Extended Data Fig. 4: Correlations between PT-PDX and PDX-PDX pairs.
a, The 5-95% inter-percentile range of CNA profiles between PT-PDX or PDX-PDX sample pairs from the same model on different platforms as shown in Fig. 3a–c. The 5-95% inter-percentile range of log2(CN ratio) values were calculated across all 100-kb windows per sample. P-values were computed by one-sided Wilcoxon rank sum test (ns: non-significant, P > 0.05). In the boxplots, the center line is the median, box limits are the upper and lower quantiles, whiskers extend 1.5× the interquartile range, and dots represent the outliers. b, Pearson correlation of the samples versus the ratio of 5-95% inter-percentile range between two samples (PT/PDX or PDX-1/PDX-2). Samples pairs with ratio of range much greater or less than 1 (that is one sample is much less aberrant than the other) tend to have lower correlations. PDX-1, lower passage PDX; PDX-2, later passage PDX or same passage PDX of different lineage.
