CCND1 and breast cancer: Recurrent neo-TAD genes (found in ≥10% neo-TAD samples) were enriched in the KEGG breast cancer pathway (BH-adjusted P = 0.014), including breast cancer genes such as FGF19, ERBB2, CCND1, MYC, and RPS6KB1. Genes in neo-TADs were overexpressed under CN covariates (P < 0.0001, one-way ANCOVA), demonstrating the noncoding effects of SVs on gene expression (Fig. 5B; Appendix Table S7).