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Journal articles on the topic 'Fragmentomics'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Kohabir, Kavish, Rob Wolthuis, and Erik A. Sistermans. "Fragmentomic cfDNA Patterns in Noninvasive Prenatal Testing and Beyond." Journal of Biomedicine and Translational Research 7, no. 1 (2021): 38–47. http://dx.doi.org/10.14710/jbtr.v7i1.10229.

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The release of fetoplacental cell-free DNA (cfDNA) into the maternal bloodstream opened up new avenues towards noninvasive prenatal testing (NIPT) for aneuploidies, hereditary DNA mutations and other pregnancy-related developmental disorders. Increasingly, cfDNA catches interest for its noninvasive screening value in other areas as well, including oncology. Although there are indications that cfDNA fragmentation is a non-random process, the etiology and different structural aspects of cfDNA are still not well known. The emerging field of cfDNA fragmentomics investigates the existence of tissue

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Ding, Spencer C., and Y. M. Dennis Lo. "Cell-Free DNA Fragmentomics in Liquid Biopsy." Diagnostics 12, no. 4 (2022): 978. http://dx.doi.org/10.3390/diagnostics12040978.

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Cell-free DNA (cfDNA) in bodily fluids has rapidly transformed the development of noninvasive prenatal testing, cancer liquid biopsy, and transplantation monitoring. Plasma cfDNA consists of a mixture of molecules originating from various bodily tissues. The study of the fragmentation patterns of cfDNA, also referred to as ‘fragmentomics’, is now an actively pursued area of biomarker research. Clues that cfDNA fragmentation patterns might carry information concerning the tissue of origin of cfDNA molecules have come from works demonstrating that circulating fetal, tumor-derived, and transplant

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Yang, Yin, Tao Zhang, Jingbo Wang, et al. "Abstract 5400: Predicting disease progression in inoperable localized NSCLC patients using cfDNA fragmentomics assay." Cancer Research 83, no. 7_Supplement (2023): 5400. http://dx.doi.org/10.1158/1538-7445.am2023-5400.

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Abstract Background: There is an urgent clinical need to accurately predict the risk for disease progression in post-treatment NSCLC patients. However, the current ctDNA mutation profiling approaches were limited by low sensitivity, while the cfDNA fragmentomics profiling has shown an excellent capability for cancer early detection in NSCLC and therefore exhibits great potential for predicting disease progression. In this retrospective study, we aim to develop a non-invasive liquid biopsy assay utilizing cfDNA fragmentomics profiling for predicting disease progression in inoperable localized N

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Zhao, Huan, Shuang Gan, Hang Dong, et al. "Use of urinary cell-free DNA fragmentomics in urothelial carcinoma diagnosis." Journal of Clinical Oncology 43, no. 5_suppl (2025): 846. https://doi.org/10.1200/jco.2025.43.5_suppl.846.

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846 Background: Traditional diagnostic procedures for urothelial carcinoma (UC) are often limited by patient burden and reduced sensitivity, impacting diagnostic accuracy. Liquid biopsy-based molecular detection, particularly through fragmentomics analysis, offers a promising supplement to clinical applications. Fragmentomics, which examines the unique fragmentation patterns of tumor DNA, can provide crucial insights into tumor origin and behavior. This study aims to leverage urinary cell-free DNA (ucfDNA) fragmentomics patterns to enhance the diagnostic capabilities for urothelial carcinoma.

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Cobb, Meagan S., Philippe Jolivet, Kristen N. Ganjoo, Deirdre A. Lum, Matt van de Rijn, and Joanna Przybyl. "Abstract 3678: Liquid biopsy fragmentomics approach for the diagnosis of uterine tumors." Cancer Research 85, no. 8_Supplement_1 (2025): 3678. https://doi.org/10.1158/1538-7445.am2025-3678.

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Abstract Background: Leiomyomas (LM), also known as fibroids, are common benign tumors of the smooth muscle of the uterus that can cause pain, infertility, and abnormal menstrual bleeding. Diagnosing LM is challenging using clinical indications alone, as they share symptoms with leiomyosarcoma (LMS), a rare, aggressive uterine malignancy with a ∼50% disease-specific survival. Pre-operative distinction between LM and LMS is difficult because these tumors are rarely biopsied before surgery. We hypothesize that a non-invasive circulating tumor DNA (ctDNA) test based on LMS- and LM-specific molecu

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Pan, Alex C., Russell Taylor Sundby, Jeffrey J. Szymanski, et al. "Abstract 997: Cell-free DNA fragmentomics distinguish between benign, pre-malignant and malignant peripheral nerve sheath tumors in neurofibromatosis type 1." Cancer Research 83, no. 7_Supplement (2023): 997. http://dx.doi.org/10.1158/1538-7445.am2023-997.

