Fig. 2

Recurrent batch-biased variants across cancer types. a. Heatmap shows 240 recurrent batch-biased variants in the MAF file. b. Batch-dependent occurrence of batch-biased variants is shown for KIRC, LUAD and UCEC datasets, respectively. Barcodes of plate IDs in each sample are indicated by different colours. c. Gene-level frequency of recurrent batch-biased variants (n = 14). The heatmap colours indicate the significance of batch-biased calls, i.e., -log₁₀(P-value), where P was calculated using Fisher’s exact test. d. Phylogenic tree analyses for KIRC (upper) and LUAD (lower) are shown. The phylogenic trees between the mutation profiles before correction (left) and after correction (right) are compared. The corrected mutation profiles are generated by removing the indicated batch-biased variants in each data. Barcodes of plate IDs in each sample are indicated by different colours