Fig. 3.

Performance of SQUID and fusion-gene detection methods on breast cancer cell lines HCC1954 and HCC1395. Predictions are evaluated for previously validated SVs and fusions. a Fusion-gene prediction sensitivity–precision curve of different methods. b Non-fusion-gene prediction sensitivity–precision curve. Only SQUID, deFuse, and the pipeline of de novo transcriptome assembly and transcript-to-genome alignment are able to predict non-fusion-gene TSVs. c Number of fusion-gene TSVs and non-fusion-gene TSVs correctly predicted by SQUID. Non-fusion-gene TSVs make up a considerable proportion of all TSVs. TSV transcriptomic structural variant