Table 2.
Fusion identification by CREST and SVAtools.
| Sample ID | Tumor Percent | ALK FISH (%) | ALK IHC (ALK1) | ALK IHC (D5F3) | CREST* | SVAtools** |
|---|---|---|---|---|---|---|
| Y31 | N/A | − (1) | 1 | N.T | – | – |
| Y32 | N/A | − (6) | 1 | N.T | – | EZR-><-RAB3C |
| Y33 | N/A | − (2) | 0 | N.T | – | – |
| Y34 | 70% | − (N/A) | 0 | N.T | – | – |
| Y35 | N/A | − (9) | 1 | N.T | EZR->ROS1 (10) | EZR->ROS1 (4) |
| Y38 | 80% | − (2) | 0 | N.T | – | – |
| Y39 | 90% | − (N/A) | 1 | N.T | – | – |
| Y65 | 40% | − (N/A) | 1 | N.T | – | – |
| Y68 | 95% | − (N/A) | 1 | N.T | SND1->BRAF not detected by BWA-Novoalign/CREST; detected by BWAMEM/CREST (17) | SND1-> BRAF (11) |
| Y69 | 90% | − (N/A) | 0 | N.T | SND1->BRAF (9) | SND1-> BRAF (21) |
|
| ||||||
| Y56 | 60% | − (N/A) | 2 | N.T | – | – |
| Y63 | 50% | − (0) | 2 | 0 | – | – |
| Y72 | 60% | − (3) | 2 | 0 | – | – |
| Y73 | 80% | − (1) | 2 | 0 | CD74->ROS1 (40) | CD74-> ROS1 (79); ROS1->CD74 (11) |
| Y74 | 90% | − (7) | 2 | 0 | – | – |
| Y75 | 50% | − (5) | 2 | 0 | – | – |
| Y76 | 70% | − (0) | 2 | 0 | – | – |
| Y77 | 90% | − (5) | 2 | 0 | – | – |
| Y78 | 90% | − (1) | 2 | 0 | – | – |
| Y79 | 70% | − (N/A) | 2 | 0 | – | – |
| Y80 | 80% | − (1) | 2 | 0 | – | – |
| Y81 | 70% | − (5) | 2 | 0 | – | – |
|
| ||||||
| 891A | N/A | + (27) | 1 | 0 | AAK1->ALK (94); EML4->BIRC6 (160) | AAK1->ALK (152); EML4->BIRC6 (187) |
| Y20 | N/A | + (15) | 1 | 0 | – | – |
| Y53 | 70% | + (15) | 1 | 0 | – | – |
| Y60 | 60% | + (18) | 1 | 0 | – | – |
|
| ||||||
| Y02 | 90% | + (N/A) | 2 | N.T | HIP1->ALK (20) | HIP1->ALK (33) |
| Y04 | 95% | + (29) | 2 | N.T | EML4->ALK (42) | EML4->ALK (94) |
| Y05 | 90% | + (60) | 3 | N.T | ALK->EML4 (29);<-ALK:EML4-> (24) | <-ALK EML4->(25); ALK->EML4 (21) |
| Y06 | 80% | + (25) | 2 | N.T | EML4->ALK (13);ALK->EML4 (60) | EML4->ALK (43); ALK->EML4 (48) |
| Y07 | 60% | + (35) | 2 | N.T | EML4->ALK (56) | EML4->ALK (99) |
| Y08 | 90% | + (N/A) | 3 | N.T | EML4->ALK (25);ALK->EML4 (25) | EML4->ALK (46); ALK->EML4 (31) |
| Y12 | N/A | + (52) | 3 | N.T | EML4->ALK (13) | EML4->ALK (13) |
| Y15 | 60% | + (N/A) | 3 | N.T | EML4->ALK (13) | EML4->ALK (9) |
| Y18 | 60% | + (N/A) | 3 | N.T | EML4->ALK (87); ALK->EML4 (58) | EML4->ALK (98); ALK->EML4 (52) |
| Y22 | 50% | + (70) | 3 | N.T | EML4->ALK (19) | EML4->ALK (42) |
| Y26 | N/A | + (72) | 3 | N.T | EML4->ALK (43) | EML4->ALK (49) |
| Y27 | 70% | + (68) | 3 | N.T | EML4->ALK (23) | EML4->ALK (36) |
| Y52 | N/A | + (N/A) | 3 | N.T | EML4->ALK (28);ALK->EML4 (41) | EML4->ALK (76); ALK->EML4 (49) |
| Y54 | 70% | + (15) | 2 | 0 | – | – |
| Y59 | 80% | + (N/A) | 3 | N.T | EML4->ALK (30); SND1->BRAF not detected by BWA-Novoalign/CREST; detected by BWAMEM/CREST (17) | EML4->ALK (13); SND1-> BRAF(13) |
| Y61 | 80% | + (N/A) | 3 | N.T | EML4->ALK (79) | EML4->ALK (56) |
*
Number of supporting split reads is shown in parentheses.
**
Number of supporting read-pairs and split reads is shown in parentheses.
“+” FISH Positive ≥ 15%, “ − ” FISH or Fusion negative, N.T; not tested, N/A; not available