纳米孔测序的三十年。
Three decades of nanopore sequencing.
作者信息
Deamer David, Akeson Mark, Branton Daniel
机构信息
Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA.
Department of Molecular &Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.
出版信息
Nat Biotechnol. 2016 May 6;34(5):518-24. doi: 10.1038/nbt.3423.
Abstract
A long-held goal in sequencing has been to use a voltage-biased nanoscale pore in a membrane to measure the passage of a linear, single-stranded (ss) DNA or RNA molecule through that pore. With the development of enzyme-based methods that ratchet polynucleotides through the nanopore, nucleobase-by-nucleobase, measurements of changes in the current through the pore can now be decoded into a DNA sequence using an algorithm. In this Historical Perspective, we describe the key steps in nanopore strand-sequencing, from its earliest conceptualization more than 25 years ago to its recent commercialization and application.
摘要
测序领域长期以来的一个目标是利用膜中电压偏置的纳米级孔来测量线性单链（ss）DNA或RNA分子通过该孔的过程。随着基于酶的方法的发展，这些方法能使多核苷酸逐个碱基地通过纳米孔，现在通过该孔的电流变化测量结果可以使用一种算法解码为DNA序列。在这篇历史展望中，我们描述了纳米孔链测序的关键步骤，从25多年前最早的概念构思到其最近的商业化和应用。
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1
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Nature. 2016 Feb 11;530(7589):228-232. doi: 10.1038/nature16996. Epub 2016 Feb 3.
2
MinION Analysis and Reference Consortium: Phase 1 data release and analysis.MinION分析与参考联盟：第一阶段数据发布与分析
F1000Res. 2015 Oct 15;4:1075. doi: 10.12688/f1000research.7201.1. eCollection 2015.
3
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Emerg Infect Dis. 2016 Feb;22(2):331-4. doi: 10.3201/eid2202.151796.
4
Nanopore sequencing detects structural variants in cancer.纳米孔测序可检测癌症中的结构变异。
Cancer Biol Ther. 2016;17(3):246-53. doi: 10.1080/15384047.2016.1139236. Epub 2016 Jan 19.
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