Literature DB >> 22563071

BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data.

Ken Chen1, John W Wallis, Cyriac Kandoth, Joelle M Kalicki-Veizer, Karen L Mungall, Andrew J Mungall, Steven J Jones, Marco A Marra, Timothy J Ley, Elaine R Mardis, Richard K Wilson, John N Weinstein, Li Ding.   

Abstract

UNLABELLED: Despite recent progress, computational tools that identify gene fusions from next-generation whole transcriptome sequencing data are often limited in accuracy and scalability. Here, we present a software package, BreakFusion that combines the strength of reference alignment followed by read-pair analysis and de novo assembly to achieve a good balance in sensitivity, specificity and computational efficiency. AVAILABILITY: http://bioinformatics.mdanderson.org/main/BreakFusion

Mesh：

Year:  2012        PMID： 22563071      PMCID： PMC3389765          DOI： 10.1093/bioinformatics/bts272

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


  14 in total

1.  BLAT--the BLAST-like alignment tool.

Authors:  W James Kent
Journal:  Genome Res       Date:  2002-04       Impact factor: 9.043

2.  Glocal alignment: finding rearrangements during alignment.

Authors:  Michael Brudno; Sanket Malde; Alexander Poliakov; Chuong B Do; Olivier Couronne; Inna Dubchak; Serafim Batzoglou
Journal:  Bioinformatics       Date:  2003       Impact factor: 6.937

3.  De novo assembly and analysis of RNA-seq data.

Authors:  Gordon Robertson; Jacqueline Schein; Readman Chiu; Richard Corbett; Matthew Field; Shaun D Jackman; Karen Mungall; Sam Lee; Hisanaga Mark Okada; Jenny Q Qian; Malachi Griffith; Anthony Raymond; Nina Thiessen; Timothee Cezard; Yaron S Butterfield; Richard Newsome; Simon K Chan; Rong She; Richard Varhol; Baljit Kamoh; Anna-Liisa Prabhu; Angela Tam; YongJun Zhao; Richard A Moore; Martin Hirst; Marco A Marra; Steven J M Jones; Pamela A Hoodless; Inanc Birol
Journal:  Nat Methods       Date:  2010-10-10       Impact factor: 28.547

4.  Integrative analysis of the melanoma transcriptome.

Authors:  Michael F Berger; Joshua Z Levin; Krishna Vijayendran; Andrey Sivachenko; Xian Adiconis; Jared Maguire; Laura A Johnson; James Robinson; Roel G Verhaak; Carrie Sougnez; Robert C Onofrio; Liuda Ziaugra; Kristian Cibulskis; Elisabeth Laine; Jordi Barretina; Wendy Winckler; David E Fisher; Gad Getz; Matthew Meyerson; David B Jaffe; Stacey B Gabriel; Eric S Lander; Reinhard Dummer; Andreas Gnirke; Chad Nusbaum; Levi A Garraway
Journal:  Genome Res       Date:  2010-02-23       Impact factor: 9.043

Review 5.  Computational methods for transcriptome annotation and quantification using RNA-seq.

Authors:  Manuel Garber; Manfred G Grabherr; Mitchell Guttman; Cole Trapnell
Journal:  Nat Methods       Date:  2011-05-27       Impact factor: 28.547

6.  BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

Authors:  Ken Chen; John W Wallis; Michael D McLellan; David E Larson; Joelle M Kalicki; Craig S Pohl; Sean D McGrath; Michael C Wendl; Qunyuan Zhang; Devin P Locke; Xiaoqi Shi; Robert S Fulton; Timothy J Ley; Richard K Wilson; Li Ding; Elaine R Mardis
Journal:  Nat Methods       Date:  2009-08-09       Impact factor: 28.547

7.  deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.

Authors:  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; Martin Hirst; Torsten O Nielsen; S Cenk Sahinalp; David Huntsman; Sohrab P Shah
Journal:  PLoS Comput Biol       Date:  2011-05-19       Impact factor: 4.475

8.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.

