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Henry Han - One of the best experts on this subject based on the ideXlab platform.
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multi resolution independent component analysis for high performance Tumor Classification and biomarker discovery
BMC Bioinformatics, 2011Co-Authors: Henry HanAbstract:Background Although high-throughput microarray based molecular diagnostic technologies show a great promise in cancer diagnosis, it is still far from a clinical application due to its low and instable sensitivities and specificities in cancer molecular pattern recognition. In fact, high-dimensional and heterogeneous Tumor profiles challenge current machine learning methodologies for its small number of samples and large or even huge number of variables (genes). This naturally calls for the use of an effective feature selection in microarray data Classification.
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multi resolution independent component analysis for high performance Tumor Classification and biomarker discovery
BMC Bioinformatics, 2011Co-Authors: Henry HanAbstract:Although high-throughput microarray based molecular diagnostic technologies show a great promise in cancer diagnosis, it is still far from a clinical application due to its low and instable sensitivities and specificities in cancer molecular pattern recognition. In fact, high-dimensional and heterogeneous Tumor profiles challenge current machine learning methodologies for its small number of samples and large or even huge number of variables (genes). This naturally calls for the use of an effective feature selection in microarray data Classification. We propose a novel feature selection method: multi-resolution independent component analysis (MICA) for large-scale gene expression data. This method overcomes the weak points of the widely used transform-based feature selection methods such as principal component analysis (PCA), independent component analysis (ICA), and nonnegative matrix factorization (NMF) by avoiding their global feature-selection mechanism. In addition to demonstrating the effectiveness of the multi-resolution independent component analysis in meaningful biomarker discovery, we present a multi-resolution independent component analysis based support vector machines (MICA-SVM) and linear discriminant analysis (MICA-LDA) to attain high-performance Classifications in low-dimensional spaces. We have demonstrated the superiority and stability of our algorithms by performing comprehensive experimental comparisons with nine state-of-the-art algorithms on six high-dimensional heterogeneous profiles under cross validations. Our Classification algorithms, especially, MICA-SVM, not only accomplish clinical or near-clinical level sensitivities and specificities, but also show strong performance stability over its peers in Classification. Software that implements the major algorithm and data sets on which this paper focuses are freely available at https://sites.google.com/site/heyaumapbc2011/ . This work suggests a new direction to accelerate microarray technologies into a clinical routine through building a high-performance classifier to attain clinical-level sensitivities and specificities by treating an input profile as a ‘profile-biomarker’. The multi-resolution data analysis based redundant global feature suppressing and effective local feature extraction also have a positive impact on large scale ‘omics’ data mining.
Michael L Blute - One of the best experts on this subject based on the ideXlab platform.
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independent validation of the 2002 american joint committee on cancer primary Tumor Classification for renal cell carcinoma using a large single institution cohort
The Journal of Urology, 2005Co-Authors: Igor Frank, Michael L Blute, Bradley C Leibovich, John C Cheville, Christine M Lohse, Horst ZinckeAbstract:Purpose: The primary Tumor Classification for renal cell carcinoma (RCC) was updated by the American Joint Committee on Cancer in 2002. To date the new Classification has not been validated using an independent group of patients and, therefore, its accuracy for predicting patient outcome is unknown. In the current study we evaluated the 2002 primary Tumor Classification and compared its predictive ability with that of the 1997 Classification. Materials and Methods: We studied 2,746 patients treated with radical nephrectomy or nephron sparing surgery for unilateral, sporadic RCC between 1970 and 2000. Cancer specific survival was estimated using the Kaplan-Meier method. The predictive abilities of the 1997 and 2002 Classifications were compared using the concordance index. Results: There were 812 deaths from RCC a mean of 3.3 years following nephrectomy. Median followup in patients still alive at last followup was 9 years. Estimated 5-year cancer specific survival rates by the 2002 Tumor Classification were 97%, 87%, 71%, 53%, 44%, 37% and 20% in patients with pT1a, pT1b, pT2, pT3a, pT3b, pT3c and pT4 RCC, respectively. The concordance index for the association between the 2002 Classification and death from RCC was 0.752 compared with 0.737 for the 1997 Classification, indicating that the 2002 version contained more predictive ability. Conclusions: Our data suggest that the 2002 primary Tumor Classification with pT1 cancers subclassified into pT1a and pT1b provides excellent stratification of patients according to cancer specific survival and it has a predictive ability that is superior to that of the 1997 Classification.
