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Journal articles on the topic 'Sequencing method'

Author: Grafiati

Published: 4 June 2021

Last updated: 9 February 2022

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1

Ronaghi, M. "DNA SEQUENCING:A Sequencing Method Based on Real-Time Pyrophosphate." Science 281, no. 5375 (1998): 363–65. http://dx.doi.org/10.1126/science.281.5375.363.

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2

CRAXTON, M. "Linear amplification sequencing, a powerful method for sequencing DNA." Methods 3, no. 1 (1991): 20–26. http://dx.doi.org/10.1016/s1046-2023(05)80159-8.

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3

Huang, Zheng, Qibin Li, Wei Jin, Qijun Liao, and Xiao Sun. "A Novel Method for Detecting Contaminated Sample Based on Illumina Sequencing Data." International Journal of Bioscience, Biochemistry and Bioinformatics 4, no. 2 (2014): 116–20. http://dx.doi.org/10.7763/ijbbb.2014.v4.322.

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4

Nestorova, Gergana G., and Eric J. Guilbeau. "Thermoelectric method for sequencing DNA." Lab on a Chip 11, no. 10 (2011): 1761. http://dx.doi.org/10.1039/c0lc00733a.

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5

Gharizadeh, Baback, Mehran Ghaderi, Declan Donnelly, Bahram Amini, Keng-Ling Wallin, and Pål Nyrén. "Multiple-primer DNA sequencing method." ELECTROPHORESIS 24, no. 78 (2003): 1145–51. http://dx.doi.org/10.1002/elps.200390147.

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6

Esfandyarpour, Hesaam, R. Fabian W. Pease, and Ronald W. Davis. "Picocalorimetric method for DNA sequencing." Journal of Vacuum Science & Technology B: Microelectronics and Nanometer Structures 26, no. 2 (2008): 661. http://dx.doi.org/10.1116/1.2897322.

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7

Sasaki, N., M. Izawa, M. Watahiki, et al. "Transcriptional sequencing: A method for DNA sequencing using RNA polymerase." Proceedings of the National Academy of Sciences 95, no. 7 (1998): 3455–60. http://dx.doi.org/10.1073/pnas.95.7.3455.

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8

Obata, Hiroko, Tatsuya Tanaka, Tsuneko Fujii, Chikako Sasho, Yukihiro Yamaguchi, and Keiichiro Suzuki. "Dye Terminator Re-cycle-sequencing Method: Phage Plaque Direct Sequencing." Analytical Biochemistry 297, no. 1 (2001): 102–5. http://dx.doi.org/10.1006/abio.2001.5328.

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9

KRASNENKO, A. Y., I. F. STETSENKO, A. S. RAKITKO, A. V. CHUROV, and V. V. ILINSKII. "ULTRALOW COVERAGE SEQUENCING IS THE MOST ACCURATE LIBRARY QUANTIFICATION METHOD PRIOR TO EXOME SEQUENCING." Periódico Tchê Química 16, no. 32 (2019): 1010–16. http://dx.doi.org/10.52571/ptq.v16.n32.2019.1027_periodico32_pgs_1010_1016.pdf.

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Accurate DNA library quantification is very important in post-pooling captured exome sequencing. Underrepresented libraries will need additional sequencing, which takes extra time and money, whereas overexpressed DNA libraries can lead to the generation of more data than required, which leads to the waste of sequence capacity and a reduced number of samples per batch. There is a number of methods available to quantify DNA libraries prior to sequencings, such as UV absorption, use of intercalating dyes, capillary electrophoresis, 5’-hydrolysis probes (TaqMan©) coupled with quantitative PCR (qPCR) or droplet digital PCR. But there is no gold standard for the quantification of DNA libraries. This study compares common library quantification methods, including LabChip (PerkinElmer Inc., MA, USA), Qubit 3.0 (Thermo Fisher Scientific, MA, USA), several qPCR approaches, and ultralow coverage sequencing on Illumina MiSeq platform (with and without insert size correction). DNA libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, MA, USA). To compare the above-mentioned approaches, cost, time, and quantification accuracy were assessed in our study. Quantification methods involving the use of Qubit and MiSeq were found to be better than qPCR and LabChip approaches at predicting the final library concentration. It was also revealed that MiSeq with insert size correction was the most accurate method for library quantification prior to exome sequencing. This method allows for correction shifts in the ratio due to enrichment. Ultralow coverage sequencing on the Illumina MiSeq platform is the most accurate method of library quantification prior to pooling and post-pooling exome enrichment.

