MP64-02 COMPARISON OF GENETIC ALTERATIONS FROM THE CANCER GENOME ATLAS BLADDER CANCER ANALYSIS AND A PROSPECTIVE SET OF HIGH-GRADE UROTHELIAL CARCINOMA TUMORS USING A CLINICAL LABORATORY IMPROVEMENT AMENDMENTS-CERTIFIED NEXT GENERATION SEQUENCING ASSAY

2015 ◽  
Vol 193 (4S) ◽  
Author(s):  
Aditya Bagrodia ◽  
Gopa Iyer ◽  
Eugene Cha ◽  
Mariel Boyd ◽  
Ahmet Zehir ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Next Generation Sequencing ◽  
Clinical Laboratory ◽  
Genetic Alterations ◽  
The Cancer Genome Atlas ◽  
High Grade ◽  
Cancer Genome Atlas ◽  
Clinical Laboratory Improvement Amendments ◽  
Generation Sequencing ◽  
Genome Atlas

scholarly journals Genetic Alterations in the Molecular Subtypes of Bladder Cancer: Illustration in the Cancer Genome Atlas Dataset

2017 ◽  
Vol 72 (3) ◽  
pp. 354-365 ◽  
Author(s):  
Woonyoung Choi ◽  
Andrea Ochoa ◽  
David J. McConkey ◽  
Mattias Aine ◽  
Mattias Höglund ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Molecular Subtypes ◽  
Genetic Alterations ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Cancer Genome Atlas ◽  
Genome Atlas

scholarly journals Enrichment of FGFR3-TACC3 Fusions in Patients With Bladder Cancer Who Are Young, Asian, or Have Never Smoked

2018 ◽  
pp. 1-11
Author(s):  
Amin H. Nassar ◽  
Kevin Lundgren ◽  
Mark Pomerantz ◽  
Eliezer Van Allen ◽  
Lauren Harshman ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Pooled Analysis ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
High Grade ◽  
Data Set ◽  
Dana Farber Cancer Institute ◽  
Cancer Genome Atlas ◽  
Never Smokers ◽  
Genome Atlas

Purpose FGFR3-TACC3 (fibroblast growth factor receptor 3–transforming acidic coiled coil-containing protein 3) fusions have recently been identified as driver mutations that lead to the activation of FGFR3 in bladder cancer and other tumor types and are associated with sensitivity to tyrosine kinase inhibitors. We examined the clinical and molecular characteristics of patients with FGFR3-TACC3 fusions and hypothesized that they are enriched in a subset of patients with bladder cancer. Materials and Methods We correlated somatic FGFR3-TACC3 fusions with clinical and molecular features in two cohorts of patients with bladder cancer. The first cohort consisted of the muscle-invasive bladder cancer (MIBC) data set (n = 412) from The Cancer Genome Atlas. The second cohort consisted of patients with MIBC or high-grade non-MIBC at the Dana-Farber Cancer Institute that had targeted capture sequencing of a selected panel of cancer genes (n = 356). All statistical tests were two sided. The clinical response of one patient with FGFR3-TACC3 bladder cancer to an FGFR3 inhibitor was investigated. Results Overall, 751 patients with high-grade bladder cancer without FGFR3-TACC3 fusions and 17 with FGFR3-TACC3 fusions were identified in the pooled analysis of the data sets from The Cancer Genome Atlas and the Dana-Farber Cancer Institute. FGFR3-TACC3 fusions were enriched in patients age ≤ 50 years versus age 51 to 65 years versus those older than 65 years (pooled, P = .002), and were observed in four (12%) of 33 patients age ≤ 50 years in the pooled analysis. Similarly, FGFR3-TACC3 fusions were significantly more common in Asians (13%) compared with African Americans (4%) and whites (2%; pooled, P < .001), as well as in never smokers (5.6%) compared with ever smokers (1.1%; pooled, P < .001). One patient with the fusion who was treated with an FGFR3 inhibitor achieved complete remission for 10 months. Conclusion Clinical testing to identify FGFR3 fusions should be prioritized for patients with bladder cancer who are younger, never smokers, and/or Asian.

scholarly journals Validation and calibration of next-generation sequencing to identify Epstein-Barr virus-positive gastric cancer in The Cancer Genome Atlas

