scholarly journals USP6 activation in nodular fasciitis by promoter-swapping gene fusions

2017 ◽  
Vol 30 (11) ◽  
pp. 1577-1588 ◽  
Author(s):  
Nimesh R Patel ◽  
John S A Chrisinger ◽  
Elizabeth G Demicco ◽  
Stephen F Sarabia ◽  
Jacquelyn Reuther ◽  
...  
Keyword(s):  
Nodular Fasciitis ◽  
Gene Fusions ◽  
Promoter Swapping

Intraarticular nodular fasciitis—detection of USP6 gene fusions in three cases by targeted RNA sequencing

2021 ◽  
Author(s):  
Klemen Stražar ◽  
Daja Šekoranja ◽  
Alenka Matjašič ◽  
Andrej Zupan ◽  
Žiga Snoj ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Nodular Fasciitis ◽  
Gene Fusions

scholarly journals Systematic investigation of promoter substitutions resulting from somatic intrachromosomal structural alterations in diverse human cancers

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Babak Alaei-Mahabadi ◽  
Kerryn Elliott ◽  
Erik Larsson
Keyword(s):  
Systematic Investigation ◽  
Gene Fusions ◽  
Expression Data ◽  
Copy Number Alterations ◽  
Sequencing Data ◽  
Structural Genomic ◽  
Structural Alterations ◽  
Transcriptomic Sequencing ◽  
Promoter Swapping ◽  
Comprehensive Study

Abstract One of the ways in which genes can become activated in tumors is by somatic structural genomic rearrangements leading to promoter swapping events, typically in the context of gene fusions that cause a weak promoter to be substituted for a strong promoter. While identifiable by whole genome sequencing, limited availability of this type of data has prohibited comprehensive study of the phenomenon. Here, we leveraged the fact that copy number alterations (CNAs) arise as a result of structural alterations in DNA, and that they may therefore be informative of gene rearrangements, to pinpoint recurrent promoter swapping at a previously intractable scale. CNA data from nearly 9500 human tumors was combined with transcriptomic sequencing data to identify several cases of recurrent activating intrachromosomal promoter substitution events, either involving proper gene fusions or juxtaposition of strong promoters to gene upstream regions. Our computational screen demonstrates that a combination of CNA and expression data can be useful for identifying novel fusion events with potential driver roles in large cancer cohorts.

scholarly journals Platform study of genotyping-guided precision medicine for rare solid tumours: a study protocol for a phase II, non-randomised, 18-month, open-label, multiarm, single-centre clinical trial testing the safety and efficacy of multiple Chinese-approved targeted drugs and PD-1 inhibitors in the treatment of metastatic rare tumours

BMJ Open ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. e044543
Author(s):  
Shuhang Wang ◽  
Hui-Yao Huang ◽  
Dawei Wu ◽  
Hong Fang ◽  
Jianming Ying ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Targeted Therapy ◽  
Single Agent ◽  
Solid Tumours ◽  
Targeted Drugs ◽  
Gene Fusions ◽  
Single Centre ◽  
Open Label ◽  
Safety And Efficacy ◽  
Rare Tumours

IntroductionLimited clinical studies have been conducted on rare solid tumours, and there are few guidelines on the diagnosis and treatment, including experiences with targeted therapy and immunotherapy, of rare solid tumours in China, resulting in limited treatment options and poor outcomes. This study first proposes a definition of rare tumours and is designed to test the preliminary efficacy of targeted and immunotherapy drugs for the treatment of rare tumours.Methods and analysisThis is a phase II, open-label, non-randomised, multiarm, single-centre clinical trial in patients with advanced rare solid tumours who failed standard treatment; the study aims to evaluate the safety and efficacy of targeted drugs in patients with advanced rare solid tumours with corresponding actionable alterations, as well as the safety and efficacy of immune checkpoint (programmed death receptor inhibitor 1, PD-1) inhibitors in patients with advanced rare solid tumours without actionable alterations. Patients with advanced rare tumours who fail standardised treatment and carry actionable alterations (Epidermal growth factor receptor (EGFR) mutations, ALK gene fusions, ROS-1 gene fusions, C-MET gene amplifications/mutations, BRAF mutations, CDKN2A mutations, BRCA1/2 mutations, HER-2 mutations/overexpressions/amplifications or C-KIT mutations) will be enrolled in the targeted therapy arm and be given the corresponding targeted drugs. Patients without actionable alterations will be enrolled in the PD-1 inhibitor arm and be treated with sintilimab. After the patients treated with vemurafenib, niraparib and palbociclib acquire resistance, they will receive combination treatment with sintilimab or atezolizumab. With the use of Simon’s two-stage Minimax design, and the sample size was estimated to be 770. The primary endpoint of this study is the objective response rate. The secondary endpoints are progression-free survival in the targeted treatment group and single-agent immunotherapy group; the duration of response in the targeted therapy and single-agent immunotherapy groups; durable clinical benefit in the single-agent immunotherapy group; and the incidence of adverse events.Ethics and disseminationEthics approval was obtained from the Chinese Academy of Medical Sciences (ID: 20/132-2328). The results from this study will be actively disseminated through manuscript publications and conference presentations.Trial registration numbersNCT04423185; ChiCTR2000039310.

scholarly journals Identification of NTRK gene fusions in lung adenocarcinomas in the Chinese population

2021 ◽  
Author(s):  
Ruiying Zhao ◽  
Feng Yao ◽  
Chan Xiang ◽  
Jikai Zhao ◽  
Zhanxian Shang ◽  
...  
Keyword(s):  
Chinese Population ◽  
Gene Fusions ◽  
Lung Adenocarcinomas
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