Breakfusion: Targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data

Ken Chen; 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

doi:10.1093/bioinformatics/bts272

Breakfusion: Targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data

Ken Chen, 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

Bioinformatics & Computational Biology

Research output: Contribution to journal › Article › peer-review

46 Scopus citations

Abstract

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.

Original language	English (US)
Article number	bts272
Pages (from-to)	1923-1924
Number of pages	2
Journal	Bioinformatics
Volume	28
Issue number	14
DOIs	https://doi.org/10.1093/bioinformatics/bts272
State	Published - Jul 2012

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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Chen, K., Wallis, J. W., Kandoth, C., Kalicki-veizer, J. M., Mungall, K. L., Mungall, A. J., Jones, S. J., Marra, M. A., Ley, T. J., Mardis, E. R., Wilson, R. K., Weinstein, J. N., & Ding, L. (2012). Breakfusion: Targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. Bioinformatics, 28(14), 1923-1924. Article bts272. https://doi.org/10.1093/bioinformatics/bts272

Chen, K, Wallis, JW, Kandoth, C, Kalicki-veizer, JM, Mungall, KL, Mungall, AJ, Jones, SJ, Marra, MA, Ley, TJ, Mardis, ER, Wilson, RK, Weinstein, JN & Ding, L 2012, 'Breakfusion: Targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data', Bioinformatics, vol. 28, no. 14, bts272, pp. 1923-1924. https://doi.org/10.1093/bioinformatics/bts272

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title = "Breakfusion: Targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data",

abstract = "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.",

author = "Ken Chen and Wallis, {John W.} and Cyriac Kandoth and Kalicki-veizer, {Joelle M.} and Mungall, {Karen L.} and Mungall, {Andrew J.} and Jones, {Steven J.} and Marra, {Marco A.} and Ley, {Timothy J.} and Mardis, {Elaine R.} and Wilson, {Richard K.} and Weinstein, {John N.} and Li Ding",

note = "Funding Information: Funding: The Cancer Center Support Grant from NCI (P30 CA016672 to UT MD Anderson); Center for Large-Scale Genome Sequencing and Analysis from NHGRI (U54 HG003079 to R.K.W); Structural Genomic Variation analysis for the 1000 Genome project from NHGRI (U01 HG005209 to L.C.)",

year = "2012",

month = jul,

doi = "10.1093/bioinformatics/bts272",

language = "English (US)",

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pages = "1923--1924",

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AU - Wallis, John W.

AU - Kandoth, Cyriac

AU - Kalicki-veizer, Joelle M.

AU - Mungall, Karen L.

AU - Mungall, Andrew J.

AU - Jones, Steven J.

AU - Marra, Marco A.

AU - Ley, Timothy J.

AU - Mardis, Elaine R.

AU - Wilson, Richard K.

AU - Weinstein, John N.

AU - Ding, Li

N1 - Funding Information: Funding: The Cancer Center Support Grant from NCI (P30 CA016672 to UT MD Anderson); Center for Large-Scale Genome Sequencing and Analysis from NHGRI (U54 HG003079 to R.K.W); Structural Genomic Variation analysis for the 1000 Genome project from NHGRI (U01 HG005209 to L.C.)

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Breakfusion: Targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data

Abstract

ASJC Scopus subject areas

MD Anderson CCSG core facilities

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