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Table 1 Somatic structural variants predicting fusion genes

From: The Swedish childhood tumor biobank: systematic collection and molecular characterization of all pediatric CNS and other solid tumors in Sweden

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

 
  1. 1Type of Structural Variant: BND   breakend notation, translocation, DUP  duplication, INV inversion
  2. 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