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Journal articles on the topic 'Direct sequencing'

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Author: Grafiati

Published: 4 June 2021

Last updated: 11 March 2023

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1

Ozsolak, Fatih, Adam R. Platt, Dan R. Jones, Jeffrey G. Reifenberger, Lauryn E. Sass, Peter McInerney, John F. Thompson, Jayson Bowers, Mirna Jarosz, and Patrice M. Milos. "Direct RNA sequencing." Nature 461, no. 7265 (September 23, 2009): 814–18. http://dx.doi.org/10.1038/nature08390.

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2

Linder, Jodell E., Tatyana E. Plachco, Romina Libster, and E. Kathryn Miller. "Sequencing human rhinoviruses: Direct sequencing versus plasmid cloning." Journal of Virological Methods 211 (January 2015): 64–69. http://dx.doi.org/10.1016/j.jviromet.2014.09.020.

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3

Chalapati, Sachin, Conor A. Crosbie, Dixita Limbachiya, and Nimesh Pinnamaneni. "Direct oligonucleotide sequencing with nanopores." Open Research Europe 1 (August 24, 2021): 47. http://dx.doi.org/10.12688/openreseurope.13578.2.

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Third-generation DNA sequencing has enabled sequencing of long, unamplified DNA fragments with minimal steps. Direct sequencing of ssDNA or RNA gives valuable insights like base-level modifications, phosphoramidite synthesis yield estimates and strand quality analysis, without the need to add the complimentary strand. Direct sequencing of single-stranded nucleic acid species is challenging as they are non-compatible to the double-stranded sequencing adapters used by manufacturers. The MinION platform from Oxford Nanopore Technologies performs sequencing by passing single-strands of DNA through a layer of biological nanopore sensors; although sequencing is performed on single-strands, the recommended template by the manufacturer is double-stranded. We have identified that the MinION platform can perform sequencing of short, single-strand oligonucleotides directly without amplification or second-strand synthesis by performing a single annealing step before library preparation. Short 5’ phosphorylated oligos when annealed to an adapter sequence can be directly sequenced in the 5' to 3' direction via nanopores. Adapter sequences were designed to bind to the 5’ end of the oligos and to leave a 3’ adenosine overhang after binding to their target. The 3’ adenosine overhang of the adapter and the terminal phosphate makes the 5’ end of the oligo analogous to an end-prepared dsDNA, rendering it compatible with ligation-based library preparation for sequencing. An oligo-pool containing 42,000, 120 nt orthogonal sequences was phosphorylated and sequenced using this method and ~90% of these sequences were recovered with high accuracy using BLAST. In the nanopore raw data, we have identified that empty signals can be wrongly identified as a valid read by the MinION platform and sometimes multiple signals containing several strands can be fused into a single raw sequence file due to segmentation faults in the software. This direct oligonucleotide sequencing method enables novel applications in DNA data storage systems where short oligonucleotides are the primary information carriers.

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4

Chalapati, Sachin, Conor A. Crosbie, Dixita Limbachiya, and Nimesh Pinnamaneni. "Direct oligonucleotide sequencing with nanopores." Open Research Europe 1 (May 12, 2021): 47. http://dx.doi.org/10.12688/openreseurope.13578.1.

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Abstract:

Third-generation DNA sequencing has enabled sequencing of long, unamplified DNA fragments with minimal steps. Direct sequencing of ssDNA or RNA gives valuable insights like base-level modifications, phosphoramidite synthesis yield estimates and strand quality analysis, without the need to add the complimentary strand. Direct sequencing of single-stranded nucleic acid species is challenging as they are non-compatible to the double-stranded sequencing adapters used by manufacturers. The MinION platform from Oxford Nanopore Technologies performs sequencing by passing single-strands of DNA through a layer of biological nanopore sensors; although sequencing is performed on single-strands, the recommended template by the manufacturer is double-stranded. We have identified that the MinION platform can perform sequencing of short, single-strand oligonucleotides directly without amplification or second-strand synthesis by performing a single annealing step before library preparation. Short 5’ phosphorylated oligos when annealed to an adapter sequence can be directly sequenced in the 5' to 3' direction via nanopores. Adapter sequences were designed to bind to the 5’ end of the oligos and to leave a 3’ adenosine overhang after binding to their target. The 3’ adenosine overhang of the adapter and the terminal phosphate makes the 5’ end of the oligo analogous to an end-prepared dsDNA, rendering it compatible with ligation-based library preparation for sequencing. An oligo-pool containing 42,000, 120 nt orthogonal sequences was phosphorylated and sequenced using this method and ~90% of these sequences were recovered with high accuracy using BLAST. In the nanopore raw data, we have identified that empty signals can be wrongly identified as a valid read by the MinION platform and sometimes multiple signals containing several strands can be fused into a single raw sequence file due to segmentation faults in the software. This direct oligonucleotide sequencing method enables novel applications in DNA data storage systems where short oligonucleotides are the primary information carriers.

