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MediSapiens FusionSCOUT pipeline and datasets Paired end reads (fastq) Align reads to Ensembl Ensembl transcriptome ! One of the latest therapeutics angles in the fight against cancer is fusion genes and their regulation. To aid in fusion gene research and reveal the multitude of gene fusion event in cancer samples MediSapiens has developed a proprietary FusionSCOUT pipeline for identifying fusion genes from RNA sequencing datasets.! ! Currently we have analysed 7625 tumour samples from the TCGA project building a fusion gene dataset covering 28 different cancers within the TCGA project which can be accessed through our FusionSCOUT product. ! ! Using this pipeline, we have discovered 3930 samples with gene fusions with 9667 different fusion genes. We´ve discovered numerous novel gene fusions as well as new cancer types in which previously known fusions appear.! ! You can now purchase these gene fusions datasets with a few mouse clicks and get the world´s most comprehensive gene fusions from cancer sets within days.! ! You can also subscribe our pipeline for your samples and get the most out of your data!! Filter by genome alignments, sequence homology, … Identify candidate fusion genes 1 2 3 1 3 2 Find fusion junction 2 5’ junction exon 5 3 3’ junction exon Filter by: junction read mate alignment, read orientations, … Predict fusion mRNA and reading frame 1 2 3 4 5 Predict protein domains (Pfam) Interpro domain 1 Interpro domain 2 Schematic representation of FusionSCOUT pipeline! www.medisapiens.com Example of data from FusionSCOUT: With the full order you´ll receive: ! • Dataset: TCGA Breast cancer (BRCA) ! cancer types or one cancer in Excel and text format! • Number of samples analysed: 1029! • • Number of samples with fusion genes: 714! Total number of fusion genes: 2941! • Selected 5´genes ESR1 and FGFR2! • • 5´gene name ESR1! ESR1! ESR1! ESR1! ESR1! ESR1! ESR1! ESR1! ESR1! ESR1! ESR1! ESR1! ESR1! ESR1! ESR1! ESR1! FGFR2! FGFR2! FGFR2! FGFR2! FGFR2! FGFR2! 3´gene' name MTHFD1L! CCDC170! CCDC170! AKAP12! AKAP12! POLH! C6orf211! CCDC170! CCDC170! CCDC170! CCDC170! CCDC170! CCDC170! CCDC170! ASPH! ASPH! RP11-78A18.2! AP1M1! ATE1! CCDC6! ENPP2! ENPP2! Paired-end read count 18! 24! 17! 16! 16! 15! 42! 21! 14! 22! 42! 35! 35! 26! 613! 613! 50! 8! 22! 27! 83! 83! Junction read count 5! 9! 11! 17! 17! 8! 10! 16! 10! 16! 25! 25! 25! 14! 371! 371! 51! 9! 19! 20! 59! 59! TCGA sample ID:s of the samples with fusions! Exact exon junctions for the fusions, including alternatively spliced variants; data on whether reading frame is retained! Data source: TCGA project, via Cancer Genomics Hub (https://cghub.ucsc.edu/)! TCGA sample id TCGA-BH-A5J0-01! TCGA-BH-A0C0-01! TCGA-BH-A1FD-01! TCGA-BH-A1FD-01! TCGA-BH-A1FD-01! TCGA-BH-A1FD-01! TCGA-E9-A1NA-01! TCGA-D8-A27N-01! TCGA-A2-A4S3-01! TCGA-A2-A0CT-01! TCGA-BH-A18R-01! TCGA-AR-A24R-01! TCGA-AR-A24R-01! TCGA-D8-A1JP-01! TCGA-A2-A3KD-01! TCGA-A2-A3KD-01! TCGA-BH-A1EY-01! TCGA-AQ-A04L-01! TCGA-D8-A142-01! TCGA-D8-A13Z-01! TCGA-LD-A7W5-01! TCGA-LD-A7W5-01! A list of all gene fusions that involve your genes of interest, across all TCGA Canonical fusion reading frame is_in_frame! is_not_in_frame! is_not_in_frame! is_not_in_frame! is_in_frame! is_not_in_frame! is_in_frame! is_not_in_frame! is_in_frame! is_not_in_frame! is_not_in_frame! no_frame! is_not_in_frame! is_in_frame! is_not_in_frame! is_not_in_frame! is_not_in_frame! is_in_frame! is_in_frame! is_in_frame! is_in_frame! is_in_frame! • Detailed list of protein domains retained in the fusion genes! • Positions, cDNA sequences for the fusion mRNAs, and much more!! 5´protein domains Oestr_rcpt ; Znf_hrmn_rcpt! 3´protein domains Formate_THF_ligase! Oestr_rcpt ; Znf_hrmn_rcpt! Oestr_rcpt ; Znf_hrmn_rcpt! Oestr_rcpt ; Znf_hrmn_rcpt! Oestr_rcpt ; Nucl_hrmn_rcpt_lig-bd_core ; Znf_hrmn_rcpt! ! Oestr_rcpt ; Znf_hrmn_rcpt! ! ! Pkinase-A_anch_WSK-motif ; RII_binding_1! Pkinase-A_anch_WSK-motif ; RII_binding_1! DNA_repair_prot_UmuC-like ; DNA_pol_Y-fam_little_finger! ! ! ! Oestr_rcpt! ! Oestr_rcpt ; Znf_hrmn_rcpt! Oestr_rcpt ; Znf_hrmn_rcpt! Immunoglobulin ; Ig_I-set ; Ser-Thr/Tyr_kinase_cat_dom! Immunoglobulin ; Ig_I-set ; Ser-Thr/Tyr_kinase_cat_dom! ! Immunoglobulin ; Ig_I-set ; Ser-Thr/Tyr_kinase_cat_dom! Immunoglobulin ; Ig_I-set! Immunoglobulin ; Ig_I-set! Asp_Arg_b-Hydrxlase! Asp_Arg_b-Hydrxlase! ! Clathrin_mu_C ; AP_mu_sigma_su! Arg-tRNA-P_Trfase_C! DUF2046! Phosphodiest/P_Trfase ; Somatomedin_B_dom ; DNA/RNA_non-sp_Endonuclease! Phosphodiest/P_Trfase ; Somatomedin_B_dom ; DNA/RNA_non-sp_Endonuclease! ! For more information on MediSapiens and FusionSCOUT gene datasets and pipeline, please visit www.medisapiens.com/products/fusionscout or contact us via email at [email protected] www.medisapiens.com
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