Beyond the exome: exploring disease mechanisms in early onset epilepsy

Background:
Epilepsy affects 1 in 26 individuals over the course of the lifetime and is the most common neurological disorder of childhood worldwide. In the past decade, the genomic revolution has led to an explosion in genetic discovery for this patient group, with disease-associated variants now identified in more than 50% of the epilepsy patients we see at Great Ormond Street Hospital. For many of our patients, genetic diagnosis informs prognosis and genetic counselling, leads to the opportunity to participate in natural history studies, and even to changes in treatment that may change outcomes in seizures and in neurodevelopment.

The Gene-STEPS study will implement rapid genetic diagnosis with tailored management in children with seizure onset under 12 months of age and use trio whole genome sequencing to explore the genetic landscape of early onset epilepsy. In this PhD project, we plan to use cutting edge bioinformatic techniques to analyse genomic data from the Gene-STEPS study. In patients without a diagnosis on primary analysis, who are likely to represent 50-70% of the cohort, we will assess for non-coding variants and structural variants. In those patients who remain unsolved, we will use long-read sequencing to interrogate the genome for large structural variants and nucleotide repeat expansions.

Aims/Objectives:
Objective 1: Use rapid trio whole genome sequencing to identify novel genetic causes of early onset epilepsy and undertake functional analysis of variant impact.
Objective 2: Use innovative bioinformatic approaches to assess non-coding variants.
Objective 3: Use long-read sequencing in WGS negative patients to identify structural variants.

Methods:
Methods will include variant analysis with Ingenuity and Alamut. Long-range sequencing will be undertaken using Nanopore technology. Wet lab techniques will include sequencing, quantitative PCR and Western blotting.

Ethics Approval:
Application has been submitted and had initial REC review, awaiting final decision.

Collaboration with University of Toronto:
This will be a 6 month placement in the Costain lab within the Molecular Genetics department of the University of Toronto. The research program is focused on understanding the causes and consequences of rare variation in the human genome. The Costain lab uses genome sequencing to discover new disease genes and genotype-phenotype associations, in a setting of an undiagnosed paediatric disease program. Dr Costain’s group is within The Centre for Applied Genomics which will provide support to the student during the placement.

References:
1. Symonds JD et al. Incidence and phenotypes of childhood-onset genetic epilepsies: A prospective population-based national cohort. Brain. 2019;142(8):2303–18.
2. McTague A, et al. The genetic landscape of the epileptic encephalopathies of infancy and childhood. Lancet Neurol. 2015;15(3):304-16
3. Palmer EE, Sachdev R, Macintosh R, et al. Diagnostic Yield of Whole Genome Sequencing After Nondiagnostic Exome Sequencing or Gene Panel in Developmental and Epileptic Encephalopathies. Neurology. 2021Mar 30;96(13):e1770-e1782.
4. Trost B, Engchuan W, Nguyen CM, et al. Genome-wide detection of tandem DNA repeats that are expanded in autism. Nature. 2020 Oct;586(7827):80-86.
5. Sanchis-Juan A, Stephens J, French CE,et al. Complex structural variants in Mendelian disorders: identification and breakpoint resolution using short- and long-read genome sequencing. Genome Med. 2018 Dec 7;10(1):95.