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  • Test of four colon cancer risk-scores in formalin fixed paraffin embedded microarray gene expression data.

Test of four colon cancer risk-scores in formalin fixed paraffin embedded microarray gene expression data.

Journal of the National Cancer Institute (2014-09-24)
Antonio F Di Narzo, Sabine Tejpar, Simona Rossi, Pu Yan, Vlad Popovici, Pratyaksha Wirapati, Eva Budinska, Tao Xie, Heather Estrella, Adam Pavlicek, Mao Mao, Eric Martin, Weinrich Scott, Fred T Bosman, Arnaud Roth, Mauro Delorenzi
ABSTRACT

Prognosis prediction for resected primary colon cancer is based on the T-stage Node Metastasis (TNM) staging system. We investigated if four well-documented gene expression risk scores can improve patient stratification. Microarray-based versions of risk-scores were applied to a large independent cohort of 688 stage II/III tumors from the PETACC-3 trial. Prognostic value for relapse-free survival (RFS), survival after relapse (SAR), and overall survival (OS) was assessed by regression analysis. To assess improvement over a reference, prognostic model was assessed with the area under curve (AUC) of receiver operating characteristic (ROC) curves. All statistical tests were two-sided, except the AUC increase. All four risk scores (RSs) showed a statistically significant association (single-test, P < .0167) with OS or RFS in univariate models, but with HRs below 1.38 per interquartile range. Three scores were predictors of shorter RFS, one of shorter SAR. Each RS could only marginally improve an RFS or OS model with the known factors T-stage, N-stage, and microsatellite instability (MSI) status (AUC gains < 0.025 units). The pairwise interscore discordance was never high (maximal Spearman correlation = 0.563) A combined score showed a trend to higher prognostic value and higher AUC increase for OS (HR = 1.74, 95% confidence interval [CI] = 1.44 to 2.10, P < .001, AUC from 0.6918 to 0.7321) and RFS (HR = 1.56, 95% CI = 1.33 to 1.84, P < .001, AUC from 0.6723 to 0.6945) than any single score. The four tested gene expression-based risk scores provide prognostic information but contribute only marginally to improving models based on established risk factors. A combination of the risk scores might provide more robust information. Predictors of RFS and SAR might need to be different.

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Paraffin (Yellow soft), European Pharmacopoeia (EP) Reference Standard
Paraffin (hard), European Pharmacopoeia (EP) Reference Standard
Paraffin (White soft), European Pharmacopoeia (EP) Reference Standard
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Formaldehyde solution, contains 10-15% methanol as stabilizer, 37 wt. % in H2O
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Formaldehyde solution, ACS reagent, 37 wt. % in H2O, contains 10-15% Methanol as stabilizer (to prevent polymerization)
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Formaldehyde solution, meets analytical specification of USP, ≥34.5 wt. %
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Formaldehyde solution, stabilized with methanol, ~37 wt. % in H2O, certified reference material
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Formaldehyde solution, for molecular biology, 36.5-38% in H2O
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Paraffin wax, meets analytical specification of Ph. Eur., white, pastilles
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Paraffin wax, mp 53-58 °C (ASTM D 87)
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Paraffin wax, mp 58-62 °C (ASTM D 87)
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Paraffin wax, mp ≥65 °C (ASTM D 87)
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