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Abstract Background: Malignant peripheral nerve sheath tumors (MPNST) are aggressive soft tissue sarcomas that, in the setting of neurofibromatosis type 1 (NF1), arise within pre-malignant atypical neurofibroma (AN) and benign plexiform neurofibroma (PN). Early surgical resection improves prognosis, however, early detection by imaging and tissue biopsies is challenging due to tissue heterogeneity. In this multi-institutional study we analyze fragmentomic profiles of plasma cell free DNA (cfDNA) to non-invasively distinguish between NF1 associated PN, AN and MPNST. Accurate classification would

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Qi, Ting, Min Pan, Huajuan Shi, Liangying Wang, Yunfei Bai, and Qinyu Ge. "Cell-Free DNA Fragmentomics: The Novel Promising Biomarker." International Journal of Molecular Sciences 24, no. 2 (2023): 1503. http://dx.doi.org/10.3390/ijms24021503.

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Cell-free DNA molecules are released into the plasma via apoptotic or necrotic events and active release mechanisms, which carry the genetic and epigenetic information of its origin tissues. However, cfDNA is the mixture of various cell fragments, and the efficient enrichment of cfDNA fragments with diagnostic value remains a great challenge for application in the clinical setting. Evidence from recent years shows that cfDNA fragmentomics’ characteristics differ in normal and diseased individuals without the need to distinguish the source of the cfDNA fragments, which makes it a promising nove

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Zamyatnin, A. A. "Fragmentomics of natural peptide structures." Biochemistry (Moscow) 74, no. 13 (2009): 1575–85. http://dx.doi.org/10.1134/s0006297909130100.

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Wang, Mengchi, Jin Mo Ahn, Junnam Lee, et al. "Abstract 4928: REFINE Method: Novel strategy for signal enhancement." Cancer Research 84, no. 6_Supplement (2024): 4928. http://dx.doi.org/10.1158/1538-7445.am2024-4928.

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Abstract Fragmentomics has emerged as a powerful tool in the detection of early cancer malignancies. One of the challenges for fragmentomics is the low signal to noise ratio in early stage cancer samples. Fragmentomic sequencing data is also inherently noisy and susceptible to batch effects. Common strategies to address these challenges include using normalization methods, such as frequency or Z-score normalization, to scale data. However, these existing methods struggle to differentiate true signals from noise and are susceptible to experimental bias. To address the need for a strategy that r

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Zamyatnin, A. A. "Fragmentomics of proteins and natural oligopeptides." Biophysics 53, no. 5 (2008): 329–35. http://dx.doi.org/10.1134/s0006350908050011.

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Thierry, A. R. "Circulating DNA fragmentomics and cancer screening." Cell Genomics 3, no. 1 (2023): 100242. http://dx.doi.org/10.1016/j.xgen.2022.100242.

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Dai, Chao, Lisha Zhu, Yong Huang, et al. "Abstract 940: Integrated analysis of cfDNA fragmentomics, DNA methylation and cfRNA transcription in metastatic castration-resistant prostate cancer (mCRPC)." Cancer Research 84, no. 6_Supplement (2024): 940. http://dx.doi.org/10.1158/1538-7445.am2024-940.

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Abstract Background Liquid biopsies based on cell-free DNA (cfDNA) analysis provide non-invasive clinical diagnostic insights. Recently, cfDNA fragmentomics has emerged as a tool for inferring epigenomic and transcriptional information from tumor-derived cfDNA. We conducted a comprehensive profiling of cfDNA fragmentomics, whole transcriptome sequencing (WTS), and genome-wide DNA methylation on two metastatic castration-resistant prostate cancer (mCRPC) samples to systematically investigate molecular aberrations in mCRPC. Methods Two mCRPC patient plasma samples were extensively profiled using

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Yin, Lingdi, Cheng Cao, Jianzhen Lin, et al. "Fragmentomics of cell-free DNA as a sensitive biomarker for early detection of pancreatic cancer." Journal of Clinical Oncology 42, no. 16_suppl (2024): 4173. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.4173.

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4173 Background: Pancreatic ductal adenocarcinoma (PDAC) is one for the most lethal types of cancer. Nearly 80% of the PDAC patients are diagnosed at advanced unresectable stages. Therefore, an accurate early diagnosis assay is urgently needed for reducing PDAC related mortalities. In this study, we aim to utilize cfDNA fragmentomics and machine learning techniques for sensitively detecting PDAC patients. Methods: Total647 cases were prospectively enrolled in this study. Plasma samples were collected from each participant for shallow WGS (~5X). After quality control process, 166 PDAC patients

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Liu, Yaping. "At the dawn: cell-free DNA fragmentomics and gene regulation." British Journal of Cancer 126, no. 3 (2021): 379–90. http://dx.doi.org/10.1038/s41416-021-01635-z.

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AbstractEpigenetic mechanisms play instrumental roles in gene regulation during embryonic development and disease progression. However, it is challenging to non-invasively monitor the dynamics of epigenomes and related gene regulation at inaccessible human tissues, such as tumours, fetuses and transplanted organs. Circulating cell-free DNA (cfDNA) in peripheral blood provides a promising opportunity to non-invasively monitor the genomes from these inaccessible tissues. The fragmentation patterns of plasma cfDNA are unevenly distributed in the genome and reflect the in vivo gene-regulation stat

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Xu, Shun, Ji Luo, Wanxiangfu Tang, et al. "Abstract 5394: Detecting pulmonary malignancy against benign nodules using non-invasive cfDNA fragmentomics assay." Cancer Research 83, no. 7_Supplement (2023): 5394. http://dx.doi.org/10.1158/1538-7445.am2023-5394.

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Abstract Background: Early screening using Low-Dose Computed Tomography (LDCT) can reduce mortality by non-small-cell-lung cancer (NSCLC), which contributed the most cancer-related death worldwide. Yet ~25% of the “suspicious” nodules identified by LDCT are confirmed to be benign through resection surgery, which adds to patients’ discomfort and the burden of the healthcare system. In this prospective study, we set to develop a non-invasive liquid biopsy assay for distinguishing pulmonary malignancy from benign lung nodules using cfDNA fragmentomic profiling. Methods: An independent training co

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Gan, Shuang, Haoran Tang, Feng Xie, Yue Zhang, and Hang Dong. "Abstract 6611: Genome-wide cfDNA fragmentomics combined with machine learning enhance non-invasive prostate cancer detection." Cancer Research 85, no. 8_Supplement_1 (2025): 6611. https://doi.org/10.1158/1538-7445.am2025-6611.

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Abstract The liquid biopsy approach focusing on DNA molecules offers a promising non-invasive method for prostate cancer diagnosis. Next-generation sequencing (NGS) of targeted gene panels is widely used for detecting somatic mutations but is limited by confounding clonal hematopoietic variants and narrow genome coverage. We propose a solution that encompasses genome-wide DNA fragmentation features for tumor fragment evaluation. This study collected plasma samples from 209 patients with prostate cancer and 49 healthy individuals as controls. Cell-free DNA (cfDNA) was extracted and tested using

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Villanueva-Cañas, J. L., D. Rizo-Potau, A. Fornies, et al. "Characterization of global cfDNA fragmentomics in Melanoma Patients." EJC Skin Cancer 3 (2025): 100432. https://doi.org/10.1016/j.ejcskn.2025.100432.

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Zhang, Ruiyun, Hang Dong, Shuang Gan, et al. "Applying fragmentomics profiles of urinary cell-free DNA for bladder cancer detection." Journal of Clinical Oncology 42, no. 4_suppl (2024): 671. http://dx.doi.org/10.1200/jco.2024.42.4_suppl.671.

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671 Background: The liquid biopsy approach focusing on DNA molecules supports non-invasive diagnosis of bladder cancer. While utilizing cell-free DNA fragmentation characteristics for the cancer detection has shown potential in plasma, its applications in urine remained unexplored. Methods: We enrolled 70 patients with bladder cancer and 49 healthy individuals in this study. The urinary cell-free DNA (ucfDNA) was extracted and tested by PredicineSCORE, a low pass whole genome sequencing (LP-WGS) assay to identify tumor-specific features. The ucfDNA fragmentomics profiles including the coverage

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Grisolia, Piera, Antonio De Falco, Rossella Tufano, et al. "Advanced CNA-informed fragmentomics enhances cross-cohort tumor detection." Journal of Liquid Biopsy 5 (November 2024): 100256. http://dx.doi.org/10.1016/j.jlb.2024.100256.

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Zhu, Lisha, Chao Dai, Shuang Gan, Shidong Jia, and Pan Du. "Abstract 5884: Cancer subtype classification by cfDNA fragmentomics analysis." Cancer Research 85, no. 8_Supplement_1 (2025): 5884. https://doi.org/10.1158/1538-7445.am2025-5884.

