Visualizing alternative futures

Results of the single marker association tests for each of the 141 DNA repair-related SNPs with MAF ≥ 0.05 present on the SNP Cancer Panel array which have passed genotyping quality controls. (XLS 145 kb

Integrative Genome-Wide Gene Expression Profiling of Clear Cell Renal Cell Carcinoma in Czech Republic and in the United States

<div><p>Gene expression microarray and next generation sequencing efforts on conventional, clear cell renal cell carcinoma (ccRCC) have been mostly performed in North American and Western European populations, while the highest incidence rates are found in Central/Eastern Europe. We conducted whole-genome expression profiling on 101 pairs of ccRCC tumours and adjacent non-tumour renal tissue from Czech patients recruited within the “K2 Study”, using the Illumina HumanHT-12 v4 Expression BeadChips to explore the molecular variations underlying the biological and clinical heterogeneity of this cancer. Differential expression analysis identified 1650 significant probes (fold change ≥2 and false discovery rate <0.05) mapping to 630 up- and 720 down-regulated unique genes. We performed similar statistical analysis on the RNA sequencing data of 65 ccRCC cases from the Cancer Genome Atlas (TCGA) project and identified 60% (402) of the downregulated and 74% (469) of the upregulated genes found in the K2 series. The biological characterization of the significantly deregulated genes demonstrated involvement of downregulated genes in metabolic and catabolic processes, excretion, oxidation reduction, ion transport and response to chemical stimulus, while simultaneously upregulated genes were associated with immune and inflammatory responses, response to hypoxia, stress, wounding, vasculature development and cell activation. Furthermore, genome-wide DNA methylation analysis of 317 TCGA ccRCC/adjacent non-tumour renal tissue pairs indicated that deregulation of approximately 7% of genes could be explained by epigenetic changes. Finally, survival analysis conducted on 89 K2 and 464 TCGA cases identified 8 genes associated with differential prognostic outcomes. In conclusion, a large proportion of ccRCC molecular characteristics were common to the two populations and several may have clinical implications when validated further through large clinical cohorts.</p> </div

Venn diagrams showing the intersection of significant genes differentially downregulated (A) and upregulated (B) in the whole – genome expression profiling microarray dataset (K2) vs. RNA-Sequencing dataset from the Cancer Genome Atlas (TCGA).

<p>Venn diagrams showing the intersection of significant genes differentially downregulated (A) and upregulated (B) in the whole – genome expression profiling microarray dataset (K2) vs. RNA-Sequencing dataset from the Cancer Genome Atlas (TCGA).</p

Characteristics of ccRCC patients in the K2 (Czech Republic) and TCGA (US) series included in survival analysis.

*<p>p value calculated using Pearson χ² testing for categorical variables and t-test for continuous variables.</p>**<p>excluding missing category.</p

Characteristics of the 101 ccRCC patients from the “K2 study” (Czech Republic) included in the whole-genome gene expression microarray study.

*<p>p value calculated using Pearson χ² testing for categorical variables and t-test for continuous variables.</p>**<p>The two younger categories were grouped.</p>***<p>All stage IV patients had distant metastasis at diagnosis, and by definition none of stage I, II or III patients had distant metastasis. Missing stages were due to the lack of lymph nodes and/or metastasis evaluation. Out of 19 cases with missing stage, 9 were pT1a, 7 were pT1b, 1 was pT2a, and 1 was pT3a.</p

Hierarchical Classification of 100 significant differentially expressed genes in K2 series.

<p>Heatmap representing the 50 significant upregulated (in red) and 50 downregulated (in green) probes with the highest fold change following differential expression in ccRCC compared with non-tumour tissue (FDR-adjusted p-value (BH) <0.05, FC ≥2).</p

Venn diagrams representing relationship between ccRCC grades and the number of differentially expressed probes.

<p>Downregulated (A) and upregulated (B) probes with fold-change (FC) ≥2 and FDR-adjusted p-value (BH) <0.05 using paired sample information are presented.</p

Analysis of ccRCC methylation profile.

<p>Flowchart representing analysis of ccRCC methylation profile for Illumina Infinium HumanMethylation 27K (violet) and 450K (yellow) BeadChips showing the intersection of differentially methylated CpG sites (upper panel) and the intersection of significantly (un)methylated genes common to both platforms with differentially expressed genes in the K2 series analysed with Illumina HumanHT-12 v4 Expression BeadChips.</p

Characteristics of the 65 ccRCC patients included in the TCGA series (US) using RNA-Sequencing technology.

<p>Data from all paired tumour/non-tumour sets available on April 19, 2012 were retrieved from TCGA data portal.</p>*<p>p value calculated using Pearson χ² testing for categorical variables and t-test for continuous variables.</p>**<p>the younger two categories were grouped.</p>***<p>excluding missing category.</p>□<p>Of stage IV patients 15 had distant metastasis at diagnosis, and by definition none of stage I, II or III patients had distant metastasis. Missing stages were due to the lack of lymph nodes and/or metastasis evaluation>. These four patients were pT1aNXMX, pT3aNXM0, pT1bNXMX and pT3aNXMX, respectively.</p

Unsupervised Hierarchical Clustering of K2 samples.

<p>Unsupervised Hierarchical Clustering of all samples following quantile normalization highlighting two groups of samples: tumour (violet) and adjacent non-tumour (light green) tissue. Dendrogram for clustering experiments was created using centred correlation and average linkage method. Length of nodes corresponds to correlation between samples.</p