scholarly journals Accuracy of The Cancer Genome Atlas Classification vs American Joint Committee on Cancer Classification for Prediction of Metastasis in Patients With Uveal Melanoma

2020 ◽  
Vol 138 (3) ◽  
pp. 260 ◽  
Author(s):  
Mehdi Mazloumi ◽  
Pornpattana Vichitvejpaisal ◽  
Lauren A. Dalvin ◽  
Antonio Yaghy ◽  
Kathryn G. Ewens ◽  
...  
Ophthalmology ◽  
2018 ◽  
Vol 125 (8) ◽  
pp. 1139-1142 ◽  
Author(s):  
Martine J. Jager ◽  
Niels J. Brouwer ◽  
Bita Esmaeli

Ophthalmology ◽  
2019 ◽  
Vol 126 (10) ◽  
pp. 1445-1453 ◽  
Author(s):  
Pornpattana Vichitvejpaisal ◽  
Lauren A. Dalvin ◽  
Mehdi Mazloumi ◽  
Kathryn G. Ewens ◽  
Arupa Ganguly ◽  
...  

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 227 ◽  
Author(s):  
Qi Wan ◽  
Xuan Sang ◽  
Lin Jin ◽  
Zhichong Wang

Growing evidence has revealed that abnormal alternative splicing (AS) events are closely related to carcinogenic processes. However, the comprehensive study on the prognostic value of splicing events involved in uveal melanoma (UM) is still lacking. Therefore, splicing data of 80 UM patients were obtained from the Cancer Genome Atlas (TCGA) SpliceSeq and RNA sequence data of UM and patient clinical features were downloaded from the Cancer Genome Atlas (TCGA) database to identify survival related splicing events in UM. As a result, a total of 37996 AS events of 17911 genes in UM were detected, among which 5299 AS events of 3529 genes were significantly associated with UM patients’ survival. Functional enrichment analysis revealed that this survival related splicing genes are corelated with mRNA catabolic process and ribosome pathway. Based on survival related splicing events, seven types of prognostic markers and the final overall prognostic signature could independently predict the overall survival of UM patients. Finally, an 11 spliced gene was identified in the final signature. On the basis of these 11 genes, we constructed a Support Vector Machine (SVM) classifier and evaluated it with leave-one-out cross-validation. The results showed that the 11 genes could determine short- and long-term survival with a predicted accuracy of 97.5%. Besides, the splicing factors and alternative splicing events correlation network was constructed to serve as therapeutic targets for UM treatment. Thus, our study depicts a comprehensive landscape of alternative splicing events in the prognosis of UM. The correlation network and associated pathways would provide additional potential targets for therapy and prognosis.


Endocrine ◽  
2020 ◽  
Author(s):  
Anello Marcello Poma ◽  
Elisabetta Macerola ◽  
Liborio Torregrossa ◽  
Rossella Elisei ◽  
Ferruccio Santini ◽  
...  

Abstract Purpose The 8th edition of the American Joint Committee on Cancer (AJCC) staging led to a significant downstaging of well differentiated thyroid cancer patients. However, some patients who had been downstaged still experienced death. By using data from the thyroid cancer dataset of The Cancer Genome Atlas (TCGA), we aimed to find molecular features that could improve survival prediction. Methods TCGA data were downloaded from cBioPortal. Restaging of cases was performed according to the pathological reports. Results Out of 496 cases, 204 (41.1%) were downstaged, and the proportion of deaths increased in stages III and IV. TERT promoter mutations were no longer enriched in stage IV only, but significantly redistributed also in stages II and III. TERT mutation was the only alteration predictive of poor survival; however, in this series it was not independent from the AJCC staging. Five proteins (4E-BP1_pT70, Chk1_pS345, Snail, STAT5 alpha and PAI-1) were significantly associated with survival, and their use as a panel refined the risk stratification independently from the AJCC staging, with a hazard ratio for a positive result of 21.2 (95%CI 3.7–122.2, P = 0.0006). Conclusions In the TCGA series, the proportion of deaths is in line with the expected survival of the latest AJCC staging, with a neat separation of risk among stages. Nevertheless, the use of protein expression can be useful in refining the stratification. Finally, after the restaging, a considerable number of tumors with TERT mutations will be allocated in lower stages; hence, dedicated studies should define the prognostic usefulness of these mutations in low-stage diseases.


2019 ◽  
Vol 67 (12) ◽  
pp. 1959 ◽  
Author(s):  
CarolL Shields ◽  
LaurenA Dalvin ◽  
Pornpattana Vichitvejpaisal ◽  
Mehdi Mazloumi ◽  
Arupa Ganguly ◽  
...  

Cancers ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 1061 ◽  
Author(s):  
Mathieu F. Bakhoum ◽  
Bita Esmaeli

The Cancer Genome Atlas (TCGA) uveal melanoma project was a comprehensive multi-platform deep molecular investigation of 80 uveal melanoma primary tissue samples supported by the National Cancer Institute. In addition to identification of important mutations for the first time, it identified four different clusters (subgroups) of patients paralleling prognosis. The findings of the TCGA marker paper are summarized in this review manuscript and other investigations that have stemmed from the findings of the TCGA project are reviewed.


2021 ◽  
Vol 69 (7) ◽  
pp. 1839
Author(s):  
CarolL Shields ◽  
EileenL Mayro ◽  
Zeynep Bas ◽  
PhilipW Dockery ◽  
Antonio Yaghy ◽  
...  

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