Genetic Architecture of an Adult Epilepsy Surgery Cohort: Functional Characterisation of Germline and Somatic Variation

Summary The focus of our research is to understand the basic neurobiology of human epilepsy, speech disorders and deafness, and translate this knowledge into improved treatment of patients

Project Details

Our understanding of the genetics underlying brain malformations and focal epilepsy is incomplete. Somatic mosaicism has emerged as an important mechanism. That occurs post-zygotically, is largely confined to the brain, and is difficult or impossible to detect by sequence analysis of venous blood samples. Furthermore, bi-allelic germline and somatic variants affecting the same gene have now been found in resection surgical tissue from several non-malignant brain malformations associated with epilepsy. In these patients, an inherited germline mutation may lead to a predisposition to developing the brain malformation, with a somatic ‘second hit’ mutation required within the affected tissues to produce each lesion. In addition, the discovery that brain malformations appear to be largely driven by mutations in genes involving the mTOR pathway means there is the potential for the development of genetically targeted therapies. This is a rapidly evolving area of research and access to genomic sequencing for patients with brain malformations is a high clinical priority.

While analysis of DNA solely from blood may not identify a mutation in patients with brain malformations and epilepsy, analysis of brain tissue specimens collected at neurosurgery can reveal causative somatic mosaic variants. Precision case management and support are required to explain complex genomic tests and facilitate sample collection. Molecular diagnosis of a somatic variant can inform clinical management, prognosis, treatment strategies and recurrence risk for these individuals and their families. Technologies such as high-depth sequencing or droplet digital PCR are key in detecting and quantifying mosaic variants even at low frequency in brain tissue. Tissue immunostaining combined with laser capture microdissection facilitates characterisation and quantification of mosaic variants in different cell populations.

Aims:

1. To identify germline and somatic variants in individuals with brain malformations and epilepsy

2. To characterise pathogenic gene variants by studying protein signalling in brain tissue

3. To isolate different cell populations from brain tissue      

4. To determine the frequency of pathogenic gene variants in different brain cell populations

Methodology:

1. Application of basic bioinformatics analysis to screen for candidate germline and somatic mutations.

2. Application of tissue immunostaining to measure mTOR signalling.

3. Application of laser capture microdissection to procure subpopulations of cells from brain tissue.

4. Application of current genomic testing technologies (e.g. Sanger sequencing and droplet digital PCR) using DNA extracted from laser-captured cells to study candidate mutations.