Skip to main content

Advertisement

Log in

Circulating Tumor DNA—the Potential of Liquid Biopsies

  • Translational Research (T King and E Mittendorf, Section Editors)
  • Published:
Current Breast Cancer Reports Aims and scope Submit manuscript

Abstract

Recent studies suggest circulating cell-free tumor DNA offers advantages compared to tissue biopsies for mutation profiling. This concept of “liquid biopsy” allows for a more global genomic picture of metastatic disease since blood serves as a reservoir for all metastatic sites. In addition, cell-free tumor DNA can be measured quantitatively, presenting the possibility of using circulating tumor DNA as a biomarker to measure disease burden and response to therapies. Here, we review historic and recent studies demonstrating the clinical potential of measuring cell-free tumor DNA in breast cancer patients and future steps needed to translate liquid biopsies from research to clinical practice.

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1

Similar content being viewed by others

References

Papers of particular interest, published recently, have been highlighted as: • Of importance

  1. Pao W, Girard N. New driver mutations in non-small-cell lung cancer. Lancet Oncol. 2011;12:175–80.

    Article  CAS  PubMed  Google Scholar 

  2. Crowley E, Di Nicolantonio F, Loupakis F, et al. Liquid biopsy: monitoring cancer-genetics in the blood. Nat Rev Clin Oncol. 2013;10:472–84.

    Article  CAS  PubMed  Google Scholar 

  3. Kim ST, Lee WS, Lanman RB, et al. Prospective blinded study of somatic mutation detection in cell-free DNA utilizing a targeted 54-gene next generation sequencing panel in metastatic solid tumor patients. Oncotarget 2015.

  4. Mandel P, Metais P. Les acides nucleiques du plasma sanguin chez l'homme. C R Seances Soc Biol Fil. 1947;142:241–3.

    Google Scholar 

  5. Leon SA, Shapiro B, Sklaroff DM, et al. Free DNA in the serum of cancer patients and the effect of therapy. Cancer Res. 1977;37:646–50.

    CAS  PubMed  Google Scholar 

  6. Ke WL, Zhao WH, Wang XY. Detection of fetal cell-free DNA in maternal plasma for Down syndrome, Edward syndrome and Patau syndrome of high risk fetus. Int J Clin Exp Med. 2015;8:9525–30.

    PubMed  PubMed Central  Google Scholar 

  7. Benachi A, Letourneau A, Kleinfinger P, et al. Cell-free DNA analysis in maternal plasma in cases of fetal abnormalities detected on ultrasound examination. Obstet Gynecol. 2015;125:1330–7.

    Article  CAS  PubMed  Google Scholar 

  8. Wagner AJ, Mitchell ME, Tomita-Mitchell A. Use of cell-free fetal DNA in maternal plasma for noninvasive prenatal screening. Clin Perinatol. 2014;41:957–66.

    Article  PubMed  Google Scholar 

  9. Konorova IL, Maximova M, Smirnova IN, et al. Circulating in blood plasma cell-free DNA in the pathogenesis of ischemic stroke: the role of the transcribed region of ribosomal repeat. Patol Fiziol Eksp Ter 2014: 13-23.

  10. Lou X, Hou Y, Liang D, et al. A novel Alu-based real-time PCR method for the quantitative detection of plasma circulating cell-free DNA: sensitivity and specificity for the diagnosis of myocardial infarction. Int J Mol Med. 2015;35:72–80.

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Stroun M, Anker P, Maurice P, et al. Neoplastic characteristics of the DNA found in the plasma of cancer patients. Oncology. 1989;46:318–22.

    Article  CAS  PubMed  Google Scholar 

  12. El Messaoudi S, Rolet F, Mouliere F, et al. Circulating cell free DNA: preanalytical considerations. Clin Chim Acta. 2013;424:222–30.

    Article  PubMed  Google Scholar 

  13. Vasioukhin V, Anker P, Maurice P, et al. Point mutations of the N-ras gene in the blood plasma DNA of patients with myelodysplastic syndrome or acute myelogenous leukaemia. Br J Haematol. 1994;86:774–9.

    Article  CAS  PubMed  Google Scholar 

  14. van Kamp H, de Pijper C, Verlaan-de Vries M, et al. Longitudinal analysis of point mutations of the N-ras proto-oncogene in patients with myelodysplasia using archived blood smears. Blood. 1992;79:1266–70.

    PubMed  Google Scholar 

  15. Shaw JA, Smith BM, Walsh T, et al. Microsatellite alterations plasma DNA of primary breast cancer patients. Clin Cancer Res. 2000;6:1119–24.

