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deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

Andrew McPherson, Fereydoun Hormozdiari, Abdalnasser Zayed, Ryan Giuliany, Gavin Ha, Mark G. F. Sun, Malachi Griffith, Alireza Heravi Moussavi, Janine Senz, Nataliya Melnyk, Marina Pacheco, Marco A. Marra (+6 others)
2011 PLoS Computational Biology  
We have developed deFuse, a novel computational method for fusion discovery in tumor RNA-Seq data.  ...  However, algorithmic methods for the discovery of gene fusions using RNA-Seq data remain underdeveloped.  ...  We have developed a novel computational method called deFuse for detecting gene fusions in RNA-Seq data and have applied it to the discovery of novel gene fusions in sarcoma and ovarian tumors.  ... 
doi:10.1371/journal.pcbi.1001138 pmid:21625565 pmcid:PMC3098195 fatcat:ffuvx4dbgreibegxwtgqkoytfi

FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples

Giulia Paciello, Elisa Ficarra
2017 BMC Bioinformatics  
Results: In this work we propose a novel methodological approach and tool named FuGePrior for the prioritization of gene fusions from paired-end RNA-Seq data.  ...  In particular gene fusion detection and comprehension have been deeply enhanced by these methods. However, state of the art algorithms for gene fusion identification are still challenging.  ...  To this aim we propose a novel computational approach and tool named FuGePrior for the prioritization of gene fusions from paired-end RNA-Seq data.  ... 
doi:10.1186/s12859-016-1450-6 pmid:28114882 pmcid:PMC5260008 fatcat:kis7jzfzlncjdod7sz6pzfzjjm

Computational proteogenomic identification and functional interpretation of translated fusions and micro structural variations in cancer [article]

Yen-Yi Lin, Alexander Gawronski, Faraz Hach, Sujun Li, Ibrahim Numanagic, Iman Sarrafi, Swati Mishra, Andrew William McPherson, Colin C Collins, Milan Radovich, Haixu Tang, S. Cenk Sahinalp
2017 bioRxiv   pre-print
We have applied our framework to all The Cancer Genome Atlas (TCGA) breast cancer Whole Genome Sequencing (WGS) and/or RNA-Seq data sets, spanning all four major subtypes, for which proteomics data from  ...  Coupled with deFuse, a popular gene fusion detection method we developed earlier, MiStrVar can provide an accurate profile of structurally aberrant transcripts in cancer samples.Given the breakpoints obtained  ...  Acknowledgement The WGS and RNA-Seq datasets were retrieved from the Cancer Genomics Hub (https: //; the proteomics data was released by the National Cancer Institute Clinical Proteomic  ... 
doi:10.1101/168377 fatcat:5nucafpn5veqth2jcyvh32auym

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data

Liqing Tian, Yongjin Li, Michael N. Edmonson, Xin Zhou, Scott Newman, Clay McLeod, Andrew Thrasher, Yu Liu, Bo Tang, Michael C. Rusch, John Easton, Jing Ma (+9 others)
2020 Genome Biology  
To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, we develop CICERO, a local assembly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate  ...  Re-analysis of TCGA glioblastoma RNA-seq unveils previously unreported kinase fusions (KLHL7-BRAF) and a 13% prevalence of EGFR C-terminal truncation.  ...  Dennis Kennetz for their assistance in data analysis.  ... 
doi:10.1186/s13059-020-02043-x pmid:32466770 fatcat:skdtwwflzvey7oecb5m4zl4chy

State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues?

Matteo Carrara, Marco Beccuti, Federica Cavallo, Susanna Donatelli, Fulvio Lazzarato, Francesca Cordero, Raffaele A Calogero
2013 BMC Bioinformatics  
More recently, two fusion genes in normal tissues were detected using both RNA-seq and protein data.  ...  Due to heterogeneous results in identifying chimeras in normal tissue, we decided to evaluate the efficacy of state of the art fusion finders in detecting chimeras in RNA-seq data from normal tissues.  ...  , using the 75 nts single-end reads RNA-seq Body Map 2.0 dataset, was used as positive control of the ability of FusionMap to detect chimers in normal tissues RNA-seq data. # of genes also detected in  ... 
doi:10.1186/1471-2105-14-s7-s2 pmid:23815381 pmcid:PMC3633050 fatcat:2c4em6dk7jhkvm3jhnnomolicq

Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives

Q. Wang, J. Xia, P. Jia, W. Pao, Z. Zhao
2012 Briefings in Bioinformatics  
Major advancements have been made in computational approaches for fusion gene discovery over the past 3 years due to improvements and widespread applications of high-throughput next generation sequencing  ...  In this article, we review the NGS and computational features of existing methods for fusion gene detection and suggest directions for future development.  ...  ACKNOWLEDGEMENTS We would like to thank Dr Jingchun Sun and Dr Min Zhao in the Bioinformatics and Systems Medicine Laboratory for valuable suggestions and discussion on this work.  ... 
doi:10.1093/bib/bbs044 pmid:22877769 pmcid:PMC3713712 fatcat:u3bquoibbvcstjdbr2hrnnqgee

SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data

Wenlong Jia, Kunlong Qiu, Minghui He, Pengfei Song, Quan Zhou, Feng Zhou, Yuan Yu, Dandan Zhu, Michael L Nickerson, Shengqing Wan, Xiangke Liao, Xiaoqian Zhu (+4 others)
2013 Genome Biology  
We have developed a new method, SOAPfuse, to identify fusion transcripts from paired-end RNA-Seq data.  ...  We applied SOAPfuse to RNA-Seq data from two bladder cancer cell lines, and confirmed 15 fusion transcripts, including several novel events common to both cell lines. SOAPfuse is available at  ...  We thank D Kim (TopHat-Fusion group), SL Salzberg (TopHat-Fusion group), and A McPherson (deFuse group) for help on operating software.  ... 
doi:10.1186/gb-2013-14-2-r12 pmid:23409703 pmcid:PMC4054009 fatcat:5m5jzaq4bjgbpkiayis5pqppl4

A Novel Pipeline for Identification and Prioritization of Gene Fusions in Patient-derived Xenografts of Metastatic Colorectal Cancer

Giulia Paciello, Andrea Acquaviva, Consalvo Petti, Claudio Isella, Enzo Medico, Elisa Ficarra
2014 Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms  
To identify gene fusions in RNA-Seq data obtained from such PDX samples, we propose a novel pipeline that tackles the following issues: (i) discriminating human from murine RNA, to filter out transcripts  ...  The pipeline, built on top of Chimerascan(R.Iyer, 2011) and deFuse(McPherson, 2011) aligner tools, was successfully applied to RNA-Seq data from 11 PDX samples.  ...  of the detected fusions in public RNA-seq dataset (TCGA).  ... 
doi:10.5220/0004799401420148 dblp:conf/biostec/PacielloAPIMF14 fatcat:k5m4fdpu6nexvn3bdvt23e2lge

Intratumor heterogeneity and clonal evolution in an aggressive papillary thyroid cancer and matched metastases

Soazig Le Pennec, Tomasz Konopka, David Gacquer, Danai Fimereli, Maxime Tarabichi, Gil Tomás, Frédérique Savagner, Myriam Decaussin-Petrucci, Christophe Trésallet, Guy Andry, Denis Larsimont, Vincent Detours (+1 others)
2015 Endocrine-Related Cancer  
We searched for non-synonymous single-nucleotide variants (nsSNVs), gene fusions, alternative transcripts, and loss of heterozygosity (LOH) by paired-end massively parallel sequencing of cDNA (RNA-Seq)  ...  Three new gene fusions were identified. A novel cancer-specific KAZN alternative transcript was detected in this aggressive PTC and in dozens of additional thyroid tumors.  ...  Acknowledgements The authors thank Jacques Emile Dumont for his great help with manuscript revision and Chantal Degraef for excellent technical assistance.  ... 
doi:10.1530/erc-14-0351 pmid:25691441 fatcat:5v7uyfgiejdvlh2wnlaf5avw3e

SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads

Jikun Wu, Wenqian Zhang, Songbo Huang, Zengquan He, Yanbing Cheng, Jun Wang, Tak-Wah Lam, Zhiyu Peng, Siu-Ming Yiu
2013 Computer applications in the biosciences : CABIOS  
Results: We present a novel tool SOAPfusion for fusion discovery with paired-end RNA-Seq reads. SOAPfusion is accurate and efficient for fusion discovery with high sensitivity (!  ...  From real data of Universal Human Reference RNA (UHRR) samples, SOAPfusion detected 7 novel fusion genes, more than other existing tools and all genes have been validated through reverse transcription-polymerase  ...  We will investigate these additional fusion genes in our future work. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btt522 pmid:24123671 fatcat:r4dx4teizfebxm5egfpvqtz2t4

Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer

Francesco Abate, Sakellarios Zairis, Elisa Ficarra, Andrea Acquaviva, Chris H Wiggins, Veronique Frattini, Anna Lasorella, Antonio Iavarone, Giorgio Inghirami, Raul Rabadan
2014 BMC Systems Biology  
Pegasus dramatically streamlines the search for oncogenic gene fusions, bridging the gap between raw RNA-Seq data and a final, tractable list of candidates for experimental validation.  ...  Conclusion: We show the effectiveness of Pegasus in predicting new driver fusions in 176 RNA-Seq samples of glioblastoma multiforme (GBM) and 23 cases of anaplastic large cell lymphoma (ALCL).  ...  RNA-Seq samples were first analyzed with ChimeraScan and deFuse [14, 15] for fusion detection.  ... 
doi:10.1186/s12918-014-0097-z pmid:25183062 pmcid:PMC4363948 fatcat:vurz3e3gtzd2tpchf3wkk7fjia

Identifying fusion transcripts using next generation sequencing

Shailesh Kumar, Sundus Khalid Razzaq, Angie Duy Vo, Mamta Gautam, Hui Li
2016 Wiley Interdisciplinary Reviews - RNA  
Fusion transcripts (i.e. chimeric RNAs) resulting from gene fusions have been used successfully for cancer diagnosis, prognosis, and therapeutic applications.  ...  In the past decade, major advancements have been made for chimeric RNA discovery due to the development of advanced sequencing platform and software packages.  ...  Daniel Nicorici for helpful discussion. We thank Loryn Facemire for her help on editing the manuscript.  ... 
doi:10.1002/wrna.1382 pmid:27485475 pmcid:PMC5065767 fatcat:sfnddjrtm5e4ngm2c27dfr7veu

Whole Transcriptome Sequencing Reveals Extensive Unspliced mRNA in Metastatic Castration-Resistant Prostate Cancer

Adam G. Sowalsky, Zheng Xia, Liguo Wang, Hao Zhao, Shaoyong Chen, Glenn J. Bubley, Steven P. Balk, Wei Li
2014 Molecular Cancer Research  
, and a novel SND1:BRAF gene fusion.  ...  To identify the mechanism that drives these advanced tumors, paired-end RNA-sequencing (RNA-seq) was performed on a panel of CRPC bone marrow biopsy specimens.  ...  Paired-end sequencing of metastatic CRPC reveals expression of novel fusion genes We performed post-processing for the discovery of fusion genes using both an annotation-dependent algorithm (ChimeraScan  ... 
doi:10.1158/1541-7786.mcr-14-0273 pmid:25189356 pmcid:PMC4312515 fatcat:7nip4afmpnhydkih4ambnokpay

INTEGRATE: gene fusion discovery using whole genome and transcriptome data

Jin Zhang, Nicole M. White, Heather K. Schmidt, Robert S. Fulton, Chad Tomlinson, Wesley C. Warren, Richard K. Wilson, Christopher A. Maher
2015 Genome Research  
Therefore, we developed a gene fusion discovery tool, INTEGRATE, that leverages both RNA-seq and WGS data to reconstruct gene fusion junctions and genomic breakpoints by split-read mapping.  ...  Currently, there are many computational tools that predict structural variations (SV) and gene fusions using whole genome (WGS) and transcriptome sequencing (RNA-seq) data separately.  ...  Larson for their help in improving the code quality. We also thank C. Cabanski, N. Rockweiler, and A. Ramu for their feedback on the website.  ... 
doi:10.1101/gr.186114.114 pmid:26556708 pmcid:PMC4691743 fatcat:vkv4jl4u3ncphplex4uxgnefwu

Transcriptome Profiling of the Cancer, Adjacent Non-Tumor and Distant Normal Tissues from a Colorectal Cancer Patient by Deep Sequencing

Yan'an Wu, Xuetao Wang, Fangbo Wu, Ruolei Huang, Fangqin Xue, Guantao Liang, Min Tao, Pengwei Cai, Yi Huang, Antonio Moschetta
2012 PLoS ONE  
In addition, one tumor-restricted gene fusion, PRTEN-NOTCH2, was also detected and experimentally confirmed.  ...  Compared with microarray technology, which is commonly used to identify transcriptional changes, the recently developed RNA-seq technique has the ability to detect other abnormal regulations in the cancer  ...  Bioinformatics prediction of gene fusion events We used two algorithms, deFuse and TopHat-Fusion, to detect gene fusion based on the pair-ends reads in different samples.  ... 
doi:10.1371/journal.pone.0041001 pmid:22905095 pmcid:PMC3414479 fatcat:t24fey5jr5hlpahcy2aawmj5yy
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