bims-tumhet Biomed News
on Tumor heterogeneity
Issue of 2025–09–28
sixteen papers selected by
Sergio Marchini, Humanitas Research
  1. Application of cfDNA methylation in cancer prognostic assessment: Progress and challenges (Review).
  2. Early detection, clinicopathological subtyping, and prognosis prediction for endometrial cancer patients using fragmentomics liquid biopsy assay.
  3. Tertiary Lymphoid Structures Across Organs: Context, Composition, and Clinical Levers.
  4. Mapping chromatin and DNA methylation landscapes at single-cell and single-molecule resolution.
  5. And the award goes to ….
  6. Ovarian Cancer: Many Diseases Under One Name.
  7. Comparison of imaging based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed paraffin-embedded tumor samples.
  8. The Years 2015-2025 as a Prospective Decade for the Identification of Specific Methylation Biomarkers of Prostate Cancer.
  9. gwSPADE: gene frequency-weighted reference-free deconvolution in spatial transcriptomics.
  10. Leveraging Real-World Data From a Clinicogenomic Database Addresses the Treatment Gap in Patients With High-Grade Serous Ovarian Cancer.
  11. Mismatch Repair as a Dynamic and Clinically Actionable Vulnerability in Cancer.
  12. Cell-free DNA fragmentomics: a universal framework for early cancer detection and monitoring.
  13. The molecular and functional landscape of resistance to FOLFIRI chemotherapy in metastatic colorectal cancer.
  14. Application of circulating tumor DNA analysis in detecting Minimal residual disease (MRD) after surgery for locally advanced head and neck squamous cell carcinoma: a preliminary study.
  15. CCNV: a user-friendly R package enabling large-scale cumulative copy number variation analyses of DNA methylation data.
  16. Special Issue "Biomarkers and Early Detection Strategies of Ovarian Tumors".
  1. Int J Oncol. 2025 Dec;pii: 98. [Epub ahead of print]67(6):
    Application of cfDNA methylation in cancer prognostic assessment: Progress and challenges (Review).
    Chenxi Su, Jiaqi Wu, Liping Jiang, Tongtong Lv, Wenxi Liu, Jintong Zhang, Yanhua Zhang, Xiaochun Peng, Jie Tan.
      Cancer prognostic assessment constitutes an essential component of cancer treatment and management. It encompasses the prediction of patients' disease progression, treatment effect and survival. Circulating free DNA (cfDNA) refers to highly fragmented DNA that exists extracellularly in the human bloodstream. Its methylation status is not only a reliable indicator for the prognosis of cancer, but also a highly accurate predictor of the prognosis of cancer. As an emerging non‑invasive biomarker, cfDNA has demonstrated considerable potential in cancer prognostic assessment in recent years. The present review provided a comprehensive review of the promising applications of cfDNA methylation in cancer prognostic assessment, while also discussing the challenges that must be addressed to fully realize its clinical potential. As technology advances and research deepens, cfDNA methylation is expected to play an increasingly pivotal role in the field of cancer precision medicine.
    Keywords:  cancer; circulating free DNA; methylation; prognostic assessment
    DOI:  https://doi.org/10.3892/ijo.2025.5804
  2. ESMO Open. 2025 Sep 23. pii: S2059-7029(25)01639-4. [Epub ahead of print]10(10): 105770
    Early detection, clinicopathological subtyping, and prognosis prediction for endometrial cancer patients using fragmentomics liquid biopsy assay.
    Q Rao, H Zhou, W Weng, Y He, N Li, P He, W Tang, M He, X Zhu, D Zhu, H Bao, X Wu, H Wang, Z Lin, B Zhang.
       BACKGROUND: Endometrial cancer (EC) is among the most prevalent gynecological malignancies worldwide. This study explores the use of cell-free DNA (cfDNA) fragmentomics to develop a non-invasive liquid biopsy assay, aiming to improve early detection, subtyping, and prognostication of EC, thereby enhancing therapeutic outcomes and reducing associated mortality.
    MATERIALS AND METHODS: A cohort of 120 patients with diagnosed EC and 120 healthy volunteers was used to develop a novel non-invasive liquid biopsy assay for EC. Five distinct fragmentomic features were analyzed from preoperative plasma samples using low-pass whole-genome sequencing. Ensemble models were created by integrating base models that utilized four different machine learning algorithms for early cancer detection, clinicopathological subtyping, and prediction of recurrence-free survival. An independent test cohort of 62 EC patients and 62 healthy controls was used to assess the final ensemble model's performance.
