Extended Data Fig. 8: Genetic variation across multiple strains of additional cancer and non-cancer cell lines.

a, The fraction of non-silent SNVs that are discordant between pairs of strains of the same cell line. Data are mean ± s.e.m. n, number of strain pairs compared. b, Arm-level CNAs arise in RPE1 samples. Plots show CNAs detected by an e-karyotyping analysis of 26 RPE1 samples. Red, gains; blue, losses. c, Comparison of variability in non-silent SNVs between non-transformed, partially transformed and fully transformed MCF10A samples. Box plots show the fraction of discordant non-silent SNVs between pairs of samples within each category. Bar, median; box, 25th and 75th percentiles; whiskers, data within 1.5× IQR of lower or upper quartile; circles, all data points. One-tailed Wilcoxon rank-sum test, n = 28, 112 and 14 strain pairs, for the non-transformed, partially transformed and the fully transformed groups, respectively. d, Comparison of the Broad–Sanger allelic fraction correlations of cell lines derived from primary tumours and those derived from metastases. Bar, median; coloured rectangle, 25th and 75th percentiles; width of the violin indicates frequency at that value. One-tailed Wilcoxon rank-sum test. e, Top, comparison of the chromosomal instability (CIN70) gene expression signature score between CCLE lines derived from primary tumours and those derived from metastases. Bottom, comparison of the weighted-genomic integrity index (wGII) between CCLE lines derived from primary tumours and those derived from metastases. Bar, median; coloured rectangle, 25th and 75th percentiles; width of the violin indicates frequency at that value. One-tailed Wilcoxon rank-sum test. f, Comparison of the Broad–Sanger allelic fraction correlations of microsatellite-stable cell lines (MSS) and microsatellite-unstable cell lines (MSI). Bar, median; box, 25th and 75th percentiles; whiskers, data within 1.5× IQR of lower or upper quartile; circles, all data points. One-tailed Wilcoxon rank-sum test. g, Heat maps show the allelic fractions of non-silent mutations in multiple strains of cancer cell lines. The presence of a mutation is shown in colour according to its allelic fraction. h, Heat maps show the allelic fractions of non-silent mutations in multiple strains of the non-cancer cell lines HA1E and MCF10A. The presence of a mutation is shown in colour according to its allelic fraction. Also shown is an unsupervised hierarchical clustering of the 15 MCF10A strains, which represent different degrees of cellular transformation, based on their non-silent mutation profiles.