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From cfDNA to Sequencing: Workflows and Potentials

  • Michela TebaldiEmail author
  • Samanta Salvi
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1909)

Abstract

Cell-free DNA (cfDNA) is acquiring increasingly importance in oncologic clinical practice, mostly due to its role in predicting the onset of therapy resistance by following the mutation status changes of patients. In this field, high-sensitivity methods like next-generation sequencing (NGS) could help to accurately detect somatic mutations at low frequency. Here, we report some advantages and limitations of NGS approaches for cfDNA mutation analyses with the aim of choosing the most suitable in terms of sensitivity, specificity, data output, costs, and time work.

Key words

Cell-free DNA Next-generation sequencing Sequencing Amplicon-based panel Hybridization capture-based panel 

References

  1. 1.
    Li T, Kung HJ, Mack PC et al (2013) Genotyping and genomic profiling of non-small-cell lung cancer: implications for current and future therapies. J Clin Oncol 31(8):1039–1049CrossRefGoogle Scholar
  2. 2.
    Gonzalez de Castro D, Clarke PA, Al-Lazikani B et al (2013) Personalized cancer medicine: molecular diagnostics, predictive biomarkers, and drug resistance. Clin Pharmacol Ther 93(3):252–259CrossRefGoogle Scholar
  3. 3.
    Diehl F, Schmidt K, Choti MA et al (2008) Circulating mutant DNA to assess tumor dynamics. Nat Med 14(9):985–990CrossRefGoogle Scholar
  4. 4.
    Olsson E, Winter C, George A et al (2015) Serial monitoring of circulating tumor DNA in patients with primary breast cancer for detection of occult metastatic disease. EMBO Mol Med 7(8):1034–1047CrossRefGoogle Scholar
  5. 5.
    Tie J, Wang Y, Tomasetti C et al (2016) Circulating tumor DNA analysis detects minimal residual disease and predicts recurrence in patients with stage II colon cancer. Sci Transl Med 8(346):346ra92CrossRefGoogle Scholar
  6. 6.
    Diehl F, Li M, Dressman D et al (2005) Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci U S A 102(45):16368–16373CrossRefGoogle Scholar
  7. 7.
    Christensen E, Nordentoft I, Vang S et al (2018) Optimized targeted sequencing of cell-free plasma DNA from bladder cancer patients. Sci Rep 8(1):1917CrossRefGoogle Scholar
  8. 8.
    Anderson MW, Schrijver I (2010) Next generation DNA sequencing and the future of genomic medicine. Genes (Basel) 1(1):38–69CrossRefGoogle Scholar
  9. 9.
    Abel HJ, Duncavage EJ (2013) Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches. Cancer Genet 206(12):432–440CrossRefGoogle Scholar
  10. 10.
    Day E, Dear PH, McCaughan F (2013) Digital PCR strategies in the development and analysis of molecular biomarkers for personalized medicine. Methods 59(1):101–107CrossRefGoogle Scholar
  11. 11.
    Heitzer E, Ulz P, Geigl JB (2015) Circulating tumor DNA as a liquid biopsy for cancer. Clin Chem 61(1):112–123CrossRefGoogle Scholar
  12. 12.
    Raptis L, Menard HA (1980) Quantitation and characterization of plasma DNA in normals and patients with systemic lupus erythematosus. J Clin Invest 66(6):1391–1399CrossRefGoogle Scholar
  13. 13.
    Meldrum C, Doyle MA, Tothill RW (2011) Next-generation sequencing for cancer diagnostics: a practical perspective. Clin Biochem Rev 32(4):177–195PubMedPubMedCentralGoogle Scholar
  14. 14.
    Tindall KR, Kunkel TA (1988) Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase. Biochemistry 27(16):6008–6013CrossRefGoogle Scholar
  15. 15.
    Kinde I, Wu J, Papadopoulos N et al (2011) Detection and quantification of rare mutations with massively parallel sequencing. Proc Natl Acad Sci U S A 108(23):9530–9535CrossRefGoogle Scholar
  16. 16.
    Liang RH, Mo T, Dong W et al (2014) Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing. Nucleic Acids Res 42(12):e98CrossRefGoogle Scholar
  17. 17.
    Newman AM, Bratman SV, To J et al (2014) An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat Med 20(5):548–554CrossRefGoogle Scholar
  18. 18.
    Dawson SJ, Tsui DW, Murtaza M et al (2013) Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med 368(13):1199–1209CrossRefGoogle Scholar
  19. 19.
    Thress KS, Paweletz CP, Felip E et al (2015) Acquired EGFR C797S mutation mediates resistance to AZD9291 in non-small cell lung cancer harboring EGFR T790M. Nat Med 21(6):560–562CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Biosciences LaboratoryIstituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCSMeldolaItaly

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