CircFusion

CircFusion detects linear fusion transcripts and fusion circular RNAs (f-circRNAs) from RNA-seq data to identify chimeric and backspliced transcripts arising from chromosomal translocations in cancer genomics.

Key Features:

• Detection Capability: Identifies linear fusion transcripts and f-circRNAs from RNA-seq data and operates with both known and unknown fusion breakpoints.
• Handling Complex Genomic Rearrangements: Detects chimeric transcripts resulting from main and reciprocal translocations, including events with multiple breakpoints.
• Benchmarking Performance: Demonstrated reliable predictions in benchmarking on simulated and real cancer datasets and outperformed existing methods for f-circRNA detection.
• Novel Discoveries: Identified and validated novel f-circRNAs in acute leukemia samples with KMT2A::AFF1 rearrangements.

Scientific Applications:

• Cancer Genomics: Detection of fusion transcripts and f-circRNAs to study chimeric proteins, backsplicing events, and their contributions to oncogenic processes.
• Functional Characterization: Enables discovery and validation of novel f-circRNAs (for example in KMT2A::AFF1 acute leukemia) to support downstream functional studies of oncogenesis.

Methodology:

Analyzes RNA-seq data using algorithms that identify fusion and backsplice junctions and supports analysis in both known and unknown breakpoint scenarios.