Neonatal Encephalopathy: Novel Phenotypes and Genotypes Identified by Genome Sequencing.

Abstract

Background and objectives: Neonatal encephalopathy (NE) is characterized by an abnormal level of consciousness with or without seizures in the neonatal period. It affects 1-6/1,000 live term newborns. We applied genome sequencing (GS) in term newborns with NE to investigate the underlying genetic causes.

Methods: We enrolled term newborns according to inclusion/exclusion criteria during their Neonatal Intensive Care admission. We performed GS trio and applied bioinformatic tools. We developed pipelines for manual filters. We applied in silico prediction tools, protein 3D modeling, and functional characterization to assess the pathogenicity of variants.

Results: Seventeen newborns fulfilled inclusion criteria. We identified 12 variants in 10 genes. We classified 4 variants in PPP2R5D, BCOR, CFL2, and SCN2A (previously established disease genes) as pathogenic/likely pathogenic; 7 variants in DST (previously established disease gene), STAB2, CELF4, SORCS2, CTNND2, and ASTN1 (5 candidate genes) as variants of uncertain significance (VUS); and one variant in STAB2 as likely benign. The CELF4 and ASTN1 copy number variants (CNVs) resulted in structural changes in protein 3D models. The functional characterization of SORCS2 VUS revealed disruption of SorCS2 dimer formation and confirmed its pathogenicity. The functional characterization of STAB2 variants updated their characterization from VUS/likely benign to benign. The CTNND2 VUS resulted in a shift in 3D protein structure. We were not able to perform protein 3D modeling and functional characterization of two DST VUS. We are not certain whether CTNND2 and DST variants may be causative of NE in our study.

Discussion: The diagnostic rate of research GS was 41% in our prospective study. We broaden the phenotypic spectrum of PPP2R5D-associated Hogue-Janssens syndrome 1, CFL2-associated nemaline myopathy 7, and BCOR-associated oculo-facio-cardio-dental syndrome to include NE and/or neonatal seizures. We identified 3 candidate genes (SORCS2, CELF4, ASTN1) that may cause NE. We believe that protein 3D modeling is an important tool to assess the pathogenicity of CNVs and may advance the discoveries of novel genetic diseases. However, functional characterization of missense variants is essential for discoveries of novel genetic diseases. It seems that GS can help identify more candidate genes compared with ES.