Calling patterns of the somatic variant callers.

<p>Hierarchical cluster analysis of mutations called by the somatic variant callers in exome and deep sequencing data in left and right panel, respectively. Each red line represents a called somatic mutation.</p

Inter-caller agreement.

<p>Pairwise comparisons of the nine studied variant callers in exome sequencing of five breast cancer samples in exome sequencing and deep sequencing data in upper and lower panels, respectively. The matrix depicts the agreement among the studied variant callers. In each horizontal line, the number reflects the fraction of calls found by the caller that are also reported by the other callers. For instance, looking at EBCall in the first line, Mutect reports 51% of the calls reported by EBCall. Deep sequencing data includes only data covered by 200 x at minimum in both tumor and normal sample. The color reflects the degree of agreement, with the highest color intensity depicting high agreement between the two callers.</p

Fold changes for the 5 genes in ET, PV, and PMF compared to control subjects.

<p>Patient groups and genes are shown on the x-axis and fold changes on the Y-axis. NS: non-significant; S: significant. All genes FDR<0.05.</p

Identification of metastasis driver genes by massive parallel sequencing of successive steps of breast cancer progression

<div><p>Cancer results from alterations at essential genomic sites and is characterized by uncontrolled cell proliferation, invasion and metastasis. Identification of driver genes of metastatic progression is essential, as metastases, not primary tumors, are fatal. To gain insight into the mutational concordance between different steps of malignant progression we performed exome sequencing and validation with targeted deep sequencing of successive steps of malignant progression from pre-invasive stages to asynchronous distant metastases in six breast cancer patients. Using the ratio of non-synonymous to synonymous mutations, a surprisingly large number of cancer driver genes, ranging between 3 and 145, were estimated to confer a selective advantage in the studied primary tumors. We report a substantial amount of metastasis specific mutations and a number of novel putative metastasis driver genes. Most notable are the <i>DCC</i>, <i>ABCA13</i>, <i>TIAM2</i>, <i>CREBBP</i>, <i>BCL6B</i> and <i>ZNF185</i> genes, mainly mutated exclusively in metastases and highly likely driver genes of metastatic progression. We find different genes and pathways to be affected at different steps of malignant progression. The Adherens junction pathway is affected in four of the six studied patients and this pathway most likely plays a vital role in the metastatic process.</p></div

Hierarchical Cluster analysis with euclidean distance in ET, PV and PMF patients.

<p>Rows in the heat map represent the five genes DEFA4, ELA2, CTSG, OLFM4, and AZU1, and columns represent patients. The color key ranges from green to red representing standardized expression values of −3.0 to 3.0. Green indicates low expression, black intermediate expression, and red high expression. Five major clusters can be identified. Cluster 1 (green, low expression), cluster 2 (green-black, low-intermediate expression), cluster 3 (black-red, intermediate expression), cluster 4 (red-black, intermediate-high expression), and cluster 5 (red, high expression).The dendogram shows the degree of similarity between patients.</p

Clinical and Biochemical Data in Cluster 1–5 with low, low-intermediate, intermediate, intermediate-high, and high expression values of the 5 genes, respectively.

<p>Median and range are shown. Abbreviations: ET =  Essential Thrombocythemia; PV =  Polycythemia Vera; PMF =  Primary Myelofibrosis; *  =  blood tests at the time of blood sampling for gene expression profiling; disease duration at the time of blood sampling; **:from diagnosis as assessed January 2013.</p

The top 20 most downregulated oxidative stress and antioxidative defense genes in patients with ET, PV, and PMF (FDR <0.05).

<p>FC: fold change. FDR: false discovery rate.</p><p>The results from data set 1 are compared with results from data set 2.</p><p>The top 20 most downregulated oxidative stress and antioxidative defense genes in patients with ET, PV, and PMF (FDR <0.05).</p