Next Generation Sequencing in Clinical Oncology: Applications, Challenges and Promises: A Review Article
Background: The aim of this mini-review is to highlight the potential applications of next-generation sequencing technology to the field of clinical oncology with respect to genetic diagnosis, cancer classification, predictive biomarkers and personalized medicine.
Methods: Scientific databases were searched to collect relative data.
Results: Effective systematic analysis of whole-genome sequence and whole-exome sequence of tumors, targeted genome profiling, transcriptome sequencing and tumor- normal comparisons can be performed using NGS in order to diagnosis of several types of cancer.
Conclusion: NGS technology can be powerful enough to discover new and infrequent gene alterations, identify hereditary cancer mutation carriers and provide a reliable molecular portrait of wide range of cancers in a quick and cost-effective manner.
2. Rao DD, Wang Z, Senzer N, Nemunaitis J (2013). RNA interference and personalized cancer therapy. Discov Med, 15:101-10.
3. Verma M (2012). Personalized medicine and cancer. J Pers Med, 2:1-14.
4. Mehta S, Shelling A, Muthukaruppan A et al (2010). Predictive and prognostic molecular markers for cancer medicine. Ther Adv Med Oncol, 2:125-48.
5. Hutchison CA (2007). DNA sequencing: bench to bedside and beyond. Nucleic Acids Res, 35:6227-37.
6. Tipu HN, Shabbir A (2015). Evolution of DNA sequencing. J Coll Physicians Surg Pak, 25:210-5.
7. Wang XV, Blades N, Ding J, Sultana R, Parmigiani G (2012). Estimation of sequencing error rates in short reads. BMC Bioinformatics, 13:185.
8. Rizzo JM, Buck MJ (2012). Key principles and clinical applications of "next-generation" DNA sequencing. Cancer Prev Res (Phila), 5:887-900.
9. Hardwick SA, Deveson IW, Mercer TR (2017). Reference standards for next-generation sequencing. Nat Rev Genet, 18:473-484.
10. Morozova O, Marra MA (2008). Applications of next-generation sequencing technologies in functional genomics. Genomics, 92:255-64.
11. Shyr D, Liu Q (2013). Next generation sequencing in cancer research and clinical application. Biol Proced Online, 15:4.
12. Kamps R, Brandao RD, Bosch BJ et al (2017). Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification. Int J Mol Sci, 18: 308.
13. Spencer DH, Sehn JK, Abel HJ et al (2013). Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens. J Mol Diagn, 15:623-33.
14. Boutros PC (2015). The path to routine use of genomic biomarkers in the cancer clinic. Genome Res, 25:1508-13.
15. Chen Y, Sun J, Huang LC, Xu H, Zhao Z (2015). Classification of Cancer Primary Sites Using Machine Learning and Somatic Mutations. Biomed Res Int, 2015:491502.
16. Meldrum C, Doyle MA, Tothill RW (2011). Next-generation sequencing for cancer diagnostics: a practical perspective. Clin Biochem Rev, 32:177-95.
17. Tulbah A, Chaudhri N, Al Dayel F, Akhtar M (2014). The journey toward personalized cancer therapy. Adv Anat Pathol, 21:36-43.
18. Kalia M (2013). Personalized oncology: recent advances and future challenges. Metabolism, 62 Suppl 1:S11-4.
19. Simon R, Roychowdhury S (2013). Implementing personalized cancer genomics in clinical trials. Nat Rev Drug Discov, 12:358-69.
20. Dienstmann R, Jang IS, Bot B et al (2015). Database of genomic biomarkers for cancer drugs and clinical targetability in solid tumors. Cancer Discov, 5:118-23.
21. Hammerman PS, Sos ML, Ramos AH et al (2011). Mutations in the DDR2 kinase gene identify a novel therapeutic target in squamous cell lung cancer. Cancer Discov, 1:78-89.
22. Chalhoub N, Baker SJ (2009). PTEN and the PI3-kinase pathway in cancer. Annu Rev Pathol, 4:127-50.
23. Populo H, Lopes JM, Soares P (2012). The mTOR signalling pathway in human cancer. Int J Mol Sci, 13:1886-918.
24. Petrucelli N, Daly MB, Pal T (1993). BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer. In: GeneReviews(R). Ed(s), Pagon RA, Adam MP, Ardinger HH, Wallace SE, Amemiya A, Bean LJH, Bird TD, Ledbetter N, Mefford HC, Smith RJH, Stephens K. Seattle (WA): University of Washington, Seattle
25. Fong PC, Boss DS, Yap TA et al (2009). Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers. N Engl J Med, 361:123-34.
26. Rupnik A, Grenon M, Lowndes N (2008). The MRN complex. Curr Biol, 18:R455-7.
27. Zhu ML, He J, Wang M et al (2014). Potentially functional polymorphisms in the ERCC2 gene and risk of esophageal squamous cell carcinoma in Chinese populations. Sci Rep, 4:6281.
28. Mouw KW (2017). DNA Repair Pathway Alterations in Bladder Cancer. Cancers (Basel), 9(4):E28.
29. Jancik S, Drabek J, Radzioch D, Hajduch M (2010). Clinical relevance of KRAS in human cancers. J Biomed Biotechnol, 2010:150960.
30. Haimovich AD (2011). Methods, challenges, and promise of next-generation sequencing in cancer biology. Yale J Biol Med, 84:439-46.
31. Sun XX, Yu Q (2015). Intra-tumor heterogeneity of cancer cells and its implications for cancer treatment. Acta Pharmacol Sin, 36:1219-27.
32. Perez-Gracia JL, Sanmamed MF, Bosch A et al (2017). Strategies to design clinical studies to identify predictive biomarkers in cancer research. Cancer Treat Rev, 53:79-97.
|Issue||Vol 47 No 10 (2018)|
|Next generation sequencing, Cancer, Genetic diagnosis, Biomarkers, Personalized medicines|
|Rights and permissions|
|This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.|