Telomere-to-telomere diploid genome assembly of a melanoma and matched normal sample reveals that 16% of somatic variants occur in sequences absent from standard references, with satellite repeats serving as major hotspots for UV-induced mutagenesis due to sequence-intrinsic mutability, centromere kinetochore domains undergoing extensive genetic and epigenetic remodeling, telomeres experiencing punctuated cycles of attrition and telomerase-mediated extension, and copy number alterations plus epimutations—rather than point mutations—predominantly rewiring cancer gene regulatory programs.

Oncogenesis involves widespread genetic and epigenetic alterations, yet the full spectrum of somatic variation genome-wide remains unresolved. We generated a near-telomere-to-telomere (T2T) diploid assembly of a donor paired with deep short- and long-read sequencing of their melanoma. This revealed that 16% of somatic variants occur in sequences absent from GRCh38, with satellite repeats acting as hotspots for UV-induced damage due to sequence-intrinsic mutability and inefficient repair. Centromere kinetochore domains emerged as focal sites of structural, genetic, and epigenetic variation, leading to remodeling of centromere kinetochore binding domains during tumor evolution. Single-molecule telomere reconstructions uncovered cycles of attrition, deletion, and telomerase-mediated extension that shape cancer telomeres. Finally, diploid chromatin maps exposed that copy number alterations and epimutations, rather than point mutations, predominate in rewiring cancer regulatory programs. These findings define the full landscape of a cancer’s somatic variation and their functional impact, establishing a blueprint for T2T studies of mosaicism.