The Impact of Panel Size in Next Generation Sequencing in Pediatric Epilepsy

Introduction: Next-generation sequencing (NGS) is a helpful tool to identify monogenic epilepsy syndromes and thus significantly influences therapeutic approaches. However, the numbers of genes tested in such panels varies greatly. In Germany panels up to 25kb of length are tested frequently – as German public health insurers cover the costs of panels up to this size – but there are also tests of much larger panels carried out in certain cases. At present there is no evidence if and under which circumstances tests of larger panels are superior.

Methods: This retrospective cohort study investigated data of 190 patients of 18 years and younger (102 female and 88 male) that have undergone NGS diagnostic from October 2013 to April 2018. The distribution of variants of uncertain significance (VUS), pathogenic, likely pathogenic, likely benign and benign mutations was analysed across different subsets of panels. The yield of small panels (less than 10 genes) and large panels (over 60 genes) was compared using the Fisher’s exact test. The patient’s clinic was considered by differentiating between panels for patients with severe early onset epilepsy encephalopathies (EOEE) and patients with more benign forms of early-onset epilepsies (non-EOEE).

Results: Overall the diagnostic yield of large panels was significantly increased (25% vs. 13%, p = 0,01). By differentiating between non-EOEE and EOEE panels the increased yield of large panels was highly significant in non-EOEE patients (p = 0,0004). However, there was no significant difference between small and large panels in EOEE patients. In contrast, the proportion of genetic mutations of uncertain significance (VUS) was more than 10-times higher in large panels (p = 0,0001).

Discussion: This study indicates that large panels are superior for patients with early-onset epilepsy forms without encephalopathy (non-EOEE). For patients with EOEE small panels of a maximum of 10 genes seem to show similar yields compared with larger panels. It was also shown that the portion of VUS increases with rising panel sizes.

Conclusion: When deciding on NGS panel sizes the clinic and suspected diagnosis of a patient should be considered.