Investigational Assay for Haplotype Phasing of the Huntingtin Gene
| Autor: | Daniel Dorset, Ramakrishna Boyanapalli, Kenneth Longo, Jeffrey M. Brown, Aaron J. Morris, Nripesh Prasad, Scott Yourstone, Shawn Levy, Chandra Vargeese, Nenad Svrzikapa, Jaya Goyal, Jason Powers |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
antisense oligonucleotide lcsh:QH426-470 mRNA Mutant Single-nucleotide polymorphism Biology Loss of heterozygosity 03 medical and health sciences 0302 clinical medicine Huntington's disease Genotype Genetics medicine Allele lcsh:QH573-671 Molecular Biology lcsh:Cytology Haplotype single-nucleotide polymorphism medicine.disease lcsh:Genetics 030104 developmental biology 030220 oncology & carcinogenesis long-read sequencing Molecular Medicine Original Article Trinucleotide repeat expansion Huntington’s disease |
| Zdroj: | Molecular Therapy. Methods & Clinical Development Molecular Therapy: Methods & Clinical Development, Vol 19, Iss, Pp 162-173 (2020) |
| ISSN: | 2329-0501 |
| Popis: | Novel treatments for Huntington’s disease (HD), a progressive neurodegenerative disorder, include selective targeting of the mutant allele of the huntingtin gene (mHTT) carrying the abnormally expanded disease-causing cytosine-adenine-guanine (CAG) repeat. WVE-120101 and WVE-120102 are investigational stereopure antisense oligonucleotides that enable selective suppression of mHTT by targeting single-nucleotide polymorphisms (SNPs) that are in haplotype phase with the CAG repeat expansion. Recently developed long-read sequencing technologies can capture CAG expansions and distant SNPs of interest and potentially facilitate haplotype-based identification of patients for clinical trials of oligonucleotide therapies. However, improved methods are needed to phase SNPs with CAG repeat expansions directly and reliably without need for familial genotype/haplotype data. Our haplotype phasing method uses single-molecule real-time sequencing and a custom algorithm to determine with confidence bases at SNPs on mutant alleles, even without familial data. Herein, we summarize this methodology and validate the approach using patient-derived samples with known phasing results. Comparison of experimentally measured CAG repeat lengths, heterozygosity, and phasing with previously determined results showed improved performance. Our methodology enables the haplotype phasing of SNPs of interest and the disease-causing, expanded CAG repeat of the huntingtin gene, enabling accurate identification of patients with HD eligible for allele-selective clinical studies. Graphical Abstract Svrzikapa et al. describe a method using single-molecule real-time long-read sequencing and a custom algorithm to determine bases at SNPs on mutant alleles. Accurate haplotype phasing of SNPs in relationship to the expanded CAG repeat of the huntingtin gene enables identification of patients with Huntington’s disease eligible for allele-selective clinical studies. |
| Databáze: | OpenAIRE |
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