    RESULTS: The liquid biopsy assay demonstrated high efficacy in early EC detection, achieving an area under the curve (AUC) of 0.96, with 75.8% sensitivity and 96.8% specificity in the independent test cohort. Consistent sensitivities were observed across EC stages I-IV at 74.4%, 85.7%, 75%, and 75%, respectively. The assay moderately predicted clinicopathological features including stage (AUC = 0.72), histological subtypes (AUC = 0.73), and microsatellite instability status (AUC = 0.77). The model also effectively predicted recurrence-free survival, identifying high-risk patients [hazard ratio (HR) 8.6, P < 0.001]. Additionally, similarity network fusion stratified patients into high- and low-risk clusters, with high-risk individuals exhibiting a notably increased recurrence risk (HR 6.2, P = 0.049). Patients identified as high-risk by both methods exhibited an even greater risk (HR 10.1, P < 0.0001) for recurrence.
    CONCLUSIONS: This DECIPHER-UCEC-2 study (Detecting Early Cancer by Inspecting ctDNA Features) demonstrates that by integrating cfDNA fragmentomics with machine learning, our liquid biopsy assay shows significant promise for EC's early detection, subtyping, and prognosis, potentially paving the way for enhanced patient outcomes.
    Keywords:  cell-free DNA; early diagnosis; endometrial cancer; fragmentomics; whole-genome sequencing
    DOI:  https://doi.org/10.1016/j.esmoop.2025.105770
  3. Immunol Rev. 2025 Oct;335(1): e70063
    Tertiary Lymphoid Structures Across Organs: Context, Composition, and Clinical Levers.
    Stephane M Guillaume, Cristian G Beccaria, Matteo Iannacone, Michelle A Linterman.
      Tertiary lymphoid structures (TLSs) arise in non-lymphoid tissues in response to persistent antigen stimulation and chronic inflammation. Spanning organs from lung and liver to meninges, skin, and beyond, TLSs range from loose aggregates of immune cells to fully mature structures containing functional germinal centers (GC). In this review, we provide a comprehensive overview of TLS formation, architecture, and function across diverse tissues, highlighting both shared features and tissue-specific adaptations. We then explore the clinical relevance of TLS in infections, autoimmunity, cancer, and allergy, emphasizing their dual roles in mediating protective immunity and driving pathology. Finally, we discuss emerging technologies that are transforming our ability to dissect TLSs at high resolution (including spatial multi-omics, advanced imaging, and digital pathology), enabling mechanism-guided strategies to modulate TLSs therapeutically. Framing TLSs through the lens of maturation and tissue context provides a foundation for interpreting their clinical associations and for enhancing or dismantling these niches according to need.
    Keywords:  B cells; germinal centers; tertiary lymphoid structures
    DOI:  https://doi.org/10.1111/imr.70063
  4. Nat Methods. 2025 Sep 26.
    Mapping chromatin and DNA methylation landscapes at single-cell and single-molecule resolution.
      
    DOI:  https://doi.org/10.1038/s41592-025-02848-3
  5. Nat Methods. 2025 Sep 24.
    And the award goes to ….
    Vivien Marx.
      
    DOI:  https://doi.org/10.1038/s41592-025-02842-9
  6. J Insur Med. 2025 Sep 22.
    Ovarian Cancer: Many Diseases Under One Name.
    Clifton P Titcomb.
      In the United States, ovarian cancer is the second most common form of gynecologic cancer and the second leading cause of gynecologic cancer death. It is a heterogeneous disease with many different types and subtypes. The most common variety (70%-80%) is the high-grade serous epithelial tumor. A positive family history and/or the presence of susceptibility genes (BRCA1, BRCA2, and mismatch repair genes) increase the risk for developing the disease. Due to the lack of effective screening tools, even in those with known increased risk, most ovarian cancers are diagnosed at advanced stages. Diagnosis and accurate staging usually require tissue sampling and extensive debulking surgery performed by a surgeon who specializes in gynecologic oncology. Combination chemotherapy, before or after surgery, or as primary treatment for advanced disease is commonly needed. Mortality rates vary by stage, grade, and type of tumor. For the most common histotypes, due to the presence of advanced disease at presentation in most individuals, overall death rates remain high. Survival is better with some of the less common subtypes including sex cord stromal, germ cell and borderline epithelial ovarian tumors.
