Figures & data
Figure 1. Selection of candidate genes by cDNA microarray analysis.
(A) Strategy to find biomarkers is schematically shown. First, DEGs were screened by cDNA microarray and the expression levels of screened genes were verified by quantitative RT-PCR using 30 glioblastoma multiforme patients in a discovery set. Second, these verified DEGs were validated using different 23 GBM patients in a validation set. Finally, only SDC-4 was identified as a biomarker. (B) A volcano plot was generated. Each dot corresponds to one gene. X- and y-axes indicate fold change (log2[short/long]) of signal intensities of individual genes and the statistical significance (-log10[p-value]) of the difference in the signal intensities of individual genes between long- and short-term survivors, respectively. Dashed line indicates y = |x|–1, y = 1 and |x| = 0.5. (C) Thirty-two candidate DEGs were extracted as described in the text. Gene names and their statistical evaluations are shown in .
DEG: Differentially expressed gene.
![Figure 1. Selection of candidate genes by cDNA microarray analysis.(A) Strategy to find biomarkers is schematically shown. First, DEGs were screened by cDNA microarray and the expression levels of screened genes were verified by quantitative RT-PCR using 30 glioblastoma multiforme patients in a discovery set. Second, these verified DEGs were validated using different 23 GBM patients in a validation set. Finally, only SDC-4 was identified as a biomarker. (B) A volcano plot was generated. Each dot corresponds to one gene. X- and y-axes indicate fold change (log2[short/long]) of signal intensities of individual genes and the statistical significance (-log10[p-value]) of the difference in the signal intensities of individual genes between long- and short-term survivors, respectively. Dashed line indicates y = |x|–1, y = 1 and |x| = 0.5. (C) Thirty-two candidate DEGs were extracted as described in the text. Gene names and their statistical evaluations are shown in Table 2.DEG: Differentially expressed gene.](/cms/asset/0529dda8-b9f5-4bb1-9534-ddce30c72520/ifso_a_12363932_f0001.jpg)
Figure 2. SDC-4 is a prediction marker for overall survival.
(A) AUC-maximized receiver operating characteristic curve was generated. Optimal cut-off value, 0.001 of SDC-4 relative expression levels (log2[1 + 2−ΔCT]) discriminates between long-term (OS ≥256 days) and short-term (OS <256 days) survivors, and SDC-4 expression levels in long-term survivors are ≤0.001. Statistical capabilities are 70.4% sensitivity, 76.0% specificity, 76.0% positive predictive value, 70.4% negative predictive value and 73.1% accuracy, and a Chi-square test shows a statistical significance (p < 0.001). All the 53 patients in the discovery and validation sets are included in this analysis. (B) Kaplan–Meier curves of OS (days) of patients with ≤0.001 (SDC-4 low) and >0.001 (SDC-4 high) of SDC-4-expression levels are shown. Comparison of OS between the two groups is performed using a two-sided log-rank test, and the difference in OS is statistically significant (p < 0.001). One-year OS rates were 64.0 and 18.5% in SDC-4-low and -high patients, respectively.
OS: Overall survival.
![Figure 2. SDC-4 is a prediction marker for overall survival.(A) AUC-maximized receiver operating characteristic curve was generated. Optimal cut-off value, 0.001 of SDC-4 relative expression levels (log2[1 + 2−ΔCT]) discriminates between long-term (OS ≥256 days) and short-term (OS <256 days) survivors, and SDC-4 expression levels in long-term survivors are ≤0.001. Statistical capabilities are 70.4% sensitivity, 76.0% specificity, 76.0% positive predictive value, 70.4% negative predictive value and 73.1% accuracy, and a Chi-square test shows a statistical significance (p < 0.001). All the 53 patients in the discovery and validation sets are included in this analysis. (B) Kaplan–Meier curves of OS (days) of patients with ≤0.001 (SDC-4 low) and >0.001 (SDC-4 high) of SDC-4-expression levels are shown. Comparison of OS between the two groups is performed using a two-sided log-rank test, and the difference in OS is statistically significant (p < 0.001). One-year OS rates were 64.0 and 18.5% in SDC-4-low and -high patients, respectively.OS: Overall survival.](/cms/asset/776828eb-ed15-4285-befe-0b23f614daa1/ifso_a_12363932_f0002.jpg)
Table 1. Patients’ characteristics in a discovery set.
Table 2. Thirty-two candidate genes that differentially expressed between long- and short-term survivors in peripheral blood mononuclear cells prior to WT1 peptide vaccination in 30 glioblastoma multiforme patients in a discovery set.
Table 3. Verification of 32 candidate genes by quantitative RT-PCR.
Table 4. Patients’ characteristics in a validation set.
Table 5. Validation of 15 candidate genes using different 23 glioblastoma multiforme patients in a validation set.