Table 1 Candidate gene fusions detected by LongGF on long-read RNA-seq data for universal human reference mRNA sample and for a patient with AML. “A:B” denotes a gene fusion of gene A and gene B. The 6 known gene fusions for ‘UHR Nanopore’ rows are used for evaluating gene fusion detection, but additional gene fusions may be present for UHR samples
Gene fusion | Datasets | #Supporting reads | Read coverage | Fusion points (hg38 coordinate) | Benchmark | |
|---|---|---|---|---|---|---|
Breakpoint 1 | Breakpoint 2 | |||||
BCAS4:BCAS3 | UHR Nanopore | 8 | 23 | chr20:50,795,173 | chr17:61,368,325 | Yes |
MGAT5:IGLC7 | 7 | 12 | chr2:134,120,290 | chr22:22,922,718 | ||
GAS6:RASA3 | 2 | 8 | chr13:11,3826,995 | chr13:113,981,855 | Yes | |
ARFGEF2:SULF2 | 2 | 5 | chr20:48,922,009 | chr20:47,736,942 | Yes | |
AP3D1:JSRP1 | 2 | 41 | chr19:2,127,153 | chr19:2,252,480 | ||
VMP1:RPS6KB1 | 2 | 78 | chr17:59,838,294 | chr17:59,910,610 | Yes | |
BCAS4:BCAS3 | UHR PacBio | 206 | 520 | chr20:50795172 | chr17:61368324 | Yes |
ARFGEF2:SULF2 | 70 | 389 | chr20:48922011 | chr20:47736941 | Yes | |
FGFR1:NSD3 | 42 | 53 | chr8:38457533 | chr8:38381797 | In [64] | |
LDLR:ZNF333 | 36 | 51 | chr19:11108452 | chr19:14701590 | In [64] | |
SMARCA4:CARM1 | 28 | 1126 | chr19:10986591 | chr19:10904949 | In [64] | |
VMP1:RPS6KB1 | 26 | 2601 | chr17:59838295 | chr17:59910609 | Yes | |
GAS6:RASA3 | 22 | 103 | chr13:113826995 | chr13:113981856 | Yes | |
GANAB:B3GAT3 | 20 | 33 | chr11:62627352 | chr11:62620496 | In [65] | |
RPS6KB1:DIAPH3 | 19 | 2738 | chr17:59930173 | chr13:59666845 | In [64] | |
NUP214:XKR3 | 19 | 39 | chr9:131199013 | chr22:16808083 | In [64] | |
MYH6:HOMEZ | 15 | 27 | chr14:23386622 | chr14:23285911 | In [38] | |
PAPOLA:AK7 | 15 | 78 | chr14:96502599 | chr14:96437835 | In [64] | |
CBX3:CCDC32 | 14 | 26 | chr7:26201744 | chr15:40561981 | In [64] | |
MYH9:EIF3D | 14 | 65 | chr22:36387806 | chr22:36526134 | In [64] | |
DCAF6:SEMA4A | 14 | 885 | chr1:167951860 | chr1:156153370 | ||
ZBTB45:UBE2M | 11 | 35 | chr19:58518739 | chr19:58557605 | ||
RSBN1:AP4B1 | 10 | 15 | chr1:113811708 | chr1:113899869 | ||
GCN1:MSI1 | 10 | 65 | chr12:120190297 | chr12:120347515 | In [64] | |
ESR1:CCDC170 | 9 | 29 | chr6:151702003 | chr6:151573171 | In [64] | |
NUP210L:GATAD2B | 8 | 501 | chr1:154027597 | chr1:153922729 | In [64] | |
ABL1:BCR | 8 | 298 | chr9:130854065 | chr22:23290408 | Yes | |
ZFP64:ATP1A1 | 8 | 18 | chr20:52052134 | chr1:116396734 | ||
GOPC:ROS1 | 8 | 13 | chr6:117566853 | chr6:117321395 | In [64] | |
RUNX1T1:RUNX1 | A patient with AML | 9 | 2373 | chr8:92,017,366 | chr21:34,859,474 | Yes |
NBEAL1:RPL12 | 8 | 7244 | chr2:203,190,790 | chr9:127,451,392 | ||