Fusion genes in solid tumors: an emerging target for cancer diagnosis and treatment

Parker, Brittany C.; Zhang, Wei

doi:10.5732/cjc.013.10178

Cited by 87 publications

(71 citation statements)

References 92 publications

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“…Fusion genes play a critical role in investigating causes and development of various cancer types 56 . RNA-seq has been shown as a valuable source for detecting fusion genes 6 .…”

Section: Resultsmentioning

confidence: 99%

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

Sahraeian¹,

Mohiyuddin²,

et al. 2017

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RNA-sequencing (RNA-seq) is an essential technique for transcriptome studies, hundreds of analysis tools have been developed since it was debuted. Although recent efforts have attempted to assess the latest available tools, they have not evaluated the analysis workflows comprehensively to unleash the power within RNA-seq. Here we conduct an extensive study analysing a broad spectrum of RNA-seq workflows. Surpassing the expression analysis scope, our work also includes assessment of RNA variant-calling, RNA editing and RNA fusion detection techniques. Specifically, we examine both short- and long-read RNA-seq technologies, 39 analysis tools resulting in ~120 combinations, and ~490 analyses involving 15 samples with a variety of germline, cancer and stem cell data sets. We report the performance and propose a comprehensive RNA-seq analysis protocol, named RNACocktail, along with a computational pipeline achieving high accuracy. Validation on different samples reveals that our proposed protocol could help researchers extract more biologically relevant predictions by broad analysis of the transcriptome.

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“…Fusion genes play a critical role in investigating causes and development of various cancer types 56 . RNA-seq has been shown as a valuable source for detecting fusion genes 6 .…”

Section: Resultsmentioning

confidence: 99%

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

Sahraeian¹,

Mohiyuddin²,

et al. 2017

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“…Such gene-fusions can lead to chimeric proteins able to suppress tumour-suppressor genes or activate oncogenes and their assessment provides an opportunity to expand the available prognostic and treatment options (reviewed by Parker et al [224]).…”

Section: Cancer Somatic Mutation Analysismentioning

confidence: 99%

Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification

Kamps

Brandão

Bosch

et al. 2017

IJMS

398

294

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Next-generation sequencing (NGS) technology has expanded in the last decades with significant improvements in the reliability, sequencing chemistry, pipeline analyses, data interpretation and costs. Such advances make the use of NGS feasible in clinical practice today. This review describes the recent technological developments in NGS applied to the field of oncology. A number of clinical applications are reviewed, i.e., mutation detection in inherited cancer syndromes based on DNA-sequencing, detection of spliceogenic variants based on RNA-sequencing, DNA-sequencing to identify risk modifiers and application for pre-implantation genetic diagnosis, cancer somatic mutation analysis, pharmacogenetics and liquid biopsy. Conclusive remarks, clinical limitations, implications and ethical considerations that relate to the different applications are provided.

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“…Studies over the past decades have uncovered the oncogenic role of fusion genes in hematological malignancies and mesenchymal tumors, and have highlighted the diagnostic and therapeutic advantages provided by the detection of these chimeric transcripts and their tumor‐specific expression 15. A similar search for fusion transcripts in ovarian cancer has shown that they are not common.…”

Section: Discussionmentioning

confidence: 99%

Identification of novel cyclin gene fusion transcripts in endometrioid ovarian carcinomas

Agostini

Brunetti

Davidson

et al. 2018

Intl Journal of Cancer

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Formation of fusion genes is pathogenetically crucial in many solid tumors. They are particularly characteristic of several mesenchymal tumors, but may also be found in epithelial neoplasms. Ovarian carcinomas, too, may harbor fusion genes but only few of these were found to be recurrent with a rate ranging from 0.5 to 5%. Because most attempts to find specific and recurrent fusion transcripts in ovarian carcinomas focused exclusively on high‐grade serous carcinomas, the situation in the other carcinoma subgroups remains largely uninvestigated as far as fusion genes are concerned. We performed transcriptome sequencing on a series of 34 samples from ovarian tumors that included borderline, clear cell, mucinous, endometrioid, low‐grade and high‐grade serous carcinomas in search of fusion genes typical of these subtypes. We found a total of 24 novel fusion transcripts. The PCMTDI‐CCNL2 fusion transcript, which involves a member of the cyclin family, was found recurrently involved but only in endometrioid carcinomas (4 of 18 tumors; 22%). We also found three additional fusion transcripts involving genes belonging to the cyclin family: ANXA5‐CCNA2 and PDE4D‐CCNB1 were detected in two endometrioid carcinomas, whereas CCNY‐NRG4 was identified in a clear cell carcinoma. The recurrent involvement of CCNL2 in four fusions and of three other genes of the cyclin family in three additional transcripts hints that deregulation of cyclin genes is important in the pathogenesis of ovarian carcinomas in general but of endometrioid carcinomas particularly.

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Fusion genes in solid tumors: an emerging target for cancer diagnosis and treatment

Cited by 87 publications

References 92 publications

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification

Identification of novel cyclin gene fusion transcripts in endometrioid ovarian carcinomas

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