Kaplan-Meier survival plot for NOB G-CIMP+ (n = 7), NOB G-CIMP− (n = 123), TCGA G-CIMP+ (n = 30) and TCGA G-CIMP− (n = 361) samples.

<p>Kaplan-Meier survival plot for NOB G-CIMP+ (n = 7), NOB G-CIMP− (n = 123), TCGA G-CIMP+ (n = 30) and TCGA G-CIMP− (n = 361) samples.</p

Overview of detected chromosomal aberrations by cCGH and aCGH

<p>Overview of detected chromosomal aberrations by cCGH and aCGH</p

Data processing flowchart for predicting G-CIMP calls of NOB samples from TCGA gene expression data.

<p>Data processing flowchart for predicting G-CIMP calls of NOB samples from TCGA gene expression data.</p

Comparison of TCGA G-CIMP labels and our G-CIMP calls.

<p>Comparison of TCGA G-CIMP labels and our G-CIMP calls.</p

PCA plot of TCGA and NOB samples in combined methylation data set.

<p>Samples are labeled by histopathology check results.</p

Box-Whisker plot of age of NOB and TCGA G-CIMP positive and G-CIMP negative samples.

<p>Limits of box and whiskers plot are 10%, 25%, 50%, 75% and 90%.</p

PCA plot of TCGA and NOB samples in combined methylation data set.

<p>This data set includes 394 samples and 1438 methylation sites.</p

Comparison of cCGH (A, C) and arrayCGH (B, D) results from chromosome 9 of CWR22 and chromosome 14 of DU145-MN1.

<p>A small region of gain on 9p close to the centromer (B, arrowhead) and a small deletion on 14q (D, arrowhead) are only detected by arrayCGH.</p

PCA plot of TCGA and NOB samples after batch effect removal.

<p>As expected, normal brain samples are clustered together, and TCGA and NOB samples are not separated. We used high variation 1482 probe sets (std. dev. >1) in combined data set.</p

Validation of amplicons by FISH analysis on cell lines.

<p>Identification of increased copies of signals of the BAC clone RP11-165H19 mapped to 9p13.3 amplicon in cell line CWR22 and CWR22-Rv1 (A and B). C Optimal signal and lack of cross hybridization was verified using normal metaphase spreads showing two signals for each probe. BAC clone RP11-165H19 signals are green; red signals indicate chromosome 9 centromere (D9Z1).</p