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Genomic and Transcriptomic Sequencing and Analysis Approaches

Year 2018, Volume: 4 Issue: 1, 34 - 42, 20.04.2018
https://doi.org/10.19127/mbsjohs.370490

Abstract


















In
this review, we explained that genomic and transcriptomic sequences and
analysis assays. First of all, we detailed information of genomic and
transcriptomic terms and related analyses. Genomics is aimed to elucidate the
structural and functional properties of the genomes. Transcriptomics are used
to express quantities of transcripts in a physiological state and specific
developmental stage. The methods of genomic and transcriptomic analyses imply
highly productive sequence analysis or microarray hybridization analysis as
well as bioinformatics analyses. The sequencing technologies include set of methods
such as preparing template, sequencing, imaging and data analysis. Firstly, the
nucleotide information peculiar to DNA and RNA is obtained by means of the
chosen technology in accordance with the goal and scope of the study. The
obtained sequences are aligned with respect to a familiar reference sequence,
or are combined as de novo. Subsequently,
it is determined whether the distinct genomic sets are connected with the other
genomic sets by overlapping distinct genomic sets, such as aligned sequence
readings, gene annotation, EST, genetic
polymorphism, and mobile elements. So, the structural variant to which the
obtained sequence data are peculiar is determined. Within the scope of the study,
giving information about sequencing technologies and the methods of analyses of
the obtained sequences is aimed for researchers work on this subject.

References

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  • Kim JB, Porreca GJ, Song L, Greenway SC, Gorham JM, George M, et al. Polony Multiplex Analysis of Gene Expression (PMAGE) in Mouse Hypertrophic Cardiomyopathy. Science 2007;316:1481-85.
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  • Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res 2009;19:294-305.
  • Ronaghi M, Karamohamed S, Pettersson B, Uhle´n M, Nyre´n P. Real-time DNA sequencing using detection of pyrophosphate release. Analytical Biochemistry 1996;242:84-9.
  • Salzberg CT, Steven L. How to map billions of short reads onto genomes. Nature Biotechnology 2009;27:455-57.
  • Shendure J, Ji H. Next-generation DNA sequencing. Nature Biotechnology 2008;26: 1135-45.
  • Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005;309:1728-32.
  • Shinkai K, Sakurai S. Molecular recognition of adenine, cytosine, and uracil in a single-stranded RNA by a natural polysaccharide: Schizophyllan. J Am Chem Soc 2000;122(18):4520-4521.
  • Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, Cerrina F. 1999. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nature Biotechnology 1999;17:974-78.
  • Song L, Wang W. Genomes and evolutionary genomics of animals. Current Zoology 2013;59:87-98.
  • Sugnet CW, Kent WJ, Ares M, Haussler D. Transcriptome and genome conservation of alternative splicing events in humans and mice. Pac Symp Biocomput 2004;66-77.
  • Taylor R, William A. Hierarchical method to align large numbers of biological sequences. Elsevier 1990;183:456-74.
  • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010;26:841-42.
  • Wang L, Weinshilboum RM. Pharmacogenomics: candidate gene identification, functional validation and mechanisms. Hum Mol Genet 2008;17:174-9.
  • Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews and Genetics 2009;10:57-63. Watson JD, Crick FHC. The Structure of DNA. Cold Spring Harbor Symposia on Quantitative Biology 1953;18:123-31.
  • Wold B, Myers RM. Sequence census methods for functional genomics. Nat Methods 2008; 5:19-21.
Year 2018, Volume: 4 Issue: 1, 34 - 42, 20.04.2018
https://doi.org/10.19127/mbsjohs.370490

