Literature DB >> 21840877

ChimeraScan: a tool for identifying chimeric transcription in sequencing data.

Matthew K Iyer1, Arul M Chinnaiyan, Christopher A Maher.   

Abstract

SUMMARY: Next generation sequencing (NGS) technologies have enabled de novo gene fusion discovery that could reveal candidates with therapeutic significance in cancer. Here we present an open-source software package, ChimeraScan, for the discovery of chimeric transcription between two independent transcripts in high-throughput transcriptome sequencing data. AVAILABILITY: http://chimerascan.googlecode.com CONTACT: cmaher@dom.wustl.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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Year:  2011        PMID： 21840877      PMCID： PMC3187648          DOI： 10.1093/bioinformatics/btr467

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  12 in total

1.  Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer.

Authors:  Scott A Tomlins; Daniel R Rhodes; Sven Perner; Saravana M Dhanasekaran; Rohit Mehra; Xiao-Wei Sun; Sooryanarayana Varambally; Xuhong Cao; Joelle Tchinda; Rainer Kuefer; Charles Lee; James E Montie; Rajal B Shah; Kenneth J Pienta; Mark A Rubin; Arul M Chinnaiyan
Journal:  Science       Date:  2005-10-28       Impact factor: 47.728

2.  A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome.

Authors:  Oliver A Hampton; Petra Den Hollander; Christopher A Miller; David A Delgado; Jian Li; Cristian Coarfa; Ronald A Harris; Stephen Richards; Steven E Scherer; Donna M Muzny; Richard A Gibbs; Adrian V Lee; Aleksandar Milosavljevic
Journal:  Genome Res       Date:  2008-12-03       Impact factor: 9.043

3.  Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs).

Authors:  Yijun Ruan; Hong Sain Ooi; Siew Woh Choo; Kuo Ping Chiu; Xiao Dong Zhao; K G Srinivasan; Fei Yao; Chiou Yu Choo; Jun Liu; Pramila Ariyaratne; Wilson G W Bin; Vladimir A Kuznetsov; Atif Shahab; Wing-Kin Sung; Guillaume Bourque; Nallasivam Palanisamy; Chia-Lin Wei
Journal:  Genome Res       Date:  2007-06       Impact factor: 9.043

4.  Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.

Authors:  Marcus Kinsella; Olivier Harismendy; Masakazu Nakano; Kelly A Frazer; Vineet Bafna
Journal:  Bioinformatics       Date:  2011-02-16       Impact factor: 6.937

5.  MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers.

Authors:  Christian Steidl; Sohrab P Shah; Bruce W Woolcock; Lixin Rui; Masahiro Kawahara; Pedro Farinha; Nathalie A Johnson; Yongjun Zhao; Adele Telenius; Susana Ben Neriah; Andrew McPherson; Barbara Meissner; Ujunwa C Okoye; Arjan Diepstra; Anke van den Berg; Mark Sun; Gillian Leung; Steven J Jones; Joseph M Connors; David G Huntsman; Kerry J Savage; Lisa M Rimsza; Douglas E Horsman; Louis M Staudt; Ulrich Steidl; Marco A Marra; Randy D Gascoyne
Journal:  Nature       Date:  2011-03-02       Impact factor: 49.962

6.  Chimeric transcript discovery by paired-end transcriptome sequencing.

Authors:  Christopher A Maher; Nallasivam Palanisamy; John C Brenner; Xuhong Cao; Shanker Kalyana-Sundaram; Shujun Luo; Irina Khrebtukova; Terrence R Barrette; Catherine Grasso; Jindan Yu; Robert J Lonigro; Gary Schroth; Chandan Kumar-Sinha; Arul M Chinnaiyan
Journal:  Proc Natl Acad Sci U S A       Date:  2009-07-10       Impact factor: 11.205

7.  Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma.

Authors:  Nallasivam Palanisamy; Bushra Ateeq; Shanker Kalyana-Sundaram; Dorothee Pflueger; Kalpana Ramnarayanan; Sunita Shankar; Bo Han; Qi Cao; Xuhong Cao; Khalid Suleman; Chandan Kumar-Sinha; Saravana M Dhanasekaran; Ying-bei Chen; Raquel Esgueva; Samprit Banerjee; Christopher J LaFargue; Javed Siddiqui; Francesca Demichelis; Peter Moeller; Tarek A Bismar; Rainer Kuefer; Douglas R Fullen; Timothy M Johnson; Joel K Greenson; Thomas J Giordano; Patrick Tan; Scott A Tomlins; Sooryanarayana Varambally; Mark A Rubin; Christopher A Maher; Arul M Chinnaiyan
Journal:  Nat Med       Date:  2010-06-06       Impact factor: 53.440

8.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Authors:  Ben Langmead; Cole Trapnell; Mihai Pop; Steven L Salzberg
Journal:  Genome Biol       Date:  2009-03-04       Impact factor: 13.583

9.  Decoding the fine-scale structure of a breast cancer genome and transcriptome.

Authors:  Stanislav Volik; Benjamin J Raphael; Guiqing Huang; Michael R Stratton; Graham Bignel; John Murnane; John H Brebner; Krystyna Bajsarowicz; Pamela L Paris; Quanzhou Tao; David Kowbel; Anna Lapuk; Dmitri A Shagin; Irina A Shagina; Joe W Gray; Jan-Fang Cheng; Pieter J de Jong; Pavel Pevzner; Colin Collins
Journal:  Genome Res       Date:  2006-02-03       Impact factor: 9.043