    CAS  PubMed  Google Scholar 

  16. Fujiwara K, Fujimoto N, Tabata M, et al. Identification of epigenetic aberrant promoter methylation in serum DNA is useful for early detection of lung cancer. Clin Cancer Res. 2005;11:1219–25.

    Article  CAS  PubMed  Google Scholar 

  17. Choi JJ, Reich 3rd CF, Pisetsky DS. The role of macrophages in the in vitro generation of extracellular DNA from apoptotic and necrotic cells. Immunology. 2005;115:55–62.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Stroun M, Lyautey J, Lederrey C, et al. Alu repeat sequences are present in increased proportions compared to a unique gene in plasma/serum DNA: evidence for a preferential release from viable cells? Ann N Y Acad Sci. 2001;945:258–64.

    Article  CAS  PubMed  Google Scholar 

  19. Yu SC, Lee SW, Jiang P, et al. High-resolution profiling of fetal DNA clearance from maternal plasma by massively parallel sequencing. Clin Chem. 2013;59:1228–37.

    Article  CAS  PubMed  Google Scholar 

  20. Diehl F, Schmidt K, Choti MA, et al. Circulating mutant DNA to assess tumor dynamics. Nat Med. 2008;14:985–90. This was one of the first papers to assess ctDNA as a method to measure tumor burden and response to therapies.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Henry NL, Hayes DF. Cancer biomarkers. Mol Oncol. 2012;6:140–6.

    Article  CAS  PubMed  Google Scholar 

  22. Toro PV, Erlanger B, Beaver JA, et al. Comparison of cell stabilizing blood collection tubes for circulating plasma tumor DNA. Clin Biochem 2015.

  23. Sjoblom T, Jones S, Wood LD, et al. The consensus coding sequences of human breast and colorectal cancers. Science. 2006;314:268–74.

    Article  PubMed  Google Scholar 

  24. Reuter JA, Spacek DV, Snyder MP. High-throughput sequencing technologies. Mol Cell. 2015;58:586–97.

    Article  CAS  PubMed  Google Scholar 

  25. Baker M. Digital PCR, hits its stride. Nat Methods. 2012;9:541–4.

    Article  CAS  Google Scholar 

  26. Higgins MJ, Jelovac D, Barnathan E, et al. Detection of tumor PIK3CA status in metastatic breast cancer using peripheral blood. Clin Cancer Res. 2012;18:3462–9. This paper was one of the first prospective mutational concordance studies on ptDNA and tissue biopsies.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Dressman D, Yan H, Traverso G, et al. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci U S A. 2003;100:8817–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Gerlinger M, Rowan AJ, Horswell S, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med. 2012;366:883–92.

    Article  CAS  PubMed  Google Scholar 

  29. Rothe F, Laes JF, Lambrechts D, et al. Plasma circulating tumor DNA as an alternative to metastatic biopsies for mutational analysis in breast cancer. Ann Oncol. 2014;25:1959–65. This paper was one of the first prospective studies using NGS for assessing concordance between ctDNA and tissue biopsies.

    Article  CAS  PubMed  Google Scholar 

  30. Chu D, Paoletti C, Gersch C, et al. ESR1 mutations in circulating plasma tumor DNA from metastatic breast cancer patients. Clin Cancer Res 2015. This was the first prospective study of correlating ESR1 mutations in ptDNA and metastatic tissue biopsies.

  31. Bettegowda C, Sausen M, Leary RJ, et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014;6:224ra224. One of the largest studies of mutational concordance between tumors and ctDNA across many tumor types.

    Article  Google Scholar 

  32. Murtaza M, Dawson SJ, Tsui DW, et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature. 2013;497:108–12. The first paper to serially follow changes in clonal population of metastatic patients using whole exome sequencing.

    Article  CAS  PubMed  Google Scholar 

  33. Gevensleben H, Garcia-Murillas I, Graeser MK, et al. Noninvasive detection of HER2 amplification with plasma DNA digital PCR. Clin Cancer Res. 2013;19:3276–84.

    Article  CAS  PubMed  Google Scholar 

  34. Lanman RB, Mortimer SA, Zill OA, et al. Analytical and clinical validation of a digital sequencing panel for quantitative, highly accurate evaluation of cell-free circulating tumor DNA. PLoS One. 2015;10:e0140712.

    Article  PubMed  PubMed Central  Google Scholar 

  35. Sozzi G, Conte D, Leon M, et al. Quantification of free circulating DNA as a diagnostic marker in lung cancer. J Clin Oncol. 2003;21:3902–8.

