Skip to main content
SpringerLink
Log in

Molecular Methods in Oncology: Genomic Analysis

  • Chapter
  • First Online:
Book cover Precision Molecular Pathology of Neoplastic Pediatric Diseases

Part of the book series: Molecular Pathology Library ((MPLB))

  • 508 Accesses

Abstract

Next-generation sequencing (NGS) and chromosomal microarrays represent major technological advances—elegant combinations of biochemistry and microfluidics and laser optics—used in brute force approaches that rely on advanced computing to assemble and align the data from thousands or millions of individual reactions. NGS solutions comprise a spectrum of methods to obtain DNA sequence data in a massively parallel and automated fashion, which are faster and more efficient than the linear sequencing approach of three decades ago. Microarrays allow the simultaneous interrogation of numerous probes or targets, using sequence complementarity testing to identify similarities or differences in the genome. NGS and array-based comparative genomic hybridization provide insights into the whole spectrum of DNA aberrations, from single base substitutions to large-scale chromosomal deletions, which in turn help physicians diagnose and treat human disease.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 79.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 99.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 129.99
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. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977;74(12):5463–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M. Nucleotide sequence of bacteriophage phi X174 DNA. Nature. 1977;265(5596):687–95.

    Article  CAS  PubMed  Google Scholar 

  3. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, International Human Genome Sequencing Consortium, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860–921. Erratum in: Nature 2001 Jun 7;411(6838):720. Szustakowki, J [corrected to Szustakowski, J]. Nature 2001 Aug 2;412(6846):565.

    Article  CAS  PubMed  Google Scholar 

  4. Prober JM, Trainor GL, Dam RJ, Hobbs FW, Robertson CW, Zagursky RJ, Cocuzza AJ, Jensen MA, Baumeister K. A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science. 1987;238(4825):336–41.

    Article  CAS  PubMed  Google Scholar 

  5. Smith LM, Sanders JZ, Kaiser RJ, Hughes P, Dodd C, Connell CR, Heiner C, Kent SB, Hood LE. Fluorescence detection in automated DNA sequence analysis. Nature. 1986;321(6071):674–9.

    Article  CAS  PubMed  Google Scholar 

  6. Mardis ER. DNA sequencing technologies: 2006-2016. Nat Protoc. 2017;12(2):213–8.

    Article  CAS  PubMed  Google Scholar 

  7. Metzker ML. Emerging technologies in DNA sequencing. Genome Res. 2005;15(12):1767–76.

    Article  CAS  PubMed  Google Scholar 

  8. Pettersson E, Lundeberg J, Ahmadian A. Generations of sequencing technologies. Genomics. 2009;93(2):105–11.

    Article  CAS  PubMed  Google Scholar 

  9. Illumina. Illumina sequencing technology. 2010. Product literature online at https://www.illumina.com/documents/products/techspotlights/techspotlight_sequencing.pdf.

  10. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol. 2008;26(10):1135–45.

    Article  CAS  PubMed  Google Scholar 

  11. Canard B, Sarfati RS. DNA polymerase fluorescent substrates with reversible 3′-tags. Gene. 1994;148(1):1–6.

    Article  CAS  PubMed  Google Scholar 

  12. Ion Torrent. Exome sequencing using the Ion Proton system. 2012. Product literature online at https://tools.thermofisher.com/content/sfs/brochures/Proton-Exome-Product-Bulletin.pdf.

  13. Zhu Z, Jenkins G, Zhang W, Zhang M, Guan Z, Yang CJ. Single-molecule emulsion PCR in microfluidic droplets. Anal Bioanal Chem. 2012;403(8):2127–43.

    Article  CAS  PubMed  Google Scholar 

  14. Pachauri V, Ingebrandt S. Biologically sensitive field-effect transistors: from ISFETs to NanoFETs. Essays Biochem. 2016;60(1):81–90.

    Article  PubMed  PubMed Central  Google Scholar 

  15. Nakano K, Shiroma A, Shimoji M, Tamotsu H, Ashimine N, Ohki S, et al. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Hum Cell. 2017;30(3):149–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Rhoads A, Au KF. PacBio sequencing and its applications. Genomics Proteomics Bioinformatics. 2015;13(5):278–89.

    Article  PubMed  PubMed Central  Google Scholar 

  17. Applied Biosystems. SOLiD™ system accuracy with the exact call chemistry module. 2011. White paper available at https://tools.thermofisher.com/content/sfs/brochures/cms_091372.pdf.

  18. Huang YF, Chen SC, Chiang YS, Chen TH, Chiu KP. Palindromic sequence impedes sequencing-by-ligation mechanism. BMC Syst Biol. 2012;6(Suppl 2):S10.

    Article  PubMed  PubMed Central  Google Scholar 

  19. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456(7218):53–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Gan C, Love C, Beshay V, Macrae F, Fox S, Waring P, Taylor G. Applicability of next generation sequencing technology in microsatellite instability testing. Genes (Basel). 2015;6(1):46–59.

    Article  CAS  Google Scholar 

  21. Nowak JA, Yurgelun MB, Bruce JL, Rojas-Rudilla V, Hall DL, Shivdasani P, Garcia EP, Agoston AT, Srivastava A, Ogino S, Kuo FC, Lindeman NI, Dong F. Detection of mismatch repair deficiency and microsatellite instability in colorectal adenocarcinoma by targeted next-generation sequencing. J Mol Diagn. 2017;19(1):84–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Salipante SJ, Scroggins SM, Hampel HL, Turner EH, Pritchard CC. Microsatellite instability detection by next generation sequencing. Clin Chem. 2014;60(9):1192–9.