10.  MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

Authors:  Kai Wang; Darshan Singh; Zheng Zeng; Stephen J Coleman; Yan Huang; Gleb L Savich; Xiaping He; Piotr Mieczkowski; Sara A Grimm; Charles M Perou; James N MacLeod; Derek Y Chiang; Jan F Prins; Jinze Liu
Journal:  Nucleic Acids Res       Date:  2010-08-27       Impact factor: 16.971
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  142 in total

1.  Spatiotemporal genomic architecture informs precision oncology in glioblastoma.

Authors:  Jin-Ku Lee; Jiguang Wang; Jason K Sa; Erik Ladewig; Hae-Ock Lee; In-Hee Lee; Hyun Ju Kang; Daniel S Rosenbloom; Pablo G Camara; Zhaoqi Liu; Patrick van Nieuwenhuizen; Sang Won Jung; Seung Won Choi; Junhyung Kim; Andrew Chen; Kyu-Tae Kim; Sang Shin; Yun Jee Seo; Jin-Mi Oh; Yong Jae Shin; Chul-Kee Park; Doo-Sik Kong; Ho Jun Seol; Andrew Blumberg; Jung-Il Lee; Antonio Iavarone; Woong-Yang Park; Raul Rabadan; Do-Hyun Nam
Journal:  Nat Genet       Date:  2017-03-06       Impact factor: 38.330

2.  RNA-seq identifies clinically relevant fusion genes in leukemia including a novel MEF2D/CSF1R fusion responsive to imatinib.

Authors:  H Lilljebjörn; H Ågerstam; C Orsmark-Pietras; M Rissler; H Ehrencrona; L Nilsson; J Richter; T Fioretos
Journal:  Leukemia       Date:  2013-11-04       Impact factor: 11.528

3.  Identification of recurrent SMO and BRAF mutations in ameloblastomas.

Authors:  Robert T Sweeney; Andrew C McClary; Benjamin R Myers; Jewison Biscocho; Lila Neahring; Kevin A Kwei; Kunbin Qu; Xue Gong; Tony Ng; Carol D Jones; Sushama Varma; Justin I Odegaard; Toshihiro Sugiyama; Souichi Koyota; Brian P Rubin; Megan L Troxell; Robert J Pelham; James L Zehnder; Philip A Beachy; Jonathan R Pollack; Robert B West
Journal:  Nat Genet       Date:  2014-05-25       Impact factor: 38.330

4.  Clonal evolution of glioblastoma under therapy.

Authors:  Jiguang Wang; Emanuela Cazzato; Erik Ladewig; Veronique Frattini; Daniel I S Rosenbloom; Sakellarios Zairis; Francesco Abate; Zhaoqi Liu; Oliver Elliott; Yong-Jae Shin; Jin-Ku Lee; In-Hee Lee; Woong-Yang Park; Marica Eoli; Andrew J Blumberg; Anna Lasorella; Do-Hyun Nam; Gaetano Finocchiaro; Antonio Iavarone; Raul Rabadan
Journal:  Nat Genet       Date:  2016-06-06       Impact factor: 38.330

5.  Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing.

Authors:  Jason L Weirather; Pegah Tootoonchi Afshar; Tyson A Clark; Elizabeth Tseng; Linda S Powers; Jason G Underwood; Joseph Zabner; Jonas Korlach; Wing Hung Wong; Kin Fai Au
Journal:  Nucleic Acids Res       Date:  2015-06-03       Impact factor: 16.971

6.  Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma.

Authors:  Junfei Zhao; Andrew X Chen; Robyn D Gartrell; Andrew M Silverman; Luis Aparicio; Tim Chu; Darius Bordbar; David Shan; Jorge Samanamud; Aayushi Mahajan; Ioan Filip; Rose Orenbuch; Morgan Goetz; Jonathan T Yamaguchi; Michael Cloney; Craig Horbinski; Rimas V Lukas; Jeffrey Raizer; Ali I Rae; Jinzhou Yuan; Peter Canoll; Jeffrey N Bruce; Yvonne M Saenger; Peter Sims; Fabio M Iwamoto; Adam M Sonabend; Raul Rabadan
Journal:  Nat Med       Date:  2019-02-11       Impact factor: 53.440

7.  RAP: A Web Tool for RNA-Seq Data Analysis.

Authors:  Mattia D'Antonio; Pietro Libro; Ernesto Picardi; Graziano Pesole; Tiziana Castrignanò
Journal:  Methods Mol Biol       Date:  2021

Review 8.  Detecting and targetting oncogenic fusion proteins in the genomic era.

Authors:  Monika A Davare; Cristina E Tognon
Journal:  Biol Cell       Date:  2015-04-07       Impact factor: 4.458

9.  cDNA hybrid capture improves transcriptome analysis on low-input and archived samples.

Authors:  Christopher R Cabanski; Vincent Magrini; Malachi Griffith; Obi L Griffith; Sean McGrath; Jin Zhang; Jason Walker; Amy Ly; Ryan Demeter; Robert S Fulton; Winnie W Pong; David H Gutmann; Ramaswamy Govindan; Elaine R Mardis; Christopher A Maher
Journal:  J Mol Diagn       Date:  2014-05-09       Impact factor: 5.568

10.  Long-range transcriptome sequencing reveals cancer cell growth regulatory chimeric mRNA.

Authors:  Roberto Plebani; Gavin R Oliver; Marco Trerotola; Emanuela Guerra; Pamela Cantanelli; Luana Apicella; Andrew Emerson; Alessandro Albiero; Paul D Harkin; Richard D Kennedy; Saverio Alberti
Journal:  Neoplasia       Date:  2012-11       Impact factor: 5.715
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