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BreakTrans: uncovering the genomic architecture of gene fusions

Ken Chen12*, Nicholas E Navin13, Yong Wang3, Heather K Schmidt4, John W Wallis4, Beifang Niu4, Xian Fan12, Hao Zhao1, Michael D McLellan4, Katherine A Hoadley5, Elaine R Mardis4, Timothy J Ley46, Charles M Perou5, Richard K Wilson4 and Li Ding46*

Author Affiliations

1 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030, USA

2 Department of Computer Science, Rice University, 6100 Main St, Houston, Texas 77251, USA

3 Department of Genetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030, USA

4 The Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave, St Louis, MO 63108, USA

5 Department of Genetics, University of North Carolina School of Medicine, 120 Mason Farm Road, Chapel Hill, NC 27599, USA

6 Department of Medicine, Washington University School of Medicine, 660 S. Euclid Ave, St Louis, MO 63110, USA

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Genome Biology 2013, 14:R87  doi:10.1186/gb-2013-14-8-r87

Published: 23 August 2013

Additional files

Additional file 1:

A list of 3,498 candidate gene fusion breakpoints in SK-BR-3, used as input to BreakTrans.

Format: TSV Size: 153KB Download file

Open Data

Additional file 2:

A list of 41,615 candidate genomic breakpoints in SK-BR-3, used as input to BreakTrans.

Format: TSV Size: 3.9MB Download file

Open Data

Additional file 3:

A list of 40 genomically validated fusion breakpoints output by BreakTrans-0.0.6.

Format: TSV Size: 3KB Download file

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Additional file 4:

A list of 1,994 candidate gene fusions predicted by nFuse-0.1.4.

Format: TSV Size: 1.4MB Download file

Open Data

Additional file 5:

Figures S1 to S42. Figure S1: PREX1-CPNE1 fusion detected from SK-BR-3 WTS data. Figures S2 to S5: integrative genomics views (IGVs) of read alignments at the two GSR breakpoints (four break-ends) underlying PREX1-CPNE1. Figures S6 to S9: IGVs of GSR breakpoints underlying MTBP-SAMD12. Figures S10 and S11: IGVs of GSR breakpoints underlying WDR67-ZNF704. Figure S12: whole genome somatic copy number alteration (log2) of A09I. Figure S13: the NF1-NLE1 fusions detected in A09I. Figure S14: somatic copy number alteration on chromosome 17 of A09I with red vertical lines marking the GSR breakpoints that support the NF1-NLE1 fusion. Figures S15 to S18: IGV of the two GSR breakpoints (four break-ends) that underlie NF1-NLE1. Figure S19: the PPP1R1B-PIPOX fusion detected in A0D1. Figure S20: whole-genome somatic copy number alteration (log2) of A0D1. Figure S21: somatic copy number alteration on chromosome 17 of A0D1 with red vertical lines marking the GSR breakpoints that support the PPP1R1B-PIPOX fusion. Figures S22 to S27: IGVs of the three GSR breakpoints (6 break-ends) that underlie PPP1R1B-PIPOX. Figure S28: the PPP3R1-TTC27 fusion detected in A0YG. Figure S29: whole-genome somatic copy number alteration (log2) of A0YG. Figure S30: somatic copy number alteration on chromosome 2 of A0YG with red vertical lines marking the GSR breakpoints that support the PPP3R1-TTC27 fusion. Figure S31: zoomed-in view of Figure S29 at the chromosome 2 chromothripsis that harbors the fusion. Figures S32 to S37: IGVs of the three GSR breakpoints (6 break-ends) that underlie PPP3R1-TTC27. Figures S38 to S41: PCR validation of TCGA BRCA genomic breakpoints. Figure S42: capillary sequencing trace of a PCR product that was not visible in the gel.

Format: PPTX Size: 4.5MB Download file

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Additional file 6:

A list of 124 fusion breakpoints (42 gene pairs) produced by Tophat-fusion from the validation RNA-seq data.

Format: TXT Size: 8KB Download file

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Additional file 7:

A list of 115 fusion breakpoints (62 gene pairs) produced by BreakFusion-1.0.1 from the validation RNA-seq data.

Format: TSV Size: 6KB Download file

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Additional file 8:

Breakpoints and PCR primers for SK-BR-3 validation.

Format: XLSX Size: 47KB Download file

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Additional file 9:

A list of 177 gene fusions and corresponding genomic breakpoints produced by BreakTrans from 43 TCGA breast cancer samples.

Format: XLSX Size: 63KB Download file

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Additional file 10:

Experimental design for validating 20 TCGA GSR breakpoints.

Format: XLSX Size: 52KB Download file

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Additional file 11:

PCR validation of 20 TCGA GSR breakpoints in 9 TCGA samples.

Format: XLSX Size: 10KB Download file

Open Data