annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

BMC Bioinformatics

Table 4 Validation of annoFuse prioritization using PPTC PDX fusion calls

Histology	PPTC STAR-Fusion/FusionCatcher/SOAPFuse/ deFuse (n detected)	PPTC STAR-Fusion/Arriba (n detected)	annoFuse STAR-Fusion/Arriba (n retained)	% Retained with annoFuse
ALL	117	75	72	96
CNS Embryonal	4	3	3	100
Ependymoma	2	0	0	NA
Ewing Sarcoma	11	10	10	100
Glioblastoma	1	1	0	0
Osteosarcoma	18	15	15	100
Other Brain	1	1	1	100
Other Sarcoma	4	3	3	100
Rhabdomyosarcoma	7	6	6	100
Wilms	1	0	0	NA
Total	166	114	110	96
ALL truth set	27	23	23	100

Retention of high-confidence, putative oncogenic calls averaged 96% across the entire PPTC PDX dataset and was 100% for the ALL truth set (ALL = acute lymphoblastic leukemia). Column 1 = PPTC histology, Column 2 = fusion calls from STAR-Fusion, FusionCatcher, deFuse, and SOAPFuse which were filtered and reported as high-confidence in the PPTC dataset, Column 3 = PPTC reported fusions detected from STAR-Fusion and Arriba, Column 4 = Fusions retained following annoFuse filtering, Column 5 = Percent of fusions retained after applying annoFuse

ISSN: 1471-2105