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Next-Generation Sequencing in Cancer

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Journal of Maxillofacial and Oral Surgery Aims and scope Submit manuscript

Abstract

Objective

In this article, we provide a gestalt idea about NGS technologies and their applications in cancer research and molecular diagnosis.

Background

Next-generation sequencing (NGS) advancements like DNA sequencing and RNA sequencing allow uncovering of genomic, transcriptomic, and epigenomic scenes of individual malignant growths. An assortment of genomic abnormalities can be screened at the same time, for example common and uncommon variations, auxiliary variations like insertions and deletions, copy-number variation, and fusion transcripts.

Conclusion

NGS innovations together with bioinformatics investigation, which extend our insight, are progressively used to analyze multiple genes in a cost-effective way and have been applied in examining clinical cancer samples and offering NGS-based molecular diagnosis.

Application

NGS is progressively significant as a device for the diagnosis of cancers.

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Abbreviations

NGS:

Next generation sequencing

DNA:

Deoxy ribonucleic acid

RNA:

Ribonucleic acid

WES:

Whole exome sequencing

WGS:

Whole genome sequencing

NCDs:

Non-communicable diseases

WHO:

World Health Organization

HNCs:

Head and neck cancers

SCC:

Squamous cell carcinoma

GWAS:

Genome-wide association study

SBS:

Sequencing by synthesis

SMRT:

Single-molecule real-time

CNV:

Copy number variations

SNPs:

Single-nucleotide polymorphisms

TCGA:

The cancer genome atlas

WGBS:

Whole genome bisulphite sequencing

RRBS:

Reduced representation bisulfite sequencing

PC:

Prostrate cancer

BC:

Breast cancer

HNSCC:

Head and neck squamous cell carcinoma

References

  1. Marziali A, Akeson M (2001) New DNA sequencing methods. Annu Rev Biomed Eng 3:195–223

    Article  CAS  Google Scholar 

  2. World Health Organization (2018) Global Health Observatory. World Health Organization: Geneva. https://www.who.int/gho/database/en/. Accessed 21 June 21

  3. Ferlay J, Soerjomataram I, Ervik M et al (2012) GLOBOCAN v1.0, cancer incidence and mortality worldwide. IARC Cancer Base No. 11. Lyon, International Agency for Research on Cancer, 2012. http://globocan.iarc.fr. Accessed 19 Oct 2015

  4. van Oijen MG, Slootweg PJ (2000) Oral field cancerization: carcinogen-induced independent events or micrometastatic deposits? Cancer Epidemiol Biomark Prev 9:249–256

    Google Scholar 

  5. Byakodi R, Byakodi S, Hiremath S et al (2012) Oral cancer in India: an epidemiologic and clinical review. J Community Health 37:316–319

    Article  Google Scholar 

  6. Furness S, Glenny AM, Worthington HV, Pavitt S, Oliver R, Clarkson JE et al (2010) Interventions for the treatment of oral cavity and oropharyngeal cancer: chemotherapy. Cochrane Database Syst Rev 9:CD006386

    Google Scholar 

  7. Gersten O, Wilmoth JR (2002) The cancer transition in Japan since 1951. Demogr Res 7:271–306

    Article  Google Scholar 

  8. Bray F (2014) Transitions in human development and the global cancer burden. In: Stewart BW, Wild CP (eds) World cancer report 2014. IARC Press, Lyon, pp 42–55

    Google Scholar 

  9. Maule M, Merletti F (2012) Cancer transition and priorities for cancer control. Lancet Oncol 13:745–746

    Article  Google Scholar 

  10. Gomy I, Diz Mdel P (2016) Hereditary cancer risk assessment: insights and perspectives for the next-generation sequencing era. Genet Mol Biol 39:184–188

    Article  Google Scholar 

  11. Wang Q, Lu Q, Zhao H (2015) A review of study designs and statistical methods for genomic epidemiology studies using next generation sequencing. Front Genet 6:149

    PubMed  PubMed Central  Google Scholar 

  12. Wang KS, Zuo L, Luo X (2014) Genetic factors for alcohol dependence and schizophrenia: common and rare variants. Austin J Drug Abuse Addict 1:id1001

    Google Scholar 

  13. Li W, Zhao K, Kirberger M, Liao W, Yan Y (2015) Next generation sequencing technologies in cancer diagnostics and therapeutics: a mini review. Cell Mol Biol 61:91–102

    CAS  PubMed  Google Scholar 

  14. Luthra R, Chen H, Roy-Chowdhuri S, Singh RR (2015) Next-generation sequencing in clinical molecular diagnostics of cancer: advantages and challenges. Cancers 7:2023–2036

    Article  CAS  Google Scholar 

  15. Corless CL (2016) Next-generation sequencing in cancer diagnostics. J Mol Diagn 18:813–816

    Article  Google Scholar 

  16. Serratì S, De Summa S, Pilato B, Petriella D, Lacalamita R et al (2016) Next-generation sequencing: advances and applications in cancer diagnosis. Onco Targets Ther 9:7355–7365

    Article  Google Scholar 

  17. Kamps R, Brandão RD, Bosch BJ, Paulussen AD, Xanthoulea S et al (2017) Next-generation sequencing in oncology: genetic diagnosis, risk prediction and cancer classification. Int J Mol Sci 18:308