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10

Kubát, Z. "Chromosome walking with BAC clones as a method of genome mapping." Plant, Soil and Environment 53, No. 10 (2008): 447–50. http://dx.doi.org/10.17221/2198-pse.

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Current sequencing projects are often based on random sequencing of genomic libraries followed by contig assembly by means of bioinformatics tools. This approach is convenient for whole genome sequencing projects. Chromosome walking described here is suitable for mapping and sequencing of short genomic regions in species where whole genome sequencing is not possible or for cloning gene from its closest known marker. This method is based on searching for overlapping BAC clones specific for the genomic region of interest.

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11

CHEN, ELLSON Y., and PETER H. SEEBURG. "Supercoil Sequencing: A Fast and Simple Method for Sequencing Plasmid DNA." DNA 4, no. 2 (1985): 165–70. http://dx.doi.org/10.1089/dna.1985.4.165.

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12

ISHII, Kazuo, and Masahira HATTORI. "Technical Course “Method of DNA Sequencing”." Japanese Journal of Thrombosis and Hemostasis 9, no. 3 (1998): 190–95. http://dx.doi.org/10.2491/jjsth.9.190.

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13

Williams, WT, JS Bunt, and HJ Clay. "Yet another method of species-sequencing." Marine Ecology Progress Series 72 (1991): 283–87. http://dx.doi.org/10.3354/meps072283.

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14

Tang, J. Y., A. M. Roskey, and S. Agrawal. "Method for Sequencing Synthetic Oligodeoxynucleotide Phosphorothioates." Analytical Biochemistry 212, no. 1 (1993): 134–37. http://dx.doi.org/10.1006/abio.1993.1302.

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15

Zoler, Mitchel L. "CalTech Develops New DNA Sequencing Method." Nature Biotechnology 3, no. 5 (1985): 395–99. http://dx.doi.org/10.1038/nbt0585-395.

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16

Hyman, Edward David. "A new method of sequencing DNA." Analytical Biochemistry 174, no. 2 (1988): 423–36. http://dx.doi.org/10.1016/0003-2697(88)90041-3.

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17

Chen, Sixing, and Xihong Lin. "Analysis in case–control sequencing association studies with different sequencing depths." Biostatistics 21, no. 3 (2018): 577–93. http://dx.doi.org/10.1093/biostatistics/kxy073.

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Summary With the advent of next-generation sequencing, investigators have access to higher quality sequencing data. However, to sequence all samples in a study using next generation sequencing can still be prohibitively expensive. One potential remedy could be to combine next generation sequencing data from cases with publicly available sequencing data for controls, but there could be a systematic difference in quality of sequenced data, such as sequencing depths, between sequenced study cases and publicly available controls. We propose a regression calibration (RC)-based method and a maximum-likelihood method for conducting an association study with such a combined sample by accounting for differential sequencing errors between cases and controls. The methods allow for adjusting for covariates, such as population stratification as confounders. Both methods control type I error and have comparable power to analysis conducted using the true genotype with sufficiently high but different sequencing depths. We show that the RC method allows for analysis using naive variance estimate (closely approximates true variance in practice) and standard software under certain circumstances. We evaluate the performance of the proposed methods using simulation studies and apply our methods to a combined data set of exome sequenced acute lung injury cases and healthy controls from the 1000 Genomes project.

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18

Ohara, Reiko, Ayako Tanaka, and Osamu Ohara. "Automated Fluorescent DNA Sequencing by a Simplified Solid-Phase Chemical Sequencing Method." BioTechniques 22, no. 4 (1997): 653–56. http://dx.doi.org/10.2144/97224bm18.

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19

Aksenenko, Maria B., and T. G. Ruksha. "Sequencing methods in dermatology." Russian Journal of Skin and Venereal Diseases 19, no. 1 (2016): 7–12. http://dx.doi.org/10.18821/1560-9588-2016-19-1-7-12.

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Review of the literature devoted to the application of sequencing methods (genome research method) at various dermatological diseases. DNA sequencing technology is described in the article. Sanger Sequencing Method and Next-Generation Sequencing are discussed. Examples of genes and mutations found by sequencing methods are presented. Clinical meaning of mutations in BRAF, NRAS, KIT, GNAQ, GNA11 genes that play an important role in the pathogenesis of different clinical pathological forms of melanoma is described. Reveling tumor subtypes provides a selective approach in treatment of cutaneous melanoma, that can be useful in different therapeutic methods and makes it possible to predict the development of chemoresistance. Furthermore, data about another genes, that play an important role in pathogenesis of different dermatological diseases with tumor and non-tumor genesis are presented.