    Article  CAS  PubMed  Google Scholar 

  23. Campesato LF, Barroso-Sousa R, Jimenez L, Correa BR, Sabbaga J, Hoff PM, Reis LF, Galante PA, Camargo AA. Comprehensive cancer-gene panels can be used to estimate mutational load and predict clinical benefit to PD-1 blockade in clinical practice. Oncotarget. 2015;6(33):34221–7.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Goodman AM, Kato S, Bazhenova L, Patel SP, Frampton GM, Miller V, Stephens PJ, Daniels GA, Kurzrock R. Tumor mutational burden as an independent predictor of response to immunotherapy in diverse cancers. Mol Cancer Ther. 2017;16(11):2598–608.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Johnson DB, Frampton GM, Rioth MJ, Yusko E, Xu Y, Guo X, Ennis RC, Fabrizio D, Chalmers ZR, Greenbowe J, Ali SM, Balasubramanian S, Sun JX, He Y, Frederick DT, Puzanov I, Balko JM, Cates JM, Ross JS, Sanders C, Robins H, Shyr Y, Miller VA, Stephens PJ, Sullivan RJ, Sosman JA, Lovly CM. Targeted next generation sequencing identifies markers of response to PD-1 blockade. Cancer Immunol Res. 2016;4(11):959–67.

    Article  PubMed  PubMed Central  Google Scholar 

  26. Rosenberg JE, Hoffman-Censits J, Powles T, van der Heijden MS, Balar AV, Necchi A, Dawson N, O’Donnell PH, Balmanoukian A, Loriot Y, Srinivas S, Retz MM, Grivas P, Joseph RW, Galsky MD, Fleming MT, Petrylak DP, Perez-Gracia JL, Burris HA, Castellano D, Canil C, Bellmunt J, Bajorin D, Nickles D, Bourgon R, Frampton GM, Cui N, Mariathasan S, Abidoye O, Fine GD, Dreicer R. Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial. Lancet. 2016;387(10031):1909–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Gubin MM, Artyomov MN, Mardis ER, Schreiber RD. Tumor neoantigens: building a framework for personalized cancer immunotherapy. J Clin Invest. 2015;125(9):3413–21.

    Article  PubMed  PubMed Central  Google Scholar 

  28. du Manoir S, Speicher MR, Joos S, Schröck E, Popp S, Döhner H, et al. Detection of complete and partial chromosome gains and losses by comparative genomic in situ hybridization. Hum Genet. 1993;90(6):590–610.

    Article  PubMed  Google Scholar 

  29. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science. 1992;258(5083):818–21.

    Article  CAS  PubMed  Google Scholar 

  30. Pinkel D, Albertson DG. Array comparative genomic hybridization and its applications in cancer. Nat Genet. 2005;37(Suppl):S11–7.

    Article  CAS  PubMed  Google Scholar 

  31. Bier FF, von Nickisch-Rosenegk M, Ehrentreich-Förster E, Reiss E, Henkel J, Strehlow R, et al. DNA microarrays. Adv Biochem Eng Biotechnol. 2008;109:433–53.

    PubMed  CAS  Google Scholar 

  32. Coughlin CR 2nd, Scharer GH, Shaikh TH. Clinical impact of copy number variation analysis using high-resolution microarray technologies: advantages, limitations and concerns. Genome Med. 2012;4(10):80.

    Article  PubMed  PubMed Central  Google Scholar 

  33. Hacia JG, Collins FS. Mutational analysis using oligonucleotide microarrays. J Med Genet. 1999;36(10):730–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. McGall GH, Christians FC. High-density genechip oligonucleotide probe arrays. Adv Biochem Eng Biotechnol. 2002;77:21–42.

    PubMed  CAS  Google Scholar 

  35. Suomalainen A, Syvänen AC. Analysis of nucleotide sequence variations by solid-phase minisequencing. Methods Mol Biol. 2003;226:361–6.

    PubMed  CAS  Google Scholar 

  36. Goto S, Takahashi A, Kamisango K, Matsubara K. Single-nucleotide polymorphism analysis by hybridization protection assay on solid support. Anal Biochem. 2002;307(1):25–32.

    Article  CAS  PubMed  Google Scholar 

  37. Palmisano GL, Delfino L, Fiore M, Longo A, Ferrara GB. Single nucleotide polymorphisms detection based on DNA microarray technology: HLA as a model. Autoimmun Rev. 2005;4(8):510–4.

    Article  CAS  PubMed  Google Scholar 

  38. Watson MA. Microarrays. In: Pfeifer JD, editor. Molecular genetic testing in surgical pathology. Philadelphia: Lippincott Williams & Wilkins; 2006.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Division of Pediatric Pathology, Medical College of Wisconsin, Milwaukee, WI, USA

    Jason A. Jarzembowski MD, PhD

Authors
  1. Jason A. Jarzembowski MD, PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jason A. Jarzembowski MD, PhD .

Editor information

Editors and Affiliations

  1. Department of Pathology, University of Utah/ARUP Laboratories, Salt Lake City, Utah, USA

    Larissa V. Furtado

  2. Department of Pathology, University of Chicago, Chicago, Illinois, USA

    Aliya N. Husain

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG, part of Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Jarzembowski, J.A. (2018). Molecular Methods in Oncology: Genomic Analysis. In: Furtado, L., Husain, A. (eds) Precision Molecular Pathology of Neoplastic Pediatric Diseases . Molecular Pathology Library. Springer, Cham. https://doi.org/10.1007/978-3-319-89626-7_3

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-89626-7_3

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-89625-0

  • Online ISBN: 978-3-319-89626-7

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics

Search

Navigation