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Multimodal analysis of cell-free DNA whole-methylome sequencing for cancer detection and localization

Author

Listed:
  • Fenglong Bie

    (Chinese Academy of Medical Sciences and Peking Union Medical College
    Shandong Provincial Hospital Affiliated to Shandong First Medical University)

  • Zhijie Wang

    (Chinese Academy of Medical Sciences and Peking Union Medical College)

  • Yulong Li

    (Genecast Biotechnology Co., Ltd.)

  • Wei Guo

    (Chinese Academy of Medical Sciences and Peking Union Medical College)

  • Yuanyuan Hong

    (Genecast Biotechnology Co., Ltd.)

  • Tiancheng Han

    (Genecast Biotechnology Co., Ltd.)

  • Fang Lv

    (Genecast Biotechnology Co., Ltd.)

  • Shunli Yang

    (Genecast Biotechnology Co., Ltd.)

  • Suxing Li

    (Genecast Biotechnology Co., Ltd.)

  • Xi Li

    (Genecast Biotechnology Co., Ltd.)

  • Peiyao Nie

    (Genecast Biotechnology Co., Ltd.)

  • Shun Xu

    (The First Hospital of China Medical University)

  • Ruochuan Zang

    (Chinese Academy of Medical Sciences and Peking Union Medical College)

  • Moyan Zhang

    (Chinese Academy of Medical Sciences and Peking Union Medical College)

  • Peng Song

    (Chinese Academy of Medical Sciences and Peking Union Medical College)

  • Feiyue Feng

    (Chinese Academy of Medical Sciences and Peking Union Medical College)

  • Jianchun Duan

    (Chinese Academy of Medical Sciences and Peking Union Medical College)

  • Guangyu Bai

    (Chinese Academy of Medical Sciences and Peking Union Medical College)

  • Yuan Li

    (Chinese Academy of Medical Sciences and Peking Union Medical College)

  • Qilin Huai

    (Chinese Academy of Medical Sciences and Peking Union Medical College)

  • Bolun Zhou

    (Chinese Academy of Medical Sciences and Peking Union Medical College)

  • Yu S. Huang

    (Genecast Biotechnology Co., Ltd.)

  • Weizhi Chen

    (Genecast Biotechnology Co., Ltd.)

  • Fengwei Tan

    (Chinese Academy of Medical Sciences and Peking Union Medical College)

  • Shugeng Gao

    (Chinese Academy of Medical Sciences and Peking Union Medical College)

Abstract

Multimodal epigenetic characterization of cell-free DNA (cfDNA) could improve the performance of blood-based early cancer detection. However, integrative profiling of cfDNA methylome and fragmentome has been technologically challenging. Here, we adapt an enzyme-mediated methylation sequencing method for comprehensive analysis of genome-wide cfDNA methylation, fragmentation, and copy number alteration (CNA) characteristics for enhanced cancer detection. We apply this method to plasma samples of 497 healthy controls and 780 patients of seven cancer types and develop an ensemble classifier by incorporating methylation, fragmentation, and CNA features. In the test cohort, our approach achieves an area under the curve value of 0.966 for overall cancer detection. Detection sensitivity for early-stage patients achieves 73% at 99% specificity. Finally, we demonstrate the feasibility to accurately localize the origin of cancer signals with combined methylation and fragmentation profiling of tissue-specific accessible chromatin regions. Overall, this proof-of-concept study provides a technical platform to utilize multimodal cfDNA features for improved cancer detection.

Suggested Citation

  • Fenglong Bie & Zhijie Wang & Yulong Li & Wei Guo & Yuanyuan Hong & Tiancheng Han & Fang Lv & Shunli Yang & Suxing Li & Xi Li & Peiyao Nie & Shun Xu & Ruochuan Zang & Moyan Zhang & Peng Song & Feiyue F, 2023. "Multimodal analysis of cell-free DNA whole-methylome sequencing for cancer detection and localization," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41774-w
    DOI: 10.1038/s41467-023-41774-w
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    Cited by:

    1. Jiaqi Liu & Lijun Dai & Qiang Wang & Chenghao Li & Zhichao Liu & Tongyang Gong & Hengyi Xu & Ziqi Jia & Wanyuan Sun & Xinyu Wang & Minyi Lu & Tongxuan Shang & Ning Zhao & Jiahui Cai & Zhigang Li & Hon, 2024. "Multimodal analysis of cfDNA methylomes for early detecting esophageal squamous cell carcinoma and precancerous lesions," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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