Table 1.
Main characteristics of the whole series of patients included in the study.
Fig 1.
Recurrent chromothripsis on chromosome 13 in high-risk MDS.
(A) Whole genome view ratio plots derived from aCGH data of MDS patients (#026, #027 and #072) showing chromothripsis on chromosome 13, indicated by the red-shaded box. The three patients had complex karyotypes: patient #026 had 33 aberrations and affecting seven chromosomes; patient #027 had 19 abnormalities affecting five chromosomes; patient #072 had 21 aberrations affecting six chromosomes. The Y-axis represents the log2 ratio values of MDS:control signal intensities for each probe. The X-axis illustrates all the probes in the array sorted by chromosome and physical mapping position. Chromosome numbers are indicated below the X-axis. (B) Detailed view of the whole chromosome 13 in patients #026, #027 and #072 showing a complex pattern of alternating copy number gains and losses. The grey area represents the thresholds of signal values (log2 ratio) to call CNAs, red lines indicate segmented copy number profiles, and boxes shaded in pale-red and pale-blue depict copy number losses and gains, respectively. Patient #026 had 18 alternating copy number changes, patient #027 had 11, and patient #072 had 16 changes along the whole chromosome 13. Copy number profiles differed between these patients. The Y-axis represents log2 ratios and the X-axis shows all probes of chromosome 13 sorted by chromosome position. Genomic location (Mb) is indicated below the X-axis. (C) Distribution of TP53 mutations identified by amplicon-based deep sequencing in the three MDS patients with chromothripsis. All TP53 mutations were located in the sequence-specific DNA binding domain. One patient had two mutations in heterozygosis, while the other two patients had one mutation each in homozygosis. The variant allele frequencies (VAFs) are represented in brackets. Each circle represents a mutation found in one patient. Green and red circles depict missense and nonsense mutations, respectively. Each patient is illustrated by a different-colour triangle. The complete coding region of TP53 is illustrated and the respective exons and amino acid (AA) positions are indicated at the bottom. The following protein domains are shown: TAD1 and TAD2, amino-terminal transactivation domains 1 and 2; DBD, sequence-specific DNA-binding domain; NLS, nuclear localization signalling domain; 4D, carboxy-terminal tetramerization domain; Neg, negative regulation domain. Gene variants were represented using the R package “R453PlusToolbox” [53].
Table 2.
Summary of mutations found in the analyzed genes.
Fig 2.
Summary of recurrent CNAs found in the global series.
(A) Proportion of the whole series of patients with normal and abnormal aCGH profiles. Each aCGH category is then divided by the cytogenetic subgroups detected by CC studies: normal, abnormal and non-informative karyotype. Percentages represent the proportion of patients from the total number of patients within each cytogenetic subgroup. (B) Frequency of large recurrent genomic abnormalities and frequency of cryptic recurrent CNAs involving genes of known significance in MDS and MDS/MPN patients only seen by aCGH. All abnormalities are classified by MDS and MDS/MPN subtypes and color-coded as indicated on the right panel of the figure.
Fig 3.
Combination of aCGH and NGS analysis for regions with frequently mutated genes in MDS and MDS/MPN.
(A, C, D, E, G) Detailed view of the whole chromosomes 2, 4, 17, 21 and X, where recurrent regions of deletion where found by aCGH, indicated by the red-shaded box. A magnified view of the minimal deleted regions with a schematic diagram showing the genes included within the deletion. For all figures, genomic locations are indicated in Mb, and the chromosome position (bp) and size (kb) of the minimal deleted regions are indicated in the upper part of each chromosome view ratio plots. The Y-axis represents the log2 ratio values and all probes for each chromosome are sorted by genomic position along the X-axis. (A) A 533.4-kb deletion on 2p23.3 affecting the DNMT3A locus. (C) A 298.7-kb deletion on 21q22.12 affecting the RUNX1 locus. (D) A 697.1-kb deletion on Xp11.4 affecting the BCOR locus. (E) A 381.2-kb deletion on 4q24 affecting the TET2 locus. (G) An 11.14-Mb deletion on 17p13.3-p12 affecting the TP53 locus. Genes were represented using the R package “GenomeGraphs”. (B, F, H) Distribution of DNMT3A, TET2 and TP53 mutations identified by targeted amplicon-based deep sequencing. The variant allele frequencies (VAFs) are represented in brackets. The complete coding regions of DNMT3A, TET2 and TP53 are illustrated and the respective exons and amino acid (AA) positions are indicated below. Each circle represents a mutation found in a single patient. Green, red and blue circles depict missense, nonsense and frameshift mutations, respectively. (B) One patient carried a DNMT3A missense mutation located in the MTase domain. The following protein domains are shown: PWWP, proline-tryptophan-tryptophan-proline domain; ZNF, zinc finger domain; MTase, methyltransferase domain. (F) Three patients with a TET2 deletion harbored one nonsense, one missense and one frameshift mutation each. The two evolutionarily conserved domains, boxes 1 and 2, are shown. (H) Four patients carried one TP53 missense mutation each. The following protein domains are shown: TAD1 and TAD2, amino-terminal transactivation domains 1 and 2; DBD, sequence-specific DNA-binding domain; NLS, nuclear localization signalling domain; 4D, carboxy-terminal tetrame-rization domain; Neg, negative regulation domain. Gene variants were represented using the R package “R453PlusToolbox” [53].