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20

França, Lilian T. C., Emanuel Carrilho, and Tarso B. L. Kist. "A review of DNA sequencing techniques." Quarterly Reviews of Biophysics 35, no. 2 (2002): 169–200. http://dx.doi.org/10.1017/s0033583502003797.

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1. Summary 1692. Introduction 1703. Sanger's method and other enzymic methods 1703.1 Random approach 1713.2 Direct approach 1713.3 Enzyme technology 1753.4 Sample preparation 1753.5 Labels and DNA labelling 1763.5.1 Radioisotopes 1763.5.2 Chemiluminescent detection 1763.5.3 Fluorescent dyes 1773.6 Fragment separation and analysis 1803.6.1 Electrophoresis 1803.6.2 Mass spectrometry – an alternative 1824. Maxam & Gilbert and other chemical methods 1835. Pyrosequencing – DNA sequencing in real time by the detection of released PPi 1876. Single molecule sequencing with exonuclease 1907. Conclusion 1928. Acknowledgements 1929. References 193The four best known DNA sequencing techniques are reviewed. Important practical issues covered are read-length, speed, accuracy, throughput, cost, as well as the automation of sample handling and preparation. The methods reviewed are: (i) the Sanger method and its most important variants (enzymic methods); (ii) the Maxam & Gilbert method and other chemical methods; (iii) the PyrosequencingTM method – DNA sequencing in real time by the detection of released pyrophosphate (PPi); and (iv) single molecule sequencing with exonuclease (exonuclease digestion of a single molecule composed of a single strand of fluorescently labelled deoxynucleotides). Each method is briefly described, the current literature is covered, advantages, disadvantages, and the most suitable applications of each method are discussed.

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21

Debuire, B., A. Chabli, and N. Frenoy. "Fast, manual, nonradioactive method for DNA sequencing." Clinical Chemistry 39, no. 8 (1993): 1682–85. http://dx.doi.org/10.1093/clinchem/39.8.1682.

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Abstract We describe a protocol that allows nonradioactive detection of sequencing products after manual, direct, solid-phase sequencing of polymerase chain reaction-amplified DNA. The amplified DNA fragment to be studied is biotinylated at the 5' end of one of the two oligonucleotide primers used for amplification, allowing coupling to streptavidin-coated magnetic beads. The immobilized double-stranded DNA is then separated into single strands by alkaline treatment. A 5'-biotinylated sequencing primer is used after saturating with a biotin solution any possible remaining affinity sites on the streptavidin-coated magnetic beads. Sequencing is performed by using T7 DNA polymerase, and the sequencing products are electrophoresed in denaturing polyacrylamide sequencing gel. After transfer of the products to a nylon membrane, the sequencing pattern is revealed by chemiluminescence. Biotinylated alkaline phosphatase is bound to the 5' end of the sequencing primer via a streptavidin bridge and catalyzes the reaction by cleaving a phosphate group from a chemiluminescent substrate. The emitted photons are detected by exposing the membrane to x-ray film. This method is simple, rapid, and consistently successful and reproducible.

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22

Rani, Bibha. "RNA Sequencing (RNA-Seq): Method and Applications." International Journal of Pure & Applied Bioscience 6, no. 1 (2018): 167–73. http://dx.doi.org/10.18782/2320-7051.5046.

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23

IMAMURA, TAKUYA. "DNA methylation analysis with bisulfite sequencing method." Newsletter of Japan Society for Comparative Endocrinology, no. 113 (2004): 25–29. http://dx.doi.org/10.5983/nl2001jsce.2004.113_25.

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24

Kim, Suhyeon, Hyun Ju Yoo, and Jong Hoon Hahn. "Postelectrophoresis Capillary Scanning Method for DNA Sequencing." Analytical Chemistry 68, no. 5 (1996): 936–39. http://dx.doi.org/10.1021/ac9508107.

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25

YASUDA, Shuhay, Naohiro NAKAYAMA, Hiroyuki JEKUYA, and Eiichi SOEDAT. "An improved method for shotgun DNA sequencing." Agricultural and Biological Chemistry 49, no. 5 (1985): 1525–26. http://dx.doi.org/10.1271/bbb1961.49.1525.