2015 ◽  
Vol 19 (2) ◽  
pp. 676-681 ◽  
Author(s):  
M. Constanza Camargo ◽  
Reanne Bowlby ◽  
Andy Chu ◽  
Chandra Sekhar Pedamallu ◽  
Vesteinn Thorsson ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Next Generation Sequencing ◽  
Epstein Barr Virus ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Barr Virus ◽  
Cancer Genome Atlas ◽  
Epstein Barr ◽  
Generation Sequencing ◽  
Genome Atlas

scholarly journals A comprehensive analysis of the angiogenesis-related genes in glioblastoma multiforme vs. brain lower grade glioma

2020 ◽  
Vol 78 (1) ◽  
pp. 34-38
Author(s):  
Burcu BITERGE-SUT
Keyword(s):  
Glioblastoma Multiforme ◽  
Malignant Gliomas ◽  
Genetic Alterations ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Lower Grade ◽  
Nonsense Mutations ◽  
Lower Grade Glioma ◽  
Cancer Genome Atlas ◽  
Genome Atlas

Abstract Brain tumors are one of the most common causes of cancer-related deaths around the world. Angiogenesis is critical in high-grade malignant gliomas, such as glioblastoma multiforme. Objective: The aim of this study is to comparatively analyze the angiogenesis-related genes, namely VEGFA, VEGFB, KDR, CXCL8, CXCR1 and CXCR2 in LGG vs. GBM to identify molecular distinctions using datasets available on The Cancer Genome Atlas (TCGA). Methods: DNA sequencing and mRNA expression data for 514 brain lower grade glioma (LGG) and 592 glioblastoma multiforme (GBM) patients were acquired from The Cancer Genome Atlas (TCGA), and the genetic alterations and expression levels of the selected genes were analyzed. Results: We identified six distinct KDR mutations in the LGG patients and 18 distinct KDR mutations in the GBM patients, including missense and nonsense mutations, frame shift deletion and altered splice region. Furthermore, VEGFA and CXCL8 were significantly overexpressed within GBM patients. Conclusions: VEGFA and CXCL8 are important factors for angiogenesis, which are suggested to have significant roles during tumorigenesis. Our results provide further evidence that VEGFA and CXCL8 could induce angiogenesis and promote LGG to progress into GBM. These findings could be useful in developing novel targeted therapeutics approaches in the future.

scholarly journals Detection of EGFR Mutation Distribution and Transcriptional Variants in IDH-Wildtype High-Grade Gliomas Using a Next-Generation Sequencing Oncopanel

2021 ◽  
Author(s):  
Nayuta Higa ◽  
Toshiaki Akahane ◽  
Taiji Hamada ◽  
Hajime Yonezawa ◽  
Hiroyuki Uchida ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Receptor Gene ◽  
Kinase Domain ◽  
The Cancer Genome Atlas ◽  
Cancer Center ◽  
High Grade ◽  
Next Generation ◽  
Transcriptional Variants ◽  
High Grade Gliomas ◽  
Generation Sequencing

Abstract \Purpose: To detect the epidermal growth factor receptor gene (EGFR) mutation profile and transcriptional variants in high-grade gliomas (HGGs), we sequenced EGFR and evaluated the EGFR splicing profile using a next-generation sequencing (NGS) oncopanel. Methods: We analyzed 124 HGGs—10 grade Ⅲ IDH-wildtype anaplastic astrocytomas (AAs) and 114 grade Ⅳ IDH-wildtype glioblastomas (GBMs). Results: The EGFR mutations were observed in 6.0% of grade Ⅳ GBMs and in 33% of grade Ⅲ AAs. Four cases harbored missense mutations in the EGFR kinase domain (L747A, S768I, V774M, and T790M). A total of 25% of the GBMs showed EGFR amplification. Moreover, 27% of the EGFR mutations occurred in the kinase domain. EGFRvⅢ positivity was detected in 8.0% of EGFR-amplified GBMs. We identified two other EGFR variants in GBM cases with deletions of exons 6–7 (Δe 6-7) (one case) and exons 2–14 (Δe 2-14) (two cases). Interestingly, in one case, the initial EGFRvIII mutation transformed into an EGFR Δe 2-14 mutation during recurrence. The frequency of EGFR alterations in our cohort was lower but the frequency of EGFR mutations in the kinase domain in our cohort was higher than that in The Cancer Genome Atlas and Memorial Sloan Kettering Cancer Center cohorts. Conclusions: We suggested that the EGFR gene profiles of GBM differ among cohorts and identified rare EGFR variants with longitudinal and temporal transformations of EGFRvⅢ.

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