Evaluation of the Correctable Decoding Sequencing As a New Powerful Strategy for DNA Sequencing

Overview

Journal Life Sci Alliance

Specialties Biochemistry
Biology
Cell Biology
Molecular Biology

Date 2022 Apr 15

PMID 35422436

Authors

Chu Cheng

Pengfeng Xiao

Affiliations

Soon will be listed here.

Abstract

Next-generation sequencing (NGS) promises to revolutionize precision medicine, but the existing sequencing technologies are limited in accuracy. To overcome this limitation, we propose the correctable decoding sequencing strategy, which is a duplex sequencing protocol with conservative theoretical error rates of 0.0009%. This rate is lower than that for Sanger sequencing. Here, we simulate the sequencing reactions by the self-developed software, and find that this approach has great potential in NGS in terms of sequence decoding, reassembly, error correction, and sequencing accuracy. Besides, this approach can be compatible with most SBS-based sequencing platforms, and also has the ability to compensate for some of the shortcomings of NGS platforms, thereby broadening its application for researchers. Hopefully, it can provide a powerful new protocol that can be used as an alternative to the existing NGS platforms, enabling accurate identification of rare mutations in a variety of applications in biology and medicine.

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References

Pu D, Qi Y, Cui L, Xiao P, Lu Z . A real-time decoding sequencing based on dual mononucleotide addition for cyclic synthesis. Anal Chim Acta. 2014; 852:274-83. DOI: 10.1016/j.aca.2014.09.009. View

Pourmand N, Elahi E, Davis R, Ronaghi M . Multiplex Pyrosequencing. Nucleic Acids Res. 2002; 30(7):e31. PMC: 101855. DOI: 10.1093/nar/30.7.e31. View

Chen Z, Zhou W, Qiao S, Kang L, Duan H, Xie X . Highly accurate fluorogenic DNA sequencing with information theory-based error correction. Nat Biotechnol. 2017; 35(12):1170-1178. DOI: 10.1038/nbt.3982. View

Drmanac R . The advent of personal genome sequencing. Genet Med. 2011; 13(3):188-90. DOI: 10.1097/GIM.0b013e31820f16e6. View

Wang X, Blades N, Ding J, Sultana R, Parmigiani G . Estimation of sequencing error rates in short reads. BMC Bioinformatics. 2012; 13:185. PMC: 3495688. DOI: 10.1186/1471-2105-13-185. View

Ambardar S, Gupta R, Trakroo D, Lal R, Vakhlu J . High Throughput Sequencing: An Overview of Sequencing Chemistry. Indian J Microbiol. 2016; 56(4):394-404. PMC: 5061697. DOI: 10.1007/s12088-016-0606-4. View

Nyren P, Pettersson B, Uhlen M . Solid phase DNA minisequencing by an enzymatic luminometric inorganic pyrophosphate detection assay. Anal Biochem. 1993; 208(1):171-5. DOI: 10.1006/abio.1993.1024. View

van Dijk E, Auger H, Jaszczyszyn Y, Thermes C . Ten years of next-generation sequencing technology. Trends Genet. 2014; 30(9):418-26. DOI: 10.1016/j.tig.2014.07.001. View

Cirulli E, Goldstein D . Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet. 2010; 11(6):415-25. DOI: 10.1038/nrg2779. View

10.

Ahmadian A, Ehn M, Hober S . Pyrosequencing: history, biochemistry and future. Clin Chim Acta. 2005; 363(1-2):83-94. DOI: 10.1016/j.cccn.2005.04.038. View

11.

Forgetta V, Leveque G, Dias J, Grove D, Lyons Jr R, Genik S . Sequencing of the Dutch elm disease fungus genome using the Roche/454 GS-FLX Titanium System in a comparison of multiple genomics core facilities. J Biomol Tech. 2013; 24(1):39-49. PMC: 3526337. DOI: 10.7171/jbt.12-2401-005. View

12.

Sims P, Greenleaf W, Duan H, Xie X . Fluorogenic DNA sequencing in PDMS microreactors. Nat Methods. 2011; 8(7):575-80. PMC: 3414871. DOI: 10.1038/nmeth.1629. View

13.

Zhou G, Kamahori M, Okano K, Chuan G, Harada K, Kambara H . Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extension reactions (BAMPER). Nucleic Acids Res. 2001; 29(19):E93. PMC: 60253. DOI: 10.1093/nar/29.19.e93. View

14.

Metzker M . Sequencing technologies - the next generation. Nat Rev Genet. 2009; 11(1):31-46. DOI: 10.1038/nrg2626. View

15.

Guo J, Xu N, Li Z, Zhang S, Wu J, Kim D . Four-color DNA sequencing with 3'-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides. Proc Natl Acad Sci U S A. 2008; 105(27):9145-50. PMC: 2442126. DOI: 10.1073/pnas.0804023105. View

16.

Chan E . Advances in sequencing technology. Mutat Res. 2005; 573(1-2):13-40. DOI: 10.1016/j.mrfmmm.2005.01.004. View

17.

Chen Z, Duan H, Qiao S, Zhou W, Qiu H, Kang L . Fluorogenic sequencing using halogen-fluorescein-labeled nucleotides. Chembiochem. 2015; 16(8):1153-7. DOI: 10.1002/cbic.201500117. View

18.

Rieber N, Zapatka M, Lasitschka B, Jones D, Northcott P, Hutter B . Coverage bias and sensitivity of variant calling for four whole-genome sequencing technologies. PLoS One. 2013; 8(6):e66621. PMC: 3679043. DOI: 10.1371/journal.pone.0066621. View

19.

Ju J, Kim D, Bi L, Meng Q, Bai X, Li Z . Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc Natl Acad Sci U S A. 2006; 103(52):19635-40. PMC: 1702316. DOI: 10.1073/pnas.0609513103. View

20.

Goodwin S, McPherson J, McCombie W . Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 2016; 17(6):333-51. PMC: 10373632. DOI: 10.1038/nrg.2016.49. View