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Table 1 EML4-ALK co-occurring fusion genes and chimeric transcripts detected with TRUP 1.0

From: Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data

PatID HistoID Chimeric_transcript Sp Enc Total Type-I Type-II Domains Validated
H2228 Cell-line EML4-ALK_v3 8 (8 + 8) 13 21 Intra IF Protein_kinase .
SND1-CFTR 6 (6 + 4) 5 11 Intra IF Snase/ABC_tran RT-PCR
DCBLD2-STXBP5L 7 (7 + 2) 2 9 Intra IF CUB/LCCL/F5_F8_type_C RT-PCR
H3122 Cell-line SOS1-ADCY3 16 (16 + 15) 16 32 Intra IF RhoGEF/Guanylate_cyc RT-PCR
EML4-ALK_v1 22 (22 + 7) 9 31 Intra IF Protein_kinase .
S00006 AD EML4-ALK_v2 15 (15 + 4) 5 20 Intra IF Protein_kinase FISH
S00054 AD EML4-ALK_v1 24 (24 + 16) 30 54 Intra IF Protein_kinase FISH
PIGF-CHMP3 13 (13 + 0) 4 17 Intra IF Snf7 RT-PCR
SNAP29-CELSR1 8 (8 + 2) 6 14 Intra IF EGF/LamininG2/LamininEGF/HRM/GPS/7tm2 RT-PCR
APOBEC3F-SBF1 4 (4 + 0) 1 5    Not validated  
S01122 AD EML4-ALK_v1 29 (29 + 8) 12 41 Intra IF Protein_kinase FISH
BMI1-ABI1 14 (14 + 4) 7 21 Intra OF . RT-PCR
MYO10-GPC5 12 (12 + 0) 0 12 Inter IF Myosin_head/IQ/PH RT-PCR
ARHGEF7-ZDHHC11 8 (8 + 2) 0 8 Inter IF CH/SH3/RhoGEF RT-PCR
S01124 AD EML4-ALK_v1 0 4 4 Intra IF Protein_kinase FISH
TAF4-LSM14B 12 (12 + 1) 2 14 Intra IF FDF RT-PCR
S01320 AD EML4-ALK_v1 21 (21 + 7) 6 27 Intra IF Protein_kinase FISH
NUP85-GPC3 12 (12 + 2) 0 12 Inter IF Nucleopor_Nup85 RT-PCR
NR2C1-PTPRB 15 (15 + 4) 4 19    Not validated  
KRIT-MAGI2 2 (2 + 3) 3 5    Not validated  
  1. Table summarizing the chimeric transcripts detected in two lung cancer cell-lines and five lung adenocarcinoma (AD) EML4-ALK-positive tumors. Information about the EML4-ALK variant detected is indicated (v1, v2, v3). The number of spanning (Sp) and encompassing (Enc) reads is given, as well as additional information of the chimeric transcripts: intra-chromosomal (Intra), inter-chromosomal (Inter), in-frame (IF), out-of-frame (OF).