Genetic Analysis of Uveal Melanoma in 658 Patients Using the Cancer Genome Atlas Classification of Uveal Melanoma as A, B, C, and D

Ophthalmology ◽  
2019 ◽  
Vol 126 (10) ◽  
pp. 1445-1453 ◽  
Author(s):  
Pornpattana Vichitvejpaisal ◽  
Lauren A. Dalvin ◽  
Mehdi Mazloumi ◽  
Kathryn G. Ewens ◽  
Arupa Ganguly ◽  
...  
Ophthalmology ◽  
2018 ◽  
Vol 125 (8) ◽  
pp. 1139-1142 ◽  
Author(s):  
Martine J. Jager ◽  
Niels J. Brouwer ◽  
Bita Esmaeli

2021 ◽  
Vol 145 (11) ◽  
pp. 1367-1378
Author(s):  
Minhua Wang ◽  
Pei Hui

Context.— Endometrial carcinoma is the most common gynecologic malignancy in the United States and has been traditionally classified based on histology. However, the distinction of certain histologic subtypes based on morphology is not uncommonly problematic, and as such, immunohistochemical study is often needed. Advances in comprehensive tumor sequencing have provided novel molecular profiles of endometrial carcinomas. Four distinct molecular subtypes with different prognostic values have been proposed by The Cancer Genome Atlas program: polymerase epsilon ultramutated, microsatellite instability hypermutated, copy number low (microsatellite stable or no specific molecular profile), and copy number high (serouslike, p53 mutant). Objective.— To discuss the utilities of commonly used immunohistochemical markers for the classification of endometrial carcinomas and to review the recent advancements of The Cancer Genome Atlas molecular reclassification and their potential impact on treatment strategies. Data Sources.— Literature review and authors' personal practice experience. Conclusions.— The current practice of classifying endometrial cancers is predominantly based on morphology. The use of ancillary testing, including immunohistochemistry, is helpful in the identification, differential diagnosis, and classification of these cancers. New developments such as molecular subtyping have provided insightful prognostic values for endometrial carcinomas. The proposed The Cancer Genome Atlas classification is poised to gain further prominence in guiding the prognostic evaluation for tailored treatment strategies in the near future.


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.


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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