Conception-calibrated male pediatric tumor mitotic clocks

Molecular clocks can reconstruct tumorigenesis, but their calibration is limited by uncertainty in cancer ages. Pediatric cancers simplify this problem because age ranges are narrowly bounded by conception and a minimum of ~30 divisions. We developed mitotic clocks from rapidly fluctuating CpG (fCpG) DNA methylation on the X chromosome in male cancers, applying a two-state Markov model to estimate mitotic age and epimutation rates. Across acute lymphoblastic leukemia, acute myeloid leukemia, neuroblastoma, and embryonal brain tumors, modeled and observed methylation data were highly concordant, yielding epimutation rates of ~10^-3 per division and tumor mitotic ages between 30 and several hundred divisions. The clocks also resolved remission dynamics, inferring relapses seeded by small numbers of variably dormant residual cancer cells. By exploiting the unique age constraints of male pediatric tumors, calibrated fCpG clocks provide a quantitative framework to reveal otherwise hidden features of human tumor evolution.