eISSN: 2221-6197 DOI: 10.31301/2221-6197

Brief history of high-throughput nucleic acid sequencing methods

Year: 2021

Pages: 27-46

Number: Volume 13, issue 1

Type: scientific article

Summary:

The processes occurring during the enzymatic growth of the DNA chain in the form of elongation of the molecules, the release of pyrophosphate, proton, thermal energy, and an increase in electrical impedance, which are used in various methods of high-throughput DNA sequencing by synthesis, are briefly considered. The detection of DNA chain growth is controlled by high-voltage gel electrophoresis and has limited scalability. As for mentioned above other by-products of DNA chain polymerization, their detection can be easily scalable, which has led to the emergence of methods for whole genome sequencing of new generations of DNA, which have received the widely used abbreviation NGS - Next Generation Sequencing. However, the attribution of any new sequencing method to a particular generation is sometimes difficult due to the fact that the principle used in it was born earlier than the other one was implemented, which turned out to be less productive in the end. In addition, it is more important to distinguish the methods of new DNA sequencing into two groups in which the massive parallel sequencing of identical matrices takes place or the sequencing of single DNA molecules takes place and last one have received the designation monomolecular sequencing. In this review, along with the classical Sanger method of DNA sequencing, which is still the "gold standard", pyrosequencing, semiconductor sequencing, thermosequencing, electronic sequencing, fluorescent bridge sequencing and sequencing using nanoballs from the first group, as well as monomolecular methods – tSMS sequencing, SMRT sequencing and nanopore sequencing are considered. Attention is paid to the costs of DNA sequencing and the prospects for its development.

Keywords:

DNA sequencing, high-throughput sequencing, pyrosequencing, semiconductor sequencing, thermosequencing, electronic sequencing, fluorescent bridge sequencing, nanoball fluorescence sequencing, massive parallel sequencing, monomolecular sequencing, nanopore sequencing, NGS

References:

1. Astbury W.T., Bell F.O. X-Ray study of thymonucleic acid. Nature. 1938. V. 141. P.747–748. doi:10.1038/141747b0

2. Avery O.T., MacLeod C.M., McCarty M. Studies of the chemical nature of the substance inducing transformation of pneumococcal types. Induction of transformation by a desoxyribonucleic acid fraction isolated from Pneumococcus Type III. J. Exp. Med. 1944. V.79(2). P.137–158. DOI: 10.1084/jem.79.2.137

3. Brenner S., Johnson M., Bridgham J., Golda G., Lloyd D.H., Johnson D., Luo S., McCurdy S., Foy M., Ewan M., Roth R., George D., Eletr S., Albrecht G., Vermaas E., Williams S.R., Moon K., Burcham T., Pallas M., DuBridge R.B., Kirchner J., Fearon K., Mao J-i., Corcoran K. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbeads arrays. Nat. Biotechnol. 2000. V.18(6). P.630-634. doi: 10.1038/76469

4. Chargaff E. What really is DNA? Remarks on the changing aspects of a scientific concept // Prog. Nucl. Acid Res. Mol. Biol. 1968. V.8. P.297-333. 10.1016/s0079-6603(08)60549-8

5. Chemeris A.V., Akhunov E.D., Vakhitov V.A. DNA sequencing. Moscow. Nauka. 1999. 429 p.

6. Chen F., Dong M., Ge M., Zhu L., Ren L., Liu G., Mu R. The history and advances of reversible terminators used in new generations of sequencing technology // Genomics, Proteomics, Bioinformatics. 2013. V.11(1). P.34-40. doi: 10.1016/j.gpb.2013.01.003

7. Chin C-S., Peluso P., Sedlazeck F.J., Nattestad M., Concepcion G.T., Clum A., Dunn C., O’Malley R., Figueroa-Balderas R., Morales-Cruz A., Cramer G.R., Delledonne M., Luo C., Ecker J.R., Cantu D., Rank D.R., Schatz M.C. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods. 2016. V.13(12). P.1050-1054. doi: 10.1038/nmeth.4035

8. Deamer D., Akeson M., Branton D. Three decades of nanopore sequencing // Nature Biotechnol. 2016. V.34(5). P.518-524. doi: 10.1038/nbt.3423.

