Project Summary PROJECT SUMMARY Although somatic mosaicism is a known cause of malformations of cortical development (MCD), it is still difficult to detect sparse somatic variants in patient tissue and study their molecular and functional effects. The long- term goal of this project is to unravel the cellular and molecular complexity of MCD and translate this knowledge into improved diagnostic and treatment opportunities for patients. The overall objectives in this application are to (i) improve somatic variant detection, (ii) identify transcriptional correlates of somatic variants, and (iii) test functional effects of somatic variants in relevant cell types. The central hypothesis is that somatic variants are enriched in particular cell lineages in MCD and that cell identity is an important determinant of a variant’s molecular and functional effects. The rationale for this project is that understanding somatic variation and its consequences at cell-type resolution will ultimately improve gene discovery for MCD and help advance the field toward targeted therapies for drug-resistant epilepsy associated with MCD. The central hypothesis will be tested by pursuing three specific aims: (1) Improve somatic variant detection in patients with focal cortical malformations, (2) Evaluate cell-type-specific transcriptional effects of somatic mutations, and (3) Functionally validate the cell-type-specific contribution of somatic mutations to disease features. Under the first aim, relevant cell types will be enriched from affected patient tissue and sequenced as a strategy to improve somatic variant detection. For the second aim, integrated single-nuclei genotyping and transcriptomic analyses of patient tissue will be used to evaluate gene expression signatures of somatic mosaicism. The third aim will leverage a novel transgenic mouse model of MCD to drive somatic variation in particular cell types and determine how cell identity contributes to specific components of disease. The research proposed in this application is innovative because it takes a new approach to gene discovery in MCD, leverages leading-edge techniques such as integrated single- nuclei genotyping/transcriptomics, and takes advantage of a unique mouse model generated by the applicant’s lab. The proposed research is significant because it is expected to yield new causal somatic variants for MCD and new knowledge of their molecular and functional effects in appropriate cellular contexts. Ultimately, such knowledge has the potential to provide new opportunities to develop or apply targeted treatments.