Long-read Sequencing in Inherited Retinal Dystrophies: A Systematic Review

Inherited retinal dystrophies (IRDs) encompass a group of phenotypically and genetically heterogeneous disorders leading to progressive visual impairment. The advent of next-generation sequencing (NGS) has substantially improved genetic diagnosis rates; however, approximately 30% of IRD cases remain genetically unsolved ("missing heritability"). Long-read sequencing (LRS) has emerged as a complementary approach for identifying complex, inaccessible variants, including structural and deep intronic variants. This study systematically reviews the application of LRS in IRD genetics with descriptive synthesis.

Inherited retinal dystrophies collectively affect approximately 1 in 3000 individuals and are a leading cause of inherited blindness worldwide. Accurate molecular diagnosis informs prognosis, genetic counseling, and eligibility for emerging gene therapies. While NGS represents the current standard diagnosis, its inability to capture certain variant types limits its diagnostic sensitivity. Integrating LRS could bridge this diagnostic gap and enhance personalized management.

A systematic search on PubMed (September 1, 2025) identified 26 studies investigating the use of LRS in patients with IRD (published between 2018 and September 1, 2025). Studies were eligible if they applied LRS for the genetic diagnosis of IRDs in humans, were available in full-text English, and reported IRD variants. Data extraction and synthesis followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Methodological quality was assessed using Murad's tool for case reports and case series, the Joanna Briggs Institute Checklist for Case Series, and the Quality Assessment of Diagnostic Accuracy Studies-2 tool. The review was registered prospectively on the International Prospective Register of Systematic Reviews (identifier, CRD42024602173).

Our analysis identified 88 IRD variants described by LRS. Of these, 31% were structural, 31% single nucleotide, 19% splice site, 11% insertions/deletions, and 8% deep intronic. Long-read sequencing expanded the IRD genetic landscape by identifying or refining pathogenic variants in 34 genes across 81 patients. Studies also validated LRS for phasing and resolving technically challenging regions.

Long-read sequencing overcomes key limitations of short-read sequencing in the genetic diagnosis of IRDs. Although existing studies show high analytical rigor and increased diagnostic yield, most lack formal diagnostic accuracy metrics. Current evidence supports the potential incorporation of LRS into clinical workflows, with further prospective studies needed to define diagnostic accuracy, clinical utility, and implementation standards.

The authors have no proprietary or commercial interest in any materials discussed in this article.