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Holistic determination of ends of cfDNA molecules

Peiyong Jiang1, Mary-Jane L Ma2, Rong Qiao2

  • 1Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, the Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China; State Key Laboratory of Translational Oncology, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China.

Cell Genomics
|February 7, 2026
PubMed

Insights

New fragmentomics markers from cell-free DNA (cfDNA) 3' ends improve hepatocellular carcinoma (HCC) detection. This novel approach enhances liquid biopsy for cancer diagnostics.

Area of Science:

  • Oncology
  • Genomics
  • Biomarkers

Background:

  • Cell-free DNA (cfDNA) end motifs are emerging fragmentomics biomarkers for cancer detection.
  • Previous research overlooked 3' cfDNA ends due to sequencing artifacts, limiting biomarker discovery.

Purpose of the Study:

  • To investigate native 5' and 3' end motifs (EM5, EM3) and associated nucleotide motifs (PREMs, POEMs) in cfDNA.
  • To evaluate the diagnostic performance of these novel fragmentomics markers for hepatocellular carcinoma (HCC).
  • To explore fragmentomics-based methylation analysis (3' FRAGMA) and advanced sequencing techniques for enhanced cancer detection.

Main Methods:

  • Utilized single-stranded library preparation for "2-end sequencing" to analyze native cfDNA ends.
  • Developed and applied pre-end motifs (PREMs) and post-end motifs (POEMs) analysis.
  • Implemented fragmentomics-based methylation analysis (3' FRAGMA) and "4-end sequencing".

Main Results:

  • Fragmentomics markers achieved an AUC of 0.95 for HCC detection.
  • 3' FRAGMA significantly improved HCC detection with an AUC of 0.97.
  • "4-end sequencing" further enhanced fragmentomics-based cancer detection capabilities.

Conclusions:

  • Native cfDNA end motifs, including 3' ends and associated nucleotide patterns, are powerful biomarkers for HCC detection.
  • Advanced sequencing and methylation analysis of cfDNA ends represent a significant advancement in liquid biopsy.
  • Holistic end profiling offers new insights into cfDNA fragmentation biology and improves cancer diagnostics.
Keywords:
cancer detectionend motifsfragmentomicsnoninvasive

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