High grade prostate cancer (Gleason score 8 and above) biomarker gene list and differential expression ratio in Cohort II verification sample set (80 disease and 102 controls).

<p># The 7 biomarkers were picked up from the 10 that were verified in Cohort II samples, using gene-ratio algorithm, based on the best AUC of combined gene-pair.</p>†<p>Determined by qRT-PCR analysis using SAMSN1 as a partner gene, gene ratio was calculated using delta delta Ct calculation.</p>‡<p>Calculated by Mann-Whitney test.</p>*<p>area under receiver-operating-characteristic curve.</p

PCR data from a sample set of 122 PAXgene samples of prostate cancer from the G8 group and 138 PAXgene samples from the control group were performed in a 1000×2-fold cross-validation test.

<p>Histograms of AUC were plotted and compared; results showed AUCs from the PCR data were well separated from the null sets, with an overlap of less than 5%.</p

Predictions for independent Cohort III and Cohort IV samples.

<p>The negative prediction rate for control cases is charted along with the positive prediction rates for cancer cases. PSA alone has high positive predictive rates for all cancer grades (>87%) but the combined PSA and RNA panel has lower positive prediction rates for the less aggressive G6 and G7(3+4) subgroups, 55%, and 49% respectively) while nearly the same positive prediction rate for the more aggressive G7(4+3) as G8 groups (79% and 83% respectively.</p

Gene identification and validation process.

<p>Gene Identification using Affymetrix U133Plus 2.0 GeneChip oligonucleotide arrays was carried out in Toronto, Canada, and Penang, Malaysia, in parallel. In Toronto, analysis was conducted on 166 samples (G8 = 42, G0 = 124). At the Malaysian site, 89 samples were profiled (49 G8, 40 G0). From microarray data analysis, 85 genes identified at both sites were tested in a series of quantitative real-time PCR verification studies. Twenty genes were verified through a Cohort I study on several cohorts of EDTA samples (total 245). These 20 genes were further tested in a Cohort II series of experiments on PAXgene samples (total 182), executed independently in Penang, Malaysia. 10 of the genes were verified, of which 7 genes became our final biomarkers and also confirmed in another independent sample set-Cohort III test (total 121).</p

Combined PSA and mRNA model.

<p>Inputs are CT values for genes and Log2 transformation of PSA in ng/ml.</p