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cfDNA feature families - Coggle Diagram
cfDNA feature families
Fragmentation features / patterns
Global fragmentation
Fragment-length distribution
Fraction of fragments having distinct lengths
Short-fragment enrichment
90-150 bp fragments
Regional fragmentation
Regional fragment-length patterns
Short-to-long fragment ratio
90-150 bp short fragments
151-220 bp long fragments
Z-scored regional differences
100 kb genomic bins
Chromosome-arm-specific fragmentation
Exclusion of CNA regions
Fragmentation-based classification
Global fragmentation classifier
Regional fragmentation classifier
Extended fragmentomics features
Window protection score features
Nucleosome occupancy
Chromatin organization
Indirect gene-expression information
End-motif features
Fragment end-motif features
End-motif frequencies
5-prime end-motif patterns
ML classifier on end-motif features
Fragment-end-position features
Preferred end-coordinate features
Nucleosome-positioning features
Fragment periodicity features
Chromatin-signature features
Coverage/depletion/enrichment patterns
Active or inactive chromatin regions
Tumor-specific active chromatin regions
Universal DNase I hypersensitivity sites
Regulatory regions
Regions of interest
Region-set analysis
Mean coverage around regions of interest
Neighboring genomic regions
About 20 kb windows
About 500 bp bins
Output signal
Significant coverage drops or gains
Comparison with reference set / healthy controls
Bias correction
Correction using CNA information
Analysis tools
Chromatin-signature analysis tools
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