Bu derlemede genel olarak dizileme teknolojilerinden ve yeni nesil dizileme teknolojisinin kullanıldığı omik alanlardan bahsedilmektedir.
📌 3 Key Takeaways
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Objective & Hypothesis:DNA, RNA ve metilasyon dizilemesi için kullanılan yeni nesil dizileme teknolojileri bir çok bilim dalı üzerinde büyük etkiler oluşturarak bilimsel çalışmalara yeni bakış açıları kazandırmıştır.
📊
Key Findings & Data:Yeni nesil dizileme büyük ölçekli dizileme kapasitesi ile Sanger dizilemesine kıyasla çok daha düşük maliyetlere sahiptir.
💡
Conclusion & Impact:Bu derlemede genel olarak dizileme teknolojilerinden ve yeni nesil dizileme teknolojisinin kullanıldığı omik alanlardan bahsedilmektedir.
🔬Design:Survey & Empirical Study
📍Scope:Comprehensive Sample
⚙️Variables:Yeni Nesil Dizileme · Yüksek Çıktılı Dizileme · Omik
Özet
DNA, RNA ve metilasyon dizilemesi için kullanılan yeni nesil dizileme teknolojileri bir çok bilim dalı üzerinde büyük etkiler oluşturarak bilimsel çalışmalara yeni bakış açıları kazandırmıştır. Yeni nesil dizileme büyük ölçekli dizileme kapasitesi ile Sanger dizilemesine kıyasla çok daha düşük maliyetlere sahiptir. Yeni nesil dizilemenin maliyet ve hız avantajları daha önceden neredeyse imkansız olarak düşünülen çalışmaların yapılabilir hale gelmesine olanak sağlamıştır. Bu gelişmeler yapısal ve işlevsel genomik anlayışımızı, temel genomikten entegre sistomiğe kadar değişen bir çok omik kavramı ile genişletmiştir. Bu derlemede genel olarak dizileme teknolojilerinden ve yeni nesil dizileme teknolojisinin kullanıldığı omik alanlardan bahsedilmektedir.
Darcan, C., Türkyılmaz, O. (2018). Yeni Nesil Dizileme Teknolojisine Genel Bakış. Bilecik Şeyh Edebali Üniversitesi Fen Bilimleri Dergisi, Cilt: 5 Sayı: 1, 41–49. https://ajindex.com/articles/1264716
Heather, J.M., Chain, B. “The sequence of sequencers: The history of sequencing DNA”, Genomics, vol. 107, pp. 1–8, 2016
Fiers, W., Contreras, R., Duerinck, F., Haegeman, G., Iserentant, D., et al., “Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene”, Nature, vol. 260, pp. 500–507, 1976
Maxam, A.M., Gilbert, W., “A new method for sequencing DNA”, Proc Natl Acad Sci USA, vol. 74, pp. 560 – 564, 1977
Sanger, F., Nicklen, S., Coulson, A.R., “DNA sequencing with chain-terminating inhibitors”, Proc Natl Acad Sci, vol. 74, pp. 5463−5467, 1977
Mardis, E.R., “The impact of next-generation sequencing technology on genetics”, Trends in Genetics, vol. 24, pp. 133-141, 2008
Metzker, M., “Sequencing technologies — the next generation”, Nature Rev. Genet, vol. 11, pp. 31–46,2010
Holley, R.W., “Structure of a ribonucleic acid”, Science, vol. 147, pp. 1462–1465, 1965
Chidgeavadze, Z., Beabealashvilli, R.S., “2′, 3′-Dideoxy-3'aminonucleoside 5′-triphosphates are the terminators of DNA synthesis catalyzed by DNA polymerases”, Nucleic Acids Res, vol. 12, pp. 1671–1686, 1984
Artuso, R., Fallerini, C., Dosa, L., Scionti, F., Clementi, M., et al, “Advances in Alport syndrome diagnosis using next-generation sequencing”, Eur. J. Hum. Genet, vol. 20, pp. 50-57, 2012
Anderson,S., “Shotgun DNA sequencing using cloned DNase I-generated fragments”, Nucleic Acids Res, 1981;9:3015–3027
