Somatic Mosaicism in PIK3CA Variant Correlates With Stereoelectroencephalography-Derived Electrophysiology
H Westley Phillips1, Alissa M D'Gama1, Yilan Wang1
1From the Department of Neurosurgery (H.W.P.), Stanford School of Medicine, Palo Alto, CA; Department of Neurosurgery (H.W.P., J.R.M., J.P., S.S.S.), Boston Children's Hospital, Harvard Medical School; Broad Institute of MIT and Harvard (H.W.P., Y.W., Y.C., E.A.L., A.Y.H., C.A.W.), Cambridge; Division of Genetics and Genomics (H.W.P., Y.W., E.A.L., A.Y.H., C.A.W.), Manton Center for Orphan Disease Research; Division of Newborn Medicine (A.M.D.G., B.A.), Department of Pediatrics; Epilepsy Genetics Program (A.M.D.G., J.B.B., A.P.), Department of Neurology; Department of Pediatrics (A.M.D.G., J.B.B., E.A.L., A.Y.H., C.A.W.), Harvard Medical School, Boston Children's Hospital; Program in Biological and Biomedical Sciences (Y.W.); Department of Neurology (M.C., J.B.B., A.P., C.A.W.), Boston Children's Hospital, Harvard Medical School; Translational Neuroscience Center (A.C.S.), Boston Children's Hospital; Department of Radiology (S.P.P.), Division of Neuroradiology; Department of Pathology (H.G.L.), Division of Neuropathology, Boston Children's Hospital, Harvard Medical School; and Howard Hughes Medical Institute (C.A.W.), Boston, MA.
Objectives:
Brain-limited pathogenic somatic variants are associated with focal pediatric epilepsy, but reliance on resected brain tissue samples has limited our ability to correlate epileptiform activity with abnormal molecular pathology. We aimed to identify the pathogenic variant and map variant allele fractions (VAFs) across an abnormal region of epileptogenic brain in a patient who underwent stereoelectroencephalography (sEEG) and subsequent motor-sparing left frontal disconnection.
Methods:
We extracted genomic DNA from peripheral blood, brain tissue resected from peri-sEEG electrode regions, and microbulk brain tissue adherent to sEEG electrodes. Samples were mapped based on an anatomic relationship with the presumed seizure onset zone (SOZ). We performed deep panel sequencing of amplified and unamplified DNA to identify pathogenic variants with subsequent orthogonal validation.
Results:
We detect a pathogenic somatic PIK3CA variant, c.1624G>A (p.E542K), in the brain tissue samples, with VAF inversely correlated with distance from the SOZ. In addition, we identify this variant in amplified electrode-derived samples, albeit with lower VAFs.
Discussion:
We demonstrate regional mosaicism across epileptogenic tissue, suggesting a correlation between variant burden and SOZ. We also validate a pathogenic variant from individual amplified sEEG electrode-derived brain specimens, although further optimization of techniques is required.
