The role of recessive inheritance in early-onset epileptic encephalopathies: a combined whole-exome sequencing and copy number study

Abstract

Early-onset epileptic encephalopathy (EE) and combined developmental and epileptic encephalopathies (DEE) are clinically and genetically heterogeneous severely devastating conditions. Recent studies emphasized de novo variants as major underlying cause suggesting a generally low-recurrence risk. In order to better understand the full genetic landscape of EE and DEE, we performed high-resolution chromosomal microarray analysis in combination with whole-exome sequencing in 63 deeply phenotyped independent patients. After bioinformatic filtering for rare variants, diagnostic yield was improved for recessive disorders by manual data curation as well as molecular modeling of missense variants and untargeted plasma-metabolomics in selected patients. In total, we yielded a diagnosis in ∼42% of cases with causative copy number variants in 6 patients (∼10%) and causative sequence variants in 16 established disease genes in 20 patients (∼32%), including compound heterozygosity for causative sequence and copy number variants in one patient. In total, 38% of diagnosed cases were caused by recessive genes, of which two cases escaped automatic calling due to one allele occurring de novo. Notably, we found the recessive gene SPATA5 causative in as much as 3% of our cohort, indicating that it may have been underdiagnosed in previous studies. We further support candidacy for neurodevelopmental disorders of four previously described genes (PIK3AP1, GTF3C3, UFC1, and WRAP53), three of which also followed a recessive inheritance pattern. Our results therefore confirm the importance of de novo causative gene variants in EE/DEE, but additionally illustrate the major role of mostly compound heterozygous or hemizygous recessive inheritance and consequently high-recurrence risk.

Fig. 1

Summary of genetic findings. a Percentage of patients with ≥ 1 de novo or inherited rare copy number variants and their respective classification of clinical relevance. b Total numbers, and medians, minimum and maximum numbers per patients of variants following the respective modes of inheritance identified by whole-exome sequencing in 51 child–parent trios. c Percentage of patients with (likely) disease-associated CNV or SV findings in established EE genes or with potentially disease-causing candidate genes. d Distribution of inheritance modes in diagnosed patients with (likely) EE-associated CNV or SV in established disease genes. e Results of (re-) classification of 56 secondary findings from whole-exome sequencing, of which 16% represented carriership of single alleles of recessive disorders and 12% indicated mainly dominant disease alleles as secondary findings. CNV copy number variant, SV sequence variant, VOUS  variants of unknown clinical significance, XL dom. X-linked dominant, XL rec. inh. X-linked recessive inherited

Fig. 2

Disease causing biallelic SPATA5 variants in two independent families demonstrating the value of hypothesis driven manual data analysis (variant nomenclature and exon numbering according to NM_145207.2 and NG_051570.1, respectively). a, b Pedigree of patient 73068 (a) summarizing the segregation of the maternally inherited variant p.(Met1?) and the de novo variant p.(Pro797Ala) on the paternal allele; (b) Whole-exome sequencing data of exon 15 in the patient demonstrating the localization of both, the de novo variant c.2389 C > G (p.(Pro797Ala)) and the paternally inherited single nucleotide polymorphism (SNP) rs35206443 (c.2485 G > T, p.(Asp829Tyr)) on the same allele. c-e Pedigree of patient 47651 illustrating the compound heterozygous constellation of the maternally inherited, heterozygous 51 kb deletion comprising exon 12 and 13 (c.2080_2213del; p.(Gly694Phefs*23)) detected by high-resolution chromosomal microarray analysis (d), and the paternally inherited disease-associated sequence variant c.989_991del (p.(Thr330del)) detected by whole-exome sequencing (e)