Extended Data Fig. 3: Genetic variation across 27 MCF7 strains.

a, Variation in the copy number status of nine selected genes across 27 MCF7 strains. Red, copy number gains; blue, copy number losses. Thresholds for relative gains and losses were set at 0.1 and −0.1, respectively. b, Western blots of the relative protein expression levels of ERα across strains. The expression of β-actin was used for normalization. For gel source data, see Supplementary Fig. 1. The experiment was repeated twice with similar results. c, Quantification of the relative expression of ERα. Strains Q and M were excluded from the comparison. Bar, median; box, 25th and 75th percentiles; whiskers, data within 1.5× IQR of lower or upper quartile; circles, all data points. One-tailed t-test. d, The allelic fractions of non-silent mutations in seven selected genes across 27 MCF7 strains. e, The number of non-silent point mutations (SNVs) across the 27 MCF7 strains. f, The number of COSMIC non-silent point mutations shared by each number of MCF7 strains. g, Top, unsupervised hierarchical clustering of 27 MCF7 strains, based on all of their SNVs. Groups of strains expected to cluster together based on their evolutionary history are highlighted, as in Fig. 1. Bottom, a corresponding heat map, showing the mutation status of all mutations across the 27 MCF7 strains. Mutations that were identified in only a subset of the strains that were detected in above 5% of the reads (AF > 0.05) are shown. Yellow, presence of a mutation; grey, absence of a mutation. h, The number of large (>15-bp) indels and rearrangements across the 27 MCF7 strains. Grey, indels; black, rearrangements. i, The recurrence of structural variants in each of the 42 (out of 60) genes for which at least one event was detected. j, The number of structural variants shared by each number of MCF7 strains. Note that this analysis is limited to the 60 genes listed in Supplementary Table 2.