Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival

Overview of the two-stage procedure detecting for non-coding elements with cancer-specific and conserved mutations and its application to a pan-cancer whole-genome data set. a Summary of the input data, showing the cancer type (Cancer), mutation type (Mut.), number of samples (N), and number of mutations per sample in the whole-genome data set.7 SNVs are indicated by red color, INDELs by blue color, and the median number of mutations is indicated with a black bar. b, c Genomic span and count of input elements for each element type. d Workflow of ncDriver, a two-stage procedure for non-coding driver detection. Elements passing the Mutational recurrence test of the first stage are passed on to the second-stage tests Cancer specificity test (i), Local conservation test (ii), and Global conservation test (iii). e Counts of elements that passed the Mutational recurrence test at a 25% FDR threshold for SNVs (red) and INDELs (blue). f Counts of significant elements that passed the combined significance using Fisher’s method and 25% FDR threshold. g, h Relative contribution of the Cancer specificity test (i; orange), Local conservation test (ii; red), Global conservation test (iii; yellow) to the combined significance of the significant elements of each element type for INDELs and SNV