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


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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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.

Author information




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.

Corresponding author

Correspondence to Yanyi Huang.

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Competing interests

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).

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