Epileptic encephalopathy (EE) is an umbrella-term for a class of severe epilepsies characterized by debilitating seizures. Epileptic activity often begins in early adolescence, contributing to developmental, cognitive, and behavioral abnormalities. Identification of genetic mutations in EE-patients has implicated >50 genes, with clinical diagnostic labs reporting a molecular diagnosis in 24-40% of cases. Current EE gene discovery focuses primarily on identifying de novo mutations in genomic coding regions, which alter the amino acid sequence of the resulting protein, disrupting the protein’s function and leading to neural abnormalities. A de novo mutation is not inherited from either unaffected parent; it first occurs in an affected individual, suggesting a genetic cause for the phenotype. My research focuses on identifying novel noncoding mutations in a cohort of 167 patients with EE of unknown cause. The proportion of rare diseases caused by noncoding mutations is unknown and relatively few examples of functional noncoding causative mutations exist. My goal is to identify de novo variants in intronic and untranslated genomic regions, and also to identify synonymous variants in which the resulting amino acid is unaltered. Initially, the 167-patient cohort was screened for variants in 44 established EE genes using targeted next-generation DNA sequencing. I have filtered this data for high-quality noncoding variants, which are unreported in a healthy population. I am currently screening patients’ parents for these noncoding variants to determine the mode of inheritance. Confirmed de novo variants will be followed-up with functional studies to test their molecular consequences (via mRNA, splicing, gene expression). Determining genetic causes of EE unveils molecular mechanisms behind phenotypes, allowing for precise diagnoses, and leading to treatment of severe epilepsies based on their causes. I hope to identify causative noncoding variants in epilepsy genes to expand epigenetic analysis of EE, and contribute to a better understanding of EE genotype-phenotype relationship.

Epileptic encephalopathies (EE) are severe forms of childhood epilepsies. Recent studies have shown that some cases of pediatric EE are caused by copy number variants (CNV), which are chromosomal deletions, duplications, or insertions of DNA. CNVs may contain genes that are important for neural health, causing disease when there is a copy number change. I am investigating rare CNVs in EE patients where the genetic cause is not known. I will screen EE patients for CNVs using a technique called array comparative genomic hybridization (aCGH) to identify rare CNVs that may be disease-causing. If a CNV is found, I will conduct aCGH on parents to determine if the CNV is de novo (arising for the first time in that individual and not inherited from either parent). We also expect that in cases with multiple affected family members, patients may inherit rare mutations from an affected parent. Preliminary results show that out of 69 patients screened thus far, 15 rare CNVs that range in size and number of genes affected have been identified in 13 patients. Of these, 3 de novo CNVs were identified that include a single exon deletion of the gene SLC2A1, a partial deletion of the gene NRXN1, and a 2.4 mb deletion in chromosomal region 7q11.23, affecting 40 genes. In addition, 2 patients each have a 1.4-1.5 mb deletion encompassing the region 16p13.11, which has been reported to be associated with epilepsy and developmental delay. Parental and segregation testing is ongoing for many patients. Rare CNVs can highlight genes implicated for proper neural function and development. This will help advance our understanding of the pathology and genetic basis of epilepsy. Furthermore, identification of particular pathogenic genes will be useful in the clinical setting for genetic counseling of affected patients and families.