    Article  CAS  PubMed  Google Scholar 

  36. Kim K, Shin DG, Park MK, et al. Circulating cell-free DNA as a promising biomarker in patients with gastric cancer: diagnostic validity and significant reduction of cfDNA after surgical resection. Ann Surg Treat Res. 2014;86:136–42.

    Article  PubMed  PubMed Central  Google Scholar 

  37. Nawroz H, Koch W, Anker P, et al. Microsatellite alterations in serum DNA of head and neck cancer patients. Nat Med. 1996;2:1035–7.

    Article  CAS  PubMed  Google Scholar 

  38. Garcia-Olmo DC, Picazo MG, Toboso I, et al. Quantitation of cell-free DNA and RNA in plasma during tumor progression in rats. Mol Cancer. 2013;12:8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Cristofanilli M, Budd GT, Ellis MJ, et al. Circulating tumor cells, disease progression, and survival in metastatic breast cancer. N Engl J Med. 2004;351:781–91.

    Article  CAS  PubMed  Google Scholar 

  40. Beaver JA, Jelovac D, Balukrishna S, et al. Detection of cancer DNA in plasma of patients with early-stage breast cancer. Clin Cancer Res. 2014;20:2643–50. The first prospective study evaluating the ability of ddPCR to detect ptDNA in early stage breast cancer and identifying minimal residual disease post-operatively.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Dawson SJ, Tsui DW, Murtaza M, et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med. 2013;368:1199–209. One of the first prospective studies in metastatic breast cancer patients showning prognostic and predictive value of measuring ctDNA.

    Article  CAS  PubMed  Google Scholar 

  42. Spindler KL, Appelt AL, Pallisgaard N, et al. Cell-free DNA in healthy individuals, noncancerous disease and strong prognostic value in colorectal cancer. Int J Cancer. 2014;135:2984–91.

    Article  CAS  PubMed  Google Scholar 

  43. Spindler KL, Pallisgaard N, Vogelius I, et al. Quantitative cell-free DNA, KRAS, and BRAF mutations in plasma from patients with metastatic colorectal cancer during treatment with cetuximab and irinotecan. Clin Cancer Res. 2012;18:1177–85.

    Article  CAS  PubMed  Google Scholar 

  44. Garcia-Murillas I, Schiavon G, Weigelt B, et al. Mutation tracking in circulating tumor DNA predicts relapse in early breast cancer. Sci Transl Med. 2015;7:302ra133.

    Article  PubMed  Google Scholar 

  45. Lynch TJ, Bell DW, Sordella R, et al. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med. 2004;350:2129–39.

    Article  CAS  PubMed  Google Scholar 

  46. Paez JG, Janne PA, Lee JC, et al. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science. 2004;304:1497–500.

    Article  CAS  PubMed  Google Scholar 

  47. Pao W, Miller V, Zakowski M, et al. EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib. Proc Natl Acad Sci U S A. 2004;101:13306–11.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Taniguchi K, Uchida J, Nishino K, et al. Quantitative detection of EGFR mutations in circulating tumor DNA derived from lung adenocarcinomas. Clin Cancer Res. 2011;17:7808–15.

    Article  CAS  PubMed  Google Scholar 

  49. Mok T, Wu YL, Lee JS, et al. Detection and dynamic changes of EGFR mutations from circulating tumor DNA as a predictor of survival outcomes in NSCLC patients treated with first-line intercalated Erlotinib and chemotherapy. Clin Cancer Res. 2015;21:3196–203.

    Article  CAS  PubMed  Google Scholar 

  50. Pao W, Miller VA, Politi KA, et al. Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the EGFR kinase domain. PLoS Med. 2005;2:e73.

    Article  PubMed  PubMed Central  Google Scholar 

  51. Oxnard GR, Paweletz CP, Kuang Y, et al. Noninvasive detection of response and resistance in EGFR-mutant lung cancer using quantitative next-generation genotyping of cell-free plasma DNA. Clin Cancer Res. 2014;20:1698–705.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Piotrowska Z, Niederst MJ, Karlovich CA, et al. Heterogeneity underlies the emergence of EGFRT790 wild-type clones following treatment of T790M-positive cancers with a third-generation EGFR inhibitor. Cancer Discov. 2015;5:713–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. De Roock W, Claes B, Bernasconi D, et al. Effects of KRAS, BRAF, NRAS, and PIK3CA mutations on the efficacy of cetuximab plus chemotherapy in chemotherapy-refractory metastatic colorectal cancer: a retrospective consortium analysis. Lancet Oncol. 2010;11:753–62.

