Distinct genomic characteristics between embryonic and clonal expansion pSNMs.

(A-C) Mutation spectrums in NpG and non-NpG sites for embryonic pSNMs (A), clonal expansion pSNMs in BBLD1005’s liver (B), and clonal expansion pSNMs in BBL11121’s breast (C). Mutation rate was normalized by the total number of sites in the human genome. For embryonic pSNMs, CpG sites showed significantly higher rate of C>T mutations than non-CpG sites. (D) Varied DNA replication timing of the two pSNMs types. The grey line denotes the genomic average. Embryonic pSNMs were enriched in early-replicating regions, whereas clonal expansion pSNMs were enriched in late-replicating regions. (E-G) Proportion of pSNMs locating in open or closed chromatin regions in the HepG2 (E), HMEC (F), and K562 (G) cell-lines. Significantly higher proportions of embryonic pSNMs were observed in transcribed chromatin regions of all three cell types.