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Orientation-aware Fragmentation (OCF)

Command: krewlyzer ocf

Purpose

Computes orientation-aware cfDNA fragmentation (OCF) values in tissue-specific open chromatin regions.

Biological Context

OCF (Sun et al., 2019) measures the phasing of upstream (U) and downstream (D) fragment ends in open chromatin, informing tissue-of-origin of cfDNA.

Usage

krewlyzer ocf sample.bed.gz --output output_dir/ [options]

Output

  • {sample}.OCF.tsv: Summary of OCF calculations per tissue type.
  • {sample}.OCF.sync.tsv: Detailed sync scores.

Options

  • --threads, -t: Number of processes

Calculation Details

  1. Alignment: Fragments are mapped relative to the center of the Open Chromatin Region (OCR).
  2. Counting:
    • Left ends (Start) and Right ends (End) are counted in 10bp bins across a ±1000bp window.
    • Counts are normalized by total sequencing depth.
  3. OCF Score: $$ OCF = \sum_{Peak} P_{signal} - \sum_{Peak} P_{background} $$
    • Signal: Right ends at -60bp and Left ends at +60bp (Phased nucleosome boundaries).
    • Background: Left ends at -60bp and Right ends at +60bp (Unphased).

Clinical Interpretation

Healthy Plasma Baseline

In healthy individuals, cfDNA primarily originates from:

Tissue OCF Value
T-cells (hematopoietic) Highest
Liver Second highest
Other tissues Near zero

Detecting Tumor-Derived cfDNA

When comparing a sample to healthy plasma:

Pattern Interpretation
↑ Tissue-specific OCF Tumor shedding from that tissue
↓ T-cell OCF Dilution of hematopoietic cfDNA by tumor DNA
OCF correlates with tumor fraction Higher ctDNA → stronger tissue signal

Cancer-Specific Patterns

Cancer Type Expected OCF Change
Hepatocellular carcinoma ↑ Liver OCF
Colorectal cancer ↑ Intestine OCF, ↓ T-cell OCF
Lung cancer ↑ Lung OCF, ↓ T-cell OCF

Reference: See Citation & Scientific Background for detailed paper summary.