DNA sequencing using polymerase substrate-binding kinetics

• Published in: Nature communications Vol. 6; no. 1; p. 5936
• Main Authors: Previte, Michael John Robert, Zhou, Chunhong, Kellinger, Matthew, Pantoja, Rigo, Chen, Cheng-Yao, Shi, Jin, Wang, BeiBei, Kia, Amirali, Etchin, Sergey, Vieceli, John, Nikoomanzar, Ali, Bomati, Erin, Gloeckner, Christian, Ronaghi, Mostafa, He, Molly Min
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 23.01.2015; Nature Publishing Group; Nature Pub. Group
• Subjects: 631/208/514/1948; 631/57/2272/1590; 631/92; 82; Bacteriophage phi X 174 - genetics; Base Pair Mismatch; Base Sequence; DNA - chemistry; DNA-Directed DNA Polymerase - chemistry; Equipment Design; Genome, Viral; Genomics; High-Throughput Nucleotide Sequencing - instrumentation; High-Throughput Nucleotide Sequencing - methods; Humanities and Social Sciences; Kinetics; Molecular Sequence Data; multidisciplinary; Nucleotides - genetics; Polymers; Science; Science (multidisciplinary); Sequence Analysis, DNA
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms6936

Next-generation sequencing (NGS) has transformed genomic research by decreasing the cost of sequencing. However, whole-genome sequencing is still costly and complex for diagnostics purposes. In the clinical space, targeted sequencing has the advantage of allowing researchers to focus on specific genes of interest. Routine clinical use of targeted NGS mandates inexpensive instruments, fast turnaround time and an integrated and robust workflow. Here we demonstrate a version of the Sequencing by Synthesis (SBS) chemistry that potentially can become a preferred targeted sequencing method in the clinical space. This sequencing chemistry uses natural nucleotides and is based on real-time recording of the differential polymerase/DNA-binding kinetics in the presence of correct or mismatch nucleotides. This ensemble SBS chemistry has been implemented on an existing Illumina sequencing platform with integrated cluster amplification. We discuss the advantages of this sequencing chemistry for targeted sequencing as well as its limitations for other applications. Next-generation sequencing technologies vary in performance, which is often measured by metrics such as sequencing speed, accuracy and read length. Here, the authors present a new sequencing by synthesis method that monitors polymerase binding to DNA, and suggest that this method has the potential to generate longer and faster reads.