遗传 ›› 2018, Vol. 40 ›› Issue (11): 929-937.doi: 10.16288/j.yczz.18-179

• 领域前瞻 • 上一篇    下一篇

实现“终极版”核苷酸测序仪的技术要素

于军1,2   

  1. 1. 中国科学院北京基因组研究所,中国科学院基因组科学与信息重点实验室,北京 100101
    2. 中国科学院大学,北京 100049
  • 收稿日期:2018-07-02 修回日期:2018-09-26 出版日期:2018-11-20 发布日期:2018-10-22
  • 基金资助:
    中国科学院前沿科学重点研究项目“高速纳米孔核苷酸序列分析仪”资助(QYZDY-SSW-SMC017)

Possible technical elements for the ultimate nucleotide sequencers

Jun Yu1,2   

  1. 1. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
    2. University of Chinese Academy of Sciences, Beijing 100049, China
  • Received:2018-07-02 Revised:2018-09-26 Online:2018-11-20 Published:2018-10-22
  • Supported by:
    Supported by the “High-Speed Nanopore Analysis System For Nuclear Acid”(QYZDY-SSW-SMC017)

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摘要：

20世纪70年代发明的第一代DNA测序技术,尽管测序通量有限,却成功地保证了“人类基因组计划”的实施;世纪之交出现的下一代(第二代) DNA测序技术经历了通量飞跃,为各种精准医学项目的实施提供了保障;目前的第三代技术,尽管通量居二代之后,但读长和单分子测序优势也让其有立足之本;第四代测序技术的基本标志是不经过cDNA (以RNA为模版合成的互补DNA),无PCR扩增,而直接测定单分子RNA序列,以及确定单分子RNA上的修饰核苷酸位点。从技术的角度看,第三、四代技术有一定技术要素共享(比如在单分子水平测定DNA序列),但是就测序对象而言,第四代应该属于“终极版”核苷酸测序仪：可以从单细胞出发,既能测定DNA序列,也可以测定RNA序列,也可以直接确定修饰核苷酸位点。因此,要实现这个“终极版”核苷酸测序仪,就要调动相关核心技术要素,而这些要素毫无疑问地会涉及物理、化学、工程学、生物学、半导体科学、计算机科学等领域的前沿技术,包括纳米科学、单分子光学、单分子拉曼光谱、单分子核磁共振、单分子酶学、人工智能等所谓的“硬科技”。其功能是从单细胞的裂解开始,经微纳结构实现组分分流后,直接导入RNA序列测定单元,定量分析细胞RNA分子的种类、数量、序列和修饰核苷酸位点的存在频率。本文系统介绍了第四代测序仪的可能技术要素,以及应用需求和新研究范式。

关键词: 核苷酸测序技术, 单分子, 单细胞, 纳米技术, 纳米孔

Abstract:

The DNA sequencing technology invented in 1970’s has been a leading tool for genomics and its sequel — precision medicine. The needs for advancement of the DNA sequencing technology comes from increasing resolutions in cellular and molecular studies, not only DNA or cDNA sequences but also their covalent modifications, such as various kinds of DNA or RNA methylations. Sequencing single RNA molecules directly without conversion into cDNAs appears to be the last generation of nucleotide sequencers. Some cutting-edge technological elements are clearly expected for the ultimate design of nucleotide sequencers, which must include, but not limited to, nanopores, nanofabrication, surface- or tip-enhanced Raman spectrometry, single-molecule photonics and plasmonics, artificial-intelligence based data analysis tools. The complexity of biological systems is also calling for new syntheses, frameworks, paradigms and more concerted efforts and projects internationally. Here we discuss possible roles and capacities of such technical elements for the fourth-generation nucleotide sequencers in details.

Key words: DNA sequencing, RNA direct sequencing, single cell, single molecule, nanopores