Prioritizing variants of uncertain significance for reclassification using a rule-based algorithm in inherited retinal dystrophies

Abstract

Inherited retinal dystrophies (IRD) are a highly heterogeneous group of rare diseases with a molecular diagnostic rate of >50%. Reclassification of variants of uncertain significance (VUS) poses a challenge for IRD diagnosis. We collected 668 IRD cases analyzed by our geneticists using two different clinical exome-sequencing tests. We identified 114 unsolved cases pending reclassification of 125 VUS and studied their genomic, functional, and laboratory-specific features, comparing them to pathogenic and likely pathogenic variants from the same cohort (N = 390). While the clinical exome used did not show differences in diagnostic rate, the more IRD-experienced geneticist reported more VUS (p = 4.07e-04). Significantly fewer VUS were reported in recessive cases (p = 2.14e-04) compared to other inheritance patterns, and of all the genes analyzed, ABCA4 and IMPG2 had the lowest and highest VUS frequencies, respectively (p = 3.89e-04, p = 6.93e-03). Moreover, few frameshift and stop-gain variants were found to be informed VUS (p = 6.73e-08 and p = 2.93e-06). Last, we applied five pathogenicity predictors and found there is a significant proof of deleteriousness when all score for pathogenicity in missense variants. Altogether, these results provided input for a set of rules that correctly reclassified ~70% of VUS as pathogenic in validation datasets. Disease- and setting-specific features influence VUS reporting. Comparison with pathogenic and likely pathogenic variants can prioritize VUS more likely to be reclassified as causal.

Inherited Retinal Diseases Due to RPE65 Variants: From Genetic Diagnostic Management to Therapy

“…Philp and colleagues have developed and validated an algorithm termed "estimate of pathogenic probability" (EPP) that predicts the pathogenicity of VUS based on its prevalence, segregation and predicted effects on protein structure [63]. In addition, Iancu and colleagues have recently developed a strategy for the reclassification of VUS that considers five pathogenicity predictors, resulting in an algorithm able to correctly reclassify approximately 70% of VUS as pathogenic in validation datasets [64]. The ACMG algorithm has been updated to incorporate new evidence.…”

Aggregated genomic data as cohort-specific allelic frequencies can boost variants and genes prioritization in non-solved cases of inherited retinal dystrophies

“…Up to 10 non-solved cases gained new insights due to the reevaluation of our prioritized variants. Our variant prioritization approach was also applied for VUS reclassification, a major challenge to unlock the diagnosis of rare pathologies [10,[55][56][57]. Indeed, in our IRD subcohort, top 5 genes with more deleterious variants in IRD solved cases, present a higher degree of uncertainty in variant annotation (proportion of VUS and deleterious variants) in unsolved IRD cases.…”

“…Variants are classified using ACMG guides. In the IRD subcohort, there were reported 100 VUS fulfilling these criteria [10] (Additional file 1:Table S7). Of these, 63 fulfilled criteria to be within the database generated in this work, and were still classified as VUS according to ACMG (information taken from VarSome at the time of the analysis).…”

New Developments and Possibilities in Reanalysis and Reinterpretation of Whole Exome Sequencing Datasets for Unsolved Rare Diseases Using Machine Learning Approaches

“…A recent study using a rules-based algorithmic approach showed that 125 VUS were reclassified in 114 unsolved rare inherited retinal dystrophy patients which helped in the diagnosis of the disease. It was shown using validation datasets that ~70% of VUS in these patients were reclassified as pathogenic [ 49 ].…”