a, Distribution of somatic alterations. For each tumour genome, copy number (solid lines), density of mutations per 5-Mb window (bars) and protein-coding mutations (dots) are shown. The shaded rectangle indicates the location of the 13q14 deletion that was present in three of the four CLL cases. Chromosome numbers are listed below the four profiles. b, Frequency of substitutions in each CLL tumour for the six possible classes of mutation. c, Distribution of the four possible NpA dinucleotides for the A to C transversion in each tumour genome, compared with the expected distribution across the genome. The total number of A to C substitutions per case is indicated at the top (**, P < 0.001).

a, Schematic representation of human NOTCH1, showing the main domains and locations of the three different somatic mutations identified in CLL. NEC, NOTCH1 extracellular subunit; NTM, NOTCH1 transmembrane subunit; ICN, intracellular domain of NOTCH1; LNR, Lin-12 NOTCH repeats; RAM, RAM domain; ANK, ankyrin repeat domain; PEST, PEST domain. b, Electropherogram showing the heterozygous CT deletion recurrently identified in CLL. c, Western blot showing NOTCH1 protein levels in CLL cases with or without the NOTCH1 p.P2515Rfs*4 mutation, and in Jurkat cells as a control. The arrow indicates the band corresponding to the NTM; the large arrowhead indicates the smaller band corresponding to the mutant form. d, Heat map showing the 23 genes of the NOTCH1 pathway that are differentially expressed in NOTCH1-mutated versus non-mutated CLL. e, Distribution of disease stage (Binet), ZAP-70 expression status, CD38 expression status and IGHV mutational status (UM, unmutated IGHV) in patients with or without mutations in NOTCH1 (*, P < 0.02; **, P < 0.01). f, Actuarial probability of overall survival of CLL patients with mutated or unmutated NOTCH1 (*, P = 0.03).

a, Multiple sequence alignment of MyD88 around the mutated residue (arrow) in different species. Cons., degree of conservation. b, Electropherogram showing the recurrent heterozygous p.L265P MYD88 mutation (arrow) detected in CLL. c, Cell extracts from a MYD88-mutated CLL (L265P) and a MYD88-unmutated CLL (WT) were immunoprecipitated with anti-MyD88 antibody. The immunoprecipitated and unbound fractions were analysed by western blot using anti-IRAK1 and anti-MyD88 antibodies. d, Western blot analysis of phosphorylated STAT3 (p-STAT3 (Tyr 705)) and total STAT3 in cell extracts from MYD88-mutated or unmutated CLL tumour cells. β-Actin was used as a control to show equal loading. e, Western blots showing phosphorylated IκBα (p-IκBα), total IκBα, phosphorylated p65 subunit of NF-κB (p-p65) and total p65 subunit of NF-κB in cell extracts from MYD88-mutated or unmutated CLL tumour cells. f, Heat map representing the cytokine levels secreted by B cells from eight individuals after Toll-like receptor stimulation. Only the five cytokines that showed the most significant differences between MYD88-mutated and MYD88-unmutated CLL are shown. ‘E52DEL’ indicates B cells from two patients with an inactivating MYD88 mutation, ‘WT’ corresponds to tumour cells from CLL patients without MYD88 mutation and ‘L265P’ indicates tumour cells from patients carrying a mutated MYD88. The stimulation experiments for each of the Toll-like receptors (TLRs) are represented in different colours. NS, no stimulus. g, Distribution of disease stage (Binet), ZAP-70 expression status, CD38 expression status and IGHV mutational status (UM, unmutated IGHV) in patients according to the presence or absence of p.L265P MYD88 mutation (*, P < 0.03).