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Introduction: Nucleosome occupancy patterns at transcription factor binding sites (TFBS) exhibit differences between circulating tumor DNA (ctDNA) in cancer patients and normal plasma controls, as well as among different tumor subtypes. Therefore, cell-free DNA (cfDNA) fragmentomics can be employed for cancer subtyping analysis. The tumor fraction in cfDNA can affect the performance of nucleosome profiling, and a minimal tumor fraction is required to obtain high sensitivity of cancer subtyping. This study investigated the detection sensitivity - specifically, the minimal tumor fraction require

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Shan, Zhen, Wanna Chen, Bo Lin, et al. "A non-invasive cfDNA fragmentomics assay for differentiating malignant and benign thyroid nodules." Journal of Clinical Oncology 42, no. 16_suppl (2024): 6110. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.6110.

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6110 Background: Thyroid cancer (TC) is the most common endocrine malignancy in the world. Although it has a high survival rate, distinguishing between the common benign thyroid nodules and malignant ones remains a clinical challenge. We introduce a non-invasive assay based on cfDNA fragmentomics, aimed at accurately identifying TCs, thus reducing the discomfort and risks linked to surgical biopsies. Methods: We conducted a study involving 322 participants, comprising 161 early-stage thyroid cancer patients (154 stage I and 7 stage II) and 161 patients with benign thyroid nodules, of whom 68 w

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Liu, Jiaqi, Yalun Li, Wanxiangfu Tang, et al. "Detecting early stage breast cancer using low-depth cell-free DNA fragmentomics: A multi-center cohort study." Journal of Clinical Oncology 41, no. 16_suppl (2023): 3075. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.3075.

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3075 Background: Breast cancer (BC) has contributed to the most cancer-related mortalities among females in 2020. Early detection using breast imaging methods, such as mammography and ultrasound, has significantly improved patients' survival. However, these early-screening methods suffer from high false-positive rates, resulting in many unnecessary biopsies which add to patients' discomfort. Cell-free DNA (cfDNA) fragmentomics assays have recently illustrated prominent abilities for detecting various cancer. In this multi-center prospective cohort study, we aim to develop a non-invasive liquid

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Peng, Yulu, Tingxuan Huang, Zhaohui Zhou, et al. "Early detection of renal cell carcinoma: A novel cfDNA fragmentomics-based liquid biopsy assay." Journal of Clinical Oncology 43, no. 16_suppl (2025): 4534. https://doi.org/10.1200/jco.2025.43.16_suppl.4534.

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4534 Background: Renal cell carcinoma (RCC) is a leading cause of cancer-related mortality, with a rapidly rising global incidence. Early detection greatly improves the outcomes of RCC, yet current diagnostic methods have limitations in sensitivity, specificity, and accessibility. This study develops and evaluates a cfDNA fragmentomics-based liquid biopsy integrated with machine learning as a non-invasive and scalable tool for RCC early detection. Methods: This case-control cohort study recruited 442 participants (223 RCC patients and 219 non-cancer controls, including healthy individuals and

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Zhong, Yunshi, Dong-Li He, Zhi-Guo Xiong, et al. "GaEsSeer: Early detection of gastric and esophageal cancer by integrating methylation and fragmentomics signatures in cfDNA." Journal of Clinical Oncology 41, no. 16_suppl (2023): 4069. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.4069.

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4069 Background: Esophageal and gastric cancer (EC and GC) are two common cancer types that severely impact patients’ health. The 5-year survival rate for EC and GC is as low as 19% and 31%, respectively. However, early detection will significantly increase the survival rate: stage-1 EC has a 5-year survival rate of 51%, while for stage-1 GC it’s 69%. Invasive screening methods, such as endoscopy and biopsy, caused low compliance. Computational tomography and carcinoembryonic antigen were limited by low sensitivity. To address this problem, we developed GaEsSeer, a non-invasive targeted-sequen

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Zhu, Lisha, Chao Dai, Shuang Gan, Shidong Jia, and Pan Du. "Abstract 3505: Classification of cancer subtypes by cfDNA fragmentomics analysis." Cancer Research 84, no. 6_Supplement (2024): 3505. http://dx.doi.org/10.1158/1538-7445.am2024-3505.

