Department of Bioinformatics and Computational Biology

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

Bioinformatics 28 (14):1923-4
Jul 2012

Chen K, Wallis J, Kandoth C, Kalicki-Veizer J, Mungall K, Mungall A, Jones S, Marra M, Ley T, Mardis E, Wilson R, Weinstein J, Ding L

Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, The Genome Institute, Department of Genetics, Washington University, St Louis, MO, USA, Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada and Department of Internal Medicine, Division of Oncology, Washington University, St Louis, MO, USA.warning.pngString representation "Department of B … Louis, MO, USA." is too long.

Abstract

SUMMARY: 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

CONTACT: kchen3@mdanderson.org; lding@genome.wustl.edu

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.