A real-time decoding sequencing technology—new possibility for high throughput sequencing

Abstract

The challenges and corresponding solutions for a decoding sequencing to be compatible with high throughput sequencing (HTS) technologies are provided.

Methods to improve the accuracy of next-generation sequencing

“…Ion Torrent is a NGS platform that utilizes semiconductors. Similar to Roche/ 454 system, the pH change detected by the sensor has poor linearity with respect to the number of nucleotides incorporated in a single reaction cycle, thus limiting its accuracy in measuring the homopolymer regions (Pu and Xiao, 2017). SOLiD is a NGS sequencer that is based on SBL, of which a single sequencing cycle is composed of various two-base encoded probes that bind, ligate, image and cleave.…”

“…The read length of dual-base sequencing based on SBS is nearly three times longer than that of single-base addition (Pu and Xiao, 2017). Therefore, dual-base sequencing has high accuracy and can significantly increase the potential read length.…”

Analysis of mutational genotyping using correctable decoding sequencing with superior specificity

“…If this possibility is calculated according to a con- servative sequencing error rate of 1.8% (454 Roche 1%, 11 Illumina 0.26-0.8%, 12,27 Ion Torrent 1.78% 8 ), this sequencing platform can provide seven types of specific signal information (0, 1, 2, 3, 4, 5, ≥6) and the error rate is 1.8% × 1.8% × 1/6 × 1/ 6 = 0.0009%, in which the theoretical background error rate is less than one artifactual error per 10 5 nucleotides (lower than that for Sanger sequencing). [28][29][30] Thus, this proposed approach can be used to assess the correctness of a single sequencing read and it is expected to be the most accurate high-throughput gene sequencing technique.…”

Pyrosequencing with di-base addition for the identification of pathogenic bacteria

“…Therefore, it is necessary to explore an additional method for the identification of pathogenic bacteria. We have proposed a novel sequencing method in which a template is cyclically sequenced twice in two parallel sequencing runs with different combinations of di-base addition (AG/CT, AT/CG, or AC/GT) and two sets of encodings are obtained ( [9]). The two sets of encodings allow for the bases to be sequentially decoded, moving from first to last, in a deterministic manner.…”

“…The two sets of encodings allow for the bases to be sequentially decoded, moving from first to last, in a deterministic manner. This approach is compatible with most of the SBS-based sequencing platforms, such as traditional pyrosequencing, Roach 454, Ion torrent PGM ( [9]). When the novel sequencing technique is combined with traditional pyrosequencing, we call it pyrosequencing with di-base addition (PDBA).…”