Revolution of DNA Sequencing Method from the Past until Today

Authors
M. A. Daneshpour 1
M. S. Fallah 2
P. Eshraghi 3
1 Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shaheed Beheshti University of Medical Sciences, Tehran, Iran
2 1- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shaheed Beheshti University of Medical Sciences, Tehran, Iran 2- Kawsar Human Genetics Research Center, Tehran, Iran
3 Max plung Institute, Ulm uniMax Plung Institute, Ulm University, Ulm, Germany
Abstract
DNA sequence determination is a tremendous human achievement. DNA sequencing includes several methods and technologies in use for determining the order of the nucleotide bases (adenine, guanine, cytosine, and thymine) in a molecule of DNA. Knowledge of DNA sequences has become indispensable for basic biological research, other research branches utilizing DNA sequencing, and in numerous applied fields such as diagnostic, biotechnology, forensic biology and biological systematics. The advent of DNA sequencing has significantly accelerated biological research and discovery. Rapid sequencing, the result of modern DNA sequencing technology, is instrumental in the sequencing of the human genome for the Human Genome Project. Related projects, often by scientific collaboration across continents, have generated complete DNA sequences of humans as well as numerous animals, plants and microbial genomes. DNA sequencing methods currently under development include labeling DNA polymerase and reading the sequence as a DNA strand transits through nanopores. Additional methods include microscopy-based techniques such as atomic force microscopy or transmission electron microscopy that are used to identify the positions of individual nucleotides within long DNA fragments (>5000 bp) by nucleotide labeling with heavier elements (e.g., halogens) for visual detection and recording. Third generation technologies aim to increase throughput and decrease the time to result and cost by eliminating the need for excessive reagents and harnessing the processivity of DNA polymerase. Researchers in the field of genetics in Iran use this technology in their studies, but unfortunately our literature lack proper Persian language resources. The authors intend to write a series of review articles in this field. The present paper is an introduction to the summary of important techniques in DNA sequencing.

Keywords

[1]     Olsvik O, Wahlberg J, Petterson B, Uhlén M, Popovic T, Wachsmuth IK, Fields PI. Use of automated sequencing of polymerase chain reaction-generated amplicons to identify three types of cholera toxin subunit B in Vibrio cholerae O1 strains. J Clin Microbiol 1993; 31(1): 22-5.
[2]     Fiers W, Contreras R, Duerinck F, Haegeman G, Iserentant D, Merregaert J, Min Jou W, Molemans F, Raeymaekers A, Van den Berghe A, Volckaert G, Ysebaert M. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene. Nature 1976; 260(5551): 500-7.
[3]     Min Jou W, Haegeman G, Ysebaert M, Fiers W. Nucleotide sequence of the gene coding for the bacteriophage MS2 coat protein. Nature 1972; 237(5350): 82-8.
[4]     Pettersson E, Lundeberg J, Ahmadian A. Generations of sequencing technologies. Genomics 2009; 93(2): 105-11.
[5]     Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A 1977; 74(2): 560-4.
[6]     Gilbert W, Maxam A. The nucleotide sequence of the lac operator. Proc Natl Acad Sci U S A 1973; 70(12): 3581-4.
[7]     Sanger F, Coulson AR. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 1975; 94(3): 441-8.
[8]     Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 1977; 74(12): 5463-7.
[9]     Murphy KM, Berg KD, Eshleman JR. Sequencing of genomic DNA by combined amplification and cycle sequencing reaction. Clin Chem 2005; 51(1): 35-9.
[10]  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, Goodwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, 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 open microfabricated high density picoliter reactors. Nature 2005; 437(7057): 376-80.
[11]  Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005; 309(5741): 1728-32.
[12]  Braslavsky I, Hebert B, Kartalov E, Quake SR. Sequence information can be obtained from single DNA molecules. Proc Natl Acad Sci U S A 2003; 100(7): 3960-4.
[13]  Church GM. Genomes for all. Sci Am 2006; 294(1): 46-54.
[14]  Hall N. Advanced sequencing technologies and their wider impact in microbiology. J Exp Biol 2007; 210(Pt 9): 1518-25.
[15]  Schuster SC. Next-generation sequencing transforms today's biology. Nat Methods 2008; 5(1): 16-8.
[16]  Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008; 9: 387-402.
[17]  Blow N. Metagenomics: exploring unseen communities. Nature 2008; 453(7195): 687-90.
[18]  Daneshpour MS, Faam B, Mansournia MA, Hedayati M, Halalkhor S, Mesbah-Namin SA, Shojaei S, Zarkesh M, Azizi F. Haplotype analysis of Apo AI-CIII-AIV gene cluster and lipids level: Tehran Lipid and Glucose Study. Endocrine 2012; 41(1): 103-10.
[19]  Daneshpour MS, Alfadhli S, Houshmand M, Zeinali S, Hedayati M, Zarkesh M, Momenan AA, Azizi F. Allele frequency distribution data for D8S1132, D8S1779, D8S514, and D8S1743 in four ethnic groups in relation to metabolic syndrome: Tehran Lipid and Glucose Study. Biochem Genet 2009; 47(9-10): 680-7.
[20]  Daneshpour MS, Hosseinzadeh N, Zarkesh M, Azizi F. Haplotype frequency distribution for 7 microsatellites in chromosome 8 and 11 in relation to the metabolic syndrome in four ethnic groups: Tehran Lipid and Glucose Study. Gene 2012; 495(1): 62-4.
[21]  Daneshpour MS, Rebai A, Houshmand M, Alfadhli S, Zeinali S, Hedayati M, Zarkesh M, Azizi F. 8q24.3 and 11q25 chromosomal loci association with low HDL-C in metabolic syndrome. Eur J Clin Invest 2011; 41(10): 1105-12.
[22]  Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 2008; 18(7): 1051-63.
[23]  Hanna GJ, Johnson VA, Kuritzkes DR, Richman DD, Martinez-Picado J, Sutton L, Hazelwood JD, D'Aquila RT. Comparison of sequencing by hybridization and cycle sequencing for genotyping of human immunodeficiency virus type 1 reverse transcriptase. J Clin Microbiol 2000; 38(7): 2715-21.
Pathobiology Reserach
Volume 16, Issue 4
February 2014
Pages 1-13