bims-fragic 2026-08-02 papers

Issue of 2026–08–02
four papers selected by
Laura Mannarino, Humanitas Research

Int J Mol Sci. 2026 Jul 17. pii: 6372. [Epub ahead of print]27(14):

Cell-Free DNA Fragmentation Patterns as Biomarkers for Human Papillomavirus-Related Cancers: A Systematic Review of Methodological Diversity and Diagnostic Performance.

Fernanda Santos, Marta S Silva, Francisco A Caramelo, Magda M Santana, Rui J Nobre, Jorge M P Tomaz, Luís P Almeida, Margarida Figueiredo-Dias.

Novel blood biomarkers are crucial for HPV-related cancers to overcome the limitations of imaging and biopsies. This review evaluates the diagnostic performance of circulating cell-free DNA (cfDNA) fragmentomic patterns, distinguishing host-genome integrity from specific viral signatures. Following PRISMA guidelines, we searched PubMed, EMBASE, and Web of Science up to February 2026. Methodological quality was assessed via QUADAS-2, and diagnostic performance was synthesized using a random-effects model. From 489 records, six studies (215 patients, 209 controls) met inclusion criteria. Lacking host-derived fragmentomics data, the analysis focused exclusively on the structural size profiles of circulating viral DNA (cfHPV-DNA). Meta-analysis of four cohorts specifically evaluating these viral fragmentation patterns yielded a pooled Diagnostic Odds Ratio (DOR) of 205.73 (95% CI: 44.72-946.38). Specificity was robust (~100%), with high sensitivity (>90%) for macroscopic disease. However, sensitivity decreased in low-tumor-burden cohorts. cfHPV-DNA fragmentation patterns shows promising diagnostic potential for macroscopic HPV-driven malignancies. However, further studies must determine whether fragment sizing truly outperforms binary viral detection and correlates with disease severity. Furthermore, while current assays exploit the analytical simplicity of viral targets, host-derived fragmentomics remains an overlooked compartment that warrants exploration to determine its true clinical value regarding underlying tumor dynamics. Systematic Review Registration: PROSPERO, identifier: CRD420251052768.

Keywords: HPV-related cancers; TTMV-HPV DNA; cell-free DNA; diagnostic performance; fragmentomics

DOI: https://doi.org/10.3390/ijms27146372

J Cancer. 2026 ;17(7): 1318-1330

Cell-Specific DNA Methylation Markers in Plasma cfDNA Reveal Diagnostic Potential for Head and Neck Cancer.

Tianci Wang, Fei Han, Yuxuan She, Mengju He, Yicen Ding, Qi Mei, Yani Kang.

Purpose: Head and neck cancer ranks as the seventh most common type of cancer worldwide. For patients diagnosed at advanced stages, the five-year survival rate remains below 40%, underscoring the urgent need for early detection strategies. However, current diagnostic approaches face considerable limitations. Furthermore, tissue biopsy remains invasive and impractical for routine screening. In light of these challenges, this study aims to identify and validate plasma cell-free DNA (cfDNA) methylation markers capable of enabling auxiliary assessment and facilitating prognosis assessment in head and neck cancer.
Methods: To achieve this goal, we first analyzed whole-genome bisulfite sequencing (WGBS) data from 205 samples covering 39 healthy tissue types. This comprehensive analysis was conducted to establish a baseline methylation landscape and identify methylation sites specifically associated with head and neck cells. Subsequently, differentially methylated CpG sites were screened by comparing head and neck tissues with other healthy tissues. To enhance the robustness and specificity of potential markers, more than 5 adjacent cell-specific methylated CpG sites located within 150 base pairs of each other were clustered into composite methylation markers, thereby reducing background noise and improving signal detection. These candidate markers then underwent a stringent specificity test to confirm their exclusive enrichment in head and neck tissues. Finally, one of the most promising markers was experimentally validated in plasma cfDNA samples collected from head and neck cancer patients compared with healthy controls, using targeted bisulfite sequencing to assess their detection performance in liquid biopsies.
Results: Through comprehensive analysis of WGBS data from healthy tissue samples, a total of 1,157 tissue-specific methylation sites were identified, including 146 hypermethylated and 1,011 hypomethylated sites exclusive to head and neck tissues. By clustering adjacent CpG sites within a 150-base-pair window, these were consolidated into 11 composite methylation markers, each representing a distinct genomic region with coordinated methylation patterns. Subsequent specificity testing confirmed that all composite markers exhibited strong cell-type specificity, with minimal background methylation signals detected across other tissue types. This high specificity underscores their potential for accurate tissue-of-origin inference. Validation experiments in plasma cfDNA samples further demonstrated that methylation fragments corresponding to these composite markers were consistently detectable in cancer patients but entirely absent in healthy individuals.
Conclusion: This study systematically characterizes cell-specific methylation signatures of head and neck tissues and provides preliminary evidence for the feasibility of utilizing composite cfDNA methylation markers for non-invasive cancer detection. By integrating multiple adjacent CpG sites into composite markers, our approach achieves enhanced specificity and robustness compared to conventional single-site markers, providing a strategy to overcome limitations associated with tumor heterogeneity and low cfDNA abundance in early-stage disease. These findings not only provide a methodological framework for cfDNA-based auxiliary assessment but also offer promising candidate biomarkers for tracing the tissue of origin in head and neck cancer. This work is limited by a small sample size and pending further investigation in larger, prospective cohorts. However, this work illustrates the potential of cell-specific methylation analysis to contribute to improved disease monitoring and tissue-of-origin determination.

