Skip to main content

Next-Generation Sequencing for Gene Panels

  • Chapter
  • First Online:
Genomic Applications in Pathology
  • 1858 Accesses

Abstract

Many molecular diagnostic laboratories are implementing next-generation sequencing (NGS)-based gene panels by harnessing the power of massively parallel sequencing technologies. NGS has dramatically expanded the capabilities of laboratories by multiplexing and streamlining DNA sequencing workflows. Replacing traditional target amplification techniques with in-solution enrichment technologies has simplified sequencing template preparation, greatly increasing the productivity of individual laboratories. Multigene panels can be performed with gene-specific target enrichment probes or by gene list-driven informatic analysis of exomes or genomes. Improved efficiency of molecular genetic testing, driven by the development and implementation of comprehensive disease-targeted gene panels, is propelling the advancement of genomic medicine.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 249.99
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

References

  1. Metzker ML. Sequencing technologies—the next generation. Nat Rev Genet. 2010;11:31–46.

    Article  CAS  PubMed  Google Scholar 

  2. Rehm HL. Disease-targeted sequencing: a cornerstone in the clinic. Nat Rev Genet. 2013;14:295–300. https://doi.org/10.1038/nrg3463.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Teekakirikul P, Kelly MA, Rehm HL, Lakdawala NK, Funke BH. Inherited cardiomyopathies: molecular genetics and clinical genetic testing in the postgenomic era. J Mol Diagn. 2013;15(2):158–70.

    Article  PubMed  Google Scholar 

  4. Pritchard CC, Smith C, Salipante SJ, Lee MK, Thornton AM, Nord AS, Gulden C, Kupfer SS, Swisher EM, Bennett RL, Novetsky AP, Jarvik GP, Olopade OI, Goodfellow PJ, King MC, Tait JF, Walsh T. ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing. J Mol Diagn. 2012;14(4):357–66.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Gecz J, Shoubridge C, Corbett M. The genetic landscape of intellectual disability arising from chromosome X. Trends Genet. 2009;25(7):308–16.

    Article  CAS  PubMed  Google Scholar 

  6. Lionel AC, Costain G, Monfared N, Walker S, Reuter MS, Hosseini SM, Thiruvahindrapuram B, Merico D, Jobling R, Nalpathamkalam T, Pellecchia G, Sung WWL, Wang Z, Bikangaga P, Boelman C, Carter MT, Cordeiro D, Cytrynbaum C, Dell SD, Dhir P, Dowling JJ, Heon E, Hewson S, Hiraki L, Inbar-Feigenberg M, Klatt R, Kronick J, Laxer RM, Licht C, MacDonald H, Mercimek-Andrews S, Mendoza-Londono R, Piscione T, Schneider R, Schulze A, Silverman E, Siriwardena K, Snead OC, Sondheimer N, Sutherland J, Vincent A, Wasserman JD, Weksberg R, Shuman C, Carew C, Szego MJ, Hayeems RZ, Basran R, Stavropoulos DJ, Ray PN, Bowdin S, Meyn MS, Cohn RD, Scherer SW, Marshall CR. Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole-genome sequencing as a first-tier genetic test. Genet Med. 2018 Apr;20(4):435–43. https://doi.org/10.1038/gim.2017.119.

    Article  CAS  PubMed  Google Scholar 

  7. ACMG Board of Directors. Points to consider in the clinical application of genomic sequencing. Genet Med. 2012;14:759–61.

    Article  Google Scholar 

  8. Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ. Target-enrichment strategies for next-generation sequencing. Nat Methods. 2010;7(2):111–8.

    Article  CAS  PubMed  Google Scholar 

  9. Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, Gabriel S, Jaffe DB, Lander ES, Nusbaum C. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol. 2009;27(2):182–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Fisher S, Barry A, Abreu J, Minie B, Nolan J, Delorey TM, Young G, Fennell TJ, Allen A, Ambrogio L, Berlin AM, Blumenstiel B, Cibulskis K, Friedrich D, Johnson R, Juhn F, Reilly B, Shammas R, Stalker J, Sykes SM, Thompson J, Walsh J, Zimmer A, Zwirko Z, Gabriel S, Nicol R, Nusbaum C. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol. 2011;12(1):R1.

    Article  PubMed  PubMed Central  Google Scholar 

  11. Shearer AE, Hildebrand MS, Smith RJ. Solution-based targeted genomic enrichment for precious DNA samples. BMC Biotechnol. 2012;12:20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Nord AS, Lee M, King MC, Walsh T. Accurate and exact CNV identification from targeted high-throughput sequence data. BMC Genomics. 2011;12:184.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. DePristo M, Banks E, Poplin R, Garimella K, Maguire J, Hartl C, Philippakis A, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell T, Kernytsky A, Sivachenko A, Cibulskis K, Gabriel S, Altshuler D, Daly M. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31(3):213–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis ER, Wilson RK, Ding L. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics. 2012;28(3):311–7.

    Article  CAS  PubMed  Google Scholar 

  18. Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP. SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics. 2010;26(6):730–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Roth A, Ding J, Morin R, Crisan A, Ha G, Giuliany R, Bashashati A, Hirst M, Turashvili G, Oloumi A, Marra MA, Aparicio S, Shah SP. JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics. 2012;28(7):907–13.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2012;14:178–92. https://doi.org/10.1093/bib/bbs017.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Michael O. Dorschner .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer International Publishing AG, part of Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Dorschner, M.O. (2019). Next-Generation Sequencing for Gene Panels. In: Netto, G., Kaul, K. (eds) Genomic Applications in Pathology. Springer, Cham. https://doi.org/10.1007/978-3-319-96830-8_16

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-96830-8_16

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-96829-2

  • Online ISBN: 978-3-319-96830-8

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics