Derleme
Yıl 2018,
Cilt: 5 Sayı: 1, 41 - 49, 28.06.2018
Öz
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.
Anahtar Kelimeler
Kaynakça
- [1] Heather, J.M., Chain, B. “The sequence of sequencers: The history of sequencing DNA”, Genomics, vol. 107, pp. 1–8, 2016. [2] 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. [3] Maxam, A.M., Gilbert, W., “A new method for sequencing DNA”, Proc Natl Acad Sci USA, vol. 74, pp. 560 – 564, 1977. [4] Sanger, F., Nicklen, S., Coulson, A.R., “DNA sequencing with chain-terminating inhibitors”, Proc Natl Acad Sci, vol. 74, pp. 5463−5467, 1977. [5] Mardis, E.R., “The impact of next-generation sequencing technology on genetics”, Trends in Genetics, vol. 24, pp. 133-141, 2008. [6] Metzker, M., “Sequencing technologies — the next generation”, Nature Rev. Genet, vol. 11, pp. 31–46 ,2010. [7] Holley, R.W., “Structure of a ribonucleic acid”, Science, vol. 147, pp. 1462–1465, 1965. [8] 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. [9] 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. [10] Anderson,S., “Shotgun DNA sequencing using cloned DNase I-generated fragments”, Nucleic Acids Res, 1981;9:3015–3027. [11] 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. [12] Nyrén, P.l., Lundin, A., “Enzymatic method for continuous monitoring of inorganic pyrophosphate synthesis”, Anal. Biochem, vol. 509, pp. 504–509, 1985. [13] Margulies, M., Egholm, M., Altman, W., Attiya, S., “Genome sequencing in microfabricated high-density picolitre reactors”, Nature, vol. 437, pp. 376–380, 2005. [14] 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. [15] Heather, J.M., Chain, B., “The sequence of sequencers: The history of sequencing DNA”, Genomics, vol. 107, pp. 1-8, 2016.. [16] Schuster, S.C., “Next-generation sequencing transforms today's biology”, Nat. Methods, vol. 5, pp. 16-18, 2008. [17] Glenn, T.C., “Field guide to next-generation DNA sequencers”, Mol. Ecol. Resour, vol. 11, pp. 759–769, 2011. [18] Rothberg, J.M., “An integrated semiconductor device enabling non-optical genome sequencing”, Nature, vol. 475, pp. 348–352, 2011. [19] Loman, N.J., “Performance comparison of benchtop high-throughput sequencing platforms”, Nat. Biotechnol., vol. 30:pp. 434–439, 2012. [20] Greenleaf, W.J., Sidow, A., “The future of sequencing:convergence of intelligent design and market Darwinism”, Genome Biol., vol. 15, pp. 303, 2014. [21] Schadt, E.E., Turner, S., Kasarskis, A., “A window into third-generation sequencing”, Hum. Mol. Genet., vol. 19, pp. 227–240, 2010. [22] Bowers, J., “Virtual terminator nucleotides for next-generation DNA sequencing” Nat. Methods., vol. 6, pp. 593–595, 2009. [23] Pareek, C.S., Smoczynski, R., “Tretyn A. Sequencing technologies and genome sequencing”, J. Appl. Genet., vol. 52, pp. 413–435, 2011. [24] 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. [25] Grada, A., Weinbrecht K., “Next-generation sequencing: methodology and application”, J. Invest. Dermatol., vol. 133, pp. e11, 2013. [26] Pop, M., “Genome assembly reborn: recent computational challenges”, Brief. Bioinform., vol. 10, pp. 354-366, 2009. [27] 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. [28] 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. [29] Rabbani, B., Tekin, M., Mahdieh, N., “The promise of whole-exome sequencing in medical genetics” J Hum Genet., vol. 59, pp. 5–15, 2014. [30] 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. [31] 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. [32] Ozsolak, F., Milos, P.M., “RNA sequencing: Advances, challenges and opportunities” Nat Rev Genet., vol. 12, pp. 87–98, 2011. [33] Gilbert, J.A., Dupont, C.L., Microbial metagenomics: Beyond the genome” Annu Rev Mar Sci., vol. 3, pp. 347–371, 2011. [34] Weinstock, G.M., “Genomic approaches to studying the human microbiota”, Nature., vol. 489, pp. 250–256, 2012. [35] 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. [36] 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. [38] Hirst, M., “Epigenomics: Sequencing the methylome”, Methods Mol Biol., vol. 973, pp. 39– 54, 2013. [39] Esteller, M., “Cancer epigenomics: DNA methylomes and histone-modification maps”, Nat Rev Genet., vol. 8, pp. 286-298, 2007. [40] Wion, D., Casadesus, J., “N6-methyl-adenine: an epigenetic signal for DNA-protein interactions” Nature Rev. Microbiol., vol. 4, pp. 183–192, 2006. [41] 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. [42] 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.
