CrisPam: SNP-derived PAM analysis web tool and human pathogenic SNPs database for CRISPR allele-specific targeting

Background: CRISPR is a promising novel technology for treating genetic conditions. Therefore, it is essential to further develop and promote treatment’s safety and specificity. While the guide-RNA offers position-specific DNA targeting, it may tolerate small changes such as single-nucleotide polymorphisms (SNPs). To that end, an allele-specific targeting approach is in need for future treatments of heterozygous patients, suffering from genetic conditions caused by a SNP. The SNP-derived PAM approach allows highly allele-specific DNA cleavage by incorporating a protospacer adjacent motif (PAM) sequence only at the target allele. Description Here we present CrisPam, a tool that detects SNP-derived PAMs for allele-specific targeting by the CRISPR/Cas system. The algorithm scans the generation of each reported PAM for a given DNA sequence and its variations. A successful result is such that at least one PAM is generated by a SNP. Thus, the PAM shall be part of the variant allele only and the Cas protein will therefore be able to exclusively bind the variant allele for gene-editing, while the wildtype allele remains unchanged. Conclusion CrisPam is available online for researchers and also offers access to the CrisPamDB, a database that contains the CrisPam analysis for any reported pathogenic SNP in humans.