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. 2023 May 23;21:342. doi: 10.1186/s12967-023-04178-4

Table 1.

Somatic structural variants predicting fusion genes

Sample Consequence Type of SV1 Transcript1::Transcript22 Start-Stop (GRCh38 coordinates) Pathological diagnosis
P2233_115T ETV6::NTRK3 BND ENST00000396373.8|5/7::ENST00000626019.2|12/18 chr12:11880139-chr15:88000019 ATRT
P7708_114T C11orf95::RELA DUP ENST00000433688.2|3/5::ENST00000406246.7|2/11 chr11:63764600-chr11:65662555 Ependymoma
P7708_115T C11orf95::RELA double BND ENST00000433688.2|3/5::ENST00000406246.7|2/11 chr11:63764612-chr11:65662560 Ependymoma
P7708_201T C11orf95::RELA DUP ENST00000433688.2|2/5::ENST00000406246.7|2/11 chr11:63765733-chr11:65663414 Ependymoma
P7708_109T GADL1::RBMS3 INV ENST00000282538.9|12/15::ENST00000636680.1|6/17 chr3:29516136-chr3:30793136 Ependymoma
SYNPO2::HELQ INV ENST00000307142.8|1/5::ENST00000295488.7|9/18 chr4:83435026-chr4:118898900
P7708_116T ARHGEF2::NTRK1 INV + DEL ENST00000673475.1|25/26::ENST00000524377.6|12/17 chr1:155949192-chr1:156875269 Ganglioglioma
P2233_118T RERE::SLC2A5 DUP ENST00000337907.7|2/24::ENST00000377424.9|12/12 chr1:8739338-chr1:9087076
P2233_119T KIAA1549::BRAF DUP ENST00000422774.2|16/20::ENST00000288602.11|9/19 chr7:138852276-chr7:140790556 Pilocytic astrocytoma
P4551_213T KIAA1549::BRAF double INV DUP ENST00000422774.2|16/20::ENST00000644969.2|9/20 chr7:138852518-chr7:140791970 Pilocytic astrocytoma
P2233_108T KIAA1549::BRAF DUP ENST00000422774.2|16/20::ENST00000644969.2|9/20 chr7:138852755-chr7:140789812 Pilocytic astrocytoma
P2233_110T KIAA1549::BRAF DUP ENST00000422774.2|16/20::ENST00000644969.2|9/20 chr7:138853500-chr7:140792494 Pilocytic astrocytoma
P4552_104T KIAA1549::BRAF DUP ENST00000422774.2|16/20::ENST00000644969.2|9/20 chr7:138854568-chr7:140790408 Pilocytic astrocytoma
P2233_103T KIAA1549::BRAF DUP ENST00000422774.2|16/20::ENST00000644969.2|9/20 chr7:138856929-chr7:140789598 Pilocytic astrocytoma
P7708_104T KIAA1549::BRAF DUP ENST00000422774.2|16/20::ENST00000644969.2|9/20 chr7:138858793-chr7:140791924 Pilocytic astrocytoma
P4552_106T KIAA1549::BRAF DUP ENST00000422774.2|16/20::ENST00000644969.2|9/20 chr7:138859026-chr7:140791514 Pilocytic astrocytoma
P4552_105T KIAA1549::BRAF DUP ENST00000422774.2|16/20::ENST00000644969.2|9/20 chr7:138860733-chr7:140788171 Pilocytic astrocytoma
P4551_217T KIAA1549::BRAF DUP ENST00000422774.2|15/20::ENST00000644969.2|9/20 chr7:138862714-chr7:140787922 Pilocytic astrocytoma
P4552_108R KIAA1549::BRAF DUP ENST00000422774.2|15/20::ENST00000644969.2|9/20 chr7:138863829-chr7:140793843 Pilocytic astrocytoma
P4551_215T KIAA1549::BRAF DUP ENST00000422774.2|15/20::ENST00000644969.2|9/20 chr7:138867796-chr7:140792603 Pilocytic astrocytoma
P4551_216T KIAA1549::BRAF DUP ENST00000422774.2|12/20::ENST00000644969.2|9/20 chr7:138878216-chr7:140787971 Pilocytic astrocytoma
P4551_219T EWSR1::PATZ1 INV ENST00000414183.6|9/18::ENST00000266269.10|1/5 chr22:29289872-chr22:31344672 Pilocytic astrocytoma
P4552_110T QKI::RAF1 BND ENST00000361752.8|3/18::ENST00000442415.7|8/18 chr6:163496728-chr3:12604073 Pilocytic astrocytoma
P7708_105T FGFR1::TACC1 INV ENST00000425967.7|18/19::ENST00000317827.9|7/13 chr8:38413736-chr8:38835597 Oligodendroglioma
P4551_218T FGFR1::TACC1 INV ENST00000425967.7|18/19::ENST00000317827.9|7/13 chr8:38413197-chr8:38833204 Pilocytic astrocytoma anaplastic
P2233_101T PLEKHA5::PIK3C2G DUP ENST00000429027.6|3/32::ENST00000676171.1|19/33 chr12:18476311-chr12:19180500 PNET
P2233_106T ABL1::FLJ37453 BND ENST00000372348.7|1/11::ENST00000317122.2|2/2 chr9:130847932-chr1:15838837 Rhabdoid meningioma
GABRA5::NTRK3 INV ENST00000400081.7|3/11::ENST00000626019.2|9/19 chr15:26871512-chr15:88134456
MOCOS::ELP2 DUP ENST00000261326.6|6/15::ENST00000442325.6|21/23 chr18:36168162-chr18:36205353

1Type of Structural Variant: BND   breakend notation, translocation, DUP  duplication, INV inversion

25' and 3' genes and transcripts involved in the fusion transcript followed by the exon involved in the breakpoint and total number of exons in the transcript