Venter, J. C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., et al, “The sequence of the human genome”, Science, vol. 291, pp. 1304–1351, 2001
Nyrén, P.l., Lundin, A., “Enzymatic method for continuous monitoring of inorganic pyrophosphate synthesis”, Anal. Biochem, vol. 509, pp. 504–509, 1985
Margulies, M., Egholm, M., Altman, W., Attiya, S., “Genome sequencing in microfabricated high-density picolitre reactors”, Nature, vol. 437, pp. 376–380, 2005
Voelkerding, K.V., Dames, S.A., Durtschi, J.D., “Next-generation sequencing: from basic research to diagnostics”, Clin. Chem, vol. 55, pp. 641–658, 2009
Heather, J.M., Chain, B., “The sequence of sequencers: The history of sequencing DNA”, Genomics, vol. 107, pp. 1-8, 2016
Greenleaf, W.J., Sidow, A., “The future of sequencing:convergence of intelligent design and market Darwinism”, Genome Biol., vol. 15, pp. 303, 2014
Schadt, E.E., Turner, S., Kasarskis, A., “A window into third-generation sequencing”, Hum. Mol. Genet., vol. 19, pp. 227–240, 2010
Bowers, J., “Virtual terminator nucleotides for next-generation DNA sequencing” Nat. Methods., vol. 6, pp. 593–595, 2009
Pareek, C.S., Smoczynski, R., “Tretyn A. Sequencing technologies and genome sequencing”, J. Appl. Genet., vol. 52, pp. 413–435, 2011
Kasianowicz, J.J., Brandin, E., Branton, D., Deamer, D.W., “Characterization of individual polynucleotide molecules using a membrane channel”, Proc. Natl. Acad. Sci. U.S.A., vol. 93:pp. 13770–13773,1996
Grada, A., Weinbrecht K., “Next-generation sequencing: methodology and application”, J. Invest. Dermatol., vol. 133, pp. e11, 2013
Pop, M., “Genome assembly reborn: recent computational challenges”, Brief. Bioinform., vol. 10, pp. 354-366, 2009
Ng, S.B., Turner, E.H., Robertson, P.D., Flygare, S.D., Bigham, A.W., et al. “Targeted capture and massively parallel sequencing of 12 human exomes”, Nature, vol. 461, pp. 272–276, 2009
Chilamakuri, C.S.R., Lorenz, S., Madoui, M.A., Vodak, D., Sun, J.C., et al., “Performance comparison of four exome capture systems for deep sequencing”, BMC Genomics, vol. 15, pp. 449, 2014
Rabbani, B., Tekin, M., Mahdieh, N., “The promise of whole-exome sequencing in medical genetics” J Hum Genet., vol. 59, pp. 5–15, 2014
Mamanova, L., Coffey, A.J., Scott, C.E., Kozarewa, I., Turner, E.H., et al., “Target-enrichment strategies for next-generation sequencing”, Nat Methods, vol. 7, pp. 111–118, 2010
Stoddard, J.L., Niemela, J.E., Fleisher T.A., Rosenzweig S.D., “Targeted NGS: A cost-effective approach to molecular diagnosis of PIDs”, Front. Immunol., vol. 5, pp.531, 2014
Ozsolak, F., Milos, P.M., “RNA sequencing: Advances, challenges and opportunities” Nat Rev Genet., vol. 12, pp. 87–98, 2011
Gilbert, J.A., Dupont, C.L., Microbial metagenomics: Beyond the genome” Annu Rev Mar Sci., vol. 3, pp. 347–371, 2011
Weinstock, G.M., “Genomic approaches to studying the human microbiota”, Nature., vol. 489, pp. 250–256, 2012
Wylie, K.M., Weinstock, G.M., Storch, G.A., “Virome genomics:A tool for defining the human virome” Curr Opin Microbiol., vol. 16, pp. 479–484, 2013
