BreakTrans: uncovering the genomic architecture of gene fusions

Abstract

Producing gene fusions through genomic structural rearrangements is a major mechanism for tumor evolution. Therefore, accurately detecting gene fusions and the originating rearrangements is of great importance for personalized cancer diagnosis and targeted therapy. We present a tool, BreakTrans, that systematically maps predicted gene fusions to structural rearrangements. Thus, BreakTrans not only validates both types of predictions, but also provides mechanistic interpretations. BreakTrans effectively validates known fusions and discovers novel events in a breast cancer cell line. Applying BreakTrans to 43 breast cancer samples in The Cancer Genome Atlas identifies 90 genomically validated gene fusions. BreakTrans is available at http://bioinformatics.mdanderson.org/main/BreakTrans.

Figure 1

Schematic overview of BreakTrans. Plotted as an example are three genes, A, B and C, that range from genomic positions (black nodes) a to c, d to g, and h to j, respectively. Each gene contains two exons (arrow boxes) that can be transcribed from 5' to 3'. Gene A is on the positive (+) strand, while genes B and C are on the negative (-) strand. Two sets of putative novel genomic breakpoints are identified from alignments: b+

Figure 2

Copy number profile in the SK-BR-3 genome. Plotted are three gene fusions predicted by BreakTrans: (a) PREX1>CPNE1, (b) MTBP>SAMD12, (c) WDR67>ZNF704. The x-axis represents genomic positions and the y-axis represents absolute copy number in non-overlapping 10 kb windows. The vertical red lines mark the locations of the GSR breakpoints that led to these fusions.

Figure 3

Breakpoints of novel fusions in SK-BR-3. (a) The novel tumor allele supporting PREX1>CPNE1 consists of the first three exons of PREX1 (green), an intronic segment of PHF20 (orange) and the last three exons of CPNE1 (blue). The RNA PREX1>CPNE1 breakpoint between exons A and B was nominated by deFuse, while the genomic breakpoints SV1 and SV2 were detected by CREST. (b) Six genomic breakpoints from three gene fusions were selected for PCR validation (Additional file 8). SV1 and SV2 are from PREX1>CPNE1, SV3 and SV4 from MTBP-SAMD12, and SV5 and SV6 from WDR67-ZNF704. Clean PCR bands were observed at SV1, SV2, SV3 and SV6.

Figure 4

Definition of breakpoints and breakpoint strings. For intra-chromosome rearrangements, four types of breakpoints - (a) null, (b) jump, (c) inverse and (d) repeat between genomic positions x and y - can be created that involve DNA on either the positive (red arrow) or the negative (blue arrow) strands. Edges are labeled with a number (for example, 3) representing confidence scores (for example, number of supporting reads) for the predicted adjacency. Edges without a number or with the number '0' represent reference adjacency (null breakpoints). For inter-chromosomal rearrangements, four possible novel alleles - (e) A-D, (f) B-C, (g) A-B and (h) C-D - can be created by joining four breakends (A, B, C, D) from two wild-type alleles (A-C, B-D) through genomic breakpoints x and y. Each allele can be represented in two different orientations involving combinations of either the positive (red arrow) or the negative (blue arrow) strands. (i) Breakpoint strings corresponding to the above configurations are listed, where '+' represents the positive strand and '-' the negative strand. The syntax of breakpoint strings is further explained in the Materials and methods.