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5

Rudi, Heidi, Knut‐Erik Gylder, Odd Arne Rognli, and Knut Rudi. "Direct Haplotype‐Specific DNA Sequencing." Preparative Biochemistry and Biotechnology 36, no. 3 (September 2006): 253–57. http://dx.doi.org/10.1080/10826060600716687.

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6

Zhang, Jinyue, Shuanghong Yan, Le Chang, Weiming Guo, Yuqin Wang, Yu Wang, Panke Zhang, Hong-Yuan Chen, and Shuo Huang. "Direct microRNA Sequencing Using Nanopore-Induced Phase-Shift Sequencing." iScience 23, no. 3 (March 2020): 100916. http://dx.doi.org/10.1016/j.isci.2020.100916.

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7

Kilger, Christian, Matthias Krings, Hendrik Poinar, and Svante Pääbo. "“Colony Sequencing”: Direct Sequencing of Plasmid DNA from Bacterial Colonies." BioTechniques 22, no. 3 (March 1997): 412–18. http://dx.doi.org/10.2144/97223bm08.

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8

Petry, H., K. Pekrun, K. Wäse, I. Schedel, W. Lüke, and G. Hunsmann. "Direct sequencing versus cloned amplicon sequencing in HIV-1 diagnosis." Experientia 52, no. 4 (April 1996): 303–4. http://dx.doi.org/10.1007/bf01919520.

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9

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 (October 2001): 102–5. http://dx.doi.org/10.1006/abio.2001.5328.

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10

Zhang, Jinyue. "Direct MicroRNA Sequencing using Nanopore Induced Phase-Shift Sequencing (NIPSS)." Biophysical Journal 118, no. 3 (February 2020): 475a—476a. http://dx.doi.org/10.1016/j.bpj.2019.11.2638.

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11

Jakaria, J., F. Saputra, K. A. Paramitasari, P. P. Agung, and M. Maskur. "IDENTIFICATION OF UTERIN MILK PROTEIN (UTMT) GENE IN BALI CATTLE USING DIRECT SEQUENCING." Journal of the Indonesian Tropical Animal Agriculture 41, no. 1 (March 1, 2016): 1–6. http://dx.doi.org/10.14710/jitaa.41.1.1-6.

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The objective of this research was to identify diversity of exon 5 UTMP gene fragment in Bali cattle using direct sequencing. The total 60 blood samples of Bali Cattle derived from BPTU Bali in Bali siland (20 heads), BPTU Serading in Sumbawa island (20 heads) and Village Breeding Center in Barru District South Sulawesi (20 heads) were used to evaluate their genetic diversity at exon 5 UTMP gene. The forward and reverse data sequences were analyzed using Bioedit program and alignment analysis was carried out using MEGA5 program. Meanwhile haplotype analysis was performed by DnaSPv5 program. The result showed that partial sequences in exon 5 UTMP gene had 16 haplotypes with the highest number of haplotypes ware found in VBC Barru district South Sulawesi (8 haplotypes). Moreover, the highest average of haplotype (h) and nucleotide (p) diversity were found in VBC Barru district South Sulawesi were 0.7949 and 0.0016, respectively. In addition, minisatellite insersion was found in exon 5 UTMP gene fragment on Bali cattle which are consist of 5'-CCA GTC ATG AAG AAG GCA GAG GTC GTC GTG CCG GCG AAA-3'. According to our results, haplotype and minisatellite variation in exon 5 UTMP gene fragment can be used as a candidate genetic marker specific for reproductive trait in the Bali cattle and for its strategy breeding program in the future.

