Fragment-level Methylation (UXM)
Command: krewlyzer uxm
Purpose
Computes the proportions of Unmethylated (U), Mixed (X), and Methylated (M) fragments per region.
Biological Context
Fragment-level methylation (UXM, Loyfer et al., 2022) reveals cell-of-origin and cancer-specific methylation patterns in cfDNA.
Usage
# Single-end (default)
krewlyzer uxm /path/to/bam_folder --output uxm_out [options]
# Paired-end mode
krewlyzer uxm /path/to/bam_folder --output uxm_out --type PE [options]
Output
Output: {sample}.UXM.tsv
Options
--mark-input,-m: Marker BED file (default:data/MethMark/Atlas.U25.l4.hg19.bed)--map-quality,-q: Minimum mapping quality (default: 30)--min-cpg,-c: Minimum CpG per fragment (default: 4)--methy-threshold,-tM: Methylation threshold (default: 0.75)--unmethy-threshold,-tU: Unmethylation threshold (default: 0.25)--type: Fragment type: SE or PE (default: SE)--threads,-t: Number of processes
Clinical Interpretation
Fragment Classification
| Class | Threshold | Interpretation |
|---|---|---|
| U (Unmethylated) | ≤25% methylated CpGs | Cell-type specific unmethylated regions |
| X (Mixed) | 25-75% | Heterogeneous/mosaic methylation |
| M (Methylated) | ≥75% methylated CpGs | Stably methylated regions |
Healthy cfDNA Composition
Based on the Human Methylation Atlas:
| Cell Type | Contribution |
|---|---|
| Megakaryocytes | ~31% |
| Granulocytes | ~30% |
| Monocytes/Macrophages | ~20% |
| Endothelial | ~6% |
| Hepatocytes | ~3% |
| Lymphocytes | ~3% |
Cancer Detection
| Pattern | Interpretation |
|---|---|
| Altered tissue proportions | Tumor DNA shifts composition |
| Non-hematopoietic increase | Possible tumor-derived cfDNA |
| Resolution | Can detect ~0.1% tumor fractions |
Reference: See Citation & Scientific Background for detailed paper summary.