DNA copy number profiles of metastases containing a co-amplification at chromosome 8q24.21 and 6q21.

<p>DNA copy number profiles of two patients containing a co-amplification of at 8q24.21 (<i>MYC</i>) and chromosome 6q21 in the metastasis (<i>B, D, E</i>), which was not present in the primary tumor (<i>A, C</i>). The x-axis displays clones spotted on the array sorted by chromosomal position. The y-axis displays the log₂ ratios of the clones. The segments are depicted by grey lines. Boundaries of chromosomes are indicated by dotted lines.</p

Genomic overlap of primary tumors (p) and matched metastasis (m).

<p>(<i>A–B</i>) Example of a tumor metastasis pair from the group with less than 70% genomic overlap of gain, loss or normal DNA copy number (total 20 patients of which 3 patients were not joined pairwise in the dendrogram of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086833#pone-0086833-g003" target="_blank">Figure 3</a>)and (<i>C–D</i>) example of a tumor metastasis pair from the group with 70 and 95% genomic overlap of gain, loss or normal DNA copy number (38 patients of which 1 patient was not joined pairwise in the dendrogram of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086833#pone-0086833-g003" target="_blank">Figure 3</a>) The x-axis displays clones spotted on the array sorted by chromosomal position. The y-axis displays the log₂ ratios of the clones. The segments are depicted by grey lines. Boundaries of chromosomes are indicated by dotted lines. (<i>E</i>) Histogram of the percentages of genomic overlap of gain, loss or normal DNA copy number of all tumor metastasis pairs. The x-axis displays the percentages of overlap. Tthe y-axis displays the frequencies of the metastases.</p

Baseline characteristics of the 62 patients included in the analysis.

<p>Abbreviations: MSI; microsatellite instability, dMMR; deficient mismatch repair system, pMMR; proficient mismatch repair system.</p

Flowchart of data preprocessing and analysis procedures.

<p>In grey analysis performed in R, in white analysis performed in Nexus.</p

Frequency plots of DNA copy number aberrations in 62 primary tumors and 68 matched metastases.

<p>(<i>A</i>) Frequencies of aberrations based on called data for primary tumors and (<i>B</i>) metastases. The x-axis displays clones spotted on the array sorted by chromosomal position. The y-axis displays the frequency of tumors with gains (above zero) or losses (below zero). Boundaries of chromosomes are indicated by dotted lines.</p

Gene breakpoint and gene mutation frequencies of the 25 most frequently affected genes in CRC.

<p>Gene breakpoint frequencies (red bars) were based on the analysis of 352 CRC samples and gene mutation frequencies (blue bars) on the analysis of 204 samples. Genes marked with a “*” indicate a pool of genes that share probe(s) associated with chromosomal breakpoints: the <i>PCMTD2*</i> pool also includes <i>LINC00266-1; PARK2*</i> also includes <i>PACRG</i>; <i>ZNF337*</i> also includes <i>NCOR1P1</i>, <i>FAM182A</i>, <i>FAM182B</i>, <i>FRG1B</i>, <i>MIR663A</i>, <i>MLLT10P1</i>; <i>CD99*</i> also includes <i>XG</i>; <i>PARP8*</i> also includes <i>EMB</i>.</p

Four distinct core modules of putative CRC driver genes were retrieved by Multi-Dendrix analysis.

<p>The nodes comprise both gene breakpoints (red outline) and gene mutations (blue outline). Edges (grey lines) connect genes that are mutually exclusively affected. The thickness of the grey lines and the corresponding number reflect the robustness score. The strongest mutual exclusivity is observed between <i>PIBF1</i> and <i>TP53</i>. Genes marked with a “*” indicate a pool of genes that share probe(s) associated with chromosomal breakpoints: the <i>ZNF337*</i> pool also includes <i>NCOR1P1</i>, <i>FAM182A</i>, <i>FAM182B</i>, <i>FRG1B</i>, <i>MIR663A</i>, <i>MLLT10P1</i>; <i>ZNF519*</i> also includes <i>ANKRD20A5P</i>, <i>ANKRD30B</i>.</p

Clustering of 203 CRC patients by NBS based on gene breakpoints and gene mutations revealed four CRC subtypes.

<p>(A) Co-clustering matrix of CRC samples generated by NBS analysis. The matrix color intensity represents the similarity score. The color bar on top indicates the groups of patients related to the four CRC subtypes (k = 4) as determined by hierarchical clustering after NBS analysis. (B) Kaplan-Meier plot for overall survival (in days) of CRC subtype 1 (n = 80 patients), subtype 2 (n = 45 patients), subtype 3 (n = 27 patients) and subtype 4 (n = 51 patients). There are significant differences in OS among the four CRC subtypes (log-rank <i>P</i> = 0.001), with poorest OS for subtype 3 CRC patients. (C) Kaplan-Meier plot for OS of CRC subtype 3 patients <i>versus</i> patients in other CRC subtypes, showing a hazard ratio (HR) of 2.17 and a median OS of 392 days <i>versus</i> 610 days, respectively (log-rank <i>P</i> = 0.0002).</p