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12

Mazars, Georges-Raoul, Caroline Moyret, Philippe Jeanteur, and Charles-Guy Theillet. "Direct sequencing by thermal asymmetric PCR." Nucleic Acids Research 19, no. 17 (1991): 4783. http://dx.doi.org/10.1093/nar/19.17.4783.

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13

Bashir, Rashid. "Direct DNA Sequencing Using Nanopore Sensors." Genetic Engineering & Biotechnology News 33, no. 7 (April 2013): 34–35. http://dx.doi.org/10.1089/gen.33.7.15.

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14

Green, Peter M., and Francesco Giannelli. "Direct sequencing of PCR-amplified DNA." Molecular Biotechnology 1, no. 2 (April 1994): 117–24. http://dx.doi.org/10.1007/bf02921552.

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15

Porter, K. W., J. D. Briley, and B. R. Shaw. "Direct PCR Sequencing with Boronated Nucleotides." Nucleic Acids Research 25, no. 8 (April 1, 1997): 1611–17. http://dx.doi.org/10.1093/nar/25.8.1611.

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16

Zimmerman, Lisa J., and James C. Fuscoe. "Direct DNA sequencing of PCR products." Environmental and Molecular Mutagenesis 18, no. 4 (1991): 274–76. http://dx.doi.org/10.1002/em.2850180413.

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17

Petersen, I., H. Ohgaki, B. Ludeke, and P. Kleihues. "Direct DNA Sequencing Following SSCP Analysis." Analytical Biochemistry 218, no. 2 (May 1994): 478–79. http://dx.doi.org/10.1006/abio.1994.1216.

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18

Kim, Jung Heon, Jiyeon Kim, Bon-Sang Koo, Hanseul Oh, Jung-Joo Hong, and Eung-Soo Hwang. "Rapid Whole-genome Sequencing of Zika Viruses using Direct RNA Sequencing." Journal of Bacteriology and Virology 49, no. 3 (2019): 115. http://dx.doi.org/10.4167/jbv.2019.49.3.115.

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19

Fan, Jianguo, and Rajinder S. Ranu. "Direct Cycle Sequencing with ΔTaqr`DNA Polymerase." DNA Sequence 7, no. 5 (January 1997): 285–88. http://dx.doi.org/10.3109/10425179709034047.

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20

Ibrahim, Ashraf, and Anders Sjöstedt. "Direct Sequencing of PCR-Amplified 23S rDNA." BioTechniques 23, no. 2 (August 1997): 216–20. http://dx.doi.org/10.2144/97232bm07.

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21

Kant, J. A. "Direct DNA sequencing in the clinical laboratory." Clinical Chemistry 41, no. 10 (October 1, 1995): 1407–9. http://dx.doi.org/10.1093/clinchem/41.10.1407.

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22

Kocher, T. D. "PCR, direct sequencing, and the comparative approach." Genome Research 1, no. 4 (May 1, 1992): 217–21. http://dx.doi.org/10.1101/gr.1.4.217.

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23

Nilsen, Timothy W. "Direct Chemical Sequencing of End-Labeled RNA." Cold Spring Harbor Protocols 2015, no. 1 (January 2015): pdb.prot080937. http://dx.doi.org/10.1101/pdb.prot080937.

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24

Hwang, David M., Ruo-Xiang Wang, and Choong-Chin Liew. "Direct Automated Sequencing of Single λ-Phage Plaques by Exponential Amplification Sequencing." Analytical Biochemistry 231, no. 2 (November 1995): 460–63. http://dx.doi.org/10.1006/abio.1995.0082.

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25

Sarkar, Gobinda, and Mark E. Bolander. "Direct sequencing of unpurified PCR-amplified DNA by semi-exponential cycle sequencing (SECS)." Molecular Biotechnology 8, no. 3 (December 1997): 269–77. http://dx.doi.org/10.1007/bf02760780.

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26

Salih, Gaza F., and Hersh Abdul Hamakarim. "IDENTIFICATION OF β-GLOBIN MUTATIONS WHICH PRODUCED β-THALASSEMIA BY ARMS-PCR ASSAY AND DIRECT SEQUENCING." Journal of Sulaimani Medical College 6, no. 2 (December 1, 2016): 123–32. http://dx.doi.org/10.17656/jsmc.10096.