Abstract

References

  • References
  • Altshuler D, Daly MJ, Lander ES. Genetic Mapping in Human Disease. Science 2008; 322:881-88.
  • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000;25:25-9.
  • Aury JM, Cruaud C, Barbe V, Rogier O, Mangenot S, Samson G, et al. High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies. BMC Genomics 2008;9:603.
  • Bai Y, Sartor M, Cavalcoli J. Current status and future perspectives for sequencing livestock genomes. Journal of Animal Science and Biotechnology 2012;3:1-6.
  • Buchanan-Wollaston V, Page T, Harrison E, Breeze E, Lim PO, Nam HG, et al. Comparative transcriptome analysis reveals significant differences in gene expression and signalling pathways between developmental and dark/starvation-induced senescence in Arabidopsis. Plant J 2005;42:567-85.
  • Chaisson MJ, Brinza D, Pevzner PA. De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Res 2009;19:336-46.
  • Clarke L. The 1000 Genomes Project A History, Results and Tools. 2012.
  • Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005;21:3674-76.
  • Consortium. A global reference for human genetic variation. Nature 2015;526:68-74.
  • Dressman D, Yan H, Traverso G, Kinzler KW, Vogelstein B. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci 2003;100:8817-22.
  • Eid J, Adrian F, Gray J, Luong K, Lyle J, Otto G, et al. Real-Time DNA Sequencing from Single Polymerase Molecules. Science 2009;23:133-38.
  • Fedurco M, Romieu A, Williams S, Lawrence I, Turcatti G. BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res 2006;34:e22.
  • Frazer KA, Murray SS, Schork NJ, Topol EJ. Human genetic variation and its contribution to complex traits. Nat Rev Genet 2009;10:241-51.
  • Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 2016;17: 333-51.
  • Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, et al. Single-molecule DNA sequencing of a viral genome. Science 2008;320:106-9.
  • Kim JB, Porreca GJ, Song L, Greenway SC, Gorham JM, George M, et al. Polony Multiplex Analysis of Gene Expression (PMAGE) in Mouse Hypertrophic Cardiomyopathy. Science 2007;316:1481-85.
  • Leamon JH, Lee WL, Tartaro KR, Lanza JR, Sarkis GJ, deWinter AD, et al. A massively parallel PicoTiterPlate based platform for discrete picoliter-scale polymerase chain reactions. Electrophoresis 2003;24:3769-77.
  • Lee BM, Christopher M. A genomic view of alternative splicing. Nature 2002;30:13-9.
  • Levene MJ, Korlach J, Turner SW, Foquet M, Craighead HG, Webb WW. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 2003;299:682-6.
  • Luscombe NM, Greenbaum D, Gerstein M. 2001. What is Bioinformatics? A Proposed Definition and Overview of the Field. Method Inform Med 2001;40:346-58.
  • Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet 2010;11:31-46.
  • Metzker ML, Raghavachari R, Richards S, Jacutin SE, Civitello A, Burgess K, et al. Termination of DNA synthesis by novel 3'-modified- deoxyribonucleoside 5'-triphosphates. Nucleic Acids Research 1994;22:4259-67.
  • Michael TP, Jackson S. The First 50 Plant Genomes. The Plant Genome 2013;6:10.
  • Myers JL, Weber B, Eugene W. Human Whole-Genome Shotgun Sequencing. Genome Research 1997;7:401-09.
  • Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, et al. Analysis of the mouse transcriptome based on functional annotation of 60, 770 full-length cDNAs. Nature 2002;420:563-73.
  • Orita M, Suzuki Y, Sekiya T, Kenshi H. Rapid and sensitive detection of point mutations and dna polymorphisms using the polymerase chain reaction. Genomics 1989;5:874-79.
  • Özsolak F, Platt AR, Jones DR, Reifenberger JG, Sass LE, McInerney P. et al. Direct RNA sequencing. Nature 2009;461:814-8.
  • Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res 2009;19:294-305.
  • Ronaghi M, Karamohamed S, Pettersson B, Uhle´n M, Nyre´n P. Real-time DNA sequencing using detection of pyrophosphate release. Analytical Biochemistry 1996;242:84-9.
  • Salzberg CT, Steven L. How to map billions of short reads onto genomes. Nature Biotechnology 2009;27:455-57.
  • Shendure J, Ji H. Next-generation DNA sequencing. Nature Biotechnology 2008;26: 1135-45.
  • Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005;309:1728-32.
  • Shinkai K, Sakurai S. Molecular recognition of adenine, cytosine, and uracil in a single-stranded RNA by a natural polysaccharide: Schizophyllan. J Am Chem Soc 2000;122(18):4520-4521.
  • Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, Cerrina F. 1999. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nature Biotechnology 1999;17:974-78.
  • Song L, Wang W. Genomes and evolutionary genomics of animals. Current Zoology 2013;59:87-98.
  • Sugnet CW, Kent WJ, Ares M, Haussler D. Transcriptome and genome conservation of alternative splicing events in humans and mice. Pac Symp Biocomput 2004;66-77.
  • Taylor R, William A. Hierarchical method to align large numbers of biological sequences. Elsevier 1990;183:456-74.
  • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010;26:841-42.
  • Wang L, Weinshilboum RM. Pharmacogenomics: candidate gene identification, functional validation and mechanisms. Hum Mol Genet 2008;17:174-9.
  • Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews and Genetics 2009;10:57-63. Watson JD, Crick FHC. The Structure of DNA. Cold Spring Harbor Symposia on Quantitative Biology 1953;18:123-31.
  • Wold B, Myers RM. Sequence census methods for functional genomics. Nat Methods 2008; 5:19-21.
There are 42 citations in total.

Details

Primary Language English
Subjects Health Care Administration
Journal Section Case reports
Authors

Ümmügülsüm Tanman Zıplar This is me

Demet Cansaran-duman

Mine Türktaş

Publication Date April 20, 2018
Published in Issue Year 2018 Volume: 4 Issue: 1

Cite

Vancouver Tanman Zıplar Ü, Cansaran-duman D, Türktaş M. Genomic and Transcriptomic Sequencing and Analysis Approaches. Mid Blac Sea J Health Sci. 2018;4(1):34-42.

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