9. Droege M, Hill B. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. J Biotechnol. 2008. V.136(1-2). P.3-10. doi: 10.1016/j.jbiotec.2008.03.021

10. Eid J., Fehr A., Gray J., Luong K., Lyle J., Otto G., Peluso P., Rank D., Baybayan P., Bettman B., Bibillo A., Bjornson K., Chaudhuri B., Christians F., Cicero R., Clark S., Dalal R., Dewinter A., Dixon J., Foquet M., Gaertner A., Hardenbol P., Heiner C., Hester K., Holden D., Kearns G., Kong X., Kuse R., Lacroix Y., Lin S., Lundquist P., Ma C., Marks P., Maxham M., Murphy D., Park I., Pham T., Phillips M., Roy J., Sebra R., Shen G., Sorenson J., Tomaney A., Travers K., Trulson M., Vieceli J., Wegener J., Wu D., Yang A., Zaccarin D., Zhao P., Zhong F., Korlach J., Turner S. Real-time DNA sequencing from single polymerase molecules // Science. 2009. V.323. P.133-138. doi: 10.1126/science.1162986

11. Esfandyarpour H., Davis R.W. An integrated differential nanocalimeter with on-chip microfluidic multiplexing for high throughput genomics and proteomics // 14th International Conference on Miniaturized Systems for Chemistry and Life Sciences, 3 - 7 October 2010, Groningen. P.1349-1351.

12. Esfandyarpour H., Zheng B., Pease R.F., Davis R.W. Structural optimization for heat detection of DNA thermosequencing platform using finite element analysis // Biomicrofluidics. 2008. V.2. P.24102. doi: 10.1063/1.2901138

13. Esfandyarpour H., Parizi K.B., Barmi M.R. <...> Dong B., Witney F.R., Davis R.W. High accuracy DNA sequencing on a small, scalable platform via electrical detection of single base incorporations. bioRxiv preprint. 2020. doi: 10.1101/604553

14. Fang G, Munera D, Friedman DI, Mandlik A, Chao MC, Banerjee O, Feng Z, Losic B, Mahajan MC, Jabado OJ, Deikus G, Clark TA, Luong K, Murray IA, Davis BM, Keren-Paz A, Chess A, Roberts RJ, Korlach J, Turner SW, Kumar V, Waldor MK, Schadt EE. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing // Nat. Biotechnol. 2012. V.30. P.1232-1239. doi: 10.1038/nbt.2432

15. Flusberg B.A., Webster D.R., Lee J.H., Travers K.J., Olivares E.C., Clark T.A., Korlach J., Turner S.W. Direct detection of DNA methylation during singlemolecule, real-time sequencing // Nat. Methods. 2010. V.7. P.461-465. doi: 10.1038/nmeth.1459

16. Fraser C.M., Gocayne J.D., White O., Adams M.D., Clayton R.A., Fleischmann R.D., Bult C.J., Kerlavage A.R., Sutton G., Kelley J.M., Fritchman J.L., Weidman J.F., Small K.V., Sandusky M., Fuhrmann J., Nguyen D., Utterback T.R., Saudek D.M., Phillips C.A., Merrick J.M., Tomb J-F., Dougherty B.A., Bott K.F., Hu P-C., Lucier T.S., Peterson S.N., Smith H.O., Hutchinson C.A., III, Venter J.C. The minimal gene complement of Mycoplasma genitalium // Science. 1995. V.270. P.397-403. DOI: 10.1126/science.270.5235.397

17. Hyman E.D. A new method of sequencing DNA // Anal. Biochem. 1988. V.174. P.423-436. DOI: 10.1016/0003-2697(88)90041-3

18. Jain M., Koren S., Miga K.H., Quick J., Rand A.C., Sasani T.A., Tyson J.R., Beggs A.D., Dilthey A.T., Fiddes I.T., Malla S., Marriott H., Nieto T., O'Grady J., Olsen H.E., Pedersen B.S., Rhie A., Richardson H., Quinlan A.R., Snutch T.P., Tee L., Paten B., Phillippy A.M., Simpson J.T., Loman N.J., Loose M. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat. Biotechnol. 2018. V. 36(4). P.338-345. doi: 10.1038/nbt.4060

19. Ivanov I., Niu L., Chueh A., Tian H., Deng S. Apparatus and methods for continuous diagnostics of macromolecules. Pat. Appl. US 2018/0230531 A1.

20. Kasianovich J.J., Bezrukov S.M. On ―three decades of nanopore sequencing‖ // Nature Biotechnol. 2016. V.34(5). P.481-482. doi: 10.1038/nbt.3570

21. Kim D-R., Kim T-S., Kim E., Min S-J., Shin D., Ahn D-R. Synthesis of 3'-O-fluorescently mono-modified reversible terminators and their uses in sequencingby-synthesis. Bioorg Med Chem Lett. 2014. V.24(1). P.209-213. doi: 10.1016/j.bmcl.2013.11.040

22. Liu X., Milton J., Ruediger S. Labelled nucleotides. Pat. US 7,795,424 B2. (Sep 14, 2010)

23. Mak S.S.T., Gopalakrishnan S., Carøe C., Geng C., Liu S., Sinding M-H.S., Kuderna L.F.K., Zhang W., Fu S., Vieira F.G., Germonpré M., Bocherens H., Fedorov S., Petersen B., Sicheritz-Pontén T., Marques-Bonet T., Zhang G., Jiang H., Gilbert M.T.P. Comparative performance of the BGISEQ500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. Gigascience. 2017. V.6(8). P.1-13. doi: 10.1093/gigascience/gix049

24. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. Genome sequencing in microfabricated high-density picolitre reactors // Nature. 2005. V.437. P.376-380. doi: 10.1038/nature03959

25. Maxam A.M., Gilbert W. A new method for sequencing DNA // Proc. Natl. Acad. Sci. USA. 1977. V.74. P.560-564. doi: 10.1073/pnas.74.2.560

26. Moore G.E. Cramming more components onto integrated circuits // Electronics. 1965. V. 38. P. 114-117.

27. Purushothaman S., Toumazou С., Georgiou J. Towards fast solid state DNA sequencing // Circuits and Systems. 2002. V. 4. P.169-172. DOI: 10.1109/ISCAS.2002.1010416

28. Purushothaman S., Toumazou С., Ou C.P. Protons and single nucleotide polymorphism detection: A simple use for the ion sensitive field effect transistor // Sensors and Actuators. 2006. V.114(2). P.964-968. DOI: 10.1016/j.snb.2005.06.069

29. Pushkarev D., Neff N.F., Quake S.R. Singlemolecule sequencing of an individual human genome. Nat. Biotechnol. 2009. V.27(9). P.847-850. doi: 10.1038/nbt.1561

30. Rebrikov D.V., Korostin D.O., Shubina E.S., Il'inskii V.V. NGS: vysokoproizvoditel'noe sekvenirovanie. M.: Binom. Laboratoriya znanii. 2014. 232 S. [NGS: high-performance sequencing] (In Russian)

31. Ronaghi M, Karamohamed S, Pettersson B, Uhlén M, Nyrén P. Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem. 1996 Nov 1;242(1):84-9. doi: 10.1006/abio.1996.0432.

32. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J. An integrated semiconductor device enabling non-optical genome sequencing // Nature. 2011. V.475. P.348-352. doi: 10.1038/nature10242

33. Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chain-terminating inhibitors // Proc. Natl. Acad. Sci. USA. 1977. V.74. P.5463-5467. doi: 10.1073/pnas.74.12.5463.

34. Shin D., Ahn D-R., Ahn H-C. 3’-O-fluorescently mono-modified nucleotides and uses thereof / Pat. US 8,030,466. Oct., 4, 2011

35. Signer R., Caspersson T., Hammarsten E. Molecular shape of thymonucleic acid. Nature. 1938. V. 141. P.122. doi:10.1038/141122a0

36. Toumazou С., Purushothaman S. Sensing apparatus and method / GB Pat. Appl. № 0105831.2 (09.02.2001).

37. Toumazou C., Shepherd L.M., Reed S.C., Chen G.I., Patel A., Garner D.M., Wang C-J.A., Ou C-P., AminDesai K., Athanasiou P., Bai H., Brizido I.M.Q., Caldwell B., Coomber-Alford D., Georgiou P., Jordan K.S., Joyce J.C., La Mura M., Morley D., Sathyavruthan S., Temelso S., Thomas R.E., Zhang L. Simultaneous DNA amplification and detection using a pH-sensing semiconductor system. Nat. Methods. 2013. V.10(7). P.641-646. doi: 10.1038/nmeth.2520

38. Vasilenko S.K., Demushkin .P., Budovskii E.I., Knorre D.G. Opredelenie nukleotidnoi posledovatel'nosti v oligonukleotidakh // Dokl. AN SSSR. 1965. T.162. S. 694-697 [Determination of the nucleotide sequence in oligonucleotides] (In Russian)

39. Watson J.D., Crick F.H.C. A structure for deoxyribose nucleic acid. Nature. 1953. V. 171(4356). P. 737-738. doi:10.1038/171737a0

40. Wetterstrand K.A. DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP)

41. https://www.genome.gov/about-genomics/factsheets/DNA-Sequencing-Costs-Data [Accessed 02.02.2021].

42. Wheeler D.A., Srinivasan M., Egholm M., Shen Y., Chen L., McGuire A., He W., Chen Y.-J., Makhijani V., Roth G.T., Gomes X., Tartaro K., Niazi F., Turcotte C.L., Irzyk G.P., Lupski J.R., Chinault C., Song X-z., Liu Y., Yuan Y., Nazareth L., Qin X., Muzny D.M., Margulies M., Weinstock G.M., Gibbs R.A., Rothberg J.M. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008. V.452(7189). P.872-876. doi: 10.1038/nature06884

43. Yoshinaga Y., Daum C., He G., O'Malley R. Genome Sequencing. Methods Mol. Biol. 2018. V.1775. P.37-52. doi: 10.1007/978-1-4939-7804-5_4

44. Zubov V.V. Rothberg sequencing (potentials for semiconductor sequencing). Biomics. 2013. V.5(1-2). P. 62-74.

Download pdf
up
eISSN: 2221-6197 DOI: 10.31301/2221-6197