Fig. 1: 5q common deleted region and mutation landscape of −5/del(5q) AML.

A Median log-2 copy number ratio (log-2 ratio) calculated for windows of 13 Kb (depicted by gray dots; each dot represents the median value obtained for the whole −5/del(5q) WGS cohort for a specific window) covering chromosome 5 (genomic position and schematic representation of chromosome 5 are indicated along the x-axis). Gray and red squares on the schematic representation of chromosome 5 depict cytobands and the centromere, respectively. The horizontal dashed black line marks a log-2 ratio of 0 corresponding to a normal diploid state. Black solid segments represent the median log-2 ratio calculated for overlapping windows of 10 Mb (overlap = 2.5 Mb). The vertical blue zone delimits the CDR (5q31.1 to 5q31.3). The position of genes of interest are indicated by black diamonds. B Mutations heatmap of −5/del(5q) AML. Genes (y-axis) composing the heatmap were either mutated in one or more −5/del(5q) specimens (x-axis). NPM1 was conserved because its wild-type status was significantly associated with −5/del(5q) AML compared to other AML or to complex karyotype (CK) AML without −5/del(5q). Genes were ordered (from top to bottom) based on their mutation frequencies (indicated by the red bar graph on the left). Specimens were grouped according to their mutation status (from left to right). Specimens presenting a deletion of the chromosome 17p (del(17p)) spanning TP53 (identified by FISH and/or WGS) or a complex karyotype (CK) are flagged by gray cells at the top of the heatmap. Mutation types (compound heterozygous or other mutations) are depicted by dark and light blue cells in the heatmap, as indicated in the legend at the bottom of the heatmap. Significant associations or anti-associations (depicted by a (+) and a (−), respectively) compared to other AML or to complex karyotype (CK) AML without −5/del(5q) (as indicated at the bottom right of the heatmap) are shown for concerned genes (in bold) at the right of the heatmap. *, **, *** and **** stand for p < 0.05, p < 0.01, p < 0.001 and p < 1e-04, respectively. C Size of chromosome 5 deletions for patients with or without lesions of chromosome 17p. Median values are indicated by red lines. As indicated by the legend, diamonds depict patients with a combined deletion of the chromosome 17p (del(17p)) and a mutation of TP53 (TP53m), triangles depict TP53m without del(17p) and dots depict del(17p) without TP53m. Squares represent patients without lesions of the 17p (indicated as “other” on the x-axis). Blue symbols represent −5/del(5q) specimens presenting a complex karyotype (CK). P-values resulting from the tests comparing each group to the “other” AML are directly indicated on the figure.