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cancer specific survival for patients with pt3 renal cell carcinoma can the 2002 primary Tumor Classification be improved
The Journal of Urology, 2005Co-Authors: Bradley C Leibovich, Igor Frank, John C Cheville, Christine M Lohse, Horst Zincke, Eugene D Kwon, Houston R Thompson, Michael L BluteAbstract:ABSTRACT Purpose: The 2002 primary Tumor Classification for renal cell carcinoma (RCC) does not distinguish between patients with Tumor thrombus involving the renal vein only and those with inferior vena cava Tumor thrombus below the diaphragm. We evaluated the association of Tumor thrombus level and fat invasion with outcome to determine if further subClassification would improve the prognostic accuracy of the current Classification. Materials and Methods: We studied 675 patients treated with radical nephrectomy or nephron sparing surgery for pT3a (206, 30.5%), pT3b (422, 62.5%), pT3c (19, 2.8%) or pT4 (28, 4.2%) RCC at the Mayo Clinic between 1970 and 2000. Associations with outcome were evaluated using Cox proportional hazards regression. Results: There were 531 deaths from RCC at a median of 1.5 years following nephrectomy. Patients with pT3b RCC and level I, II or III Tumor thrombus were significantly more likely to die of RCC compared to patients with pT3b RCC and level 0 Tumor thrombus (risk ratio 1.62, p Conclusions: Further subClassification of the primary Tumor Classification for patients with pT3 RCC improved prognostic accuracy.
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cancer specific survival for patients with pt3 renal cell carcinoma can the 2002 primary Tumor Classification be improved
The Journal of Urology, 2005Co-Authors: Bradley C Leibovich, Igor Frank, John C Cheville, Christine M Lohse, Horst Zincke, Eugene D Kwon, Houston R Thompson, Michael L BluteAbstract:PURPOSE: The 2002 primary Tumor Classification for renal cell carcinoma (RCC) does not distinguish between patients with Tumor thrombus involving the renal vein only and those with inferior vena cava Tumor thrombus below the diaphragm. We evaluated the association of Tumor thrombus level and fat invasion with outcome to determine if further subClassification would improve the prognostic accuracy of the current Classification. MATERIALS AND METHODS: We studied 675 patients treated with radical nephrectomy or nephron sparing surgery for pT3a (206, 30.5%), pT3b (422, 62.5%), pT3c (19, 2.8%) or pT4 (28, 4.2%) RCC at the Mayo Clinic between 1970 and 2000. Associations with outcome were evaluated using Cox proportional hazards regression. RESULTS: There were 531 deaths from RCC at a median of 1.5 years following nephrectomy. Patients with pT3b RCC and level I, II or III Tumor thrombus were significantly more likely to die of RCC compared to patients with pT3b RCC and level 0 Tumor thrombus (risk ratio 1.62, p <0.001). Patients with peripheral perinephric or renal sinus fat invasion were also more likely to die of RCC compared to patients without fat invasion (risk ratio 1.87, p <0.001). Therefore, patients with pT3 RCC were reclassified into 4 groups as thrombus level 0 without fat invasion, fat invasion only, thrombus level 0 with fat invasion or thrombus level I, II or III without fat invasion, and thrombus level I, II or III with fat invasion or thrombus level IV. This reClassification significantly improved prediction of death from RCC compared with the current Classification (c indexes of 0.61 versus 0.55, respectively). CONCLUSIONS: Further subClassification of the primary Tumor Classification for patients with pT3 RCC improved prognostic accuracy.
Horst Zincke - One of the best experts on this subject based on the ideXlab platform.
