cellfree-rna-agent

Core Capabilities

1. cfRNA Profiling: Quantify mRNA, lncRNA, and small RNA from plasma.

2. Tissue Deconvolution: Identify tissue sources contributing to cfRNA pool.

3. Cancer Detection: ML models detecting cancer from cfRNA profiles.

4. Tumor Transcriptomics: Infer tumor gene expression non-invasively.

5. Integration with cfDNA: Combine RNA and DNA liquid biopsy analytes.

6. Biomarker Discovery: Identify diagnostic and prognostic RNA markers.

cfRNA Biology

Sources:

• Cell death (apoptosis, necrosis)
• Active secretion (EVs, RNA-binding proteins)
• Cell surface-associated RNA

Protection Mechanisms:

• Extracellular vesicles
• Protein complexes (AGO2, NPM1)
• Lipoproteins

Half-life: Minutes to hours (shorter than cfDNA)

Workflow

1. Input: Plasma cfRNA sequencing data (total RNA, small RNA, or targeted).

2. Quality Control: Assess library complexity, mapping rates, contamination.

3. Quantification: Normalize and quantify transcripts.

4. Deconvolution: Estimate tissue contributions.

5. Classification: Apply cancer detection models.

6. Integration: Combine with cfDNA if available.

7. Output: Tissue composition, cancer score, biomarker profiles.