Extended Data Figure 3: Genetic variation across 27 MCF7 strains.
(a) Variation in the copy number status of nine selected genes across 27 MCF7 strains. Copy number gains are shown in red, and copy number losses in blue. Thresholds for relative gains/losses were set at ±0.1. (b) Western blots presenting 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 their SNVs. Groups of strains expected to cluster together based on their evolutionary history are highlighted, as in Fig. 1. Bottom: a corresponding heatmap, showing the mutation status of all mutations across the 27 MCF7 strains. Shown are mutations identified only in a subset of the strains, which were detected in above 5% of the reads (allelic fraction>0.05). The presence of a mutation is shown in yellow, and its absence in gray. (h) The number of large (>15bp) indels and rearrangements across the 27 MCF7 strains. Indels are shown in gray, and rearrangements in black. (i) The recurrence of SVs in each of the 42 (out of 60) genes for which at least one event was detected. (j) The number of SVs shared by each number of MCF7 strains. Note that this analysis is limited to the 60 genes listed in Supplementary Table 2.