A virtual sequencer reveals the dephasing patterns in error-correction code DNA sequencing. Issue 5 (3rd September 2020)

• Record Type: Journal Article
• Authors: Zhou, Wenxiong; Kang, Li; Duan, Haifeng; Qiao, Shuo; Tao, Louis; Chen, Zitian; Huang, Yanyi
• Is Part Of: National science review. Volume 8:Issue 5(2021)
• Publication Date: 2020-09-03
• Subjects: DNA sequencing -- error-correction code -- dephasing -- computer simulation -- sequencing-by-synthesis; Science -- Periodicals; 505
• DOI: 10.1093/nsr/nwaa227
• Languages: English
• ISSNs: 2095-5138

Abstract

Abstract: 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 algorithm. The results show that our dephasing algorithm is applicable to sequencing signals with at least 500 cycles, or 1000-bp average read length, with acceptably low error rate for further parity checks and ECC deduction. Our 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. Abstract : A computational model reveals how DNA molecules get unsynchronized in error-correction code sequencing and leads to algorithms to correct the aberrant signals back.