Supplementary Material for deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data

Low Grade Serous (LGS) Ovarian cancer subtype characterized by small micropapillae that infiltrate ovarian stroma. Somatic KRAS, ERBB2, or BRAF mutations are found in two thirds of the cases and TP53 is rarely mutated. High Grade Serous (HGS) Highly proliferative ovarian carcinoma subtype characterized by genomic instability due to TP53 loss and in some cases BRCA1/2 mutations. This cancer may originate in the fallopian tube. Clear cell carcinoma (CCC) Ovarian carcinoma subtype characterized by large epithelial cells with abundant clear cytoplasm. Endometrioid tumor (EMD) Ovarian carcinoma subtype composed of tubular glands bearing a close resemblance to benign or malignant endometrium. Mucinous tumor (MUC) Ovarian carcinoma with similarities to mucinous colonic carcinomas. Yolk sac tumor (YKS) Ovarian germ cell tumor that represents a proliferation of both yolk sac endoderm and extraembryonic mesenchyme. Granulosa cell tumor (GRC) Ovarian tumors that arise from granulosa cells characterized by a single nucleotide variation in FOXL2. 1 Small cell hypercalemic (SCH) Ovarian cancer subtype characterized by diffuse sheets of cells punctured by variable numbers of follicle-like spaces. Often presents with hypercalcemia. 2 Summary of Supporting Information Table S1 Table of all gene fusion predictions Table S2 Table of predicted interrupted genes Table S3 Table of predicted CNVs Table S4 FISH probe selection table