CTAT-LR-Fusion

CTAT-LR-Fusion detects fusion transcripts from long-read RNA-seq data (PacBio Iso-seq or Oxford Nanopore) and leverages companion short-read Illumina RNA-seq data to maximize detection of fusion splicing isoforms and fusion-expressing tumor cells in bulk or single cell transcriptomes.

Key Features:

• Long-read fusion detection: Detects fusion transcripts from PacBio Iso-seq or Oxford Nanopore long-read RNA-seq data at bulk or single cell resolution.
• Short-read integration: Leverages Illumina RNA-seq data for additional exploration, quantification, and maximized detection of fusion splicing isoforms.
• Superior accuracy: Exceeds fusion detection accuracy of alternative methods as benchmarked with simulated and real long-read RNA-seq data.
• Combined read analysis: Combines short and long reads to maximize detection of fusion splicing isoforms and fusion-expressing tumor cells.

Scientific Applications:

• Cancer driver identification: Identifies gene fusions that act as cancer drivers in diverse adult and pediatric cancers.
• Clinical diagnostics and prognostics: Supports accurate detection of fusion transcripts essential for cancer clinical diagnostics and prognostics.
• Therapeutic development guidance: Informs therapeutic development through precise fusion transcript identification.
• Bulk tumor transcriptome analysis: Applied to bulk transcriptomes of tumor cell lines for comprehensive fusion detection.
• Single cell tumor analysis: Applied to tumor single cells from melanoma and metastatic high grade serous ovarian carcinoma samples.

Methodology:

CTAT-LR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit. The specific computational algorithms and steps are not explicitly detailed in the sources.