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Abstract Introduction Fragmentation patterns of cell-free DNA (cfDNA) from whole genome sequencing offer insights into nucleosome occupancy, providing a tool to infer epigenomic and transcriptomic information. The nucleosome complex, the primary protector of cfDNA, is reflected in the size distribution of cfDNA fragments, with a mode fragment size of 167 bp corresponding to the wrapping of DNA around a single nucleosome. Nucleosome occupancy patterns at transcription factor binding sites (TFBS) exhibit differences between circulating tumor DNA in cancer patients and normal plasma controls, as

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Chiu, Rossa W. K., Ellen Heitzer, Y. M. Dennis Lo, Florent Mouliere, and Dana W. Y. Tsui. "Cell-Free DNA Fragmentomics: The New “Omics” on the Block." Clinical Chemistry 66, no. 12 (2020): 1480–84. http://dx.doi.org/10.1093/clinchem/hvaa258.

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Wang, Jiwen, Xiaojian Ni, Yuxuan Zheng, et al. "Integration of cfDNA fragmentomics for early biliary tract cancer detection." Journal of Clinical Oncology 43, no. 16_suppl (2025): 4131. https://doi.org/10.1200/jco.2025.43.16_suppl.4131.

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4131 Background: Biliary Tract Cancer (BTC) is a highly aggressive malignancy with poor survival outcomes, primarily due to the lack of effective early detection methods and late-stage diagnoses. Current diagnostic tools, including imaging and invasive endoscopic procedures, are limited in their sensitivity and specificity for identifying early-stage disease. This study addresses this critical gap by developing a novel, non-invasive approach for BTC detection using circulating cell-free DNA (cfDNA) fragmentomics features. Methods: The study cohort included 163 patients diagnosed with BTC and 1

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Maansson, Christoffer Trier, Louise Skov Thomsen, Peter Meldgaard, Anders Lade Nielsen, and Boe Sandahl Sorensen. "Integration of Cell-Free DNA End Motifs and Fragment Lengths Can Identify Active Genes in Liquid Biopsies." International Journal of Molecular Sciences 25, no. 2 (2024): 1243. http://dx.doi.org/10.3390/ijms25021243.

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Multiple studies have shown that cell-free DNA (cfDNA) from cancer patients differ in both fragment length and fragment end motif (FEM) from healthy individuals, yet there is a lack of understanding of how the two factors combined are associated with cancer and gene transcription. In this study, we conducted cfDNA fragmentomics evaluations using plasma from lung cancer patients (n = 12) and healthy individuals (n = 7). A personal gene expression profile was established from plasma using H3K36me3 cell-free chromatin immunoprecipitation sequencing (cfChIP-seq). The genes with the highest express

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Jiao, Zichen, Xiaoqiang Zhang, Yulong Xuan, et al. "Leveraging cfDNA fragmentomic features in a stacked ensemble model for early detection of esophageal squamous cell carcinoma." Journal of Clinical Oncology 42, no. 16_suppl (2024): 4054. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.4054.

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4054 Background: In this study, we developed a stacked ensemble model that leverages cell-free DNA (cfDNA) fragmentation for the early detection of esophageal squamous cell carcinoma (ESCC). The model combined four fragmentomics features obtained from whole genome sequencing (WGS) and employed four machine learning algorithms. We evaluated the model’s generalizability in an independent validation cohort and an external cohort collected at different center. Additionally, the model’s robustness and repeatability were assessed across low coverage and repeated measured samples. The results undersc

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Taylor, Amy K., Kyle Helzer, Marina Nasrin Sharifi, et al. "Fragmentomics of cell-free DNA from targeted panels in genitourinary malignancies." Journal of Clinical Oncology 42, no. 4_suppl (2024): 199. http://dx.doi.org/10.1200/jco.2024.42.4_suppl.199.

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199 Background: The detection of genomic alterations in cancer is critical for identifying clinically actionable alterations for treatment decisions. Tumor samples historically have been required, but obtaining tissue for molecular profiling is not always feasible, especially in the metastatic setting. The isolation and analysis of cell-free DNA (cfDNA) including circulating tumor DNA (ctDNA) via blood-based “liquid” biopsies offers non-invasive sampling of the tumor. Recently, fragmentation patterns of cfDNA (i.e. “fragmentomics”) have emerged as a method for inferring epigenomic and transcri

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Park, Sehhoon, Jun-Kyu Kang, Hwang-Phill Kim, et al. "Exploratory analysis using cfDNA-based fragmentomics to predict disease recurrence in limited disease small cell lung cancer." Journal of Clinical Oncology 40, no. 16_suppl (2022): 8569. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.8569.

