Volume 21, Issue 3 (2018)                   mjms 2018, 21(3): 153-161 | Back to browse issues page

XML Persian Abstract Print

Download citation:
BibTeX | RIS | EndNote | Medlars | ProCite | Reference Manager | RefWorks
Send citation to:

Daneshpour M, Masjoodi S, Ghafari N, Raesi M, Fallah M. Performance of Illumina Next Generation Sequencing. mjms 2018; 21 (3) :153-161
URL: http://mjms.modares.ac.ir/article-30-12086-en.html
1- “Cellular and Molecular Research Center, Research Institute for Endocrine Sciences“ and “Celluar & Molecular Department, Research for Endocrine Sciences Faculty“ Shahid Beheshti University of Medical Sciences, Tehran, Iran , daneshpour@sbmu.ac.ir
2- “Cellular and Molecular Research Center, Research Institute for Endocrine Sciences“ and “Celluar & Molecular Department, Research for Endocrine Sciences Faculty“ Shahid Beheshti University of Medical Sciences, Tehran, Iran
3- Kawsar Human Genetics Research Center, Tehran, Iran
Abstract:   (10970 Views)
Introduction: Nowadays, new methods have been developed to reduce the cost of disease-related laboratory methods and to achieve the shortest response time, which in a short time, determine a large portion of the genome. These methods are known as the next generation sequencing techniques. One of the most common application of such as these methods is diagnosis of disease. The aim of this study was to investigate the performance of Illumina next generation sequencing.
Conclusion: With the advanced technology of sequencing the whole genome, determining the structural changes of the genes, comprehensive studies of the number of genes, the identification of polymorphism, spot mutations and small mutations, the study of the expression of genes, and other applications are possible. In this method, first, the whole genome is broken into double strand DNA fragments; then, the bumps of fragmentation are converted to the smooth end, and adapters are connected to both ends of the components, and the sample pieces of the gene are connected to the flow cell with the help of hybridization by the same adapters. In the next step, centralized colonies of fragments (clusters) are formed through amplification of samples, using the bridge method, which subsequently, could be read. In a chemical reaction, the growth inhibitors will be taken by the end of 3’ and a new cycle begins. The mentioned step is continued until the sequence of whole cycle of the fragment is detected. The sequences of the whole genome are, then, determined with reference sequences, and ultimately the results are compared with the panel of genes associated with the disease and the changes are determined. Different methods can identify changes in the gene area and, in some cases, with investigating the rare changes, the relationship between these changes and the diagnosis of certain diseases can be known.
Full-Text [PDF 1011 kb]   (3795 Downloads)    
Article Type: Review | Subject: Biochemistry
Received: 2017/06/26 | Accepted: 2018/02/14

1. King RA, Rotter JI, Motulsky AG. The genetic basis of common diseases. Oxfprd: Oxford university press; 2002. [Link]
2. Daneshpour MS, Faam B, Mansournia MA, Hedayati M, Halalkhor S, Mesbah-Namin SA, et al. Haplotype analysis of Apo AI-CIII-AIV gene cluster and lipids level: Tehran Lipid and Glucose Study. Endocrine. 2012;41(1):103-10. [Link] [DOI:10.1007/s12020-011-9526-6]
3. Daneshpour MS, Hosseinzadeh N, Zarkesh M, Azizi F. Haplotype frequency distribution for 7 microsatellites in chromosome 8 and 11 in relation to the metabolic syndrome in four ethnic groups: Tehran Lipid and Glucose Study. Gene. 2012;495(1):62-4. [Link] [DOI:10.1016/j.gene.2011.12.011]
4. Daneshpour MS, Alfadhli S, Houshmand M, Zeinali S, Hedayati M, Zarkesh M, et al. Allele frequency distribution data for D8S1132, D8S1779, D8S514, and D8S1743 in four ethnic groups in relation to metabolic syndrome: Tehran Lipid and Glucose Study. Biochem Genet. 2009;47(9-10):680-7. [Link] [DOI:10.1007/s10528-009-9265-z]
5. Daneshpour MS, Fallah MS, Eshraghi P. Revolution of DNA sequencing method from the past until today. Modares J Med Sci. 2014;16(4):1-13. [Persian] [Link]
6. Daneshpour MS, Rebai A, Houshmand M, Alfadhli S, Zeinali S, Hedayati M, et al. 8q24.3 and 11q25 chromosomal loci association with low HDL-C in metabolic syndrome. Eur J Clin Invest. 2011;41(10):1105-12. [Link] [DOI:10.1111/j.1365-2362.2011.02516.x]
7. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol. 2008;26(10):1135-45. [Link] [DOI:10.1038/nbt1486]
8. Sawicki MP, Samara G, Hurwitz M, Passaro E Jr. Human genome project. Am J Surg. 1993;165(2):258-64. [Link] [DOI:10.1016/S0002-9610(05)80522-7]
9. 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(5741):1728-32. [Link] [DOI:10.1126/science.1117389]
10. Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet. 2008;9:387-402. [Link] [DOI:10.1146/annurev.genom.9.081307.164359]
11. Bioo Scientific. NEXTflex™ Bisulfite-Seq Kit - for illumina sequencing [Internet]. Vienna: Medibena; 2011 [cited 2016 Dec 19]. Available from: http://www.medibena.at/nextflex-bisulfite-seq.html. [Link]
12. Voelkerding KV, Dames S, Durtschi JD. Next generation sequencing for clinical diagnostics-principles and application to targeted resequencing for hypertrophic cardiomyopathy: A paper from the 2009 william beaumont hospital symposium on molecular pathology. J Mol Diagn. 2010;12(5):539-51. [Link] [DOI:10.2353/jmoldx.2010.100043]
13. Quail MA, Swerdlow H, Turner DJ. Improved protocols for the illumina genome analyzer sequencing system. Curr Protoc Hum Genet. 2009; Chapter 18: Unit 18.2. [Link] [DOI:10.1002/0471142905.hg1802s62]
14. Bronner IF, Quail MA, Turner DJ, Swerdlow H. Improved protocols for illumina sequencing. Curr Protoc Hum Genet. 2014;80:18.2.1-42. [Link]
15. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, et al. A tale of three next generation sequencing platforms: Comparison of ion torrent, pacific biosciences and illumina MiSeq sequencers. BMC Genomics. 2012;13:341. [Link] [DOI:10.1186/1471-2164-13-341]
16. Cuddapah S, Barski A, Cui K, Schones DE, Wang Z, Wei G, et al. Native chromatin preparation and Illumina/Solexa library construction. Cold Spring Harb Protoc. 2009;2009(6):pdb.prot5237. [Link]
17. Dames S, Durtschi J, Geiersbach K, Stephens J, Voelkerding KV. Comparison of the illumina genome analyzer and roche 454 GS FLX for resequencing of hypertrophic cardiomyopathy-associated genes. J Biomol Tech. 2010;21(2):73-80. [Link]
18. Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, et al. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res. 2008;18(10):1638-42. [Link] [DOI:10.1101/gr.077776.108]
19. Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet. 2008;24(3):133-41. [Link] [DOI:10.1016/j.tig.2007.12.007]
20. Illumine. TruSeq™ DNA PCR-Free. [Internet] San Diego: illumine; 2013 [cited 2016 Jul 24]. Available from: https://www.illumina.com/documents/products/datasheets/datasheet_truseq_dna_pcr_free_sample_prep.pdf [Link]

Send email to the article author

Rights and permissions
Creative Commons License This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.