Cell-Free Epigenome Atlas (CFEA)

Cell-Free Epigenome Atlas (CFEA) catalogs and standardizes cell-free DNA (cfDNA) epigenomic profiles—including 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), and nucleosome positioning (NP)—across human diseases to support comparative analysis and biomarker development.

Key Features:

• Epigenetic modalities: Includes cfDNA profiles for 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), and nucleosome positioning (NP).
• Dedicated database: Aggregates human cell-free epigenomes spanning 27 different human diseases.
• Comprehensive data collection: Integrates cfDNA-based epigenome-wide profiles relevant for noninvasive disease diagnosis and classification.
• Standardized quality control: Implements bioinformatic pipelines for quality control and standardized data processing of cfDNA epigenomic datasets.
• Curated biological and clinical information: Manually curates associated biological and clinical metadata to enable comparison across disease stages such as early and metastatic cancer.

Scientific Applications:

• Liquid biopsy biomarker development: Supports development of cfDNA-based epigenetic signatures for noninvasive biomarkers.
• Disease detection and classification: Enables analysis of epigenetic alterations in cfDNA for disease detection and tumor classification.
• Comparative epigenomics across disease stages: Facilitates comparison of cfDNA epigenomes across stages including early versus metastasis.
• Molecular mechanism and translational research: Provides standardized datasets to study epigenetic mechanisms in human diseases and inform personalized medicine research.

Methodology:

Bioinformatic pipelines for quality control and standardized data processing of cfDNA-based epigenome-wide profiles.