Skip to main content
SpringerLink
Log in

Role of Next Generation Sequencing (NGS) in Hematological Disorders

  • Chapter
  • First Online:
Hematopathology

  • 1330 Accesses

Abstract

Sequencing techniques are at the forefront of medical diagnostics in the current era of personalized medicine and targeted therapy. These techniques can identify the exact genetic change at the nucleotide level which aids in delineating the molecular pathogenesis and may also help in development of tailored therapy. Different sequencing approaches can be used for either the discovery of new genetic aberrations or checking the known genetic change for diagnostic purposes, depending on the requirement. Next generation sequencing (NGS) refers to the post-Sanger technologies, i.e., sequencing technologies developed after Sanger sequencing. So, NGS includes a group of technologies having the capacity to sequence large segments of genome or entire genome in high-throughput experiments to detect genetic aberrations in a much faster and reliable way [1]. The current high-throughput NGS techniques, which are also being made available at affordable costs, are gradually replacing the conventional or first generation sequencing techniques in the clinical settings. In this chapter, the basic workflow of next generation sequencing (NGS) and its application in hematological disorders has been briefly discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
eBook
USD 16.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 139.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    Coverage: The average number of times each base pair in the target genome is covered by reads. For example, 30× coverage implies that each base in the genome was covered by 30 reads on an average.

  2. 2.

    Phred Quality score (Q) indicates base call accuracy and is logarithmically related to the probability of error (p) in base-calling. If Q is 10, then p is 1 in 10 and base call accuracy is 90%. If Q is 40, then p is 1 in 104, i.e., 1 in 10,000 and base call accuracy is 99.99%.

References

  1. Singh RR, Luthra R, Routbort MJ, Patel KP, Medeiros LJ. Implementation of next generation sequencing in clinical molecular diagnostic laboratories: advantages, challenges and potential. Expert Rev Precis Med Drug Dev. 2016;1(1):109–20.

    Article  Google Scholar 

  2. Sulonen A, Ellonen P, Almusa H, Lepisto M, Eldfors S, Hannula S, et al. Comparison of solution-based exome capture methods for next generation sequencing. Genome Biol. 2011;12(9):R94.

    Article  CAS  Google Scholar 

  3. Kohlmann A, Grossmann V, Nadarahjah N, Haferlach T. Next generation sequencing—feasibility and practicality in hematology. Br J Haematol. 2013;160(6):736–53.

    Article  CAS  Google Scholar 

  4. Merker JD, Valouev A, Gotlib J. Next-generation sequencing in hematologic malignancies: what will be the dividends? Ther Adv Hematol. 2012;3(6):333–9.

    Article  CAS  Google Scholar 

  5. 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;309:1728–32.

    Article  CAS  Google Scholar 

  6. Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, et al. DNA sequencing of a cytogenetically normal acute myeloid leukemia genome. Nature. 2008;456:66–72.

    Article  CAS  Google Scholar 

  7. Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, et al. DNMT3A mutations in acute myeloid leukemia. N Engl J Med. 2010;363:2424–33.

    Article  CAS  Google Scholar 

  8. Patel JP, Gonen M, Figueroa ME, Fernandez H, Sun Z, Racevskis J, et al. Prognostic relevance of integrated genetic profiling in acute myeloid leukemia. N Engl J Med. 2012;366:1079–89.

    Article  CAS  Google Scholar 

  9. Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS, et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature. 2012;481:506–10.

    Article  CAS  Google Scholar 

  10. Walter MJ, Shen D, Ding L, Shao J, Koboldt DC, Chen K, et al. Clonal architecture of secondary acute myeloid leukemia. N Engl J Med. 2012;366:1090–8.

    Article  CAS  Google Scholar 

  11. Cancer Genome Atlas Research Network. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013;368:2059–74.

    Article  Google Scholar 

  12. Arber DA, Orazi A, Hasserjian RP, Brunning RD, Le Beau MM, Porwit A, et al. Introduction and overview of the classification of myeloid neoplasms. In: Swerdlow SH, Campo E, Harris NL, et al., editors. WHO classification of tumours of haematopoietic and lymphoid tissues. Revised 4th ed. Lyon: IARC; 2017. p. 16–27.

    Google Scholar 

  13. Steensma DP. The evolving role of genomic testing in assessing prognosis of patients with myelodysplastic syndromes. Best Pract Res Clin Haematol. 2017;30(4):295–300.

    Article  Google Scholar 

  14. Malcovati L, Papaemmanuil E, Ambaglio I, Elena C, Galli A, Della Porta MG, et al. Driver somatic mutations identify distinct disease entities within myeloid neoplasms with myelodysplasia. Blood. 2014;124(9):1513–21.

    Article  CAS  Google Scholar 

  15. Quesada V, Conde L, Villamor N, Ordonez GR, Jares P, Bassaganyas L, et al. Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nat Genet. 2012;44:47–52.

    Article  CAS  Google Scholar 

  16. Wang L, Lawrence MS, Wan Y, Stojanov P, Sougnez C, Stevenson K, et al. SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med. 2011;365:2497–506.

