Fig. 1

Comprehensive evaluation of RNA-based Fusioncapture versus DNA-NGS in fusion detection and orthogonal validation in sarcoma. (A) Representative sarcoma cases showing fusion detection discrepancies between RNA-based Fusioncapture™ and DNA-based Onco PanScan™ panels within the 28 overlapping genes shared by both assays. The figure includes DNA-positive/RNA-negative and RNA-positive/DNA-negative fusion calls, along with their orthogonal validation results (e.g., FISH, Sanger sequencing, IHC). (B - E) Verification for 4 DNA-NGS positive/RNA-NGS negative fusions. FISH assay was performed on all the four patients, including Intergenic::NTRK1, PLEKHH2::ALK, PAPPA2::NTRK1, and SYT11::NTRK1, respectively. The Intergenic::NTRK1 (B) and PLEKHH2::ALK (C) fusions were negative. The PAPPA2::NTRK1 (D) and SYT11::NTRK1 (E) fusions were considered positive by FISH, but negative by IHC. (F - J) Validation of the 5 DNA-NGS negative/RNA-NGS positive fusions. FISH assay was performed on the two other patients, including KIAA1549::BRAF (F), and EWSR1::ATF1 (G) and the two fusions were all confirmed as true positive. Sanger sequencing was performed on the three of the 5 patients, as UBTD2::BRAF (H), NOTCH2::LOC729970 (I) and NOTCH2::CARMN (J) and all fusions were positive. (K) Clinical value of the 8 RNA-NGS detected only fusions. (L - M) The landscape of fusions covered only by Fusioncapture panel in the 788 sarcoma patients. (L) Circos plot of the 281 gene fusions from 221 cases in all the STS identified by Fusioncapture panel only. (M) Increased fusion detection ratio and clinical utility of 221 patients