Ursell, L.K., Metcalf, J.L., Parfrey, L.W., Knight, R.,”Defining the human microbiome”, Nutr Rev., vol. 70, pp. 38–44, 2012 [37] Peter, A.J., Stephen, B.B., “The Epigenomics of Cancer”, Cell., vol. 128, pp. 683-692, 2007
Hirst, M., “Epigenomics: Sequencing the methylome”, Methods Mol Biol., vol. 973, pp. 39– 54, 2013
Esteller, M., “Cancer epigenomics: DNA methylomes and histone-modification maps”, Nat Rev Genet., vol. 8, pp. 286-298, 2007
Wion, D., Casadesus, J., “N6-methyl-adenine: an epigenetic signal for DNA-protein interactions” Nature Rev. Microbiol., vol. 4, pp. 183–192, 2006
Merlo, A., Herman, J.G., Mao,L., Lee, D.J., Gabrielson, E., et al., “5' CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/CDKN2/MTS1 in human cancers” Nature Med., vol. 1, pp. 686–692, 1995
Vijayakumar, N.T., Judy, M.V., “Autism spectrum disorders: Integration of the genome, transcriptome and the environment”, J Neurol Sci. vol. 364, pp. 167-176, 2016
Heather, J.M., Chain, B. “The sequence of sequencers: The history of sequencing DNA”, Genomics, vol. 107, pp. 1–8, 2016
Fiers, W., Contreras, R., Duerinck, F., Haegeman, G., Iserentant, D., et al., “Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene”, Nature, vol. 260, pp. 500–507, 1976
Maxam, A.M., Gilbert, W., “A new method for sequencing DNA”, Proc Natl Acad Sci USA, vol. 74, pp. 560 – 564, 1977
Sanger, F., Nicklen, S., Coulson, A.R., “DNA sequencing with chain-terminating inhibitors”, Proc Natl Acad Sci, vol. 74, pp. 5463−5467, 1977
Mardis, E.R., “The impact of next-generation sequencing technology on genetics”, Trends in Genetics, vol. 24, pp. 133-141, 2008
Metzker, M., “Sequencing technologies — the next generation”, Nature Rev. Genet, vol. 11, pp. 31–46,2010
Holley, R.W., “Structure of a ribonucleic acid”, Science, vol. 147, pp. 1462–1465, 1965
Chidgeavadze, Z., Beabealashvilli, R.S., “2′, 3′-Dideoxy-3'aminonucleoside 5′-triphosphates are the terminators of DNA synthesis catalyzed by DNA polymerases”, Nucleic Acids Res, vol. 12, pp. 1671–1686, 1984
Artuso, R., Fallerini, C., Dosa, L., Scionti, F., Clementi, M., et al, “Advances in Alport syndrome diagnosis using next-generation sequencing”, Eur. J. Hum. Genet, vol. 20, pp. 50-57, 2012
Anderson,S., “Shotgun DNA sequencing using cloned DNase I-generated fragments”, Nucleic Acids Res, 1981;9:3015–3027
Venter, J. C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., et al, “The sequence of the human genome”, Science, vol. 291, pp. 1304–1351, 2001
Nyrén, P.l., Lundin, A., “Enzymatic method for continuous monitoring of inorganic pyrophosphate synthesis”, Anal. Biochem, vol. 509, pp. 504–509, 1985
Margulies, M., Egholm, M., Altman, W., Attiya, S., “Genome sequencing in microfabricated high-density picolitre reactors”, Nature, vol. 437, pp. 376–380, 2005
Voelkerding, K.V., Dames, S.A., Durtschi, J.D., “Next-generation sequencing: from basic research to diagnostics”, Clin. Chem, vol. 55, pp. 641–658, 2009
Heather, J.M., Chain, B., “The sequence of sequencers: The history of sequencing DNA”, Genomics, vol. 107, pp. 1-8, 2016
Greenleaf, W.J., Sidow, A., “The future of sequencing:convergence of intelligent design and market Darwinism”, Genome Biol., vol. 15, pp. 303, 2014
