Possible precision medicine implications from genetic testing using combined detection of sequence and intragenic copy number variants in a large cohort with childhood epilepsy

Abstract

Objective: Molecular genetic etiologies in epilepsy have become better understood in recent years, creating important opportunities for precision medicine. Building on these advances, detailed studies of the complexities and outcomes of genetic testing for epilepsy can provide useful insights that inform and refine diagnostic approaches and illuminate the potential for precision medicine in epilepsy.

Methods: We used a multi-gene next-generation sequencing (NGS) panel with simultaneous sequence and exonic copy number variant detection to investigate up to 183 epilepsy-related genes in 9769 individuals. Clinical variant interpretation was performed using a semi-quantitative scoring system based on existing professional practice guidelines.

Results: Molecular genetic testing provided a diagnosis in 14.9%-24.4% of individuals with epilepsy, depending on the NGS panel used. More than half of these diagnoses were in children younger than 5 years. Notably, the testing had possible precision medicine implications in 33% of individuals who received definitive diagnostic results. Only 30 genes provided 80% of molecular diagnoses. While most clinically significant findings were single-nucleotide variants, ~15% were other types that are often challenging to detect with traditional methods. In addition to clinically significant variants, there were many others that initially had uncertain significance; reclassification of 1612 such variants with parental testing or other evidence contributed to 18.5% of diagnostic results overall and 6.1% of results with precision medicine implications.

Significance: Using an NGS gene panel with key high-yield genes and robust analytic sensitivity as a first-tier test early in the diagnostic process, especially for children younger than 5 years, can possibly enable precision medicine approaches in a significant number of individuals with epilepsy.

Keywords: clinical management; copy number variant; diagnostic genetic testing; next‐generation sequencing panel; precision medicine; variant of uncertain significance.

Figure 1

Distribution of positive molecular diagnoses (PosMDs) in a large unselected clinical cohort with epilepsy. Panel A shows a high diagnostic yield exceeding 20% in NGS panels for the Rett/Angelman spectrum of syndromic epilepsies and early infantile epileptic encephalopathies (EIEE), while the comprehensive panel showed a 14.9% yield. These represent consolidated figures derived from data from different versions of each panel. Nearly half of the solid evidence genes (see Methods) in the current panel were discovered only within the last 5‐10 years and together contributed a significant rate of PosMDs. These newer genes contributed as much as 7% alone (PRRT2) and more than 20% together to the overall diagnostic yield. Panel B shows that the diagnostic yield tends to be higher when epilepsy is accompanied by comorbidities such as intellectual impairment (ID), autism, or developmental delay (DD; P < 0.001, chi‐squared). Error bars represent 95% confidence intervals using the Wilson method. Panel C shows the number of PosMDs by individual genes on the NGS panel. Only eight genes accounted for 50% of all PosMDs, while another 22 genes raised this yield to 80%. The remaining 20% of PosMDs were spread across 76 genes. Seventy‐eight genes had no PosMDs, and 48 genes produced no LP/P at all. Genes with precision medicine implications are shown in blue

Figure 2

Positive molecular diagnoses (PosMDs) with possible precision medicine implications (PMIs) in epilepsy. Panel A shows the percentage of PosMDs related to various categories of precision medicine in epilepsy. Half of the PosMDs with possible PMI pointed to contraindications for certain anti‐epileptic drugs (AEDs). Approximately 10% of PosMDs with PMI were consistent with biochemical disorders that have established treatment options. Panel B shows the number of PosMDs with PMIs in genes in three overlapping categories of epilepsy disorders: early infantile epileptic encephalopathy (EIEE), Rett/Angelman spectrum of syndromic neurodevelopmental epilepsies, and a third group of all other forms of epilepsy. Panel C shows the positive diagnostic yield in various age groups separated by infancy (age <1 year), early childhood (age 1‐4 years), later childhood (age 5‐17 years), and adulthood (age ≥18 years). Colors indicate the proportion of individuals who received a PosMD with possible PMIs or those with emerging evidence of PMIs. A third group of PosMDs without PMIs is also shown at the top of each column

Figure 3

Distribution of clinically reportable variants. Panel A shows that variants identified in the 183 genes on the NGS panel were distributed in a range of one to 12 per individual. Panel B summarizes the proportion of individuals who received a negative report, a report describing a positive molecular diagnosis (PosMD), or an inconclusive report with a variant of uncertain significance or a single likely pathogenic/pathogenic variant, or both, that did not contribute to a PosMD. Panel C shows the wide range of variant types identified and the clinical classifications of each type. A significant number of clinically reportable variants that are technically challenging to identify with traditional methods were identified in this cohort. Panel D illustrates the distribution of variants of uncertain significance (VUS) identified in this study. The genes on the panel showed a 100‐fold range (0.02%‐9%) in the fraction of individuals who had at least one VUS in those genes. The VUS frequency was lower in the 57 genes associated with early‐onset and highly penetrant epilepsies compared with that in the remaining 103 solid evidence genes on the panel (P = 0.002, Wilcoxon rank sum). AD, autosomal dominant; AR, autosomal recessive; LP, likely pathogenic; P, pathogenic; PE, preliminary evidence; RP, reduced penetrance; var, variant; VUS, variant of uncertain significance