Authors:  Cole Trapnell; Brian A Williams; Geo Pertea; Ali Mortazavi; Gordon Kwan; Marijke J van Baren; Steven L Salzberg; Barbara J Wold; Lior Pachter
Journal:  Nat Biotechnol       Date:  2010-05-02       Impact factor: 54.908

9.  TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.

Authors:  Daehwan Kim; Steven L Salzberg
Journal:  Genome Biol       Date:  2011-08-11       Impact factor: 13.583

10.  FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data.

Authors:  Andrea Sboner; Lukas Habegger; Dorothee Pflueger; Stephane Terry; David Z Chen; Joel S Rozowsky; Ashutosh K Tewari; Naoki Kitabayashi; Benjamin J Moss; Mark S Chee; Francesca Demichelis; Mark A Rubin; Mark B Gerstein
Journal:  Genome Biol       Date:  2010-10-21       Impact factor: 13.583
View more
  37 in total

1.  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

Review 2.  Sequence assembly demystified.

Authors:  Niranjan Nagarajan; Mihai Pop
Journal:  Nat Rev Genet       Date:  2013-01-29       Impact factor: 53.242

Review 3.  Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives.

Authors:  Qingguo Wang; Junfeng Xia; Peilin Jia; William Pao; Zhongming Zhao
Journal:  Brief Bioinform       Date:  2012-08-09       Impact factor: 11.622

4.  Genome-wide genotyping of acute myeloid leukemia with translocation t(9;11)(p22;q23) reveals novel recurrent genomic alterations.

Authors:  Michael W M Kühn; Lars Bullinger; Stefan Gröschel; Jan Krönke; Jennifer Edelmann; Frank G Rücker; Karina Eiwen; Peter Paschka; Verena I Gaidzik; Karlheinz Holzmann; Richard F Schlenk; Hartmut Döhner; Konstanze Döhner
Journal:  Haematologica       Date:  2014-05-23       Impact factor: 9.941

Review 5.  Identifying fusion transcripts using next generation sequencing.

Authors:  Shailesh Kumar; Sundus Khalid Razzaq; Angie Duy Vo; Mamta Gautam; Hui Li
Journal:  Wiley Interdiscip Rev RNA       Date:  2016-08-02       Impact factor: 9.957

6.  An improved understanding of cancer genomics through massively parallel sequencing.

Authors:  Jamie K Teer
Journal:  Transl Cancer Res       Date:  2014-06       Impact factor: 1.241

Review 7.  Collection, integration and analysis of cancer genomic profiles: from data to insight.

Authors:  Jianjiong Gao; Giovanni Ciriello; Chris Sander; Nikolaus Schultz
Journal:  Curr Opin Genet Dev       Date:  2014-02-27       Impact factor: 5.578

8.  Genomic landscape of non-small cell lung cancer in smokers and never-smokers.

Authors:  Ramaswamy Govindan; Li Ding; Malachi Griffith; Janakiraman Subramanian; Nathan D Dees; Krishna L Kanchi; Christopher A Maher; Robert Fulton; Lucinda Fulton; John Wallis; Ken Chen; Jason Walker; Sandra McDonald; Ron Bose; David Ornitz; Donghai Xiong; Ming You; David J Dooling; Mark Watson; Elaine R Mardis; Richard K Wilson
Journal:  Cell       Date:  2012-09-14       Impact factor: 41.582

Review 9.  Expanding the computational toolbox for mining cancer genomes.

Authors:  Li Ding; Michael C Wendl; Joshua F McMichael; Benjamin J Raphael
Journal:  Nat Rev Genet       Date:  2014-07-08       Impact factor: 53.242

10.  NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision.

Authors:  Trees-Juen Chuang; Chan-Shuo Wu; Chia-Ying Chen; Li-Yuan Hung; Tai-Wei Chiang; Min-Yu Yang
Journal:  Nucleic Acids Res       Date:  2015-10-05       Impact factor: 16.971
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.