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8569 Background: The current standard of care (SOC) for limited disease (LD) small cell lung cancer (SCLC) is definitive concurrent chemoradiotherapy (CCRT). Despite the high response rate to SOC, up to 70% of the patients potentially experience disease recurrence and fail to show the prolonged clinical benefit. We investigated the feasibility of cell-free DNA (cfDNA) based genomic alteration and fragmentomic analysis using pre-and post-treatment samples to investigate the predictive value of disease recurrence in LD-SCLC. Methods: The blood sample from fifty LD-SCLC who were treated with defi

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Park, Sehhoon, Jun-Kyu Kang, Hwang-Phill Kim, et al. "Exploratory analysis using cfDNA-based fragmentomics to predict disease recurrence in limited disease small cell lung cancer." Journal of Clinical Oncology 40, no. 16_suppl (2022): 8569. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.8569.

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8569 Background: The current standard of care (SOC) for limited disease (LD) small cell lung cancer (SCLC) is definitive concurrent chemoradiotherapy (CCRT). Despite the high response rate to SOC, up to 70% of the patients potentially experience disease recurrence and fail to show the prolonged clinical benefit. We investigated the feasibility of cell-free DNA (cfDNA) based genomic alteration and fragmentomic analysis using pre-and post-treatment samples to investigate the predictive value of disease recurrence in LD-SCLC. Methods: The blood sample from fifty LD-SCLC who were treated with defi

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Chauhan, Pradeep Singh, Irfan Alahi, Jessica Linford, et al. "Abstract 3258: Predicting genitourinary cancer tissue-of-origin using urine cell-free DNA fragmentomics and cell-free RNA." Cancer Research 85, no. 8_Supplement_1 (2025): 3258. https://doi.org/10.1158/1538-7445.am2025-3258.

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Abstract Introduction: We previously developed a urine liquid biopsy assay to measure urine tumor DNA (utDNA) levels in bladder cancer (BC) patients. Here, we extended this approach significantly by layering in cell-free DNA fragmentomic and cell-free RNA analysis, and extending the method to the full spectrum of genitourinary (GU) cancers, to enable both GU cancer detection and tumor tissue of origin prediction. Methods: A total of 155 GU cancer patients and 34 healthy adults were enrolled in this prospective study. Preoperative urine was collected from 94 bladder cancer (BC) patients, includ

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Lo, Y. M. Dennis, Diana S. C. Han, Peiyong Jiang, and Rossa W. K. Chiu. "Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies." Science 372, no. 6538 (2021): eaaw3616. http://dx.doi.org/10.1126/science.aaw3616.

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Liquid biopsies that analyze cell-free DNA in blood plasma are used for noninvasive prenatal testing, oncology, and monitoring of organ transplant recipients. DNA molecules are released into the plasma from various bodily tissues. Physical and molecular features of cell-free DNA fragments and their distribution over the genome bear information about their tissues of origin. Moreover, patterns of DNA methylation of these molecules reflect those of their tissue sources. The nucleosomal organization and nuclease content of the tissue of origin affect the fragmentation profile of plasma DNA molecu

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Rahat, Dolev, Lilach Schneor, Noa Liscovitch-Brauer, and Noam Shomron. "P125: Detection of pancreatic cancer in liquid biopsies using integrative fragmentomics." Genetics in Medicine Open 2 (2024): 101006. http://dx.doi.org/10.1016/j.gimo.2024.101006.

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Yin, Rong, Siwei Wang, Ming Li, et al. "Utilization of cell-free DNA fragmentomics in minimal residual disease detection for non-small cell lung cancer." Journal of Clinical Oncology 40, no. 16_suppl (2022): 3038. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.3038.

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3038 Background: Non-small-cell lung cancer (NSCLC) is the leading cause of worldwide cancer-related deaths. Currently, ̃30-55% of the NSCLC patients develop recurrence due to minimal residual disease (MRD) after receiving surgical resection of the tumor. Therefore, there is an urgent clinical need to accurately predict the MRD risk in post-surgical NSCLC patients. However, the current targeted ctDNA mutation profiling method is limited by the cost of design and synthesis of patient-specific panels and relatively low sensitivity. Cell-free DNA (cfDNA) fragmentomics have recently shown great ac

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Guzman, Carlos, Michael L. Salmans, Mengchi Wang, Byung In Lee, and Andrew R. Carson. "Abstract B058: Novel machine learning lung cancer classifier shows significant correlation with cancer-specific fragmentomics features." Clinical Cancer Research 30, no. 21_Supplement (2024): B058. http://dx.doi.org/10.1158/1557-3265.liqbiop24-b058.

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Abstract Lung cancer is the second most prevalent cancer, and the leading cause of cancer-related deaths, in the US. Since the survival rate of patients diagnosed with lung cancer at earlier stages is dramatically higher than those diagnosed at later stages, technologies that shift lung cancer diagnosis to an earlier stage would be expected to improve survival rates. Fragmentomics, the study of short circulating cell-free DNA (cfDNA) fragments in the blood, is an emerging field in cancer diagnostics that has the potential to catalyze such a shift. Studies have shown that fragmentomics features

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Bao, Hua, Xiaoxi Chen, Min Wu, et al. "Abstract 1266: Development and performance of a multi-cancer early detection test utilizing plasma cfDNA fragmentomics: A large-scale, prospective, multicenter study." Cancer Research 84, no. 6_Supplement (2024): 1266. http://dx.doi.org/10.1158/1538-7445.am2024-1266.

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Abstract Background: The implementation of the multi-cancer early detection (MCED) test offers a valuable adjunct to existing screening methods, enabling more efficient detection of cancer and potentially leading to improved treatment outcomes and prognoses for patients. Here, we report on the performance of an MCED test, which utilizes plasma cfDNA and leverages genome-wide fragmentomics-based characteristics to identify cancer signals and predict the signal origin across a diverse range of cancer types. Methods: Plasma cfDNA from evaluable blood samples was analyzed using an MCED blood test

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Abelman, Dor D., Jenna Eagles, Aimee Wong, et al. "Abstract 3250: Tumor-independent monitoring of minimal residual disease in multiple myeloma using cfDNA fragmentomics." Cancer Research 85, no. 8_Supplement_1 (2025): 3250. https://doi.org/10.1158/1538-7445.am2025-3250.

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Abstract Introduction: Monitoring minimal residual disease (MRD) is critical in multiple myeloma (MM) to predict outcomes and guide therapy. Traditional bone marrow (BM) aspirates for MRD detection are invasive and limited by sample quality. We therefore explored cell-free DNA (cfDNA) fragmentation as a less invasive alternative for MRD detection. Methods: We performed 30-40X whole-genome sequencing (WGS) on peripheral blood cfDNA from 45 MM patients, collecting baseline (n = 45) and follow-up samples (n = 98) from eight Canadian sites (M4 and IMMAGINE studies) and one U.S. site (SPORE study),

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Maansson, Christoffer Trier, Louise Skov Thomsen, Peter Meldgaard, Anders Lade Nielsen, and Boe Sandahl Sorensen. "Abstract 2290: Integration of cell-free DNA end motifs and fragment lengths can improve identification of active genes in liquid biopsies." Cancer Research 84, no. 6_Supplement (2024): 2290. http://dx.doi.org/10.1158/1538-7445.am2024-2290.

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Abstract Multiple studies have shown that the plasma cell-free DNA (cfDNA) from cancer patients differs from healthy individuals in both fragment length and fragment end motifs (FEMs). Yet, there is a lack of understanding regarding how the two factors combined can be associated with cancer and gene transcription. In this study, we evaluated cfDNA fragmentomics in plasma from lung cancer patients (n = 17) and healthy individuals (n = 7) using targeted sequencing (lung cancer: n = 12, healthy: n = 7) and whole-genome sequencing (WGS) (lung cancer: n = 5). A personal gene expression profile was

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Rolfo, Christian, and Alessandro Russo. "The Next Frontier for Colorectal Cancer Screening: Blood-Based Tests." Cancer Research 84, no. 19 (2024): 3128–29. http://dx.doi.org/10.1158/0008-5472.can-24-1620.

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Colorectal cancer is associated with substantial morbidity and mortality worldwide. Detection of early colorectal cancer is possible through approved screening tests but overall adherence is quite low. Implementation of effective noninvasive options could increase screening uptake and prevent a significant number of deaths. Noninvasive early cancer detection can potentially be achieved using a liquid biopsy. In this issue of Cancer Research, Cao and colleagues report on a novel multidimensional fragmentomics assay, named FRAGTECT, for colorectal cancer detection in circulating cell-free DNA wi

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Sirajee, Ahmad Salman, Debajyoti Kabiraj, and Subhajyoti De. "Cell-free nucleic acid fragmentomics: A non-invasive window into cellular epigenomes." Translational Oncology 49 (November 2024): 102085. http://dx.doi.org/10.1016/j.tranon.2024.102085.

