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<p>We had previously reported a convolutional neural network (CNN) based approach, called the holistic kinetic model (HK model 1), for detecting 5-methylcytosine (5mC) by single molecule real-time sequencing (Pacific Biosciences). In this study, we constructed a hybrid model with CNN and transformer layers, named HK model 2. We improve the area under the receiver operating characteristic curve (AUC) for 5mC detection from 0.91 for HK model 1 to 0.99 for HK model 2. We further demonstrate that HK model 2 can detect other types of base modifications, such as 5-hydroxymethylcytosine (5hmC) and N6-methyladenine (6mA). Using HK model 2 to analyze 5mC patterns of cell-free DNA (cfDNA) molecules, we demonstrate the enhanced detection of patients with hepatocellular carcinoma, with an AUC of 0.97. Moreover, HK model 2-based detection of 6mA enables the detection of jagged ends of cfDNA and the delineation of cellular chromatin structures. HK model 2 is thus a versatile tool expanding the applications of single molecule real-time sequencing in liquid biopsies.</p><p></p>

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Transformer-based deep learning for accurate detection of multiple base modifications using single molecule real-time sequencing

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年4月14日

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  • Xi Hu,
  • Yuwei Shi,
  • Suk Hang Cheng,
  • Zhaoyang Huang,
  • Ze Zhou,
  • Xiaoyu Shi,
  • Yi Zhang,
  • Jing Liu,
  • Mary-Jane L. Ma,
  • Spencer C. Ding,
  • Jiaen Deng,
  • Rong Qiao,
  • Wenlei Peng,
  • L. Y. Lois Choy,
  • Stephanie C. Y. Yu,
  • W. K. Jacky Lam,
  • K. C. Allen Chan,
  • Hongsheng Li,
  • Peiyong Jiang,
  • Y. M. Dennis Lo

摘要

We had previously reported a convolutional neural network (CNN) based approach, called the holistic kinetic model (HK model 1), for detecting 5-methylcytosine (5mC) by single molecule real-time sequencing (Pacific Biosciences). In this study, we constructed a hybrid model with CNN and transformer layers, named HK model 2. We improve the area under the receiver operating characteristic curve (AUC) for 5mC detection from 0.91 for HK model 1 to 0.99 for HK model 2. We further demonstrate that HK model 2 can detect other types of base modifications, such as 5-hydroxymethylcytosine (5hmC) and N6-methyladenine (6mA). Using HK model 2 to analyze 5mC patterns of cell-free DNA (cfDNA) molecules, we demonstrate the enhanced detection of patients with hepatocellular carcinoma, with an AUC of 0.97. Moreover, HK model 2-based detection of 6mA enables the detection of jagged ends of cfDNA and the delineation of cellular chromatin structures. HK model 2 is thus a versatile tool expanding the applications of single molecule real-time sequencing in liquid biopsies.