ctDNAtools

ctDNAtools provides analysis of circulating tumor DNA (ctDNA) and cell-free DNA (cfDNA) sequencing data to detect minimal residual disease and characterize cfDNA fragmentation for cancer research.

Key Features:

• Minimal Residual Disease (MRD) Detection: Implements Monte Carlo sampling to test for MRD by tracking pre-detected reporter mutations across follow-up samples.
• cfDNA Fragmentation Analysis: Computes fragment size histograms, fragment size profiles, and fragment end pattern analyses of cfDNA.

Scientific Applications:

• Oncology Monitoring: Enables non-invasive monitoring of cancer progression and treatment response using ctDNA from liquid biopsies.
• Relapse Detection and Disease Tracking: Supports early detection of relapse and longitudinal molecular tracking of tumor evolution via reporter mutation analysis.
• Biomarker Characterization: Facilitates investigation of cfDNA fragmentation patterns as biomarkers of tumor biology and patient prognosis.

Methodology:

Performs Monte Carlo sampling for MRD testing, tracks pre-detected reporter mutations across follow-up samples, and computes fragment size histograms, fragment size profiles, and fragment end pattern analyses for cfDNA fragmentation studies.