Custom Pediatric Oncology NGS Panel Identifies Somatic Mosaicism in Archival Tissue and Enhances Targeted Clinical Care

Abstract Background Disorders in the PIK3CA-related overgrowth spectrum (PROS) due to somatic mosaicism are associated with segmental overgrowth of the body in conjunction with vascular, skeletal, and brain malformations such as hemimegalencephaly. A pathogenic variant may only be detectable in affected tissue and not in peripheral blood or saliva samples; therefore, archival tissue may be the only relevant available specimen for testing. While this is a common approach for cancer testing, it is not typically used for constitutional genetic disorders. Methods PIK3CA mosaicism was assessed with a custom pediatric oncology next-generation sequencing (NGS) panel (OncoKids®) designed to capture somatic mutations in pediatric malignancies. The panel covers a wide range of targets including PIK3CA and AKT1 hotspots. We utilized OncoKids® on archival formalin-fixed, paraffin-embedded or frozen samples from seven patients with facial hemihypertrophy and lipomas, hemimegalencephaly, or hemihypertrophy with a lymphovascular malformation. The age of the archival tissue examined by NGS ranged from two to thirteen years (median 5 years). Every patient had clinical manifestations within the PIK3CA-related overgrowth spectrum and had a sample of an affected tissue available for testing from a prior surgical intervention. Results PIK3CA mosaicism was detected in all seven patients and the mutant allele fraction was lower in the lymphovascular malformation tissues (8-11%) than in brain (20-32%) and lipomatous tissues (16-23%). Conclusions Our study highlights the clinical utility of using a robust, oncology-focused NGS assay to identify PIK3CA mosaicism in non-cancer cases. It is feasible to use archival samples that are more than a decade old to obtain a molecular diagnosis which can then be used to improve healthcare management.