Next Generation Sequencing – Application in Clinical Practice

Czech version

Authors: L. Koubková ¹; B. Vojtěšek ¹; R. Vyzula ^1,2
Authors‘ workplace: Regionální centrum aplikované molekulární onkologie, Masarykův onkologický ústav, Brno ¹; Klinika komplexní onkologické péče, Masarykův onkologický ústav, Brno ²
Published in: Klin Onkol 2014; 27(Supplementum): 61-68

Overview

Development of new sequencing methods allowed faster and more economical genomic research. With these technologies, it is now possible to determine the complete sequence of human genome in a short time period and at a relatively low cost. Introduction of next generation sequencing methods to cancer research provided a comprehensive molecular characterization of cancers and enabled deeper insights into tumor complexity, heterogeneity and evolution. Next generation technologies have been applied to identify new causal mutations in genes in hereditary cancer syndromes. More than 15 various tumor types have been already sequenced and compared to that of normal cells allowing identification of new cancer driving mutations and genome structural rearrangements. In this review, we describe technical characteristics of main next generation sequencing platforms, briefly overview their pros and cons and clinical perspective.

Key words:
high‑throughput nucleotide sequencing – genomics – mutations – cancer research – clinical application – personalized treatment

This work was supported by the European Regional Development Fund and the State Budget of the Czech Republic (RECAMO, CZ.1.05/2.1.00/03.0101) and by MH CZ – DRO (MMCI, 00209805).

The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.

The Editorial Board declares that the manuscript met the ICMJE “uniform requirements” for biomedical papers.

Submitted:
4. 2. 2014

Accepted:
1. 4. 2014

Sources

1. Avery OT, Macleod CM, McCarty M. Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. J Exp Med 1944; 79(2): 137−158.

2. Watson JD, Crick FH. The structure of DNA. Cold Spring Harb Symp Quant Biol 1953; 18: 123−131.

3. Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci USA 1977; 74(2): 560−564.

4. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain‑terminating inhibitors. Proc Natl Acad Sci USA 1977; 74(12): 5463−5467.

5. Liu L, Li Y, Li S et al. Comparison of next‑ generation sequencing systems. J Biomed Biotechnol 2012; 2012: 251364. doi: 10.1155/ 2012/ 251364.

6. Metzker ML. Sequencing technologies − the next generation. Nat Rev Genet 2010; 11(1): 31−46. doi: 10.1038/ nrg2626.

7. Zhou X, Ren L, Meng Q et al. The next‑ generation sequencing technology and application. Protein Cell 2010; 1(6): 520−536. doi: 10.1007/ s13238- 010- 0065- 3.

8. Shokralla S, Spall JL, Gibson JF et al. Next‑ generation sequencing technologies for environmental DNA research. Mol Ecol 2012; 21(8): 1794−1805. doi: 10.1111/ j.1365- 294X.2012.05538.x.

9. Xuan J, Yu Y, Qing T et al. Next‑ generation sequencing in the clinic: promises and challenges. Cancer Lett 2013; 340(2): 284−295. doi: 10.1016/ j.canlet.2012.11.025.

10. Quince C, Lanzen A, Curtis TP et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 2009; 6(9): 639−641. doi: 10.1038/ nmeth.1361.

11. Illumina.com [homepage on the Internet]. Illumina, Inc.; c2014 [updated 2014; cited 2014 Mar 19]. Available from: http:/ / www.illumina.com/ systems.ilmn.

12. Nanoportech.com [homepage on the Internet]. Oxford Nanopore Technologies, Oxford, UK; c2008−2014 [updated 2014; cited 2014 Mar 17]. Available from: https:/ / www.nanoporetech.com/ technology/ introduction‑ to‑ nanopore‑sensing/ introduction‑ to‑ nanopore‑sensing.

13. Di Fiori N, Squires A, Bar D et al. Optoelectronic control of surface charge and translocation dynamics in solid‑ state nanopores. Nat Nanotechnol 2013; 8(12): 946−951. doi: 10.1038/ nnano.2013.221.

14. Squires AH, Hersey JS, Grinstaff MW et al. A nanopore‑nanofiber mesh biosensor to control DNA translocation. J Am Chem Soc 2013; 135(44): 16304−16307.

15. Anderson BN, Muthukumar M, Meller A. pH tuning of DNA translocation time through organically functionalized nanopores. ACS Nano 2013; 7(2): 1408−1414. doi: 10.1021/ nn3051677.

16. Guan YF, Li GR, Wang RJ et al. Application of next‑ generation sequencing in clinical oncology to advance personalized treatment of cancer. Chin J Cancer 2012; 31(10): 463−470. doi: 10.5732/ cjc.012.10216.

17. Shyr D, Liu Q. Next generation sequencing in cancer research and clinical application. Biol Proced Online 2013; 15(1): 4. doi: 10.1186/ 1480- 9222- 15- 4.

18. Ku CS, Cooper DN, Ziogas DE et al. Research and clinical applications of cancer genome sequencing. Curr Opin Obstet Gynecol 2013; 25(1): 3−10. doi: 10.1097/ GCO.0b013e32835af17c.

19. Ley TJ, Mardis ER, Ding L et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 2008; 456(7218): 66−72. doi: 10.1038/ nature07485.

20. Dong H, Wang S. Exploring the cancer genome in the era of next‑ generation sequencing. Front Med 2012; 6(1): 48−55. doi: 10.1007/ s11684- 012- 0182- x.

21. Jones S, Hruban RH, Kamiyama M et al. Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene. Science 2009; 324(5924): 217. doi: 10.1126/ science.1171202.

22. Comino‑ Méndez I, Gracia‑ Aznárez FJ, Schiavi F et al. Exome sequencing identifies MAX mutations as a cause of hereditary pheochromocytoma. Nat Genet 2011; 43(7): 663−667. doi: 10.1038/ ng.861.

23. Yokoyama S, Woods SL, Boyle GM et al. A novel recurrent mutation in MITF predisposes to familial and sporadic melanoma. Nature 2011; 480(7375): 99−103. doi: 10.1038/ nature10630.

24. Tran B, Dancey JE, Kamel‑ Reid S et al. Cancer genomics: technology, discovery, and translation. J Clin Oncol 2012; 30(6): 647−660. doi: 10.1200/ JCO.2011.39.2316.

25. Chang F, Li MM. Clinical application of amplicon‑based next‑ generation sequencing in cancer. Cancer Genet 2013; 206(12): 413−419. doi: 10.1016/ j.cancergen.2013.10.003.

26. Walsh T, Lee MK, Casadei S et al. Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci USA 2010; 107(28): 12629−12633. doi: 10.1073/ pnas.1007983107.

27. Ozcelik H, Shi X, Chang MC et al. Long‑range PCR and next‑ generation sequencing of BRCA1 and BRCA2 in breast cancer. J Mol Diagn 2012; 14(5): 467−475. doi: 10.1016/ j.jmoldx.2012.03.006.