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Circulating Cell-free DNA Fragmentomics Detection and Beyond

aging and disease
Circulating cell-free DNA (cfDNA) comprises DNA fragments released into bodily fluids via apoptosis, necrosis, or phagocytosis. cfDNA encapsulates both fragmentomics (structural) and non-fragmentomics (sequence/epigenetic) information from source cells, thereby representing a promising biomarker.
Tianliang, Liu, Zhicheng, Li, Shifu, Chen, Jiasheng, Zhong   +3 more
exaly   +3 more sources

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Longitudinal Noninvasive Surveillance & Fragmentomic Characterization of Follicular Lymphoma

Blood, 2023
Introduction While cell-free DNA (cfDNA) plays an increasingly defined role in aggressive lymphomas, its characteristics in indolent lymphomas are less established. Many follicular lymphoma (FL) patients experience durable remissions and late relapses ( Fig A).
Schroers-Martin, Joseph G., Mutter, Jurik, Rossi, Cédric, Liu, Chih Long, Shahrokh Esfahani, Mohammad, Sugio, Takeshi, Tessoulin, Benoit, Scherer, Florian Paul, Soo, Joanne, Alig, Stefan, Kurtz, David M., Olsen, Mari, Diehn, Maximilian, Alizadeh, Ash A.   +13 more
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Multidimensional Fragmentomics Enables Early and Accurate Detection of Colorectal Cancer

Cancer Research
Abstract Colorectal cancer is frequently diagnosed in advanced stages, highlighting the need for developing approaches for early detection. Liquid biopsy using cell-free DNA (cfDNA) fragmentomics is a promising approach, but the clinical application is hindered by complexity and cost.
Yuepeng Cao, Nannan Wang, Xuxiaochen Wu, Wanxiangfu Tang, Hua Bao, Chengshuai Si, Peng Shao, Dongzheng Li, Xin Zhou, Dongqin Zhu, Shanshan Yang, Fufeng Wang, Guoqing Su, Ke Wang, Qifan Wang, Yao Zhang, Qiangcheng Wang, Dongsheng Yu, Qian Jiang, Jun Bao, Liu Yang   +20 more
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Cell-free DNA fragmentomics and second malignant neoplasm risk in patients with PTEN hamartoma tumor syndrome

Cell Reports Medicine
<p><strong>Supplementary dataset for manuscript</strong></p> <p>Affiliations:</p> <p>¹Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA</
Darren Liu, Lamis Yehia, Andrew Dhawan   +2 more
exaly   +3 more sources

cfDNA fragmentomics for preeclampsia prediction

To investigate whether cfDNA fragmentomic features have the potential to predict early-onset or late-onset PE, we performed WGS of plasma cfDNA (>10X final read depth) from pregnant women with PE (n=109 for early-onset PE, n=333 for late-onset PE) and sampling-gestation-matched healthy controls (n=476).
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Abstract 3505: Classification of cancer subtypes by cfDNA fragmentomics analysis

Cancer Research
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 ...
Lisha Zhu, Chao Dai, Shuang Gan, Shidong Jia, Pan Du   +4 more
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Integration of cfDNA fragmentomics for early biliary tract cancer detection.

Journal of Clinical Oncology
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.
Jiwen Wang, Xiaojian Ni, Yuxuan Zheng, Qingxin Xie, Hua Bao, Kun Fan, Dongqin Zhu, Hairong Bao, Ruowei Yang, Chunyan Wang, Bohao Zheng, Shuang Chang, Xiuxiu Xu, Haimeng Tang, Xiaoling Ni, Tao Suo, Xue Wu, Sheng Shen, Han Liu, Houbao Liu   +19 more
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Abstract 1125: Characterizing the cfDNA fragmentome in patients with hepatocellular carcinoma

Cancer Research
Abstract Hepatocellular carcinoma (HCC) is the third leading cause of cancer death globally and is one of the most rapidly increasing causes of cancer mortality in North America and Europe due to metabolic and emerging risk factors. Here, we show that cell-free DNA (cfDNA) fragmentation profiles reflected underlying disease biology ...
Hope Orjuela, Carter Norton, Shashikant Koul, Daniel C. Bruhm, Akshaya V. Annapragada, Sarah Short, Keerti Boyapati, Adrianna Bartolomucci, Vilmos Adleff, Nicholas A. Vulpescu, Kauí Lebarbenchon, Jacob Carey, Carter Portwood, Andrei Sorop, Razvan Iacob, Speranta Iacob, Liana Gheorghe, Simoni Dima, Katherine A. McGlynn, Manuel Ramirez-Zea, Jillian Phallen, Robert B. Scharpf, John Groopman, Victor E. Velculescu, Zachariah Foda   +24 more
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Prospective Evaluation of cfDNA Fragmentomes for Lung Cancer Detection

C99. ADVANCES IN BIOMARKERS ACROSS THE LUNG CANCER CONTINUUM, 2023
P.J. Mazzone, K.-K. Wong, J.J. Tsay, A. Vachani, A. Ryan, J. Carey, D. Jakubowski, K. Lumbard, J. Catallini, T. Maddala, P.B. Bach, R. Scharpf, N. Dracopoli, V. Velculescu   +13 more
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Abstract 3772: Leveraging the cfDNA fragmentome to predict immunotherapy response

Cancer Research
Abstract Background: Assessing immunotherapy response presents unique challenges, driven by the heterogeneity of clinical responses that are inadequately captured by conventional imaging. Early changes in circulating tumor DNA (ctDNA), captured by mutation-based next generation sequencing (NGS), have ...
Noushin Niknafs, Lavanya Sivapalan, Bahar Alipanahi, Daniel Rabizadeh, Mimi Najjar, Zachary L. Skidmore, Gavin Pereira, Caitlin Schonewolf, Bryan Chesnick, Peter Bach, Nicholas C. Dracopoli, Robert Scharpf, Joseph Murray, Victor Velculescu, Valsamo (Elsa) K. Anagnostou   +14 more
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