Requirements for submitted TSV/CSV

TSV and CSV containing gene fusions can be used to launch a RNA-only or DNA + RNA somatic analysis (Launch analysis > New analysis > Somatic analysis from TSV/CSV)

The TSV/CSV uploaded to analyse gene fusions must be of the following manufacturers and have one of the following formats:

• Star Fusion:

#FusionName           JunctionReadCount  SpanningFragCount  SpliceType           LeftGene                        LeftBreakpoint    RightGene                        RightBreakpoint   LargeAnchorSupport  FFPM        LeftBreakDinuc  LeftBreakEntropy  RightBreakDinuc  RightBreakEntropy  annots
THRA--AC090627.1      27                 93                 ONLY_REF_SPLICE      THRA^ENSG00000126351.8          chr17:38243106:+  AC090627.1^ENSG00000235300.3     chr17:46371709:+  YES_LDAS            23875.8456  GT              1.8892            AG               1.9656             ["CCLE","FA_CancerSupp","INTRACHROMOSOMAL[chr17:8.12Mb]"]

• Fusion Catcher:

Gene_1_symbol(5end_fusion_partner)    Gene_2_symbol(3end_fusion_partner)    Fusion_description    Counts_of_common_mapping_reads    Spanning_pairs    Spanning_unique_reads    Longest_anchor_found    Fusion_finding_method    Fusion_point_for_gene_1(5end_fusion_partner)    Fusion_point_for_gene_2(3end_fusion_partner)    Gene_1_id(5end_fusion_partner)    Gene_2_id(3end_fusion_partner)    Exon_1_id(5end_fusion_partner)    Exon_2_id(3end_fusion_partner)    Fusion_sequence    Predicted_effect 
FGFR3    TACC3    known,adjacent,oncogene,cosmic,ticdb,tcga,cell_lines,18cancers,gliomas,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,oesophagus,10K<gap<100K    0    820    66    43    BOWTIE+BLAT;BOWTIE+STAR    4:1806934:+    4:1727977:+    ENSG00000068078    ENSG00000013810            AGCAGCTGGTGGAGGACCTGGACCGTGTCCTTACCGTGACGTCCACCGAC*ACAGAAGAGTGACACCCGCCTCTGAGACCCTAGAAGACCCTTGCAGGACA    in-frame

• Arriba:

#gene1    gene2    strand1(gene/fusion)    strand2(gene/fusion)    breakpoint1    breakpoint2    site1    site2    type    split_reads1    split_reads2    discordant_mates    coverage1    coverage2    confidence    reading_frame    tags    retained_protein_domains    closest_genomic_breakpoint1    closest_genomic_breakpoint2    gene_id1    gene_id2    transcript_id1    transcript_id2    direction1    direction2    filters    fusion_transcript    peptide_sequence    read_identifiers
BCR    ABL1    +/+    +/+    22:23632600    9:133729451    CDS/splice-site    CDS/splice-site    translocation    4    7    0    4    12    high    in-frame    Mitelman    Bcr-Abl_oncoprotein_oligomerisation_domain(100%),C2_domain(100%),PH_domain(100%),RhoGEF_domain(100%)|F-actin_binding(100%),Protein_kinase_domain(100%),SH2_domain(100%),SH3_domain(100%),Variant_SH3_domain(100%)    .    .    ENSG00000186716.15    ENSG00000097007.13    ENST00000305877.8    ENST00000372348.2    downstream    upstream    .    AGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAG___ATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAA|AAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAG___GTGAAAAGCTCCGGG    SFSLTSVELQMLTNSCVKLQTVHSIPLTINKEDDESPGLYGFLNVIVHSATGFKQSS|kALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLR    BCR-ABL1-10,BCR-ABL1-2,BCR-ABL1-24,BCR-ABL1-28,BCR-ABL1-58,BCR-ABL1-60,BCR-ABL1-76,BCR-ABL1-12,BCR-ABL1-18,BCR-ABL1-4,BCR-ABL1-66

• Dragen RnaFusionFilter TSO500:

Caller,Gene A,Gene B,Gene A Breakpoint,Gene B Breakpoint,Score,Filter,Precise/Imprecise,Intragenic Call,Ref A Split,Ref A Pair,Ref B Split,Ref B Pair,Alt Split,Alt Pair,CandidateAlt,Contig,ContigAlign1,ContigAlign2,KeepFusion,Ref A Dedup,Ref B Dedup,Alt Split Dedup,Alt Pair Dedup,Fusion Directionality Known
RnaFusionFilter,HFM1,ERBB2,chr1:91852917,chr17:37879582,N/A,Imprecise;LowQ,Imprecise,N/A,N/A,N/A,N/A,N/A,N/A,N/A,4,CCCGCTTTCACGGTCTGTATTCGTGAGGCCCCGCTTTCACGGTCTGTATTCGTACTGAAAATCAAGATCAAGCGAGCTTTTGCCCTTCTGCTCCACGGGAGGTTTCTGTCCTCCCTGAGCTCGCCTTAGGGAAAG,109,0,False,1,8,0,2,False

• Dragen Bio-IT platform

#FusionGene,Score,LeftBreakpoint,RightBreakpoint,Filter,SplitScore,NumSplitReads,NumSoftClippedReads,NumSoftClipReadsGene1,NumSoftClippedReadsGene2,NumPairedReads,NumRefSplitReadsGene1,NumRefPairedReadsGene1,NumRefSplitReadsGene2,NumRefPairedReadsGene2,AltToRef,UniqueAlignmentsGene1,UniqueAlignmentsGene2,MaxMapqGene1,AvgMapqGene1,MaxMapqGene2,AvgMapqGene2,CoverageBasesGene1,CoverageBasesGene2,DeltaExonBoundaryGene1,DeltaExonBoundaryGene2,IsRestrictedGene1,IsRestrictedGene2,IsEnrichedGene1,IsEnrichedGene2,CisDistance,BreakpointDistance,GenePairHomologyEval,AnchorLength1,AnchorLength2,FusionLengthGene1,FusionLengthGene2,NonFusionLengthGene1,NonFusionLengthGene2,Gene1Id,Gene2Id,Gene1Location,Gene2Location,Gene1Sense,Gene2Sense
CCDC6--RET,1,chr10:61665880:-,chr10:43612032:+,PASS,8488,4262,4226,3310,916,0,0,0,106,0,80.0755,48,35,227,116.814,250,92.2176,70,144,0,0,1,1,1,1,100000000,18053848,1,73,72,535,13768,117360,39558,ENSG00000108091.10,ENSG00000165731.13,IntactExon,IntactExon,True,True

• Archer 

Classification Report Artifact Genes SS Reads %Reads Brkpt Cat Type InFrame TO Rept Artf Known Partners Strong User-Annotated True Positive User-Annotated False Positive Mispriming Off-Target Expression Imbalance Transcriptional Readthrough Cross-contamination Known Ensembl Paralogue Intronic Fusion Low Confidence Tier I Tier II Tier III Tier IV

TrueETV6:NTRK31222875.27865chr12:12022903,chr15:88576276FusionTrue146131TrueTrueFalseFalseFalseFalseFalseFalseFalseFalseFalse0000