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Highly accurate fluorogenic DNA sequencing with information theory–based error correction

Nature Biotechnology volume 35, pages 1170–1178 (2017)Cite this article

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Abstract

Eliminating errors in next-generation DNA sequencing has proved challenging. Here we present error-correction code (ECC) sequencing, a method to greatly improve sequencing accuracy by combining fluorogenic sequencing-by-synthesis (SBS) with an information theory–based error-correction algorithm. ECC embeds redundancy in sequencing reads by creating three orthogonal degenerate sequences, generated by alternate dual-base reactions. This is similar to encoding and decoding strategies that have proved effective in detecting and correcting errors in information communication and storage. We show that, when combined with a fluorogenic SBS chemistry with raw accuracy of 98.1%, ECC sequencing provides single-end, error-free sequences up to 200 bp. ECC approaches should enable accurate identification of extremely rare genomic variations in various applications in biology and medicine.

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Figure 1: The schematic of the ECC sequencing approach.
Figure 2: Sequencing signal in a typical fluorogenic degenerate sequencing run.
Figure 3: Information communication model for ECC sequencing.
Figure 4: Dynamic programming-based decoding algorithm.
Figure 5: High accuracy of ECC sequencing.

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Acknowledgements

The authors thank Y. Men, Z. Yu, H. Qiu, C. Zheng, Y. Fu, X. Zhang, T. Chen, L. Wu, S. Zhang, X. Jiang, J. Bu, P.A. Sims, L.L. Tao, and H. Ge for experimental assistance and discussion. This work was supported by the Ministry of Science and Technology of China (863 Program 2012AA02A101), National Natural Science Foundation of China (21327808 and 21525521), Beijing Municipal Commission of Science and Technology (Z111100059111002), and Beijing Advanced Innovation Center for Genomics.

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Authors and Affiliations

  1. Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China

    Zitian Chen, Wenxiong Zhou, Shuo Qiao, Li Kang, Haifeng Duan, X Sunney Xie & Yanyi Huang

  2. Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, China

    Zitian Chen, Wenxiong Zhou, Shuo Qiao, Li Kang, Haifeng Duan, X Sunney Xie & Yanyi Huang

  3. College of Engineering, Peking University, Beijing, China

    Zitian Chen & Yanyi Huang

  4. School of Life Sciences, Peking University, Beijing, China

    Zitian Chen, Wenxiong Zhou, Shuo Qiao, Li Kang, Haifeng Duan, X Sunney Xie & Yanyi Huang

  5. Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China

    Yanyi Huang

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Contributions

Y.H. and X.S.X. conceived the project. Y.H. and Z.C. designed the experiment. Z.C., W.Z., S.Q., L.K., and H.D. performed the experiments. All authors analyzed the data and wrote the manuscript.

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Correspondence to Yanyi Huang.

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Patent applications based on this work have been filed by Peking University, and licensed to Cygnus, of which all the authors are consultants, Z.C. and H.D. are shareholders.

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Chen, Z., Zhou, W., Qiao, S. et al. Highly accurate fluorogenic DNA sequencing with information theory–based error correction. Nat Biotechnol 35, 1170–1178 (2017). https://doi.org/10.1038/nbt.3982

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