Recurrent somatic copy number alterations in resected cerebral cavernous malformations

Cerebral Cavernous Malformations (CCMs) are brain vascular lesions that occur in sporadic or inherited (autosomal dominant) forms. The malformations are driven by mutations in KRIT1, CCM2, PDCD10 or MAP3K3. Known oncogenic variants in PIK3CA accompany CCM-specific variants in lesions. While the primary genetic etiology of CCM lesions is relatively well understood, a subset of lesions does not yet have an identified molecular genetic etiology. Moreover, whether large genomic alterations occur somatically in CCM lesion tissue has been largely unexplored. In PIK3CA + cancers, large somatic copy number alterations ('CNAs') are frequent, with whole genome doubling and aneuploidy identified in most tumors. Such CNA events are known to be associated with course of disease and therapeutic response. In this study, using whole genome SNP-genotyping and Mosaic Chromosome Alteration (MoChA) analysis, we identify the presence of large (> 1 MB) somatic CNAs in CCMs, with specific enrichment of events in chromosome arms 16p,19p,17q, 20q. We also identify additional chromosome arm level events encompassing known CCM genes in a subset of lesions. Thus, we characterize a pattern of large genomic events that had remained hidden by the insensitivity of the molecular and analytical methods previously used. Finally, we propose that similar events may be found in other vascular malformations or PIK3CA overgrowth syndromes that have yet to be analyzed in this manner.