Keywords: DNA methylation; cfDNA; head and neck cancer; liquid biopsy

DOI: https://doi.org/10.7150/jca.133470

J Obstet Gynecol Neonatal Nurs. 2026 Jul 28. pii: S0884-2175(26)00180-2. [Epub ahead of print]

Interpreting False-Positive or Atypical Prenatal Cell-Free DNA Results.

Mindy B Tinkle, Abigail Reese.

Cell-free DNA (cfDNA) screening is a highly accurate method of genetic screening that relies on the presence of placenta-derived DNA circulating in maternal plasma. The widespread availability of this screening, also known as non-invasive prenatal testing, has transformed prenatal genetic screening for fetal chromosome disorders, including trisomies 21, 18, and 13. Despite the increased accuracy of the cfDNA approach, false-positive results remain a possibility. Such results have distinct biological causes and clinical implications. In this article, we review the most common causes of false-positive screening results: confined placental mosaicism; vanishing twin syndrome; and maternal factors, including maternal mosaicism and malignancies. We also review unexplained false-positive and nonreportable cfDNA results and appropriate follow-up. Clinical vignettes demonstrate scenarios that nurses and other providers may encounter in the delivery of prenatal care.

Keywords: DNA; circulating; false-positive reactions; prenatal diagnosis

DOI: https://doi.org/10.1016/j.jogn.2026.06.003

Genes (Basel). 2026 Jun 30. pii: 754. [Epub ahead of print]17(7):

The ctDNA Paradigm: Dynamic Observation, Quantitative Analysis, and Interpretive Limits in Precision Oncology.

Massimiliano Chetta, Nenad Bukvic, Alessandra Rosati.

Circulating tumor DNA (ctDNA) was initially conceived as a minimally invasive surrogate for interrogating cancer biology; however, three decades of evidence have demonstrated that plasma is not a passive reservoir of tumor-derived material, but rather a dynamic and biologically heterogeneous milieu in which multiple competing genomic signals coexist. This review explores the level of interpretive rigor required to translate ctDNA detection into clinically actionable precision oncology. Clonal hematopoiesis of indeterminate potential (CHIP) is discussed not as an occasional confounder, but as an intrinsic source of biological background noise, underscoring the critical importance of matched leukocyte sequencing to discriminate tumor-derived alterations from hematopoietic variants, particularly in older individuals and in patients previously exposed to cytotoxic therapies. The widespread assumption that variant allele frequency (VAF) directly reflects tumor burden is critically re-evaluated through the mathematical relationships linking VAF to tumor fraction, local copy-number architecture, and mutation multiplicity. Within this framework, estimation of cancer cell fraction (CCF) and probabilistic discrimination between clonal and subclonal events are examined, including the emergence of reversion mutations as molecular evidence of therapy-driven evolutionary adaptation. The review also addresses the central paradox of ultra-sensitive sequencing technologies: although unique molecular identifiers and duplex sequencing can extend analytical sensitivity below 0.01% VAF, sensitivity in the absence of contextual specificity risks conflating technical artifacts and biologically insignificant alterations with clinically meaningful disease. Equal emphasis is placed on pre-analytical variables, highlighting how sample collection, stabilization, and processing protocols define the upper limit of downstream analytical reliability. Beyond single-nucleotide variants, fragmentomic and methylation-based approaches are presented as complementary orthogonal dimensions capable of revealing tumor-associated signals even when mutational evidence is limited or absent. Longitudinal ctDNA assessment is argued to provide substantially greater biological and clinical insight than isolated static measurements, while robust clinical reporting is shown to depend on transparent disclosure of assay limitations, residual uncertainty related to CHIP, and structured bidirectional communication between molecular laboratories and treating clinicians. Ultimately, the transition from a biomarker-centered model toward an integrated systems-based framework, combining genomics, epigenomics, fragmentomics, and evolutionary modeling, emerges as the defining challenge for the next generation of liquid biopsy in precision oncology.

Keywords: cancer cell fraction; clonal hematopoiesis; ctDNA; fragmentomics; liquid biopsy; variant allele frequency

DOI: https://doi.org/10.3390/genes17070754