bims-fragic Biomed News
on Fragmentomics
Issue of 2026–07–26
two papers selected by
Laura Mannarino, Humanitas Research
  1. Epigenomic modifications define chromatin states to regulate cell-free DNA fragmentomics.
  2. Interference of Clonal Hematopoiesis in cfDNA Liquid Biopsy Testing & Identification of Actionable Alterations in Large Diverse Cohort of US Veterans.
  1. Nat Commun. 2026 Jul 18.
    Epigenomic modifications define chromatin states to regulate cell-free DNA fragmentomics.
    Fanglei Gong, Yuqi Pan, Huizhen Lin, Yunyun An, Mengqi Yang, Xiaoyi Liu, Yunxia Bai, Zhenyu Zhang, Bianbian Tang, Kun Zhang, Xin Zhao, Yu Zhao, Changzheng Du, Xuetong Shen, Kun Sun.
      Plasma cell-free DNA (cfDNA) fragmentomics offer promising cancer biomarkers, but their molecular regulation remains elusive. Here, we investigate the role of epigenomic modifications in cfDNA fragmentation. We identify strong correlations between cfDNA fragmentomic features and various epigenetic marks measured in cfDNA. We further segment the genome into different chromatin states using histone modification signals, revealing consistent associations with cfDNA fragmentomics. The association is further validated by histone modifier perturbation experiments, confirming chromatin organization as a key regulator of cfDNA fragmentation. CfDNA fragmentomic features associated with Transposon Elements (TEs) outperform genome-wide metrics in cancer diagnosis, reflecting cancer type-specific patterns. Leveraging these insights, we develop TEANA (Transposon Element Analysis in cfDNA), an AI-empowered model using a small set of TE fragmentomic features for pan-cancer detection and tumor-origin prediction, achieving robust performance across independent cohorts. Hence, chromatin states drive cfDNA fragmentation, and dysregulated TEs provide highly informative biomarkers for cancer diagnosis.
    DOI:  https://doi.org/10.1038/s41467-026-75640-2
  2. Oncologist. 2026 Jul 21. pii: oyag265. [Epub ahead of print]
    Interference of Clonal Hematopoiesis in cfDNA Liquid Biopsy Testing & Identification of Actionable Alterations in Large Diverse Cohort of US Veterans.
    Luca F Valle, Micaela Scobie, Kerry Rowe, Colin C Pritchard, Bruce Montgomery, Isla P Garraway, Nicholas G Nickols, Martin W Schoen, Amar U Kishan, Michael J Kelley, Matthew B Rettig, Kara N Maxwell.
       INTRODUCTION: Liquid biopsies using cell-free DNA (cfDNA) can identify actionable somatic alterations in prostate cancer (PCa). The presence of alterations related to clonal hematopoiesis (CH) can complicate interpretation of cfDNA results and lead to clinical inaction. We sought to determine alteration profiles identified by cfDNA testing in a large, racially diverse cohort of United States Veterans with metastatic PCa and quantify the extent of CH interference in the identification of actionable alterations.
    METHODS: Next-generation sequencing of cfDNA biopsy specimens from US Veterans with metastatic PCa was performed using Foundation Medicine through the VA National Precision Oncology Program (NPOP) from August 2020 to January 2025. Actionable and non-actionable alteration rates were compared between tests with and without identification of a CH alteration. Tests with CH interference were then stratified by the presence of a PCa-related alteration (TMPRSS2, ERG, SPOP) and rates of actionable and non-actionable alterations were compared between these groups.
    RESULTS: cfDNA alterations were identified in 2501/2657 (94.1%) cfDNA tests. CH interference was common, with 663/2657 (25%) tests identifying CH alterations only and 1615/2657 (60.8%) tests identifying CH and non-CH alterations concurrently. Accounting for tests in which no alteration was identified (156/2657; [5.9%]), only 223/2501 (8.4%) tests exhibited non-CH only alterations. Alteration rates in FDA-approved targetable genes were similar in samples with and without CH interference, except for CDK12 variants, which were more frequently identified in tests without CH interference (8.5% vs 3.8%, p < 0.01) and BRCA1 variants which were more frequently identified in tests with CH interference (2.0% vs 0%, p = 0.02). In samples with CH interference, alterations in PTEN, RB1, and TP53 were more likely and HRR alterations were less likely in samples with a PCa specific alteration versus those without (TSG 72% vs 51%, p < 0.0001; HRR 36% vs 56%, p < 0.0001).
    CONCLUSIONS: CH interference was very common in cfDNA testing in metastatic PCa patients. The absence of a CH alteration or presence of a known PCa-related alteration does not reliably modify identification frequencies of actionable alterations. Robust CH inferential platforms or analysis of a matched lymphocyte sample with cfDNA may improve clinical differentiation of CH versus PCa derived cfDNA results.
    Keywords:  CHIP; Prostate cancer; cell-free DNA; circulating tumor DNA; clonal hematopoesis
    DOI:  https://doi.org/10.1093/oncolo/oyag265
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