The landscape of structural variation in pediatric cancer

Structural variants (SVs) account for over 60% of pediatric cancer driver variants. Pan-cancer analyses on 1,616 pediatric and 2,203 adult whole genomes show that pediatric SV burden varies ∼100-fold across cancer types, is reduced 6- to 16-fold compared to adult brain and solid tumors, but is comparable in hematological malignancies. The top-ranked SV-disrupted genes are drivers in pediatric cancers and fragile sites in adult cancers. Recurrent SV hotspots near RAG recombination signal sequences disrupt immune loci and driver genes in pediatric acute lymphoblastic leukemias, but immune loci exclusively in adult lymphoid cancers. Ten extracted SV signatures implicate RAG-mediated mutagenesis as a potential etiology for COSMIC SV7 in lymphoid cancers, while clustering of spatiotemporally distinct samples from 13 patients reveals the ongoing evolutionary contributions of SVs to intra-tumor heterogeneity and driver selection. Our study expands the known scope of RAG-mediated mutagenesis, while the curated SV dataset can guide future research and clinical testing.