    Article  PubMed  Google Scholar 

  54. Siravegna G, Mussolin B, Buscarino M, et al. Clonal evolution and resistance to EGFR blockade in the blood of colorectal cancer patients. Nat Med. 2015;21:795–801.

    Article  CAS  PubMed  Google Scholar 

  55. Misale S, Yaeger R, Hobor S, et al. Emergence of KRAS mutations and acquired resistance to anti-EGFR therapy in colorectal cancer. Nature. 2012;486:532–6.

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Tie J, Kinde I, Wang Y, et al. Circulating tumor DNA as an early marker of therapeutic response in patients with metastatic colorectal cancer. Ann Oncol 2015.

  57. Ibrahim EM, Kazkaz GA, Al-Mansour MM, et al. The predictive and prognostic role of phosphatase phosphoinositol-3 (PI3) kinase (PIK3CA) mutation in HER2-positive breast cancer receiving HER2-targeted therapy: a meta-analysis. Breast Cancer Res Treat. 2015;152:463–76.

    Article  CAS  PubMed  Google Scholar 

  58. Olsson E, Winter C, George A, et al. Serial monitoring of circulating tumor DNA in patients with primary breast cancer for detection of occult metastatic disease. EMBO Mol Med. 2015;7:1034–47.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Li S, Shen D, Shao J, et al. Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts. Cell Rep. 2013;4:1116–30.

    Article  CAS  PubMed  Google Scholar 

  60. Merenbakh-Lamin K, Ben-Baruch N, Yeheskel A, et al. D538G mutation in estrogen receptor-alpha: a novel mechanism for acquired endocrine resistance in breast cancer. Cancer Res. 2013;73:6856–64.

    Article  CAS  PubMed  Google Scholar 

  61. Robinson DR, Wu YM, Vats P, et al. Activating ESR1 mutations in hormone-resistant metastatic breast cancer. Nat Genet. 2013;45:1446–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Toy W, Shen Y, Won H, et al. ESR1 ligand-binding domain mutations in hormone-resistant breast cancer. Nat Genet. 2013;45:1439–45.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Jeselsohn R, Yelensky R, Buchwalter G, et al. Emergence of constitutively active estrogen receptor-alpha mutations in pretreated advanced estrogen receptor-positive breast cancer. Clin Cancer Res. 2014;20:1757–67.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Sefrioui D, Perdrix A, Sarafan-Vasseur N, et al. Short report: monitoring ESR1 mutations by circulating tumor DNA in aromatase inhibitor resistant metastatic breast cancer. Int J Cancer. 2015;137:2513–9.

    Article  CAS  PubMed  Google Scholar 

  65. Guttery DS, Page K, Hills A, et al. Noninvasive detection of activating estrogen receptor 1 (ESR1) mutations in estrogen receptor-positive metastatic breast cancer. Clin Chem. 2015;61:974–82.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by The Avon Foundation (BHP) and NIH CA009071 (KC, BHP). We would also like to thank and acknowledge the support of NIH P30 CA006973, the Sandy Garcia Charitable Foundation, the Commonwealth Foundation, the Santa Fe Foundation, the Breast Cancer Research Foundation, the Health Network Foundation, the Marcie Ellen Foundation, The Helen Golde Trust, and The Robin Page/Lebor Foundation. None of the funding sources influenced the design, interpretation, or submission of this manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ben Ho Park.

Ethics declarations

Conflict of Interest

Karen Cravero declares no conflict of interest.

Ben Ho Park is a member of the scientific advisory boards of Horizon Discovery, LTD and Loxo Oncology and has research contracts with Genomic Health, Inc. and Foundation Medicine. Under separate licensing agreements between Horizon Discovery, LTD and The Johns Hopkins University, B.H.P. is entitled to a share of royalties received by the University on sales of products. The terms of this arrangement are being managed by the Johns Hopkins University, in accordance with its conflict of interest policies.

Human and Animal Rights and Informed Consent

This article does not contain any studies with human or animal subjects performed by any of the authors.

Additional information

This article is part of the Topical Collection on Translational Research

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Cravero, K., Park, B.H. Circulating Tumor DNA—the Potential of Liquid Biopsies. Curr Breast Cancer Rep 8, 14–21 (2016). https://doi.org/10.1007/s12609-016-0199-2

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12609-016-0199-2

Keywords

Navigation