    Keywords:  BRCA1 and BRCA2; Epithelial ovarian tumors; borderline ovarian carcinoma; cancer antigen-125 (CA-125); carcinosarcoma; endometroid carcinoma; fallopian tube cancer; germ cell tumors; hereditary nonpolyposis coli/HNOCC/Lynch syndrome; high-grade serous carcinoma; human epididymis secretory protein-4 (HE-4); low-grade serous carcinoma; primary cancer of the peritoneum; primary mucinous carcinoma; sex cord - stromal tumors
    DOI:  https://doi.org/10.17849/insm-52-3-1-10.2A
  7. Nat Commun. 2025 Sep 26. 16(1): 8499
    Comparison of imaging based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed paraffin-embedded tumor samples.
    RTI Team
      Imaging-based spatial transcriptomics (ST) is evolving as a pivotal technology in studying tumor biology and associated microenvironments. However, the strengths of the commercially available ST platforms in studying spatial biology have not been systematically evaluated using rigorously controlled experiments. We use serial 5 μm sections of formalin-fixed, paraffin-embedded surgically resected lung adenocarcinoma and pleural mesothelioma samples in tissue microarrays to compare the performance of the ST platforms (CosMx, MERFISH, and Xenium (uni/multi-modal)) in reference to bulk RNA sequencing, multiplex immunofluorescence, GeoMx, and hematoxylin and eosin staining data. In addition to an objective assessment of automatic cell segmentation and phenotyping, we perform a manual phenotyping evaluation to assess pathologically meaningful comparisons between ST platforms. Here, we show the intricate differences between the ST platforms, reveal the importance of parameters such as probe design in determining the data quality, and suggest reliable workflows for accurate spatial profiling and molecular discovery.
    DOI:  https://doi.org/10.1038/s41467-025-63414-1
  8. Biomolecules. 2025 Sep 18. pii: 1334. [Epub ahead of print]15(9):
    The Years 2015-2025 as a Prospective Decade for the Identification of Specific Methylation Biomarkers of Prostate Cancer.
    Zohair Selmani, Paul Peixoto, Alexis Overs, Eric Hervouet.
      For ten years, DNA methylation appeared as a major step in the understanding and issues of prostate cancers. Indeed, although classical biochemical parameters are still useful for prostate cancer diagnosis, they have poor sensitivity and are not specific for prostate cancer subtypes. The recent boom in the identification of specific DNA methylation profiles and the rapid development of liquid biopsies have completely modified the care of patients and may greatly influence outcomes in the future. Indeed, DNA methylation modifications could substantially improve the diagnosis by identifying specific prostate subtypes, improve follow-up to monitor residual disease, improve therapeutic efficiency by predicting the response to treatment, and improve the health quality of patients since these epigenetic modifications can easily be detected in non-invasive liquid biopsies.
    Keywords:  DNA methylation; biomarker; cancer; diagnosis; liquid biopsies; prostate
    DOI:  https://doi.org/10.3390/biom15091334
  9. Nucleic Acids Res. 2025 Sep 23. pii: gkaf966. [Epub ahead of print]53(18):
    gwSPADE: gene frequency-weighted reference-free deconvolution in spatial transcriptomics.
    Aoqi Xie, Nina G Steele, Yuehua Cui.
      Most spatial transcriptomics (ST) technologies (e.g. 10× Visium) operate at the multicellular level, where each spatial location often contains a mixture of cells with heterogeneous cell types. Thus, effective deconvolution of cell type compositions is critical for downstream analysis. Although reference-based deconvolution methods have been proposed, they depend on the availability of reference data, which may not always be accessible. Additionally, within a deconvolved cell type, cellular heterogeneity may still exist, requiring further deconvolution to uncover finer structures for a better understanding of this complexity. Here, we present gwSPADE, a gene frequency-weighted reference-free SPAtial DEconvolution method for ST data. gwSPADE requires only the gene count matrix and utilizes appropriate weighting schemes within a topic model to accurately recover cell type transcriptional profiles and their proportions at each spatial location, without relying on external single-cell reference information. In various simulations and real data analyses, gwSPADE demonstrates scalability across various platforms and shows superior performance over existing reference-free deconvolution methods such as STdeconvolve.
    DOI:  https://doi.org/10.1093/nar/gkaf966
  10. JCO Precis Oncol. 2025 Sep;9 e2400832
    Leveraging Real-World Data From a Clinicogenomic Database Addresses the Treatment Gap in Patients With High-Grade Serous Ovarian Cancer.
