ChiTaRS 8.0: the comprehensive database of chimeric transcripts and RNA-seq data with applications in liquid biopsy

Area of Science:

• Genomics and Bioinformatics
• Cancer Research
• Molecular Biology

Background:

• Gene fusions, arising from replication and transcription errors, are crucial biomarkers for cancer diagnosis and therapy.
• Accurate identification of gene fusions is vital for advancing personalized cancer medicine.
• Existing databases require updates to encompass novel fusion discoveries and functional insights.

Purpose of the Study:

• To update and enhance the Chimeric Transcripts and RNA-Sequencing database (ChiTaRS 8.0) with new human chimeric transcripts and fusion data.
• To incorporate information on chimeric breakpoints from chromosome conformation capture techniques (Hi-C datasets).
• To identify novel chimeric transcripts in various cancers, including oral squamous cell carcinoma and glioblastoma, using text mining and liquid biopsy data.

Main Methods:

• Curated 47,445 RNA transcripts and over 100,000 chimeric sequences for the ChiTaRS 8.0 database.
• Integrated 1055 chimeric breakpoints from Hi-C datasets.
• Applied text mining to RNA-sequencing data from public datasets and patient blood/plasma samples to discover novel chimeras.

Main Results:

• ChiTaRS 8.0 contains over 100,000 human chimeric sequences and 1055 novel chimeric breakpoints.
• The database includes an expanded list of gene fusions with potential as drug targets.
• Novel chimeras were identified in oral squamous cell carcinoma and glioblastoma, now catalogued in ChiTaRS 8.0.

Conclusions:

• ChiTaRS 8.0 is an enhanced repository for fusion transcripts, crucial for cancer research and personalized therapy.
• The database provides valuable insights into the functional landscape of chimeras in cancers and complex diseases.
• Integration of liquid biopsy data expands the utility of ChiTaRS for identifying disease-specific chimeras.