FusionSeq

FusionSeq identifies fusion transcripts in paired-end RNA-sequencing (RNA-Seq) data to detect known and novel gene fusions relevant to oncogenic processes.

Key Features:

• Identification of Fusion Transcripts: Detects fusion transcripts by analyzing paired-end RNA-sequencing (RNA-Seq) data and distinguishes genuine fusion events from artifacts.
• Artifact Filtering: Applies filtering mechanisms to eliminate spurious candidate fusions arising from artifacts such as misalignment or random pairing of transcript fragments.
• Candidate Ranking: Ranks fusion candidates using several statistical measures to prioritize biologically relevant events.
• Breakpoint Junction Analysis: Identifies exact sequences at breakpoint junctions for precise mapping of structural changes in genes involved in fusion events.

Scientific Applications:

• Cancer Fusion Detection: Detects known and novel fusion transcripts across various cancer types, including samples with and without previously documented rearrangements.
• Calibration Dataset Analysis: Applied to a specially sequenced calibration dataset comprising eight different cancers to evaluate performance across diverse oncological contexts.

Methodology:

Integrates statistical filtering and ranking systems to refine candidate fusion transcripts and performs breakpoint junction sequence identification.