    Chiara Maura Ciniselli, Elena Conca, Michele Bartoletti, Nicoletta Colombo, Umberto Malapelle, Salvatore Lopez, Sandro Pignata, Francesco Raspagliesi, Paolo Verderio, Claudio Zamagni, Valentina Sara Barbiero, Silvia Castellani, Emilia Sicari, Luca Agnelli, Federica Perrone, Giancarlo Pruneri.
       PURPOSE: This study used a deidentified nationwide (US-based) high-grade serous ovarian cancer (HGSOC) clinicogenomic database (CGDB) to enrich our understanding of HGSOC's genomic heterogeneity and assess the utility of comprehensive genomic profiling (CGP) in clinical settings.
    PATIENTS AND METHODS: We conducted a retrospective observational analysis on 856 patients with HGSOC profiled with CGP genomic tests, retrieved from CGDB from January 2011 to September 2023.
    RESULTS: In addition to BRCA1 (11.7%) and BRCA2 (6.5%) variants, CGP revealed further potentially actionable alterations (amplifications and/or mutations) in CCNE1 (16%), FGFR1/2/3/4 (6.5%), PIK3CA (3.9%), TP53Y220C (3.7%), ERBB2 (3.5%), CDK12 (2.3%), ARID1A (2.2%), KRAS (2.1%), and BRAF (1%) genes. Then, 439 patients were selected, presenting both CGP test performed on specimen collected at the time of surgery and initiation of first-line therapy within ±8 months from surgery, and categorized into no (NS, n = 74), interval (IS, n = 157), and upfront surgery (n = 208) groups, each comparable by clinical features. The CGP revealed BRCA mutations, at similar frequency in the three groups, in 54/439 patients (12.3%). Patients with pathogenic BRCA mutations had better event-free survival (EFS) compared with those with BRCAwt. Loss-of-heterozygosity (LOH) ≥16 (LOH-positive patients) was found in 142/433 (32.8%) patients, with different prevalence across treatment groups (12.8% NS; 9% IS; 8.8% upfront surgery). Patients treated with poly (ADP-ribose) polymerase inhibitors (PARPi) had improved EFS (hazard ratio for other drugs v PARPi 1.77 [95% CI, 1.21 to 2.58]). Interestingly, in 206 BRCAwt and LOH-negative patients, not eligible for PARPi, CGP detected potentially targetable alterations in 99 of them (48%).
    CONCLUSION: Overall, our study provides evidence that CGP significantly improves the identification of molecular targets in HGSOC, supporting its importance in the clinical practice to provide patients with more therapeutic options.
    DOI:  https://doi.org/10.1200/PO-24-00832
  11. Cancer Res. 2025 Sep 24.
    Mismatch Repair as a Dynamic and Clinically Actionable Vulnerability in Cancer.
    Eleonora Piumatti, Pietro Paolo Vitiello, Vito Amodio, Alberto Bardelli, Giovanni Germano.
      DNA mismatch repair (MMR) preserves genomic integrity by correcting replication errors. Deficiency in MMR (MMRd) results in microsatellite instability, increased tumor mutational burden, neoantigen generation, and activation of immune response. In this review, we first outlined how MMR loss promotes immune activation and responsiveness to immune checkpoint blockade (ICB), establishing MMRd status as the first tumor-agnostic biomarker for ICB therapy. Subsequently, we summarized the compelling evidence that defines MMR status as a dynamic, context-dependent process influenced by environmental and therapeutic pressures, rather than a fixed, binary trait. Accordingly, we discussed the implications of spatial and temporal heterogeneity of MMR status for both the diagnosis and treatment of cancer, the differential response of MMRd tumors to ICB, as well as the occasional benefits observed in MMR-proficient (MMRp) immune-cold cancers. We then explored strategies to exploit MMR dynamics and mimic MMRd-like phenotypes through alkylating agents, pharmacological MMR inhibition, and stress-mediated modulation, with the aim of sensitizing refractory tumors to immunotherapy. Finally, we reported emerging therapeutic opportunities in MMRd tumors, including Werner helicase inhibition, nonsense-mediated decay blockade, and neoantigen-targeted vaccines. Altogether, reframing MMR as a dynamic and targetable axis may broaden immunotherapy applicability and advance precision immune oncology across different tumor types.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-25-2255
  12. Am J Clin Exp Immunol. 2025 ;14(4): 237-240
    Cell-free DNA fragmentomics: a universal framework for early cancer detection and monitoring.