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independent validation of the 2002 american joint committee on cancer primary Tumor Classification for renal cell carcinoma using a large single institution cohort
The Journal of Urology, 2005Co-Authors: Igor Frank, Michael L Blute, Bradley C Leibovich, John C Cheville, Christine M Lohse, Horst ZinckeAbstract:Purpose: The primary Tumor Classification for renal cell carcinoma (RCC) was updated by the American Joint Committee on Cancer in 2002. To date the new Classification has not been validated using an independent group of patients and, therefore, its accuracy for predicting patient outcome is unknown. In the current study we evaluated the 2002 primary Tumor Classification and compared its predictive ability with that of the 1997 Classification. Materials and Methods: We studied 2,746 patients treated with radical nephrectomy or nephron sparing surgery for unilateral, sporadic RCC between 1970 and 2000. Cancer specific survival was estimated using the Kaplan-Meier method. The predictive abilities of the 1997 and 2002 Classifications were compared using the concordance index. Results: There were 812 deaths from RCC a mean of 3.3 years following nephrectomy. Median followup in patients still alive at last followup was 9 years. Estimated 5-year cancer specific survival rates by the 2002 Tumor Classification were 97%, 87%, 71%, 53%, 44%, 37% and 20% in patients with pT1a, pT1b, pT2, pT3a, pT3b, pT3c and pT4 RCC, respectively. The concordance index for the association between the 2002 Classification and death from RCC was 0.752 compared with 0.737 for the 1997 Classification, indicating that the 2002 version contained more predictive ability. Conclusions: Our data suggest that the 2002 primary Tumor Classification with pT1 cancers subclassified into pT1a and pT1b provides excellent stratification of patients according to cancer specific survival and it has a predictive ability that is superior to that of the 1997 Classification.
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cancer specific survival for patients with pt3 renal cell carcinoma can the 2002 primary Tumor Classification be improved
The Journal of Urology, 2005Co-Authors: Bradley C Leibovich, Igor Frank, John C Cheville, Christine M Lohse, Horst Zincke, Eugene D Kwon, Houston R Thompson, Michael L BluteAbstract:ABSTRACT Purpose: The 2002 primary Tumor Classification for renal cell carcinoma (RCC) does not distinguish between patients with Tumor thrombus involving the renal vein only and those with inferior vena cava Tumor thrombus below the diaphragm. We evaluated the association of Tumor thrombus level and fat invasion with outcome to determine if further subClassification would improve the prognostic accuracy of the current Classification. Materials and Methods: We studied 675 patients treated with radical nephrectomy or nephron sparing surgery for pT3a (206, 30.5%), pT3b (422, 62.5%), pT3c (19, 2.8%) or pT4 (28, 4.2%) RCC at the Mayo Clinic between 1970 and 2000. Associations with outcome were evaluated using Cox proportional hazards regression. Results: There were 531 deaths from RCC at a median of 1.5 years following nephrectomy. Patients with pT3b RCC and level I, II or III Tumor thrombus were significantly more likely to die of RCC compared to patients with pT3b RCC and level 0 Tumor thrombus (risk ratio 1.62, p Conclusions: Further subClassification of the primary Tumor Classification for patients with pT3 RCC improved prognostic accuracy.
