Extended Data Fig. 2: Evaluation of the composite likelihood model applied to extended nucleotide contexts.

To test the independence assumption of the composite likelihood model, we examined the interaction between any two positions (25 possible combinations) in the 11-nucleotide context around mutations of eight cancer types (bladder, n = 317 samples; breast, n = 1443; colorectal, n = 223; endometrium, n = 327; gastroesophageal, n = 833; head and neck, n = 425; lung adeno, n = 446; skin, n = 582). For any two positions, there are 96 possible nucleotide contexts and we plotted the observed mutation count of each nucleotide context (x-axis) against the predictions of the composite likelihood model (y-axis). Pearson correlation coefficients between observed and predicted data served as a measure of interaction. Each position pair is visualized in a separate correlation plot, and positions are annotated at the bottom right of the plot. For instance, pair (-1,1) refers to the trinucleotide context. Dot colors indicate the base substitution types.