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26

Yasuda, Shuhay, Naohiro Nakayama, Hiroyuki Jikuya, and Eiichi Soeda. "An Improved Method for Shotgun DNA Sequencing." Agricultural and Biological Chemistry 49, no. 5 (1985): 1525–26. http://dx.doi.org/10.1080/00021369.1985.10866935.

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27

Ma, Z., R. W. Lee, B. Li, et al. "Isothermal amplification method for next-generation sequencing." Proceedings of the National Academy of Sciences 110, no. 35 (2013): 14320–23. http://dx.doi.org/10.1073/pnas.1311334110.

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28

Margolis, Russell L., Shi-Hua Li, and Christopher A. Ross. "A rapid method for sequencing trinucleotide repeats." Nucleic Acids Research 21, no. 21 (1993): 4983–84. http://dx.doi.org/10.1093/nar/21.21.4983.

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29

Hattori, Masahira, and Yoshiyuki Sakaki. "Dideoxy sequencing method using denatured plasmid templates." Analytical Biochemistry 152, no. 2 (1986): 232–38. http://dx.doi.org/10.1016/0003-2697(86)90403-3.

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30

Raza, Shahid, and Ayesha Ameen. "Nano pore Sequencing Technology: A Review." International Journal of Advances in Scientific Research 3, no. 8 (2017): 90. http://dx.doi.org/10.7439/ijasr.v3i8.4333.

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DNA strand nucleotide order is determined by using Nano pore sequencing method can this method is under development since 1995. Many porous membranes proteins and used as Nano pores, Each nucleotide base is pass through this small hole of almost 1 nanometer and the peak is recorded in the form of chromatograph. This method is considered more accurate than gel electrophoresis because the chances of sample damage are low and more authentications of sequences were previously reported. Now a days manual methods are replaced by automated methods for less time consumption and more accurate results.

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31

Bamanga, R. A., J. N. Ja’afar, and A. I. Gali. "Progress in DNA sequencing." Bayero Journal of Pure and Applied Sciences 11, no. 1 (2018): 110–19. http://dx.doi.org/10.4314/bajopas.v11i1.20.

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The first human genome sequence took about a decade to complete and cost more than two billion dollars. This shows the major limitations of time and cost, and the development of recent technologies for DNA sequencing ultimately aimed at reducing these two factors. The major milestone of the HGP was the sequencing of the first billionth base out of the three billion base pair human genome. However, depending on the platform used in sequencing, the cost has drastically plummeted to about five thousand dollars and this is the work of a single day. The ultimate target of the HGP is to reach a one thousand dollar price mark to sequencing an entire human genome with the highest throughput, and this is slowly but steadily approaching, thanks to the refinements of existing methods, which are reducing the cost per base by the day. This review looks at the advancement of the DNA sequencing methods from the standard Sanger method, through to those applied in today’s research and also focuses on the technologies that have evolved throughout the past three decades with a possible comparison between them and finally a look at some of the limitations of these technologies.Keywords: Human genome project, DNA sequencing, Sanger method

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32

Puritz, Jonathan B., and Katie E. Lotterhos. "Expressed exome capture sequencing: A method for cost-effective exome sequencing for all organisms." Molecular Ecology Resources 18, no. 6 (2018): 1209–22. http://dx.doi.org/10.1111/1755-0998.12905.

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33

Uitdewilligen, Jan G. A. M. L., Anne-Marie A. Wolters, Bjorn B. D’hoop, Theo J. A. Borm, Richard G. F. Visser, and Herman J. van Eck. "A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato." PLoS ONE 8, no. 5 (2013): e62355. http://dx.doi.org/10.1371/journal.pone.0062355.

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34

Zhou, Ying, Erteng Jia, Min Pan, Xiangwei Zhao, and Qinyu Ge. "Encoding Method of Single-cell Spatial Transcriptomics Sequencing." International Journal of Biological Sciences 16, no. 14 (2020): 2663–74. http://dx.doi.org/10.7150/ijbs.43887.

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35

Jones, Douglas H. "An Iterative and Regenerative Method for DNA Sequencing." BioTechniques 22, no. 5 (1997): 938–46. http://dx.doi.org/10.2144/97225rr01.

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36

Grigg, Geoffrey W. "Sequencing 5-methylcytosine residues by the bisulphite method." DNA Sequence 6, no. 4 (1996): 189–98. http://dx.doi.org/10.3109/10425179609008443.