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cancer specific survival for patients with pt3 renal cell carcinoma can the 2002 primary Tumor Classification be improved
The Journal of Urology, 2005Co-Authors: Bradley C Leibovich, Igor Frank, John C Cheville, Christine M Lohse, Horst Zincke, Eugene D Kwon, Houston R Thompson, Michael L BluteAbstract:PURPOSE: The 2002 primary Tumor Classification for renal cell carcinoma (RCC) does not distinguish between patients with Tumor thrombus involving the renal vein only and those with inferior vena cava Tumor thrombus below the diaphragm. We evaluated the association of Tumor thrombus level and fat invasion with outcome to determine if further subClassification would improve the prognostic accuracy of the current Classification. MATERIALS AND METHODS: We studied 675 patients treated with radical nephrectomy or nephron sparing surgery for pT3a (206, 30.5%), pT3b (422, 62.5%), pT3c (19, 2.8%) or pT4 (28, 4.2%) RCC at the Mayo Clinic between 1970 and 2000. Associations with outcome were evaluated using Cox proportional hazards regression. RESULTS: There were 531 deaths from RCC at a median of 1.5 years following nephrectomy. Patients with pT3b RCC and level I, II or III Tumor thrombus were significantly more likely to die of RCC compared to patients with pT3b RCC and level 0 Tumor thrombus (risk ratio 1.62, p <0.001). Patients with peripheral perinephric or renal sinus fat invasion were also more likely to die of RCC compared to patients without fat invasion (risk ratio 1.87, p <0.001). Therefore, patients with pT3 RCC were reclassified into 4 groups as thrombus level 0 without fat invasion, fat invasion only, thrombus level 0 with fat invasion or thrombus level I, II or III without fat invasion, and thrombus level I, II or III with fat invasion or thrombus level IV. This reClassification significantly improved prediction of death from RCC compared with the current Classification (c indexes of 0.61 versus 0.55, respectively). CONCLUSIONS: Further subClassification of the primary Tumor Classification for patients with pT3 RCC improved prognostic accuracy.
Bradley C Leibovich - One of the best experts on this subject based on the ideXlab platform.
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independent validation of the 2002 american joint committee on cancer primary Tumor Classification for renal cell carcinoma using a large single institution cohort
The Journal of Urology, 2005Co-Authors: Igor Frank, Michael L Blute, Bradley C Leibovich, John C Cheville, Christine M Lohse, Horst ZinckeAbstract:Purpose: The primary Tumor Classification for renal cell carcinoma (RCC) was updated by the American Joint Committee on Cancer in 2002. To date the new Classification has not been validated using an independent group of patients and, therefore, its accuracy for predicting patient outcome is unknown. In the current study we evaluated the 2002 primary Tumor Classification and compared its predictive ability with that of the 1997 Classification. Materials and Methods: We studied 2,746 patients treated with radical nephrectomy or nephron sparing surgery for unilateral, sporadic RCC between 1970 and 2000. Cancer specific survival was estimated using the Kaplan-Meier method. The predictive abilities of the 1997 and 2002 Classifications were compared using the concordance index. Results: There were 812 deaths from RCC a mean of 3.3 years following nephrectomy. Median followup in patients still alive at last followup was 9 years. Estimated 5-year cancer specific survival rates by the 2002 Tumor Classification were 97%, 87%, 71%, 53%, 44%, 37% and 20% in patients with pT1a, pT1b, pT2, pT3a, pT3b, pT3c and pT4 RCC, respectively. The concordance index for the association between the 2002 Classification and death from RCC was 0.752 compared with 0.737 for the 1997 Classification, indicating that the 2002 version contained more predictive ability. Conclusions: Our data suggest that the 2002 primary Tumor Classification with pT1 cancers subclassified into pT1a and pT1b provides excellent stratification of patients according to cancer specific survival and it has a predictive ability that is superior to that of the 1997 Classification.
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cancer specific survival for patients with pt3 renal cell carcinoma can the 2002 primary Tumor Classification be improved
The Journal of Urology, 2005Co-Authors: Bradley C Leibovich, Igor Frank, John C Cheville, Christine M Lohse, Horst Zincke, Eugene D Kwon, Houston R Thompson, Michael L BluteAbstract:ABSTRACT Purpose: The 2002 primary Tumor Classification for renal cell carcinoma (RCC) does not distinguish between patients with Tumor thrombus involving the renal vein only and those with inferior vena cava Tumor thrombus below the diaphragm. We evaluated the association of Tumor thrombus level and fat invasion with outcome to determine if further subClassification would improve the prognostic accuracy of the current Classification. Materials and Methods: We studied 675 patients treated with radical nephrectomy or nephron sparing surgery for pT3a (206, 30.5%), pT3b (422, 62.5%), pT3c (19, 2.8%) or pT4 (28, 4.2%) RCC at the Mayo Clinic between 1970 and 2000. Associations with outcome were evaluated using Cox proportional hazards regression. Results: There were 531 deaths from RCC at a median of 1.5 years following nephrectomy. Patients with pT3b RCC and level I, II or III Tumor thrombus were significantly more likely to die of RCC compared to patients with pT3b RCC and level 0 Tumor thrombus (risk ratio 1.62, p Conclusions: Further subClassification of the primary Tumor Classification for patients with pT3 RCC improved prognostic accuracy.