Schadt, E.E., Turner, S., Kasarskis, A., “A window into third-generation sequencing”, Hum. Mol. Genet., vol. 19, pp. 227–240, 2010
Bowers, J., “Virtual terminator nucleotides for next-generation DNA sequencing” Nat. Methods., vol. 6, pp. 593–595, 2009
Pareek, C.S., Smoczynski, R., “Tretyn A. Sequencing technologies and genome sequencing”, J. Appl. Genet., vol. 52, pp. 413–435, 2011
Kasianowicz, J.J., Brandin, E., Branton, D., Deamer, D.W., “Characterization of individual polynucleotide molecules using a membrane channel”, Proc. Natl. Acad. Sci. U.S.A., vol. 93:pp. 13770–13773,1996
Grada, A., Weinbrecht K., “Next-generation sequencing: methodology and application”, J. Invest. Dermatol., vol. 133, pp. e11, 2013
Pop, M., “Genome assembly reborn: recent computational challenges”, Brief. Bioinform., vol. 10, pp. 354-366, 2009
Ng, S.B., Turner, E.H., Robertson, P.D., Flygare, S.D., Bigham, A.W., et al. “Targeted capture and massively parallel sequencing of 12 human exomes”, Nature, vol. 461, pp. 272–276, 2009
Chilamakuri, C.S.R., Lorenz, S., Madoui, M.A., Vodak, D., Sun, J.C., et al., “Performance comparison of four exome capture systems for deep sequencing”, BMC Genomics, vol. 15, pp. 449, 2014
Rabbani, B., Tekin, M., Mahdieh, N., “The promise of whole-exome sequencing in medical genetics” J Hum Genet., vol. 59, pp. 5–15, 2014
Mamanova, L., Coffey, A.J., Scott, C.E., Kozarewa, I., Turner, E.H., et al., “Target-enrichment strategies for next-generation sequencing”, Nat Methods, vol. 7, pp. 111–118, 2010
Stoddard, J.L., Niemela, J.E., Fleisher T.A., Rosenzweig S.D., “Targeted NGS: A cost-effective approach to molecular diagnosis of PIDs”, Front. Immunol., vol. 5, pp.531, 2014
Ozsolak, F., Milos, P.M., “RNA sequencing: Advances, challenges and opportunities” Nat Rev Genet., vol. 12, pp. 87–98, 2011
Gilbert, J.A., Dupont, C.L., Microbial metagenomics: Beyond the genome” Annu Rev Mar Sci., vol. 3, pp. 347–371, 2011
Weinstock, G.M., “Genomic approaches to studying the human microbiota”, Nature., vol. 489, pp. 250–256, 2012
Wylie, K.M., Weinstock, G.M., Storch, G.A., “Virome genomics:A tool for defining the human virome” Curr Opin Microbiol., vol. 16, pp. 479–484, 2013
Ursell, L.K., Metcalf, J.L., Parfrey, L.W., Knight, R.,”Defining the human microbiome”, Nutr Rev., vol. 70, pp. 38–44, 2012 [37] Peter, A.J., Stephen, B.B., “The Epigenomics of Cancer”, Cell., vol. 128, pp. 683-692, 2007
Hirst, M., “Epigenomics: Sequencing the methylome”, Methods Mol Biol., vol. 973, pp. 39– 54, 2013
Esteller, M., “Cancer epigenomics: DNA methylomes and histone-modification maps”, Nat Rev Genet., vol. 8, pp. 286-298, 2007
Wion, D., Casadesus, J., “N6-methyl-adenine: an epigenetic signal for DNA-protein interactions” Nature Rev. Microbiol., vol. 4, pp. 183–192, 2006
Merlo, A., Herman, J.G., Mao,L., Lee, D.J., Gabrielson, E., et al., “5' CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/CDKN2/MTS1 in human cancers” Nature Med., vol. 1, pp. 686–692, 1995
Vijayakumar, N.T., Judy, M.V., “Autism spectrum disorders: Integration of the genome, transcriptome and the environment”, J Neurol Sci. vol. 364, pp. 167-176, 2016.