Table 3. Candidate fusion transcripts in gastrointestinal stromal tumors.
| Sample | Tool | 5′ | 3′ | Read-through | ||||
|---|---|---|---|---|---|---|---|---|
| Gene | Chromosome | FC* ≥ 2 | Gene | Chromosome | FC* ≥ 2 | |||
| 01 | DF / CS | POLA2 | 11 | CDC42EP2 | 11 | Yes | ||
| 01 | DF | IGF2 | 11 | ACTB | 7 | |||
| 01 | CS | STX16 | 20 | NPEPL1 | 20 | 2.10 | Yes | |
| 02 | DF / CS | POLA2 | 11 | CDC42EP2 | 11 | Yes | ||
| 02 | DF | FBXO25 | 8 | BET1L | 11 | |||
| 03 | DF | EPS15 | 1 | OSBPL9 | 1 | |||
| 03 | DF / CS | POLA2 | 11 | CDC42EP2 | 11 | Yes | ||
| 03 | DF | IGF2 | 11 | SEPT9 | 17 | |||
| 03 | DF | GAPDH | 12 | IGF2 | 11 | |||
| 03 | DF | C8orf42 | 8 | FBXO25 | 8 | Yes | ||
| 03 | DF | IGF2 | 11 | CCND1 | 11 | 2.77 | ||
| 03 | CS | LYPLA1 | 8 | TCEA1 | 8 | |||
| 03 | CS | FXYD6-FXYD2 | 11 | DSCAML1 | 11 | 2.00 | Yes | |
| 04 | DF | IGF2 | 11 | 2.18 | EPC1 | 10 | ||
| 04 | DF | IGF2 | 11 | 2.18 | SQSTM1 | 5 | ||
| 04 | DF | IGF2 | 11 | 2.18 | TOP2B | 3 | ||
| 04 | DF | IGF2 | 11 | 2.18 | KIT | 4 | 2.59 | |
| 04 | DF | HNRNPA2B1 | 7 | PCBD2 | 5 | |||
| 04 | DF | UBR4 | 1 | 3.36 | IGF2 | 11 | 2.18 | |
| 04 | DF | C8orf42 | 8 | FBXO25 | 8 | Yes | ||
| 04 | DF / CS | POLA2 | 11 | CDC42EP2 | 11 | Yes | ||
| 04 | CS | FXYD6-FXYD2 | 11 | DSCAML1 | 11 | 3.14 | Yes | |
| 05 | DF | POLA2 | 11 | CDC42EP2 | 11 | Yes | ||
| 05 | DF | IGF2 | 11 | LASP1 | 17 | |||
| 05 | DF | IGF2 | 11 | FUS | 16 | |||
| 05 | CS | STX16 | 20 | NPEPL1 | 20 | Yes | ||
| 07 | DF / CS | P2RY6 | 11 | 5.27 | ARHGEF17 | 11 | Yes | |
| 07 | CS | CTSL3 | 9 | 4.48 | GABBR2 | 9 | ||
| 08 | DF | IGF2 | 11 | STAT5B | 17 | |||
| 08 | DF | HNRNPA2B1 | 7 | PCBD2 | 5 | |||
| 08 | DF | C8orf42 | 8 | FBXO25 | 8 | Yes | ||
| 08 | DF | CTSL1 | 9 | GAPDH | 12 | |||
| 08 | DF | IGF2 | 11 | TNPO1 | 5 | |||
| 08 | DF | KIT | 4 | IGF2 | 11 | |||
| 08 | DF | KIT | 4 | PCBD2 | 5 | |||
| 08 | CS | POLA2 | 11 | CDC42EP2 | 11 | Yes | ||
| 09 | DF | C8orf42 | 8 | FBXO25 | 8 | Yes | ||
| 09 | CS | POLA2 | 11 | CDC42EP2 | 11 | Yes | ||
| 09 | CS | STX16 | 20 | NPEPL1 | 20 | Yes | ||
| 09 | DF / CS | RALGPS1 | 9 | LRSAM1 | 9 | |||
| 10 | DF | IGF2 | 11 | RBMS1 | 2 | |||
*Fold change (FC) represents the difference in RPKM values between a sample and the mean. Bold font indicates the genes listed in the Mitelman database (DF, defuse; CS, ChimeraScan).