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.

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Chen et al. Genome Biology 2013 14:R87   doi:10.1186/gb-2013-14-8-r87