Variability Among Next-Generation Sequencing Panels for Early-Life Epilepsies

Abstract

This study compares the potential diagnostic yield of commercially available epilepsy panels to detect the genetic findings identified in a recently published cohort of early-life epilepsy.

Epilepsy genetics is an emerging field with increasing therapeutic implications resulting from genetic findings.¹ Despite an overall enthusiasm for precision medicine in epilepsy and other disciplines, there remains no consensus on the approach to genetic testing.² A recent study by Berg et al³ demonstrated a relatively similar diagnostic yield of epilepsy next-generation sequencing (NGS) gene panels compared with whole-exome sequencing (27% vs 33%). Although the utility of NGS panels are consistently demonstrated,^3,4 to our knowledge, no study has systematically evaluated the variability in genes tested among clinically available NGS panels. We compared the potential diagnostic yield of commercially available NGS epilepsy panels to detect the genetic findings identified in a recently published cohort of early-life epilepsy.³

Methods

We compared 10 commercially available NGS gene panels across 3 major vendors: Athena Diagnostics, Ambry Genetics, and GeneDx. From each source, we evaluated early-life epilepsy panels (eg, infantile spasms, epileptic encephalopathy, and stat [rapid] panels) and comprehensive epilepsy panels as of January 24, 2018. We used the list of pathogenic genetic variants from the study by Berg et al³ to evaluate the theoretical yield for each panel. The Boston Children’s Hospital Institutional Review Board waived approval of this study as it did not involve human participants.

Results

Epilepsy NGS panels displayed a wide range in genes covered: 10 to 75 genes for early-life epilepsy panels and 87 to 234 genes for comprehensive epilepsy panels. Only the largest comprehensive epilepsy panel encompassed all genes on the smaller panels. All other panels had incomplete overlap in tested genes, including those with similar indications (eg, panels for infantile spasms).

We compared the anticipated detection rate for each panel with the genetic findings identified in the study by Berg et al.³ This analysis reports the yield each panel would have if it were executed today and assuming optimal technical conditions and coverage. Early-life epilepsy panels included 7% to 40% of genes reported in the cohort (Table).³ Early-life epilepsy panels would identify between 14% and 61% of the reported pathogenic variants in the cohort since some genes (eg, SCN1A [OMIM 182389], STXBP1 [OMIM 602926], and CDKL5 [OMIM 300203]) accounted for multiple patients. The comprehensive epilepsy panels included 40% to 65% of genes and 61% to 79% of the pathogenic variants in the cohort.

Table. Pathogenic Variants and Genes Identified in a Cohort of Known Early-Life Epilepsy Genes Across Next-Generation Sequencing Epilepsy Panels^a.

Characteristic	Early-Life Epilepsy Panels							Comprehensive Panels
	1	2b	3	4	5b	6	7	8	9	10
Genes on the panel, No.	10	16	16	17	22	67	75	87	100	234
Pathogenic variants, % total reported	24	45	14	29	47	47	61	61	62	79
Genes, % identified in cohort	7	21	12	19	23	35	40	40	40	65

^aVariability in the genes tested by each next-generation sequencing panel resulted in a fraction of the 70 pathogenic single-nucleotide variants or multinucleotide variants and 6 deletions or duplications in 43 genes reported by Berg et al.³

^bRapid and stat panels.

Discussion

Epilepsy genetics is an evolving field with an expanding number of causative genes. Next-generation sequencing panels have a high yield for genetically heterogeneous conditions, such as epilepsy.⁴ However, we found inconsistency in the genes offered on epilepsy panels, which translates to variability in the diagnostic yield. Only the largest comprehensive epilepsy panels had improved detection of genetic findings compared with the early-life epilepsy panels. The yield of a rapid 16-gene panel was almost equivalent to that of a 67-gene panel. Thus, for known epilepsy genes, a bigger panel is not inherently better.

In our analysis, the early-life epilepsy panels would have missed between 41% and 86% of the patients with pathogenic variants in confirmed epilepsy genes. Epilepsy NGS panels often do not include recently identified epilepsy genes or genes associated with a syndrome in which epilepsy is not a core feature. Coverage and detection of exon-level deletions or duplications can vary across panels. Our study underscores the importance of a clinician’s diagnostic suspicion to select the appropriate test for the appropriate patient. Despite the limitations, an appropriately chosen NGS panel remains an important step in the diagnostic workup for epilepsy.

This study highlights the variability across NGS panels and leads to the following recommendations for researchers, diagnostic laboratories, and clinicians. Research using NGS panels may not be generalizable, and future research should at least report the genes that were tested. Diagnostic laboratories should use published cohorts and current literature to continually update and evaluate their panels. Clinicians must understand that NGS panels are not created equally and may consider discussing test selection with a content expert in epilepsy genetics, such as a consultant in genetics, neurogenetics, or genetic counseling.