This repo contains the code used to calculate patient population coverage with haplotype editing as compared to mutation-targeted editing. It focuses on the NEFL window for CRISPR excision.
1000 genomes phase 3 2019 release, which can be found here.
NEFL_het_combos.ipynb - Jupyter notebook that runs a greedy algorithm to select pairs of single nucleotide polymorphisms (SNPs) surrounding the NEFL gene that target the highest number of individuals in the Thousand Genomes database. This script also runs a greedy algorithm to select optimal SNPs to be paired with a single biallelic guide RNA that is held constant. Here, an optimal SNP or optimal SNP pair denotes SNPs that target the most individuals.
When using or referring to this code, please cite the following bioRxiv paper: Dua, P. H., Simon, B. M., Marley, C. B., Feliciano, C. M., Watry, H. L., Steury, D., ... & Judge, L. M. (2024). Haplotype editing with CRISPR/Cas9 as a therapeutic approach for dominant-negative missense mutations in NEFL. bioRxiv, 2024-12. The code is most relevant to Figure 6 in the preprint.