In a recent Nature paper, an improved sequencing method to more sensitively detect cell-free RNA was reported.

Sensitively detect cfRNA - RARE-seq

✨ Methodological Innovations

🔬 Optimized cfRNA Analysis Workflow

RARE-seq is a refined method for cfRNA analysis, encompassing the entire workflow—from plasma sample processing, cfRNA extraction, and library preparation to high-throughput sequencing. This method is designed to significantly enhance the sensitivity of ctRNA detection.

🩸 Addressing Platelet Contamination

For the first time, RARE-seq reveals the substantial impact of platelet contamination on cfRNA analysis. A computational approach was developed to effectively remove platelet RNA interference, ensuring more accurate detection of non-platelet-derived gene expression.

🎯 Targeted Capture of Low-Abundance Genes

Innovatively designed to target and capture rare or absent transcripts (RAGs) in healthy individuals’ plasma, RARE-seq facilitates efficient detection of genes originating from non-hematopoietic tissues—providing a powerful tool for identifying cancer-specific and organ-specific genes.

🚀 Technical Advantages

🔍 High Sensitivity

Compared to traditional whole-transcriptome RNA sequencing, RARE-seq enhances sensitivity in detecting tumor-derived cfRNA by approximately 50-fold, with a detection limit as low as 0.05%. This allows for the identification of minuscule amounts of tumor-related cfRNA in the bloodstream with remarkable precision.

🎯 Exceptional Specificity

RARE-seq effectively distinguishes tumor-derived cfRNA from background cfRNA, reducing false-positive results and improving detection accuracy.

🛠 Robust Noise Resistance

By optimizing experimental procedures and computational methods, RARE-seq successfully eliminates platelet contamination and background noise, enhancing signal clarity and result reliability.

🔬 Broad Applicability

RARE-seq is not limited to cancer detection—it also shows promising potential in tissue origin identification, therapy resistance monitoring, and evaluation of non-malignant diseases.

🔑 Key Findings

🧪 Non-Small Cell Lung Cancer (NSCLC) Detection

Among 437 plasma samples, RARE-seq efficiently detects NSCLC transcriptional signatures. Detection sensitivity increases with tumor progression, reaching 83% sensitivity and 95% specificity in stage IV patients—outperforming initial circulating tumor DNA (ctDNA) analysis.

📌 Tissue Origin Identification

Analysis of pancreatic, prostate, and liver cancer patients validates RARE-seq’s effectiveness across multiple cancer types. With an 89% accuracy rate, it provides a powerful tool for determining the tissue origin of malignancies.

🔬 Therapy Resistance Monitoring

In NSCLC patients harboring EGFR mutations, RARE-seq successfully detects histological transformations and mutation-based resistance mechanisms, equipping clinicians with a more comprehensive understanding of therapy resistance.

🩺 Non-Malignant Disease Assessment

RARE-seq identifies lung-derived cfRNA expression in patients with chronic obstructive pulmonary disease (COPD), active COVID-19 infection, and intensive care unit (ICU) admissions, demonstrating its potential for assessing non-malignant lung conditions.

💡 Clinical Applications

🔎 Early Cancer Screening

With its high sensitivity, RARE-seq holds promise for early cancer detection, particularly for small tumors that are challenging to identify through conventional imaging methods.

🏥 Tissue Origin Identification

For patients with unknown primary tumors or those requiring cancer subtype differentiation, RARE-seq enables non-invasive tumor tissue identification—enhancing clinical diagnostic precision.

💊 Therapy Monitoring & Prognostic Evaluation

By tracking ctRNA changes in real-time, RARE-seq facilitates the early detection of therapy resistance mechanisms, allowing for timely adjustments to personalized treatment plans.

🩺 Non-Malignant Disease Assessment

RARE-seq aids in monitoring tissue damage and inflammation, evaluating disease activity, and treatment response—offering a new perspective for diagnosing and managing non-malignant diseases.

🦠 RNA Vaccine Tracking

RARE-seq enables simultaneous tracking of vaccine RNA and host immune response in individuals vaccinated with mRNA-based COVID-19 vaccines, providing valuable insights for RNA vaccine development and application.