Mutated genes with a higher frequency in our cohort than expected in the 1000 genomes repository.

<p>Mutated genes with a higher frequency in our cohort than expected in the 1000 genomes repository.</p

Distribution of selected mutations along the different affected genes and their related functional categories.

<p>A) Number of mutated samples by gene according to the described mutation filtering protocol (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148346#pone.0148346.s002" target="_blank">S2 Fig</a>). Only 33 recurrent genes were included. B) Number of mutated samples by gene category (bottom). The corresponding number of genes included in each functional category (top) is also represented in order to avoid any size bias. C) The functional categories are distributed depending on the observed mutated samples and the known number of belonging genes. Both transcription factor and ubiquitination categories shown and excess of mutated samples. D) The number of mutated samples per category in the haloplex cohort were compared against a reference population of healthy samples (1000 genomes). Here, while metabolism and signalling genes categories appear poorly mutated, ubiquitination appears remarkably more mutated than the reference population.</p

Network of significant gene co-occurrences.

<p>Genes are represented by nodes and their sizes defined from the number of significant co-occurrences they are implied. Edges represent co-occurrences between pairs of genes. Every edge is labelled with the number of samples that carries the mutated pair of genes as follows: higher than expected co-occurrences are coloured in green, while lower than expected (only one) in red. Edge width is proportional to the statistical p-value of chi-square test. Those genes co-occurring only at one single patient are painted in white. Seven co-occurrence subnetworks arise from the significant co-occurrence network, where remarkably a single component connected the half of represented genes. In contrast, 3 pairs are simultaneously mutated only in 2 different individuals, and 3 significant co-occurrence subnetworks, only in 1 patient.</p

Network-based analysis (SNOW) applied to 46 selected genes (33 recurrent and <i>RARA</i>, <i>PML</i>, and <i>FLT3</i> genes).

<p>The network was complemented with the co-occurrence relationships, in order to summarize the two kind of significant results. Significant network-based analysis genes are coloured in light blue and stroked with a magenta border whether they resulted also significant in co-occurrence analysis. Genes only included by co-occurrence are coloured in magenta. Intermediate genes were painted in white and square shaped. While grey edges represent protein-protein interaction, relationships, broad orange dashed lines describe significant co-occurrences. Moreover, main genes are grouped depending on their biological role (cohesin complex, signalling pathways, spliceosome, RHO-GTPase, retinoic acid regulators and other cellular processes roles).</p

SNV and indel filtering steps for identification of somatic variants.

<p>SNV and indel filtering steps for identification of somatic variants.</p

Single-Nucleotide Polymorphism Array-Based Karyotyping of Acute Promyelocytic Leukemia

<div><p>Acute promyelocytic leukemia (APL) is characterized by the t(15;17)(q22;q21), but additional chromosomal abnormalities (ACA) and other rearrangements can contribute in the development of the whole leukemic phenotype. We hypothesized that some ACA not detected by conventional techniques may be informative of the onset of APL. We performed the high-resolution SNP array (SNP-A) 6.0 (Affymetrix) in 48 patients diagnosed with APL on matched diagnosis and remission sample. Forty-six abnormalities were found as an acquired event in 23 patients (48%): 22 duplications, 23 deletions and 1 Copy-Neutral Loss of Heterozygocity (CN-LOH), being a duplication of 8(q24) (23%) and a deletion of 7(q33-qter) (6%) the most frequent copy-number abnormalities (CNA). Four patients (8%) showed CNAs adjacent to the breakpoints of the translocation. We compared our results with other APL series and found that, except for dup(8q24) and del(7q33-qter), ACA were infrequent (≤3%) but most of them recurrent (70%). Interestingly, having CNA or <i>FLT3</i> mutation were mutually exclusive events. Neither the number of CNA, nor any specific CNA was associated significantly with prognosis. This study has delineated recurrent abnormalities in addition to t(15;17) that may act as secondary events and could explain leukemogenesis in up to 40% of APL cases with no ACA by conventional cytogenetics.</p></div

Schematic representation of CNA adjacent to the translocation breakpoints found in our series.

<p>On the left panel, the Smooth Signal of chromosome 15 and 17 from case APL_32 are represented. Results from diagnosis sample are shown in blue and from complete remission sample, in green. On the right, chromosomes 15 and 17 are depicted with G-banding and arrows pointing the location of the <i>PML</i> and <i>RARA</i> genes. Areas shaded in blue show regions duplicated and in red, deleted. Panel (A) corresponds to isochromosome der(17)t(15;17); Panel (B) shows a small duplication of the <i>PML</i> gene, and in panel (C) both the <i>PML</i> and the <i>RARA</i> genes are duplicated. These two cases had a cryptic t(15;17) by CC, that was revealed by FISH. In panel (D) two small deletions are found distally to the translocation breakpoints.</p

Comparison of type, size and number of SNP-A abnormalities in reported APL series.

<p>*one Uniparental Tetrasomy has been included both in duplication and CN-LOH group.</p><p>CNA: Copy-Number Abnormality. CN-LOH: Copy-Neutral Loss of Heterozygocity.</p

Main characteristics of our series.

<p>*PML-RARA was diagnosed by FISH or RT-PCR.</p

Karyogram of APL according to SNP-A analysis in our series.

<p>Coloured bars depict the extension of abnormalities. Gains appear in blue at the right of each chromosome; losses in red and CN-LOH in green, at the left side of it.</p