    Article  CAS  Google Scholar 

  17. Tiacci E, Trifonov V, Schiavoni G, Holmes A, Kern W, Martelli MP, et al. BRAF mutations in hairy-cell leukemia. N Engl J Med. 2011;364:2305–15.

    Article  CAS  Google Scholar 

  18. Treon SP, Xu L, Yang G, et al. MYD88 L265P somatic mutation in Waldenstrom’s macroglobulinemia. N Engl J Med. 2012;367(9):826–33.

    Article  CAS  Google Scholar 

  19. Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, Schinzel AC, et al. Initial genome sequencing and analysis of multiple myeloma. Nature. 2011;471:467–72.

    Article  CAS  Google Scholar 

  20. Koskella HL, Eldfors S, Ellonen P, van Adrichem AJ, Kuusanmaki H, Andersson EI, et al. Somatic STAT3 mutations in large granular lymphocytic leukemia. N Engl J Med. 2012;366:1905–13.

    Article  Google Scholar 

  21. Roberts KG, Li Y, Payne-Turner D, Harvey RC, Yang Y-L, Pei D, et al. Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N Engl J Med. 2014;371(11):1005–15.

    Article  Google Scholar 

  22. Shang X, Peng Z, Ye Y, Asan, Zhang X, Chen Y, et al. Rapid targeted next-generation sequencing platform for molecular screening and clinical genotyping in subjects with hemoglobinopathies. EBioMedicine. 2017;23:150–9.

    Article  Google Scholar 

  23. He J, Song W, Yang J, Lu S, Yuan Y, Guo J. Next-generation sequencing improves thalassemia carrier screening among premarital adults in a high prevalence population: the Dai nationality, China. Genet Med. 2017;19(9):1022–31.

    Article  CAS  Google Scholar 

  24. Carlberg K, Bose N, Deng J, Lal A, Erlich H, Calloway C. Towards the development of a noninvasive prenatal test for beta-thalassemia: utilization of probe capture enrichment and next generation sequencing. Blood. 2016;128(22):3622.

    Google Scholar 

  25. Yoshizato T, Dumitriu B, Hosokawa K, Makishima H, Yoshida K, Townsley D, et al. Somatic mutations and clonal hematopoiesis in aplastic anemia. N Engl J Med. 2015;373(1):35–47.

    Article  CAS  Google Scholar 

  26. Kulasekararaj AG, Jiang J, Smith AE, Mohamedali AM, Mian S, Gandhi S, et al. Somatic mutations identify a subgroup of aplastic anemia patients who progress to myelodysplastic syndrome. Blood. 2014;124(17):2698–704.

    Article  CAS  Google Scholar 

  27. Andolfo I, Russo R, Gambale A, Iolascon A. New insights on hereditary erythrocyte membrane defects. Haematologica. 2016;101(11):1284–94.

    Article  CAS  Google Scholar 

  28. Agarwal AM, Reading NS, Frizzell K, Shen W, Sorrells S, Salama ME, et al. Using a next generation sequencing panel to discover the obscure causes of hereditary hemolytic anemias. Blood. 2016;128(22):2433.

    Google Scholar 

  29. Russo RAI, Manna F, Gambale A, Pignataro P, De Rosa G, Iolascon A. RedPlex: a targeted next generation sequencing-based diagnosis for patients with hereditary hemolytic anemias. Haematologica. 2016;101(s1):1.

    Google Scholar 

  30. Lee E, Dykas DJ, Leavitt AD, Camire RM, Ebberink E, García de Frutos P, et al. Whole-exome sequencing in evaluation of patients with venous thromboembolism. Blood Adv. 2017;1:1224–37.

    Article  CAS  Google Scholar 

  31. McDonald CJ, Ostini L, Wallace DF, Lyons A, Crawford DH, Subramaniam VN. Next-generation sequencing: application of a novel platform to analyze atypical iron disorders. J Hepatol. 2015;63(5):1288–93.

    Article  CAS  Google Scholar 

  32. Kalia SS, Adelman K, Bale SJ, Chung WK, Eng C, Evans JP, et al. Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics. Genet Med. 2017;19(2):249–55.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Lab Oncology Unit, IRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, India

    Sanjeev Kumar Gupta

Authors
  1. Sanjeev Kumar Gupta
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sanjeev Kumar Gupta .

Editor information

Editors and Affiliations

  1. Department of Hematology, All India Institute of Medical Sciences, New Delhi, India

    Renu Saxena

  2. Department of Hematology, All India Institute of Medical Sciences, New Delhi, India

    Hara Prasad Pati

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Gupta, S.K. (2019). Role of Next Generation Sequencing (NGS) in Hematological Disorders. In: Saxena, R., Pati, H. (eds) Hematopathology. Springer, Singapore. https://doi.org/10.1007/978-981-13-7713-6_30

Download citation

  • DOI: https://doi.org/10.1007/978-981-13-7713-6_30

  • Published:

  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-13-7712-9

  • Online ISBN: 978-981-13-7713-6

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics

Search

Navigation