Unravelling the Complexity of Inherited Retinal Dystrophies Molecular Testing: Added Value of Targeted Next-Generation Sequencing

Abstract

To assess the clinical utility of targeted Next-Generation Sequencing (NGS) for the diagnosis of Inherited Retinal Dystrophies (IRDs), a total of 109 subjects were enrolled in the study, including 88 IRD affected probands and 21 healthy relatives. Clinical diagnoses included Retinitis Pigmentosa (RP), Leber Congenital Amaurosis (LCA), Stargardt Disease (STGD), Best Macular Dystrophy (BMD), Usher Syndrome (USH), and other IRDs with undefined clinical diagnosis. Participants underwent a complete ophthalmologic examination followed by genetic counseling. A custom AmpliSeq™ panel of 72 IRD-related genes was designed for the analysis and tested using Ion semiconductor Next-Generation Sequencing (NGS). Potential disease-causing mutations were identified in 59.1% of probands, comprising mutations in 16 genes. The highest diagnostic yields were achieved for BMD, LCA, USH, and STGD patients, whereas RP confirmed its high genetic heterogeneity. Causative mutations were identified in 17.6% of probands with undefined diagnosis. Revision of the initial diagnosis was performed for 9.6% of genetically diagnosed patients. This study demonstrates that NGS represents a comprehensive cost-effective approach for IRDs molecular diagnosis. The identification of the genetic alterations underlying the phenotype enabled the clinicians to achieve a more accurate diagnosis. The results emphasize the importance of molecular diagnosis coupled with clinic information to unravel the extensive phenotypic heterogeneity of these diseases.

The genetic profile of Leber congenital amaurosis in an Australian cohort

“…The 90% resolution achieved in this study is comparable to recent studies for LCA using targeted NGS panels (80%; Bernardis et al. ) or whole exome/genome sequencing (89%; it is acknowledged that this study was enriched for intractable cases; Carss et al. ).…”

“…The 90% resolution achieved in this study is comparable to recent studies for LCA using targeted NGS panels (80%; Bernardis et al 2016) or whole exome/genome sequencing (89%; it is acknowledged that this study was enriched for intractable cases; Carss et al 2017). This is attributable to the progression from hypothesis (LCA panel) to nonhypothesis (RD Panel) testing (refer Table S1B), which provided an alternative molecular diagnosis in 19% (6/31) pedigrees.…”

Extensive genic and allelic heterogeneity underlying inherited retinal dystrophies in Mexican patients molecularly analyzed by next‐generation sequencing

“…As NGS costs continue to decrease, it is anticipated that its application in clinical settings will be substantially expanded. NGS has been recently applied for the recognition of pathogenic variants in cohorts of RDs patients from different ethnicities, with rates of molecularly solved cases ranging from 50% to 75% (Bernardis et al, ; Birtel et al, ; Boulanger‐Scemama et al, ; Bravo‐Gil et al, ; Di Iorio et al, ; Ge et al, ; Patel et al, ; Riera et al, ; Wang et al, ; Zhao et al, ). Differences in rates of NGS‐solved cases are presumably due to several aspects such as the inclusion of sporadic versus familial cases, the type of NGS approach (gene panels vs. exome or genome sequencing), and features inherent to the particular mutational profile of a RD population (frequency of consanguineous marriages or occurrence of founder mutation effects).…”

Prevalence of mutations in inherited retinal diseases: A comparison between the United States and India

“…Studies have shown that NGS of gene panels leads to higher detection of a genetic cause for retinal disease than traditional methods such as Sanger sequencing; however, these studies often have features that do not reflect clinical practice and may prevent extrapolation of reported diagnostic rates to clinical practice. Some studies recruited patients and often their families, while others heavily weighed in silico predictions for classifying missense variants as pathogenic and only one of these studies took into account American College of Medical Genetics and Genomics (ACMG) criteria for classifying variants, which puts low value on in silico predictions (Audo et al, ; Bernardis et al, ; Carss et al, ; de Castro‐Miro et al, ; Glockle et al, ; O'Sullivan et al, ; Riera et al, ). Some studies investigated only subsets of patients or patients with well‐defined phenotypes (Audo et al, ; Licastro et al, ; O'Sullivan et al, ).…”