The HLA sgRNA Generator is a lightweight web application designed to help researchers, clinicians and students quickly identify viable target sequences for the CRISPR/Cas9 knockout of specified class-I HLA alleles.
This tool is designed specifically to retrieve target sequences for spCas9, restricted by the "NGG" protospacer adjacent motif. Up to six unique class-I alleles may be entered in the input fields using standard HLA allele nomenclature (e.g. A*01:01:01). Once allele names are entered, click "Look up accession". The application will autocomplete the HLA allele name to a four-field identity in order to fetch sequence data and return the corresponding accession details from the IPD-IMGT HLA Database. Users should ensure that the autocompleted allele matches their desired alleles to the best of their knowledge. Alleles without genomic and coding sequences abailable in the IPD-IMGT HLA database are not currently targetable using this app. Once allele accession information has been retrieved, select the boxes next to the desired target allele(s) and click "Submit selected results". Guide sequences are reported as "PAM-loss based" if the PAM is altered in all non-targeted HLA alleles entered. Guide sequences reported as "Mismatch based" have at least one potential off-target interaction site in a non-targeted HLA allele where the PAM is intact, but there is significant mismatch within the guide sequence. Reported guide sequences are not guaranteed to be efficacious, and must be tested to establish knockout efficiency.
This tool was developed by Connor Mattivi in the Jian Cao Lab at The Rutgers Cancer Institute. Please send suggestions or contributions to Connor Mattivi at clm350@rwjms.rutgers.edu.