Finally, we identified three gene fusions involving tumor-suppressor genes (TSGs) which showed a significant decrease in gene expression (p < 0.1) relative to the cancer type supergroup: ZBTB20–LSAMP (-4.0 zfpkm, p < 0.05), NF1–RAB11FIP4 (-2.4 zfpkm) and the previously mentioned ATRX–LINC01280 (-3.5 zfpkm) in a patient with osteosarcoma (Additional file 1: Supplementary results, Figure S6). Here, ATRX is linked to osteosarcoma.