Year: 2024
Type: article
Abstract: Introduction Long-read sequencing (LRS) enables accurate structural variant detection and variant phasing. When a molecular diagnosis is suspected, target enrichment can reduce the cost and duration of sequencing. Methods LRS was conducted in five inherited retinal dystrophy (IRD) patients harboring a monoallelic variant in RPE65 that remained uncharacterized after clinical exome sequencing (CES). CRISPR-Cas9 guide RNA probes were designed to target a 31 kb region, including the entire RPE65 locus. The DNA was sequenced on a MinION platform. Short-read ×30 whole-genome sequencing (WGS) was performed for five patients to validate nanopore results. Results The nanopore sequencing process yielded a median of 271 reads within the targeted region, with a mean depth of 109 and a median read size of 8 kb. All variants identified by CES have been detected using this approach, and no additional RPE65 gene causative variants were found. Nanopore variant detection demonstrated performance akin to short-read WGS at similar coverage levels, although exhibiting increased false positive calls at lower coverage. Discussion In this study, we explore the advantages of using a targeted approach together with long-read sequencing to identify variants associated with IRD. The results underscore the utility of targeted long reads for characterizing patients affected by rare diseases when first-tier diagnostic tests are non-conclusive.
Source: Frontiers in Genetics
Authors: Cristina Rodilla, Gonzalo Núñez-Moreno, Yolanda Benitez, Raquel Romero, Lidia Fernández-Caballero, Pablo Mínguez, Marta Corton, Carmen Ayuso
Language: English
Topic: Genomics and Rare Diseases
Subfield: Genetics
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,295
Awards: Estudio de patologías del desarrollo ocular mediante integración de datos multi-ómicos y modelización experimental para mejorar el diagnóstico genético y desarrollar nuevos abordajes terapéuticos, Las Distrofias de Retina: una aproximación genómica, celular, funcional y bioinformática, para acelerar su diagnóstico y tratamiento, y medir su impacto, Un estudio exhaustivo de las distrofias de retina hereditarias: mejora del diagnóstico molecular, enfoques terapéuticos, ensayos clínicos y medida del impacto en los pacientes
OpenAlex ID: W4403405288