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cancer specific survival for patients with pt3 renal cell carcinoma can the 2002 primary Tumor Classification be improved
The Journal of Urology, 2005Co-Authors: Bradley C Leibovich, Igor Frank, John C Cheville, Christine M Lohse, Horst Zincke, Eugene D Kwon, Houston R Thompson, Michael L BluteAbstract:PURPOSE: The 2002 primary Tumor Classification for renal cell carcinoma (RCC) does not distinguish between patients with Tumor thrombus involving the renal vein only and those with inferior vena cava Tumor thrombus below the diaphragm. We evaluated the association of Tumor thrombus level and fat invasion with outcome to determine if further subClassification would improve the prognostic accuracy of the current Classification. MATERIALS AND METHODS: We studied 675 patients treated with radical nephrectomy or nephron sparing surgery for pT3a (206, 30.5%), pT3b (422, 62.5%), pT3c (19, 2.8%) or pT4 (28, 4.2%) RCC at the Mayo Clinic between 1970 and 2000. Associations with outcome were evaluated using Cox proportional hazards regression. RESULTS: There were 531 deaths from RCC at a median of 1.5 years following nephrectomy. Patients with pT3b RCC and level I, II or III Tumor thrombus were significantly more likely to die of RCC compared to patients with pT3b RCC and level 0 Tumor thrombus (risk ratio 1.62, p <0.001). Patients with peripheral perinephric or renal sinus fat invasion were also more likely to die of RCC compared to patients without fat invasion (risk ratio 1.87, p <0.001). Therefore, patients with pT3 RCC were reclassified into 4 groups as thrombus level 0 without fat invasion, fat invasion only, thrombus level 0 with fat invasion or thrombus level I, II or III without fat invasion, and thrombus level I, II or III with fat invasion or thrombus level IV. This reClassification significantly improved prediction of death from RCC compared with the current Classification (c indexes of 0.61 versus 0.55, respectively). CONCLUSIONS: Further subClassification of the primary Tumor Classification for patients with pT3 RCC improved prognostic accuracy.
Igor Frank - One of the best experts on this subject based on the ideXlab platform.
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independent validation of the 2002 american joint committee on cancer primary Tumor Classification for renal cell carcinoma using a large single institution cohort
The Journal of Urology, 2005Co-Authors: Igor Frank, Michael L Blute, Bradley C Leibovich, John C Cheville, Christine M Lohse, Horst ZinckeAbstract:Purpose: The primary Tumor Classification for renal cell carcinoma (RCC) was updated by the American Joint Committee on Cancer in 2002. To date the new Classification has not been validated using an independent group of patients and, therefore, its accuracy for predicting patient outcome is unknown. In the current study we evaluated the 2002 primary Tumor Classification and compared its predictive ability with that of the 1997 Classification. Materials and Methods: We studied 2,746 patients treated with radical nephrectomy or nephron sparing surgery for unilateral, sporadic RCC between 1970 and 2000. Cancer specific survival was estimated using the Kaplan-Meier method. The predictive abilities of the 1997 and 2002 Classifications were compared using the concordance index. Results: There were 812 deaths from RCC a mean of 3.3 years following nephrectomy. Median followup in patients still alive at last followup was 9 years. Estimated 5-year cancer specific survival rates by the 2002 Tumor Classification were 97%, 87%, 71%, 53%, 44%, 37% and 20% in patients with pT1a, pT1b, pT2, pT3a, pT3b, pT3c and pT4 RCC, respectively. The concordance index for the association between the 2002 Classification and death from RCC was 0.752 compared with 0.737 for the 1997 Classification, indicating that the 2002 version contained more predictive ability. Conclusions: Our data suggest that the 2002 primary Tumor Classification with pT1 cancers subclassified into pT1a and pT1b provides excellent stratification of patients according to cancer specific survival and it has a predictive ability that is superior to that of the 1997 Classification.