    Article  Google Scholar 

  18. Illumina®. http://www.illumina.com. Accessed 10 Jan 2017

  19. Ion-Torrent®. http://www.thermofisher.com. Accessed 7 Nov 2016

  20. PacBio®. http://www.pacb.com/. Accessed 11 Nov 2016

  21. Roche®. http://www.roche.com/. Accessed 11 Nov 2016

  22. Nanopore®. https://www.nanoporetech.com/. Accessed 11 Nov 2016

  23. LeBlanc VG, Marra MA (2015) Next-generation sequencing approaches in cancer: Where have they brought us and where will they take us? Cancers 7:1925–1958

    Article  Google Scholar 

  24. Yadav SS, Li J, Lavery HJ, Yadav KK, Tewari AK (2015) Next-generation sequencing technology in prostate cancer diagnosis, prognosis, and personalized treatment. Urol Oncol 33:267

    Article  Google Scholar 

  25. Suhaimi SS, Ab Mutalib NS, Jamal R (2016) Understanding molecular landscape of endometrial cancer through next generation sequencing: What we have learned so far? Front Pharmacol 7:409

    Article  CAS  Google Scholar 

  26. Singleton AB (2011) Exome sequencing: a transformative technology. Lancet Neurol 10:942–946

    Article  CAS  Google Scholar 

  27. The cancer genome atlas (2017)

  28. International cancer genome consortium (2017)

  29. Esteller M (2011) Non-coding RNAs in human disease. Nat Rev Genet 12:861–874

    Article  CAS  Google Scholar 

  30. Farazi TA, Hoell JI, Morozov P, Tuschl T (2013) MicroRNAs in human cancer. Adv Exp Med Biol 774:1–20

    Article  CAS  Google Scholar 

  31. Gagan J, Van Allen EM (2015) Next-generation sequencing to guide cancer therapy. Genome Med 7:80

    Article  Google Scholar 

  32. Lin PH, Kuo WH, Huang AC, Lu YS, Lin CH et al (2016) Multiple gene sequencing for risk assessment in patients with early-onset or familial breast cancer. Oncotarget 7:8310–8320

    Article  Google Scholar 

  33. Johansen Taber KA, Dickinson BD, Wilson M (2014) The promise and challenges of next-generation genome sequencing for clinical care. JAMA Intern Med 174:275–280

    Article  Google Scholar 

  34. Manolio TA, Chisholm RL, Ozenberger B, Roden DM, Williams MS et al (2013) Implementing genomic medicine in the clinic: the future is here. Genet Med 15:258–267

    Article  Google Scholar 

  35. Rabbani B, Tekin M, Mahdieh N (2014) The promise of whole-exome sequencing in medical genetics. J Hum Genet 59:5–15

    Article  CAS  Google Scholar 

  36. Leyten GH, Hessels D, Smit F, Jannink S, de Jong H et al (2015) Identification of a candidate gene panel for the early diagnosis of prostate cancer. Clin Cancer Res 21:3061–3070

    Article  CAS  Google Scholar 

  37. Chen J, Zhang D, Yan W, Yang D, Shen B (2013) Translational bioinformatics for diagnostic and prognostic prediction of prostate cancer in the next-generation sequencing era. Biomed Res Int 2013:901578

    PubMed  PubMed Central  Google Scholar 

  38. Pronina IV, Loginov VI, Burdennyy AM, Fridman MV, Senchenko VN et al (2017) DNA methylation contributes to deregulation of 12 cancer-associated microRNAs and breast cancer progression. Gene 604:1–8

    Article  CAS  Google Scholar 

  39. Millis SZ, Ikeda S, Reddy S, Gatalica Z, Kurzrock R (2016) Landscape of phosphatidylinositol-3-kinase pathway alterations across 19?784 diverse solid tumors. JAMA Oncol 2:1565–1573

    Article  Google Scholar 

  40. Agrawal N, Frederick MJ, Pickering CR, Bettegowda C, Chang K, Li RJ et al (2011) Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science 333(6046):1154–1157

    Article  CAS  Google Scholar 

  41. Stransky N, Egloff AM, Tward AD, Kostic AD, Cibulskis K, Sivachenko A et al (2011) The mutational landscape of head and neck squamous cell carcinoma. Science 333(6046):1157–1160

    Article  CAS  Google Scholar 

  42. The Cancer Genome Atlas N (2015) Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature 517(7536):576–582

    Article  Google Scholar 

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Authors and Affiliations

  1. Department of Oral and Maxillofacial Surgery, P.M.S Dental College, Vattapara, Trivandrum, India

    S. Vinod Nair

  2. Department of Oral and Maxillofacial Surgery, Saveetha Dental College, Chennai, India

    Madhulaxmi

  3. Community Medicine, Regional Cancer Centre, Trivandrum, India

    Gigi Thomas

  4. Human Genome Centre, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, George Town, Malaysia

    Ravindran Ankathil

Authors
  1. S. Vinod Nair
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  2. Madhulaxmi
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  4. Ravindran Ankathil
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Correspondence to S. Vinod Nair.

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Nair, S.V., Madhulaxmi, Thomas, G. et al. Next-Generation Sequencing in Cancer. J. Maxillofac. Oral Surg. 20, 340–344 (2021). https://doi.org/10.1007/s12663-020-01462-4

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  • DOI: https://doi.org/10.1007/s12663-020-01462-4

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