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Yang, Xin-Rong, Dong-Li He, Zhi-Guo Xiong, et al. "Detection and localization of gastrointestinal cancers based on multi-dimentional signatures from a single cfDNA targeted sequencing assay." Journal of Clinical Oncology 41, no. 16_suppl (2023): 4169. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.4169.

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4169 Background: Five major gastrointestinal (GI) cancers - colorectal (CRC), gastric (GC), liver (LC), esophageal (EC), and pancreatic cancer (PC) - are responsible for hundreds of thousands of mortalities annually worldwide. Unfortunately, there is a lack of cost-effective, blood-based screening method for their early detection. To address this issue, we aimed to develop GutSeer, a noninvasive, targeted methylation sequencing-based test by leveraging methylation and fragmentomic signatures carried by cell-free DNA (cfDNA). Methods: The panel of GutSeer consists of 1656 target regions which w

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Patel, Kishen R., Anisha Mistry, Robert Monfries, et al. "Abstract 4560: Use of ctDNA fragmentomics as a predictive biomarker in locally advanced non-small cell lung cancer." Cancer Research 85, no. 8_Supplement_1 (2025): 4560. https://doi.org/10.1158/1538-7445.am2025-4560.

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Abstract Introduction: Locally advanced non-small cell lung cancer (NSCLC) is a serious condition with a poor 5-year survival rate of approximately 30%. Standard treatment involves chemoradiotherapy (CRT) followed by immunotherapy (IO). However, predicting benefit prior to CRT and monitoring response post treatment are areas of unmet need. Cancers, like many tissues, release fragments of DNA into the bloodstream, which can be detected using whole genome sequencing (WGS). Research has shown that cancer cells tend to release shorter DNA fragments, typically between 90-150 base pairs, at higher r

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Zhang, Mingguang, Qianhui Wan, Shiwen Mei, et al. "Early gastrointestinal tumour detection using cfDNA fragmentomes based on low-pass whole-genome sequencing (lp-WGS)." Journal of Clinical Oncology 41, no. 16_suppl (2023): e15511-e15511. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.e15511.

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e15511 Background: As one of the most concerning world public health issue, cancer accounted for 21% of all deaths. Early cancer detection methods help reduce the chance of dying from cancer. The fragmentation patterns of plasma circulating cell-free DNA (cfDNA) in tumor patients and healthy people are different, which reflects aberrant gene-regulation in cancer patients. Measure cfDNA fragmentomics not only identify the biomarkers to detect cancer early, but also contribute to revealing the biological regulatory mechanism of cancer. In this study, a novel method, i.e. multi-fragmentomics earl

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Wang, Haichao, Paulius D. Mennea, Yu Kiu Elkie Chan, et al. "A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data." Genome Biology 26, no. 1 (2025): 141. https://doi.org/10.1186/s13059-025-03607-5.

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Fragmentomics features of cell-free DNA represent promising non-invasive biomarkers for cancer diagnosis. A lack of systematic evaluation of biases in feature quantification hinders the adoption of such applications. We compare features derived from whole-genome sequencing of ten healthy donors using nine library kits and ten data-processing routes and validated in 1182 plasma samples from published studies. Our results clarify the variations from library preparation and feature quantification methods. We design the Trim Align Pipeline and cfDNAPro R package as unified interfaces for data pre-

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Avgeris, Margaritis, Antonios Marmarinos, Dimitrios Gourgiotis, and Andreas Scorilas. "Jagged Ends of Cell-Free DNA: Rebranding Fragmentomics in Modern Liquid Biopsy Diagnostics." Clinical Chemistry 67, no. 4 (2021): 576–78. http://dx.doi.org/10.1093/clinchem/hvab036.

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Xu, Qin, Yibin Lin, Xiaoxi Chen, et al. "Early detection of uterine corpus endometrial carcinoma utilizing plasma cell-free DNA fragmentomics." Gynecologic Oncology 190 (November 2024): S32. http://dx.doi.org/10.1016/j.ygyno.2024.07.053.

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Xu, S., J. Luo, W. Tang, et al. "Detecting pulmonary malignancy against benign nodules using noninvasive cell-free DNA fragmentomics assay." ESMO Open 9, no. 8 (2024): 103595. http://dx.doi.org/10.1016/j.esmoop.2024.103595.

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Cao, Y., N. Wang, C. Si, et al. "585P Fragmentomics early detection assay leading to potential clinical benefits in colorectal cancer." Annals of Oncology 34 (October 2023): S426. http://dx.doi.org/10.1016/j.annonc.2023.09.1776.

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