Fig. 6. Culture-associated mutagenesis in hiPSCs.

a, Mutations in F-hiPSCs were separated into two groups: (1) mutations shared between F-hiPSCs and their founding fibroblasts (left) and (2) mutations that are private to hiPSCs (right). Proportional graphs show substitution signatures of shared and private mutations. Culture-related signature (signature 18) is enriched in private mutations. b, Box plot of exposures of substitution signatures of shared (blue) and private (orange) mutations. Culture signatures (signature 18) account for ~50% of private substitutions, in contrast to nearly zero among shared mutations. Box plots denote median (horizontal line) and 25th to 75th percentiles (boxes). The lower (minima) and upper (maxima) whiskers extend to 1.5× the interquartile range. n = 324 WGS of hiPSCs. c, Number of samples carrying each signature within shared or private mutations. Most samples acquired the culture signature late in the hiPSC cloning process. d, Relationship between exposure of culture-related signature (signature 18) and passage number (Pearson’s correlation test, two sided). e, Schematic illustration of the mutational processes in fibroblasts and F-hiPSCs.