Table 1.
Characterisation of fusion genes determined by RNA-seq
| Donor gene | Acceptor gene | In-frame shift | Count | Sample ID | Mid distance | Transciption strand | Gene 1 | Break point 1 | Gene 2 | Break point 2 | deFuse | FusionMap | High expression | Function | Reference | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CRC | Other cancers | |||||||||||||||
| ANAPC1 | ZC3H8 | 2–>0 | 1 | 13 | 375,316 | − | ANAPC1 | chr2: 112614191 | ZC3H8 | chr2: 112989507 | O | O | ||||
| APC | COMMD10 | 2–>0 | 1 | 16 | 3,475,924 | ++ | APC | chr5: 112151290 | COMMD10 | chr5: 115627214 | O | O | APC; supprresor | |||
| ATIC | UXS1 | 2–>0 | 1 | 4 | 109,465,313 | +− | UXS1 | chr2: 106717570 | ATIC | chr2: 216182883 | O | O | ||||
| BOD1 | WWC1 | 2–>0 | 1 | 14 | 5,155,548 | −+ | WWC1 | chr5: 167887655 | BOD1 | chr5: 173043203 | O | O | ||||
| BOK | ING5 | 0–>1 | 1 | 6 | 142,177 | ++ | BOK | chr2: 242501891 | ING5 | chr2: 242644068 | O | O | ||||
| CHIC1 | HDX | 2–>0 | 1 | 19 | 10,812,212 | +− | CHIC1 | chrX: 72804408 | HDX | chrX: 83616620 | O | O | ||||
| 10,891,185 | +− | HDX | chrX: 83695593* | |||||||||||||
| GTF3A | CDK8 | 2–>0 | 1 | 7 | 1,075,866 | −− | CDK8 | chr13: 26923209 | GTF3A | chr13: 27999075 | O | O | Donor and acceptor | CDK8; kinase | COAD (9) | |
| LMNA | NTRK1 | 0–>1 | 1 | 18 | 739,572 | ++ | LMNA | chr1: 156105740 | NTRK1 | chr1: 156845312 | O | O | Acceptor | NTRK1; kinase, oncogene | COAD (9) | Spitzoid neoplasm (COSMIC) |
| NAGLU | IKZF3 | 0–>1 | 1 | 3 | 2,770,478 | +− | IKZF3 | chr17: 37922746 | NAGLU | chr17: 40693224 | O | O | Donor and acceptor | COAD (9) | ||
| OSBPL10 | GADL1 | 2–>0 | 1 | 15 | 1,101,625 | ++ | GADL1 | chr3: 30769907 | OSBPL10 | chr3: 31871532 | O | O | ||||
| PTPRK | RSPO3 | 0–>1 | 1 | 19 | 1,371,611 | −+ | RSPO3 | chr6: 127469793 | PTPRK | chr6: 128841404 | O | Acceptor | PTPRK-RSPO3; oncogene | COAD, READ (20) | ESCA, STAD (20) | |
| 1 | 10 | 1,035,784 | −+ | PTPRK | chr6: 128505577 | |||||||||||
| RAB1B | DPP3 | 2–>0 | 1 | 17 | 210,011 | ++ | RAB1B | chr11: 66039928 | DPP3 | chr11: 66249939 | O | O | ||||
| RASA1 | LOC644100 | 1–>2 | 1 | 11 | 28,829,615 | ++ | RASA1 | chr5: 86564807 | LOC644100 | chr5: 115394422 | O | Acceptor | RASA1; supressor | COAD (9) | ||
| RIMS3 | SCMH1 | 0–>1 | 1 | 14 | 407,181 | −− | RIMS3 | chr1: 41107381 | SCMH1 | chr1: 41514562 | O | |||||
| RNF121 | FOLR2 | 2–>0 | 1 | 9 | 291,744 | ++ | RNF121 | chr11: 71640170 | FOLR2 | chr11: 71931914 | O | O | Acceptor | |||
| 289,435 | ++ | FOLR2 | chr11: 71929605* | |||||||||||||
| STRN | ALK | 0–>1 | 1 | 14 | 7,696,827 | ++ | ALK | chr2: 29446394 | STRN | chr2: 37143221 | O | O | Acceptor | ALK; kinase, oncogene | COAD (17) | KIRP, THCA (20) |
| TAF4 | NDRG3 | 2–>0 | 1 | 12 | 25,277,811 | ++ | NDRG3 | chr20: 35294795 | TAF4 | chr20: 60572606 | O | O | ||||
| TMOD3 | MAPK6 | 2–>0 | 1 | 1 | 183,622 | ++ | TMOD3 | chr15: 52155207 | MAPK6 | chr15: 52338829 | O | O | MAPK6; kinase | |||
| 183,607 | ++ | MAPK6 | chr15: 52338814* | |||||||||||||
| TMPRSS2 | PDE9A | 0–>1 | 1 | 5 | 1,303,676 | −+ | TMPRSS2 | chr21: 42848504 | PDE9A | chr21: 44152180 | O | O | PRAD (20) | |||
| 1,303,376 | −+ | PDE9A | chr21: 44151880* | |||||||||||||
| TPM3 | NTRK1 | 0–>1 | 1 | 2 | 2,701,487 | −+ | TPM3 | chr1: 154142876 | NTRK1 | chr1: 156844363 | O | O | Acceptor | NTRK1; kinase, oncogene | COAD (9) | SARC, THCA (20) |
| 1 | 5 | 2,702,436 | −+ | NTRK1 | chr1: 156845312 | |||||||||||
| 2,702,996 | −+ | NTRK1 | chr1: 156845872 | |||||||||||||
| TRIM24 | BRAF | 0–>1 | 1 | 8 | 2,283,414 | −+ | TRIM24 | chr7: 138203934 | BRAF | chr7: 140487348 | O | O | BRAF; kinase, oncogene | READ (20) | LIHC (20) | |
| USP32 | NSF | 0–>1 | 1 | 14 | 13,631,493 | −+ | NSF | chr17: 44791351 | USP32 | chr17: 58422844 | O | O | ||||
| VTI1A | TCF7L2 | 2–>0 | 1 | 16 | 614,020 | ++ | VTI1A | chr10: 114286923 | TCF7L2 | chr10: 114900943 | O | O | COAD (COSMIC) | |||
| ZYG11A | GPX7 | 2–>0 | 1 | 13 | 236,289 | −− | GPX7 | chr1: 53072356 | ZYG11A | chr1: 53308645 | O | O | ||||
Fusion genes were identified by GFP algorithm. Bold letters in first and second rows indicate finally selected fusion genes. Break points were filled in depending on Sanger sequencing results. Transcription strand column was written in the order of donor and acceptor gene (+; sense strand, −; antisense strand). The different break points of NGS and Sanger sequencing were marked with asterisks (*). According to NGS, the break points of HDX and MAPK6 were located on chrX: 83724583 and chr15: 52342190, respectively, and FOLR2 and PDE9A had only one break point (chr11: 71931914, chr21: 44152180, respectively). Gene function was described as kinase, oncogene, or tumour suppressor gene O; cross-validated fusion gene,
COAD colon adenocarcinoma, ESCA oesophageal carcinoma, KIRP kidney renal papillary cell carcinoma, LIHC liver hepatocellular carcinoma, PRAD prostate adenocarcinoma, READ rectal adenocarcinoma, SARC sarcoma, STAD stomach adenocarcinoma, THCA thyroid carcinoma