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- Dyrskjot, L., et al.
(författare)
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Analysis of molecular intra-patient variation and delineation of a prognostic 12-gene signature in non-muscle invasive bladder cancer; technology transfer from microarrays to PCR
- 2012
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Ingår i: British Journal of Cancer. - : Springer Science and Business Media LLC. - 0007-0920 .- 1532-1827. ; 107:8, s. 1392-1398
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Multiple clinical risk factors and genetic profiles have been demonstrated to predict progression of non-muscle invasive bladder cancer; however, no easily clinical applicable gene signature has been developed to predict disease progression independent of disease stage and grade. METHODS: We measured the intra-patient variation of an 88-gene progression signature using 39 metachronous tumours from 17 patients. For delineation of the optimal quantitative reverse transcriptase PCR panel of markers, we used 115 tumour samples from patients in Denmark, Sweden, UK and Spain. RESULTS: Analysis of intra-patient variation of the molecular markers showed 71% similar classification results. A final panel of 12 genes was selected, showing significant correlation with outcome. In multivariate Cox regression analysis, we found that the 12-gene signature was an independent prognostic factor (hazard ratio = 7.4 (95% confidence interval: 3.4-15.9), P < 0.001) when adjusting for stage, grade and treatment. Independent validation of the 12-gene panel and the determined cut-off values is needed and ongoing. CONCLUSION: Intra-patient marker variation in metachronous tumours is present. Therefore, to increase test sensitivity, it may be necessary to test several metachronous tumours from a patient's disease course. A PCR-based 12-gene signature significantly predicts disease progression in patients with non-muscle invasive bladder cancer.
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| 2. |
- Karlsen, Reinert Huseby, et al.
(författare)
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A post audit and inverse modeling in reactive transport : 50 years of artificial recharge in the Amsterdam Water Supply Dunes
- 2012
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Ingår i: Journal of Hydrology. - : Elsevier BV. - 0022-1694 .- 1879-2707. ; 454, s. 7-25
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Tidskriftsartikel (refereegranskat)abstract
- This article describes the post audit and inverse modeling of a 1-D forward reactive transport model. The model simulates the changes in water quality following artificial recharge of pre-treated water from the river Rhine in the Amsterdam Water Supply Dunes using the PHREEQC-2 numerical code. One observation dataset is used for model calibration, and another dataset for validation of model predictions. The total simulation time of the model is 50 years, from 1957 10 2007, with recharge composition varying on a monthly basis and the post audit is performed 26 years after the former model simulation period. The post audit revealed that the original model could reasonably predict conservative transport and kinetic redox reactions (oxygen and nitrate reduction coupled to the oxidation of soil organic carbon), but showed discrepancies in the simulation of cation exchange. Conceptualizations of the former model were inadequate to accurately simulate water quality changes controlled by cation exchange, especially concerning the breakthrough of potassium and magnesium fronts. Changes in conceptualization and model design, including the addition of five flow paths, to a total of six, and the use of parameter estimation software (PEST), resulted in a better model to measurement fit and system representation. No unique parameter set could be found for the model, primarily due to high parameter correlations, and an assessment of the predictive error was made using a calibration constrained Monte-Carlo method, and evaluated against field observations. The predictive error was found to be low for Na+ and Ca2+, except for greater travel times, while the K+ and Mg2+ error was restricted to the exchange fronts at some of the flow paths. Optimized cation exchange coefficients were relatively high, especially for potassium, but still within the observed range in literature. The exchange coefficient for potassium agrees with strong fixation on illite, a main clay mineral in the area. Optimized CEC values were systematically lower than clay and organic matter contents indicated, possibly reflecting preferential flow of groundwater through the more permeable but less reactive aquifer parts. Whereas the artificial recharge initially acted as an intrusion of relatively saline water triggering Na+ for Ca2+ exchange, further increasing total hardness of the recharged water, the gradual long-term reduction in salinity of the river Rhine since the mid 1970s has shifted to an intrusion of fresher water causing Ca2+ for Na+ exchange. As a result, seasonal and longer term reversal of the initial cation exchange processes was observed adding to the general long-term reduction in total hardness of the recharged Rhine water.
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