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37

Pan, Wei Jun, Xuan Wang, and Chen Yu Huang. "Aircraft Sequencing Method for Staggered Parallel Runways Approach." Applied Mechanics and Materials 602-605 (August 2014): 1303–6. http://dx.doi.org/10.4028/www.scientific.net/amm.602-605.1303.

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Most research about the approaching aircraft sequencing is for single runway approach or standard parallel runways approach. Little of research is for the case of staggered parallel runways approach. In this paper, a mathematical model of aircraft approach sequencing is established for the case of staggered parallel runways approach, and also this model is optimized with improved genetic algorithm. This model is simulated with the improved genetic algorithm both for cases of non-staggered runway approach and staggered runway approach, and the result shows that, comparing with the situation of non-staggered runway, the delay time in the case of staggered parallel runways approach decreases by 1.6 minutes, and the fitness increases by 0.0394. It proves that, in a certain extent, staggered parallel runways can reduce the minimum interval between arrival flights, thus increase the capacity of parallel runways.

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38

Mann, Robert W. "A Method for Siding and Sequencing Human Ribs." Journal of Forensic Sciences 38, no. 1 (1993): 13388J. http://dx.doi.org/10.1520/jfs13388j.

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39

Kaebernick, H., B. O'Shea, and S. S. Grewal. "A Method for Sequencing the Disassembly of Products." CIRP Annals 49, no. 1 (2000): 13–16. http://dx.doi.org/10.1016/s0007-8506(07)62886-8.

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40

Hopmans, Erik S., Georges Natsoulis, John M. Bell, Susan M. Grimes, Weiva Sieh, and Hanlee P. Ji. "A programmable method for massively parallel targeted sequencing." Nucleic Acids Research 42, no. 10 (2014): e88-e88. http://dx.doi.org/10.1093/nar/gku282.

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41

Qi, Zhan, Jing Tu, Junji Li, Bei Yao, Minghua Xu, and Zuhong Lu. "A Simplified Haplotype Sequencing Method for K562 Cells." Journal of Nanoscience and Nanotechnology 16, no. 7 (2016): 7018–23. http://dx.doi.org/10.1166/jnn.2016.11305.

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42

Perrier, L., D. Heinz, S. Baffert, et al. "Cost Of Genome Analysis: The Sanger Sequencing Method." Value in Health 18, no. 7 (2015): A353. http://dx.doi.org/10.1016/j.jval.2015.09.654.

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43

Fichot, O., and M. Girard. "An improved method for sequencing of RNA templates." Nucleic Acids Research 18, no. 20 (1990): 6162. http://dx.doi.org/10.1093/nar/18.20.6162.

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44

Nordström, Tommy, Baback Gharizadeh, Nader Pourmand, Pål Nyren, and Mostafa Ronaghi. "Method Enabling Fast Partial Sequencing of cDNA Clones." Analytical Biochemistry 292, no. 2 (2001): 266–71. http://dx.doi.org/10.1006/abio.2001.5094.

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45

Olender, Kurt M., and James M. Bieman. "Algebraic specifications and sequencing: A defect detection method." Software Testing, Verification and Reliability 5, no. 1 (1995): 49–70. http://dx.doi.org/10.1002/stvr.4370050104.

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46

Syed, Fraz, Haiying Grunenwald, and Nicholas Caruccio. "Optimized library preparation method for next-generation sequencing." Nature Methods 6, no. 10 (2009): i—ii. http://dx.doi.org/10.1038/nmeth.f.269.

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47

Endo, T. A. "Probabilistic nucleotide assembling method for sequencing by hybridization." Bioinformatics 20, no. 14 (2004): 2181–88. http://dx.doi.org/10.1093/bioinformatics/bth202.

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48

Tilanus, Marcel G. J. "Sequencing as a method for high resolution typing." Human Immunology 36, no. 1 (1993): 57. http://dx.doi.org/10.1016/0198-8859(93)90064-8.

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49

Chuvpilo, S. A., and V. V. Kravchenko. "A simple and rapid method for sequencing DNA." FEBS Letters 179, no. 1 (1985): 34–36. http://dx.doi.org/10.1016/0014-5793(85)80185-x.

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50

Paul, Bonnie, Cheri Cloninger, Marilyn Felton, Ronik Khachatoorian, and Stan Metzenberg. "A nonalkaline method for isolating sequencing-ready plasmids." Analytical Biochemistry 377, no. 2 (2008): 218–22. http://dx.doi.org/10.1016/j.ab.2008.03.005.

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