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27

Hong, Ari, Dongwan Kim, V. Narry Kim, and Hyeshik Chang. "Analyzing viral epitranscriptomes using nanopore direct RNA sequencing." Journal of Microbiology 60, no. 9 (August 24, 2022): 867–76. http://dx.doi.org/10.1007/s12275-022-2324-4.

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28

ÖNELGE, Nükhet. "Direct Nucleotide Sequencing of Citrus Exocortis Viroid (CEV)." Turkish Journal of Agriculture and Forestry 21, no. 4 (January 1, 1997): 419–22. http://dx.doi.org/10.55730/1300-011x.2824.

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29

Hickman, Suzanne E., Nathan D. Kingery, Toshiro K. Ohsumi, Mark L. Borowsky, Li-chong Wang, Terry K. Means, and Joseph El Khoury. "The microglial sensome revealed by direct RNA sequencing." Nature Neuroscience 16, no. 12 (October 27, 2013): 1896–905. http://dx.doi.org/10.1038/nn.3554.

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30

Porubský, David, Ashley D. Sanders, Niek van Wietmarschen, Ester Falconer, Mark Hills, Diana C. J. Spierings, Marianna R. Bevova, Victor Guryev, and Peter M. Lansdorp. "Direct chromosome-length haplotyping by single-cell sequencing." Genome Research 26, no. 11 (September 19, 2016): 1565–74. http://dx.doi.org/10.1101/gr.209841.116.

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31

Kelley, J. "High throughput direct end sequencing of BAC clones." Nucleic Acids Research 27, no. 6 (March 15, 1999): 1539–46. http://dx.doi.org/10.1093/nar/27.6.1539.

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32

Rao, V. B. "Strategies for direct sequencing of PCR-amplified DNA." Genome Research 4, no. 1 (August 1, 1994): S15—S23. http://dx.doi.org/10.1101/gr.4.1.s15.

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33

Kretz, Keith A., Geoffrey S. Carson, and John S. O'Brien. "Direct sequencing from low-melt agarose with Sequenase@." Nucleic Acids Research 17, no. 14 (1989): 5864. http://dx.doi.org/10.1093/nar/17.14.5864.

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34

Martin, Trevor, Stephen Hughes, Kenneth Hughes, and Michael Dawson. "Direct sequencing of PCR amplified pig PrP genes." Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease 1270, no. 2-3 (April 1995): 211–14. http://dx.doi.org/10.1016/0925-4439(95)00041-2.

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35

Iannelli, Francesco, Laura Giunti, and Gianni Pozzi. "Direct sequencing of long polymerase chain reaction fragments." Molecular Biotechnology 10, no. 2 (October 1998): 183–85. http://dx.doi.org/10.1007/bf02760864.

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36

Wang, Hwei-gene Heidi, and M. J. Fraser. "Direct double-stranded DNA sequencing with baculovirus genomes." Journal of Virological Methods 31, no. 1 (January 1991): 113–18. http://dx.doi.org/10.1016/0166-0934(91)90149-t.

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37

Yao, F., R. Zhang, Z. Zhu, K. Xia, and C. Liu. "MutScreener: primer design tool for PCR-direct sequencing." Nucleic Acids Research 34, Web Server (July 1, 2006): W660—W664. http://dx.doi.org/10.1093/nar/gkl168.

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38

Clark, Tyson A., Kristi E. Spittle, Stephen W. Turner, and Jonas Korlach. "Direct Detection and Sequencing of Damaged DNA Bases." Genome Integrity 2, no. 1 (2011): 10. http://dx.doi.org/10.1186/2041-9414-2-10.

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39

Engelke, D. R., P. A. Hoener, and F. S. Collins. "Direct sequencing of enzymatically amplified human genomic DNA." Proceedings of the National Academy of Sciences 85, no. 2 (January 1, 1988): 544–48. http://dx.doi.org/10.1073/pnas.85.2.544.

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40

Ozsolak, Fatih, and Patrice M. Milos. "Single-molecule direct RNA sequencing without cDNA synthesis." Wiley Interdisciplinary Reviews: RNA 2, no. 4 (March 14, 2011): 565–70. http://dx.doi.org/10.1002/wrna.84.

