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

Flowchart of data preprocessing and analysis procedures.

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

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