bims-fragic Biomed News
on Fragmentomics
Issue of 2026–02–22
three papers selected by
Laura Mannarino, Humanitas Research
  1. Naturally-occurring DNA fragment termini correlate with methylation at CpG sites in hair and blood plasma cell-free DNA.
  2. A pan-cancer compendium of 1,294 plasma cell-free DNA methylomes and fragmentomes enabling multicancer detection.
  3. Liquid biopsy approaches to capture minimal residual disease and therapy response in patients with early stage cancers.
  1. BMC Genomics. 2026 Feb 20.
    Naturally-occurring DNA fragment termini correlate with methylation at CpG sites in hair and blood plasma cell-free DNA.
    Samuel Sacco, Joshua D Kapp, Remy Nguyen, Isha S Rao, Richard E Green.
      
    Keywords:  Ancient DNA; Blood plasma; Cell-free DNA; CpG; Epigenetics; Forensics; Fragmentomics; Hair; Keratinization; Methylation
    DOI:  https://doi.org/10.1186/s12864-025-12459-z
  2. Nat Cancer. 2026 Feb 19.
    A pan-cancer compendium of 1,294 plasma cell-free DNA methylomes and fragmentomes enabling multicancer detection.
    Yong Zeng, Dor D Abelman, Althaf Singhawansa, Nicholas Cheng, Yuanchang Fang, Sasha C Main, Emma Bell, Wenbin Ye, Ping Luo, Samantha L Wilson, Eric Y Stutheit-Zhao, Derek Wong, Nadia Znassi, Kui Chen, Suluxan Mohanraj, Enrique Sanz-Garcia, Faiyaz Notta, Anand Ghanekar, Philip Awadalla, Benjamin H Lok, Michael M Hoffman, Raymond H Kim, Gelareh Zadeh, Daniel D De Carvalho, Scott V Bratman, Mathieu Lupien, Trevor J Pugh, Housheng Hansen He.
      Cell-free DNA analysis via methylation and fragmentation profiling has advanced minimally invasive cancer detection; however, broader application has been limited by small cohorts and inconsistent data processing. Here we collated 1,074 cfMeDIP-seq profiles across 9 studies, comprising cancer samples from 11 cancer types, carriers of Li-Fraumeni syndrome and healthy controls. We developed a uniform computational workflow to mitigate technical and biological confounders across cohorts. This analysis identified 14,202 pancancer differentially methylated regions for cancer detection, along with cancer-specific markers for subtype monitoring. Fragmentomic profiling revealed distinguishing differences in 5' end motifs, fragment lengths and nucleosome footprints across cancers. Integrating methylome and fragmentome features enhanced cancer detection and classification. Validation in 220 independent samples, including 3 cancer types absent from the primary dataset, confirmed the robustness of our findings. Altogether, this work provides a pancancer cell-free DNA resource of 1,294 samples to support future methylome and fragmentome studies.
    DOI:  https://doi.org/10.1038/s43018-026-01116-3
  3. Int Rev Cell Mol Biol. 2026 ;pii: S1937-6448(24)00161-8. [Epub ahead of print]399 113-143
    Liquid biopsy approaches to capture minimal residual disease and therapy response in patients with early stage cancers.
    Blair V Landon, Jinny Huang, Ellie G Evangelopoulou, Valsamo Anagnostou, Jenna V Canzoniero.
      Liquid biopsies are emerging as promising approaches to capture minimal residual disease (MRD) and interpret the heterogeneity of pathological responses after neoadjuvant therapy for patients with early stage cancers. Minimally invasive analyses of circulating cell-free tumor DNA (ctDNA) are enabled by advances in next generation sequencing and bioinformatic methodologies, resulting in sensitive and specific ctDNA detection. Emerging data supports the clinical utility of ctDNA status at different timepoints during the treatment trajectory and ctDNA MRD has been shown to predict clinical outcomes. Herein, we critically review ctDNA technologies and their analytical performance together with an assessment of the clinical sensitivity of these approaches to predict disease recurrence.
    Keywords:  Circulating tumor DNA; Early stage cancer; Liquid biopsies; Minimal residual disease
    DOI:  https://doi.org/10.1016/bs.ircmb.2024.12.002
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