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cancer specific survival for patients with pt3 renal cell carcinoma can the 2002 primary Tumor Classification be improved
The Journal of Urology, 2005Co-Authors: Bradley C Leibovich, Igor Frank, John C Cheville, Christine M Lohse, Horst Zincke, Eugene D Kwon, Houston R Thompson, Michael L BluteAbstract:ABSTRACT Purpose: The 2002 primary Tumor Classification for renal cell carcinoma (RCC) does not distinguish between patients with Tumor thrombus involving the renal vein only and those with inferior vena cava Tumor thrombus below the diaphragm. We evaluated the association of Tumor thrombus level and fat invasion with outcome to determine if further subClassification would improve the prognostic accuracy of the current Classification. Materials and Methods: We studied 675 patients treated with radical nephrectomy or nephron sparing surgery for pT3a (206, 30.5%), pT3b (422, 62.5%), pT3c (19, 2.8%) or pT4 (28, 4.2%) RCC at the Mayo Clinic between 1970 and 2000. Associations with outcome were evaluated using Cox proportional hazards regression. Results: There were 531 deaths from RCC at a median of 1.5 years following nephrectomy. Patients with pT3b RCC and level I, II or III Tumor thrombus were significantly more likely to die of RCC compared to patients with pT3b RCC and level 0 Tumor thrombus (risk ratio 1.62, p Conclusions: Further subClassification of the primary Tumor Classification for patients with pT3 RCC improved prognostic accuracy.
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cancer specific survival for patients with pt3 renal cell carcinoma can the 2002 primary Tumor Classification be improved
The Journal of Urology, 2005Co-Authors: Bradley C Leibovich, Igor Frank, John C Cheville, Christine M Lohse, Horst Zincke, Eugene D Kwon, Houston R Thompson, Michael L BluteAbstract:PURPOSE: The 2002 primary Tumor Classification for renal cell carcinoma (RCC) does not distinguish between patients with Tumor thrombus involving the renal vein only and those with inferior vena cava Tumor thrombus below the diaphragm. We evaluated the association of Tumor thrombus level and fat invasion with outcome to determine if further subClassification would improve the prognostic accuracy of the current Classification. MATERIALS AND METHODS: We studied 675 patients treated with radical nephrectomy or nephron sparing surgery for pT3a (206, 30.5%), pT3b (422, 62.5%), pT3c (19, 2.8%) or pT4 (28, 4.2%) RCC at the Mayo Clinic between 1970 and 2000. Associations with outcome were evaluated using Cox proportional hazards regression. RESULTS: There were 531 deaths from RCC at a median of 1.5 years following nephrectomy. Patients with pT3b RCC and level I, II or III Tumor thrombus were significantly more likely to die of RCC compared to patients with pT3b RCC and level 0 Tumor thrombus (risk ratio 1.62, p <0.001). Patients with peripheral perinephric or renal sinus fat invasion were also more likely to die of RCC compared to patients without fat invasion (risk ratio 1.87, p <0.001). Therefore, patients with pT3 RCC were reclassified into 4 groups as thrombus level 0 without fat invasion, fat invasion only, thrombus level 0 with fat invasion or thrombus level I, II or III without fat invasion, and thrombus level I, II or III with fat invasion or thrombus level IV. This reClassification significantly improved prediction of death from RCC compared with the current Classification (c indexes of 0.61 versus 0.55, respectively). CONCLUSIONS: Further subClassification of the primary Tumor Classification for patients with pT3 RCC improved prognostic accuracy.