Yıl 2018,
Cilt: 5 Sayı: 1, 41 - 49, 28.06.2018
Öz
Kaynakça
- [1] Heather, J.M., Chain, B. “The sequence of sequencers: The history of sequencing DNA”, Genomics, vol. 107, pp. 1–8, 2016. [2] 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. [3] Maxam, A.M., Gilbert, W., “A new method for sequencing DNA”, Proc Natl Acad Sci USA, vol. 74, pp. 560 – 564, 1977. [4] Sanger, F., Nicklen, S., Coulson, A.R., “DNA sequencing with chain-terminating inhibitors”, Proc Natl Acad Sci, vol. 74, pp. 5463−5467, 1977. [5] Mardis, E.R., “The impact of next-generation sequencing technology on genetics”, Trends in Genetics, vol. 24, pp. 133-141, 2008. [6] Metzker, M., “Sequencing technologies — the next generation”, Nature Rev. Genet, vol. 11, pp. 31–46 ,2010. [7] Holley, R.W., “Structure of a ribonucleic acid”, Science, vol. 147, pp. 1462–1465, 1965. [8] 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. [9] 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. [10] Anderson,S., “Shotgun DNA sequencing using cloned DNase I-generated fragments”, Nucleic Acids Res, 1981;9:3015–3027. [11] 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. [12] Nyrén, P.l., Lundin, A., “Enzymatic method for continuous monitoring of inorganic pyrophosphate synthesis”, Anal. Biochem, vol. 509, pp. 504–509, 1985. [13] Margulies, M., Egholm, M., Altman, W., Attiya, S., “Genome sequencing in microfabricated high-density picolitre reactors”, Nature, vol. 437, pp. 376–380, 2005. [14] 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. [15] Heather, J.M., Chain, B., “The sequence of sequencers: The history of sequencing DNA”, Genomics, vol. 107, pp. 1-8, 2016.. [16] Schuster, S.C., “Next-generation sequencing transforms today's biology”, Nat. Methods, vol. 5, pp. 16-18, 2008. [17] Glenn, T.C., “Field guide to next-generation DNA sequencers”, Mol. Ecol. Resour, vol. 11, pp. 759–769, 2011. [18] Rothberg, J.M., “An integrated semiconductor device enabling non-optical genome sequencing”, Nature, vol. 475, pp. 348–352, 2011. [19] Loman, N.J., “Performance comparison of benchtop high-throughput sequencing platforms”, Nat. Biotechnol., vol. 30:pp. 434–439, 2012. [20] Greenleaf, W.J., Sidow, A., “The future of sequencing:convergence of intelligent design and market Darwinism”, Genome Biol., vol. 15, pp. 303, 2014. [21] Schadt, E.E., Turner, S., Kasarskis, A., “A window into third-generation sequencing”, Hum. Mol. Genet., vol. 19, pp. 227–240, 2010. [22] Bowers, J., “Virtual terminator nucleotides for next-generation DNA sequencing” Nat. Methods., vol. 6, pp. 593–595, 2009. [23] Pareek, C.S., Smoczynski, R., “Tretyn A. Sequencing technologies and genome sequencing”, J. Appl. Genet., vol. 52, pp. 413–435, 2011. [24] 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. [25] Grada, A., Weinbrecht K., “Next-generation sequencing: methodology and application”, J. Invest. Dermatol., vol. 133, pp. e11, 2013. [26] Pop, M., “Genome assembly reborn: recent computational challenges”, Brief. Bioinform., vol. 10, pp. 354-366, 2009. [27] 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. [28] 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. [29] Rabbani, B., Tekin, M., Mahdieh, N., “The promise of whole-exome sequencing in medical genetics” J Hum Genet., vol. 59, pp. 5–15, 2014. [30] 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. [31] 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. [32] Ozsolak, F., Milos, P.M., “RNA sequencing: Advances, challenges and opportunities” Nat Rev Genet., vol. 12, pp. 87–98, 2011. [33] Gilbert, J.A., Dupont, C.L., Microbial metagenomics: Beyond the genome” Annu Rev Mar Sci., vol. 3, pp. 347–371, 2011. [34] Weinstock, G.M., “Genomic approaches to studying the human microbiota”, Nature., vol. 489, pp. 250–256, 2012. [35] 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. [36] 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. [38] Hirst, M., “Epigenomics: Sequencing the methylome”, Methods Mol Biol., vol. 973, pp. 39– 54, 2013. [39] Esteller, M., “Cancer epigenomics: DNA methylomes and histone-modification maps”, Nat Rev Genet., vol. 8, pp. 286-298, 2007. [40] Wion, D., Casadesus, J., “N6-methyl-adenine: an epigenetic signal for DNA-protein interactions” Nature Rev. Microbiol., vol. 4, pp. 183–192, 2006. [41] 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. [42] 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.
Toplam 1 adet kaynakça vardır.
Ayrıntılar
| Konular | Mühendislik |
|---|---|
| Bölüm | Makaleler |
| Yazarlar | |
| Yayımlanma Tarihi | 28 Haziran 2018 |
| Gönderilme Tarihi | 2 Aralık 2017 |
| Kabul Tarihi | 27 Aralık 2017 |
| Yayımlandığı Sayı | Yıl 2018 Cilt: 5 Sayı: 1 |