    Wanyu Dong, Wenshi Hu, Yaojuan Lu, Qiping Zheng.
      Cell-free DNA (cfDNA) fragmentomics has emerged as a powerful and noninvasive approach for cancer detection, characterization, and monitoring. By analyzing genome-wide fragmentation patterns - including fragment length distributions, end motifs, nucleosome footprints, and copy number variations - cfDNA fragmentomics provides high-resolution insights into tumor-specific biological signals even at low tumor burden. This technology offers advantages over conventional mutation-based assays by capturing aggregate structural and epigenomic alterations without requiring prior knowledge of driver mutations. In non-small cell lung cancer (NSCLC), cfDNA fragmentomics enables early detection, discrimination of malignant pulmonary nodules, and post-surgical monitoring of minimal residual disease. Recent studies have demonstrated that fragmentomic risk scores can accurately stratify recurrence risk and improve prognostic sensitivity beyond traditional genomic assays. In hepatocellular carcinoma (HCC), integration of fragment size selection, CNV profiling, and end-motif analysis has led to high-performing models for early diagnosis, particularly in high-risk populations. Moreover, cfDNA fragmentomics has proven effective in detecting malignant transformation in patients with neurofibromatosis-associated peripheral nerve sheath tumors, distinguishing benign from premalignant or malignant lesions with high precision. Expanding beyond these major cancers, fragmentomic approaches have demonstrated diagnostic potential in gastric, urological, hematologic, and pediatric malignancies. Notably, the DELFI-TF (DNA Evaluation of Fragments for early Interception-Tumor Fraction) framework has shown prognostic relevance by correlating pre-treatment cfDNA features with survival outcomes in colorectal and lung cancer patients, outperforming conventional imaging. All of these results highlight the translational importance of cfDNA fragmentomics as a cutting-edge precision oncology tool. Its continued integration into clinical workflows may redefine early cancer detection, facilitate subtype-specific interventions, and enable real-time, individualized treatment monitoring.
    Keywords:  Cell-free DNA; early cancer detection; fragmentomics; liquid biopsy
    DOI:  https://doi.org/10.62347/EBRY4326
  13. Cancer Discov. 2025 Sep 22.
    The molecular and functional landscape of resistance to FOLFIRI chemotherapy in metastatic colorectal cancer.
    Marco Avolio, Simonetta M Leto, Francesco Sassi, Barbara Lupo, Elena Grassi, Irene Catalano, Eugenia R Zanella, Valentina Vurchio, Francesca Cottino, Petros K Tsantoulis, Luca Lazzari, Paolo Luraghi, Martina Ferri, Francesco Galimi, Enrico Berrino, Sara E Bellomo, Marco Viviani, Alberto Sogari, Gianluca Mauri, Federica Tosi, Federica Cruciani, Andrea Sartore-Bianchi, Salvatore Siena, Felice Borghi, Valter Torri, Elena Élez, Josep Tabernero, Maria Nieva, Clara Montagut, Noelia Tarazona, Andres Cervantes, Sabine Tejpar, Alberto Bardelli, Caterina Marchiò, Silvia Marsoni, Andrea Bertotti, Livio Trusolino.
      The combination of 5-fluorouracil and irinotecan (FOLFIRI) remains a standard-of-care treatment for metastatic colorectal cancer (mCRC), yet benefits only about half of patients. Using patient-derived xenografts (PDXs), we investigated the biological underpinnings of this heterogeneous response. FOLFIRI-resistant models showed transcriptional upregulation of innate immunity and mitochondrial metabolism genes, together with reduced expression of the DNA polymerase POLD1. Sensitive counterparts exhibited a BRCAness-like phenotype with genomic scars of homologous recombination (HR) deficiency, not caused by genetic or epigenetic loss of HR genes but by low abundance of the RAD51 recombinase. In tumoroids, forced RAD51 overexpression attenuated HR deficiency-related scars and chemotherapy-induced damage, while HR inhibition through ATM blockade enhanced drug sensitivity. The predictive relevance of key response determinants was validated in clinical samples. This work illuminates functional, non-genetic facets of BRCAness in mCRC and introduces actionable biomarkers and targets, offering prospects to improve clinical decision-making and broaden therapeutic options for chemorefractory patients.
