MSIsensor-ct

MSIsensor-ct detects microsatellite instability (MSI) status from circulating cell-free DNA (cfDNA) sequencing data for noninvasive MSI assessment to inform cancer prognosis and chemosensitivity prediction.

Key Features:

• Machine Learning-Based Protocol: Employs a machine learning approach to determine MSI status at ultra-low circulating tumor DNA (ctDNA) content.
• Noninvasive Detection Method: Analyzes cfDNA from plasma samples to detect MSI without requiring tumor tissue.
• High Sensitivity and Accuracy: Demonstrates 100% accuracy in MSI detection within a limit of detection (LOD) of 0.05% ctDNA content across various sequencing depths and ctDNA levels.
• Input Format: Processes BAM files as input, compatible with next-generation sequencing outputs.

Scientific Applications:

• Cancer Prognosis: Assessing cancer progression and patient outcomes based on MSI status detected in cfDNA.
• Chemosensitivity Prediction: Predicting tumor response to chemotherapeutic agents based on MSI status from cfDNA.

Methodology:

Processes BAM files; employs a machine learning approach to call MSI status from cfDNA; calculates and applies a stable MSI score threshold of 20%; and was evaluated on independent testing datasets with a reported LOD of 0.05% ctDNA across sequencing depths and ctDNA levels.