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A virtual sequencer reveals the dephasing patterns in error-correction code DNA sequencing

National Science Review 2021年第5期8卷 91-100页

作者： Wenxiong Zhou Li Kang Haifeng Duan Shuo Qiao Louis Tao Zitian Chen Yanyi Huang Biomedical Pioneering Innovation Center (BIOPIC) School of Life SciencesBeijing Advanced Innovation Center for Genomics(ICG)and Peking-Tsinghua Center for Life SciencesPeking University Center for Bioinformatics State Key Laboratory of Protein Engineering and Plant Genetic EngineeringPeking University Center for Quantitative Biology Peking University College of Engineering Peking University College of Chemistry and Molecular Engineering Peking University Institute for Cell Analysis Chinese Institute for Brain Research (CIBR)

An error-correction code(ECC) sequencing approach has recently been reported to effectively reduce sequencing errors by interrogating a DNA fragment with three orthogonal degenerate sequencing-by-synthesis(SBS) reactions. However, similar to other non-single-molecule SBS methods, the reaction will gradually lose its synchronization within a molecular colony in ECC sequencing. This phenomenon, called dephasing, causes sequencing error, and in ECC sequencing, induces distinctive dephasing patterns. To understand the characteristic dephasing patterns of the dual-base flowgram in ECC sequencing and to generate a correction algorithm, we built a virtual sequencer in silico. Starting from first principles and based on sequencing chemical reactions, we simulated ECC sequencing results, identified the key factors of dephasing in ECC sequencing chemistry and designed an effective dephasing *** results show that our dephasing algorithm is applicable to sequencing signals with at least 500 cycles, or1000-bp average read length, with acceptably low error rate for further parity checks and ECC *** virtual sequencer with our dephasing algorithm can further be extended to a dichromatic form of ECC sequencing, allowing for a potentially much more accurate sequencing approach.

关键词： DNA sequencing error-correction code dephasing computer simulation sequencing-by-synthesis

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