    DOI:  https://doi.org/10.1158/2159-8290.CD-24-0556
  14. Acta Otolaryngol. 2025 Sep 26. 1-6
    Application of circulating tumor DNA analysis in detecting Minimal residual disease (MRD) after surgery for locally advanced head and neck squamous cell carcinoma: a preliminary study.
    Xiaolian Fang, Zheng Yang, Jing Zhou, Xiaohong Chen, Pingdong Li.
       BACKGROUND: Traditional imaging and pathological examinations lack sufficient sensitivity for detecting minimal residual disease (MRD), limiting early identification of subclinical recurrence in head and neck squamous cell carcinoma (HNSCC).
    AIMS/OBJECTIVES: To explore the clinical utility of dynamic circulating tumor DNA (ctDNA) monitoring in detecting MRD after surgery for locally advanced HNSCC.
    MATERIAL AND METHODS: Sixteen patients with locally advanced HNSCC who underwent radical treatment were enrolled. Peripheral blood samples were collected preoperatively and one week to five years postoperatively for ctDNA analysis. Tumor tissue targeted sequencing and clinicopathological parameters were integrated to evaluate the sensitivity, specificity, and prognostic value of MRD detection.
    RESULTS: The preoperative ctDNA positivity rate was 81.3% (13/16), with a median content of 22.6 hGE/ml (range: 0.45-131.92). High-frequency genetic alterations included TP53 mutations (81.3%, 13/16), with hotspot mutations such as p.R273C, p.H193L, and p.R342. Copy number reduction in CDKN2A (43.8%, 7/16) and PIK3CA mutations (18.8%, 3/16) were the main driver alterations. One patient with hypopharyngeal carcinoma (T3N2bM0) tested ctDNA-positive 1.5 months postoperatively, which was 6.5 months earlier than radiological recurrence (tongue metastasis detected 8 months postoperatively).
    CONCLUSIONS AND SIGNIFICANCE: Dynamic ctDNA monitoring effectively identifies postoperative MRD in HNSCC.
    Keywords:  Circulating tumor DNA; head and neck squamous cell carcinoma; minimal residual disease; next-generation sequencing
    DOI:  https://doi.org/10.1080/00016489.2025.2561924
  15. BMC Bioinformatics. 2025 Sep 23. 26(1): 229
    CCNV: a user-friendly R package enabling large-scale cumulative copy number variation analyses of DNA methylation data.
    Antonia Gocke, Yannis Schumann, Jelena Navolić, Shweta Godbole, Melanie Schoof, Matthias Dottermusch, Julia E Neumann.
       BACKGROUND: Copy number variation (CNV) analyses-often inferred from DNA-methylation data-depict alterations of DNA quantities across chromosomes and have improved tumour diagnostics and classification. For the analyses of larger case series, CNV-features of multiple samples have to be combined to reliably interpret tumour-type characteristics. Established workflows mainly focus on the analyses of singular samples and do not support scalability to high sample numbers. Additionally, only plots showing the frequency of the aberrations have been considered.
    RESULTS: We present the Cumulative CNV (CCNV) R package, which combines established segmentation methods and a newly implemented algorithm for thorough and fast CNV analysis at unprecedented accessibility. Our work is the first to supplement well-interpretable CNV frequency plots with their respective intensity plots, as well as showcasing the first application of penalised least-squares regression to DNA methylation data. CCNV exceeded existing tools concerning computing time and displayed high accuracy for all available array types on simulated and real-world data, verified by our newly developed benchmarking method.
    CONCLUSIONS: CCNV is a user-friendly R package, which enables fast and accurate generation and analyses of cumulative copy number variation plots.
    Keywords:  Chromosomal aberration; Copy number variation; Cumulative CNV; DNA methylation; EPIC; EPICv2; High-throughput; Segmentation
    DOI:  https://doi.org/10.1186/s12859-025-06269-z
  16. Int J Mol Sci. 2025 Sep 18. pii: 9071. [Epub ahead of print]26(18):
    Special Issue "Biomarkers and Early Detection Strategies of Ovarian Tumors".
    Laura Aleksandra Szafron, Jolanta Kupryjanczyk, Lukasz Michal Szafron.
      Although progress has been made in developing new therapies and deepening the biological understanding of ovarian carcinoma (OvCa), it continues to be the most lethal gynecologic cancer in women [...].
    DOI:  https://doi.org/10.3390/ijms26189071
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