Photo Credit: Tetiana Lazunova

Ophthalmologist-led reanalysis of exome sequencing data, which utilized bioinformatics, improved the diagnostic yield in inherited retinal diseases.

Despite advances in next-generation sequencing (NGS), a significant proportion of inherited retinal disease (IRD) cases remain undiagnosed, primarily due to complex genetic variations undetectable by standard exome sequencing (ES).

A recent prospective study published in JAMA Network Open investigated the efficacy of ophthalmologist-led comprehensive ES reanalysis compared to conventional methods.

Initial genetic testing using ES achieved a diagnostic yield of 62.9%, according to the study results. Subsequent clinician-driven reanalysis, incorporating updated bioinformatic tools and a thorough clinical review, increased the diagnostic rate to 71.2%. This improvement was largely due to the identification of previously missed variants, including structural variations, mitochondrial mutations, and deep intronic variants. Notably, 28.6% of the detected variants were novel, and 65 different IRD-associated genes were implicated, with EYS, ABCA4, and USH2A being the most frequently affected.

The study highlighted the limitations of conventional ES, such as the exclusion of deep intronic regions and mitochondrial DNA. By extending the analysis beyond typical exonic boundaries and integrating targeted resequencing techniques, the researchers uncovered additional pathogenic variants. The reanalysis also leveraged newly discovered gene-disease associations and updated clinical information, demonstrating the dynamic nature of genetic diagnostics.

The findings underscore the importance of continuous data reanalysis in clinical settings to enhance diagnostic accuracy. The clinician’s role was pivotal, according to the researchers, as their comprehensive approach to bioinformatics, variant annotation, and genotype-phenotype correlation significantly contributed to the improved diagnostic yield. The study advocates for the integration of mitochondrial and mobile element insertion assessments in routine ES analysis and the avoidance of restrictive variant calling intervals to capture pathogenic variants effectively.

The success of this clinician-led reanalysis supports the broader application of similar methodologies in other cohorts, potentially improving diagnostic outcomes for a range of genetic disorders. Regular updates to gene sets and bioinformatic pipelines, combined with a thorough clinical evaluation, are crucial for maximizing the utility of genetic testing in IRDs.

“This comprehensive analysis included clinical data reevaluation, detection of structural variants, Sanger sequencing of low-complexity repetitive regions, and functional minigene splicing assays, the study authors concluded. “They all contributed to the increased diagnostic yield.”

“Therefore, before moving toward [genome sequencing], clinician-centered ES reanalysis with additional sequencing in the context of focused approach on phenotypically specified gene might be helpful to uncover hidden variants.”