INTRODUCTION

Transcripts fusion as a result of genomic rearrangement is an important class of somatic alteration, as a cancer initiating event and as a molecular therapeutic target for specific tumors. Our Pipeline for RNA sequencing Data Analysis (PRADA) enables us to detect fusion transcripts with high confidence comprehensively. Based on integrated analysis of paired-end RNA sequencing and DNA copy number data from The Cancer Genome Atlas(TCGA), The Tumor Fusion Gene Data Portal provides a bona-fide fusion list across many tumor types.
sample example plot
Figure 1. Fusion transcripts. Fusion transcripts are chimeric mRNAs encoded from the joined parts of two genes, and may occur as a result of genomic rearrangements.
prada paper
Figure 2. Detection of fusion transcripts.PRADA detects fusion transcripts through identification of discordant read pairs and junction spanning reads.
Table below summarizes the tumor types available across thirty three tumor types, as of July 2017. For more information, please read our Oncogene publication:The landscape and therapeutic relevance of cancer-associated transcript fusions
Tumor Type Abbreviation Tumor Sample Size Normal Sample Size (*) Total Fusion Called Valiated by Copy Number (%) WGS sample size Validated by Structural Variation (%)
Adrenocortical carcinoma ACC 79 0 233 54.5 0 NA
Bladder Urothelial Carcinoma BLCA 414 17 1110 49.55 19 65.96
Breast invasive carcinoma BRCA 1119 103 4169 57.18 90 71.98
Cervical squamous cell carcinoma and endocervical adenocarcinoma CESC 306 3 454 42.73 10 52.00
Cholangiocarcinoma CHOL 36 9 60 73.33 0 NA
Colon adenocarcinoma COAD 310 0 297 42.42 17 44.12
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma DLBC 48 0 40 55.00 2 92.31
Esophageal carcinoma ESCA 185 9 367 68.94 12 88.79
Glioblastoma multiforme GBM 180 5 288 68.75 39 80.00
Head and Neck squamous cell carcinoma  HNSC 522 44 747 42.8 30 57.7
Kidney Chromophobe KICH 66 25 43 30.23 15 40.63
Kidney renal clear cell carcinoma KIRC 541 71 270 37.78 17 61.36
Kidney renal papillary cell carcinoma KIRP 291 32 186 37.63 5 81.25
Acute Myeloid Leukemia LAML 179 0 126 19.05 11 42.86
Brain Lower Grade Glioma LGG 534 0 778 50.64 34 74.33
Liver hepatocellular carcinoma LIHC 374 48 836 57.89 37 58.64
Lung adenocarcinoma LUAD 541 58 1479 41.24 52 67.72
Lung squamous cell carcinoma LUSC 502 51 1321 47.09 42 71.35
Mesothelioma MESO 87 0 135 45.19 0 NA
Ovarian serous cystadenocarcinoma OV 428 0 414 95.65 18 79.31
Pancreatic adenocarcinoma PAAD 179 0 191 40.84 0 NA
Pheochromocytoma and Paraganglioma PCPG 184 3 127 66.93 0 NA
Prostate adenocarcinoma PRAD 502 47 1746 44.79 9 47.17
Rectum adenocarcinoma READ 95 10 130 53.08 1 50.00
Sarcoma SARC 263 0 1740 71.72 38 94.58
Skin Cutaneous Melanoma SKCM 476 0 1180 58.39 32 79.07
Stomach adenocarcinoma STAD 414 30 764 58.25 10 66.13
Testicular Germ Cell Tumors TGCT 156 0 81 38.27 0 NA
Thyroid carcinoma THCA 513 59 189 18.52 16 71.43
Thymoma THYM 120 0 48 56.25 0 NA
Uterine Corpus Endometrial Carcinoma UCEC 185 24 771 66.93 5 73.17
Uterine Carcinosarcoma UCS 57 0 380 65.79 0 NA
Uveal Melanoma UVM 80 0 31 51.61 0 NA
Total 9966 648 20731 561
For more details please contact Verhaak Lab