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

• Published in: Nature biotechnology Vol. 35; no. 12; pp. 1170 - 1178
• Main Authors: Chen, Zitian, Zhou, Wenxiong, Qiao, Shuo, Kang, Li, Duan, Haifeng, Xie, X Sunney, Huang, Yanyi
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.12.2017; Nature Publishing Group
• Subjects: 45/23; 631/61/514/2254; 639/166/985; Agriculture; Analysis; Bioinformatics; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Decoding; Deoxyribonucleic acid; DNA; DNA sequencing; Error correction; Error-correcting codes; Information theory; Life Sciences; Methods; Redundancy
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/nbt.3982

The error rate of DNA sequencing is much reduced by combining an improved fluorogenic sequencing chemistry with a new error-correction scheme. 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.