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Haplotyping SNPs for allele-specific gene editing of the expanded huntingtin allele using long-read sequencing.
- Source :
-
HGG advances [HGG Adv] 2022 Sep 26; Vol. 4 (1), pp. 100146. Date of Electronic Publication: 2022 Sep 26 (Print Publication: 2023). - Publication Year :
- 2022
-
Abstract
- Huntington's disease (HD) is an autosomal dominant neurodegenerative disease caused by CAG trinucleotide repeat expansions in exon-1 of huntingtin ( HTT ). Currently, there is no cure for HD, and the clinical care of individuals with HD is focused on symptom management. Previously, we showed allele-specific deletion of the expanded HTT allele ( mHTT) using CRISPR-Cas9 by targeting nearby (<10 kb) SNPs that created or eliminated a protospacer adjacent motif (PAM) near exon-1. Here, we comprehensively analyzed all potential PAM sites within a 10.4-kb genomic region flanking exon-1 of HTT in 983 individuals with HD using a multiplex targeted long-read sequencing approach on the Oxford Nanopore platform. We developed computational tools (NanoBinner and NanoRepeat) to de-multiplex the data, detect repeats, and phase the reads on the expanded or the wild-type HTT allele. One SNP common to 30% of individuals with HD of European ancestry emerged through this analysis, which was confirmed as a strong candidate for allele-specific deletion of the mHTT in human HD cell lines. In addition, up to 57% HD individuals may be candidates for allele-specific editing through combinatorial SNP targeting. Cumulatively, we provide a haplotype map of the region surrounding exon-1 of HTT in individuals affected with HD. Our workflow can be applied to other repeat expansion diseases to facilitate the design of guide RNAs for allele-specific gene editing.<br />Competing Interests: P.G.-A. is currently employed by Spark Therapeutics.<br /> (© 2022 The Author(s).)
Details
- Language :
- English
- ISSN :
- 2666-2477
- Volume :
- 4
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- HGG advances
- Publication Type :
- Academic Journal
- Accession number :
- 36262216
- Full Text :
- https://doi.org/10.1016/j.xhgg.2022.100146