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41

Imashimizu, Masahiko, Taku Oshima, Hiroki Takahashi, Lucyna Lubkowska, and Mikhail Kashlev. "Direct Assessment of Transcription Fidelity by RNA Sequencing." Biophysical Journal 106, no. 2 (January 2014): 486a. http://dx.doi.org/10.1016/j.bpj.2013.11.4468.

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42

Yan, Shuanghong, and Shuo Huang. "Direct Sequencing of Xeno-Nucleic Acids using Nanopore." Biophysical Journal 116, no. 3 (February 2019): 316a. http://dx.doi.org/10.1016/j.bpj.2018.11.1711.

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43

Dong, Jianli, Mae R. Gailani, Scott L. Pomeroy, David Reardon, and Allen E. Bale. "Identification ofPATCHED mutations in medulloblastomas by direct sequencing." Human Mutation 16, no. 1 (2000): 89–90. http://dx.doi.org/10.1002/1098-1004(200007)16:1<89::aid-humu18>3.0.co;2-7.

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44

Rao, V. B. "Direct Sequencing of Polymerase Chain Reaction-Amplified DNA." Analytical Biochemistry 216, no. 1 (January 1994): 1–14. http://dx.doi.org/10.1006/abio.1994.1001.

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45

Bouwens, A. G. M., W. Verduijn, H. Rozemuller, L. F. Versluis, M. G. J. Tilanus, and G. M. Th Schreuder. "DR4 high resolution typing by direct genomic sequencing." Human Immunology 36, no. 1 (January 1993): 58. http://dx.doi.org/10.1016/0198-8859(93)90069-d.

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46

Farhangdoust, Fatemeh, Li-Tao Guo, Drew Bostrom, Sara H. Rouhanifard, Anna M. Pyle, and Meni Wanunu. "Towards direct RNA sequencing with electro-optical waveguides." Biophysical Journal 122, no. 3 (February 2023): 435a. http://dx.doi.org/10.1016/j.bpj.2022.11.2352.

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47

Grädel, Carole, Miguel A. Terrazos Miani, Christian Baumann, Maria Teresa Barbani, Stefan Neuenschwander, Stephen L. Leib, Franziska Suter-Riniker, and Alban Ramette. "Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing." Viruses 12, no. 8 (July 31, 2020): 841. http://dx.doi.org/10.3390/v12080841.

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Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, enteroviruses are identified by PCR-based methods, often combined with partial sequencing for genotyping. In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. The approach was complemented by sequencing the corresponding viral cDNA via Illumina MiSeq sequencing. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% and 99.6% of the most similar reference genome sequences. The identification of the enterovirus sequences in the samples was confirmed by short-read cDNA sequencing. Sequence identity between DRS and Illumina MiSeq enterovirus consensus sequences ranged between 94% and 97%. Here, we show that nanopore DRS can be used to correctly identify enterovirus genotypes from patient stool samples with high viral load and that the approach also provides rich metatranscriptomic information on sample composition for all life domains.

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48

Brozynska, Marta, Agnelo Furtado, and Robert James Henry. "Direct Chloroplast Sequencing: Comparison of Sequencing Platforms and Analysis Tools for Whole Chloroplast Barcoding." PLoS ONE 9, no. 10 (October 17, 2014): e110387. http://dx.doi.org/10.1371/journal.pone.0110387.

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49

Marks, Michael, Maria Fookes, Josef Wagner, Rosanna Ghinai, Oliver Sokana, Yaw-Adu Sarkodie, Anthony W. Solomon, David C. W. Mabey, and Nicholas R. Thomson. "Direct Whole-Genome Sequencing of Cutaneous Strains ofHaemophilus ducreyi." Emerging Infectious Diseases 24, no. 4 (April 2018): 786–89. http://dx.doi.org/10.3201/eid2404.171726.

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50

Thomas, Niki K., Vinay C. Poodari, Miten Jain, Hugh E. Olsen, Mark Akeson, and Robin L. Abu-Shumays. "Direct Nanopore Sequencing of Individual Full Length tRNA Strands." ACS Nano 15, no. 10 (October 7, 2021): 16642–53. http://dx.doi.org/10.1021/acsnano.1c06488.

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