Name: Fragmentomics Domain
Author: msk-access

cfDNA Fragmentomics Domain Knowledge

When to use this skill

Implementing a new feature evaluator
Interpreting evaluation results
Writing documentation or exploration cells

Biology Background

Cell-free DNA (cfDNA) in plasma is released during cell death. Cancer cells contribute "circulating tumor DNA" (ctDNA) with distinct fragmentation patterns:

Shorter fragments — ctDNA tends to be shorter than normal cfDNA
Altered nucleosome positioning — different WPS patterns at regulatory regions
Epigenetic signatures — methylation and chromatin states from tissue of origin
End motif preferences — DNA cleavage enzymes leave characteristic motifs

FSC core_short_ratio	Fraction of 120-150bp fragments	↑ increased
FSR short_long_ratio	Short / Long fragment ratio	↑ increased
MDS score	Global methylation from fragment ends	Variable
OCF z-score	Tissue-of-origin signal strength	↑ if tissue contributing
ATAC z-score	Chromatin accessibility deviation from normal	↑ or ↓ depending on mark
WPS periodicity_score	Regularity of nucleosome spacing	↓ disrupted
EndMotif entropy	Diversity of end motifs	Changed

Fragmentomics Domain

cfDNA Fragmentomics Domain Knowledge

When to use this skill

Biology Background

Feature Interpretation

Fragmentomics Domain

cfDNA Fragmentomics Domain Knowledge

When to use this skill

Biology Background

Feature Interpretation

Confounders

Nanoclaw Repl

Bioinformatics

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