Table 1.
Summary of a pilot study to compare the capability of the junction capture method to detect fusion genes with that of a gDNA capture method
| Case # | Diagnosis | Sample year | RIN score | Fusion gene | TOP RNA panel (junction capture) | gDNA capture | Anchored multiplex PCR | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Split read number | Raw read number | TOP version | Split read number | Raw read number | Split read number | Raw read number | |||||
| #1 | NSCLC | 2012 | N.D. | EML4‐ALK | 232 | 28 873 868 | V1 | 12 | 53 647 702 | 68 | 1 941 324 |
| #2 | NSCLC | 2012 | N.D. | EML4‐ALK | 284 | 29 302 268 | V1 | 108 | 61 299 256 | 22 | 2 354 508 |
| #3 | NSCLC | 2013 | N.D. | EML4‐ALK | 180 | 29 903 016 | V1 | 44 | 58 450 392 | 10 | 2 639 006 |
| #4 | NSCLC | 2014 | N.D. | EML4‐ALK | 4179 | 30 546 206 | V1 | 0 | 66 769 928 | 278 | 3 019 450 |
| #5 | NSCLC | 2012 | N.D. | KIF5B‐RET | 514 | 27 969 576 | V1 | 0 | 57 830 964 | 0 | 54 170 756 |
| #6 | NSCLC | 2013 | N.D. | KIF5B‐RET | 2898 | 27 396 626 | V1 | 150 | 69 819 612 | 0 | 58 501 738 |
| #7 | NSCLC | 2014 | 1.3 | KIF5B‐RET | 1189 | 27 750 096 | V1 | 53 | 62 606 194 | 5 | 65 226 738 |
| #8 | NSCLC | 2011 | N.D. | SLC34A2‐ROS1 | 1633 | 30 614 778 | V1 | 17 | 64 415 016 | 13 | 45 395 450 |
| #9 | NSCLC | 2012 | 1.4 | CD74‐ROS1 | 5268 | 29 494 774 | V1 | 0 | 60 541 260 | 0 | 53 252 448 |
| #10 | NSCLC | 2013 | N.D. | CD74‐ROS1 | 2491 | 28 970 804 | V1 | 77 | 69 241 262 | 0 | 56 481 374 |
N.D., not detected; NSCLC, non‐small‐cell lung cancer; PCR, polymerase chain reaction; RIN, RNA integrity number.