criteria for off-target evaluation (like penalty points for mismatch positions) and rigorous filtering (like ensuring even distribution and no overlaps) to produce a high-quality, genome-wide library. This integrated system aims to drastically reduce the number of ineffective or harmful sgRNAs.

Why it matters

This technology is crucial for advancing gene editing research, particularly with CRISPR-Cas9 systems. By creating highly accurate and specific sgRNA libraries, scientists can perform large-scale genetic screens to understand gene function, identify drug targets, and develop gene therapies more efficiently. High-quality sgRNA design minimizes unintended edits, which is vital for both research validity and therapeutic safety.

Real-world examples

• 1.CRISPR screening platforms
• 2.Academic gene function studies
• 3.Drug discovery pipelines using genetic screens
• 4.Biotechnology companies developing gene therapies