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Circulating Plasma Tumor DNA

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Novel Biomarkers in the Continuum of Breast Cancer

Part of the book series: Advances in Experimental Medicine and Biology ((BCRF,volume 882))

Abstract

Circulating cell-free DNA (ccfDNA)—first identified in 1947—is “naked” DNA that is free-floating in the blood, and derived from both normal and diseased cells. In the 1970s, scientists observed that patients with cancer had elevated levels of ccfDNA as compared to their healthy, cancer-free counterparts. The maternal fetal medicine community first developed techniques to identify the small fraction of fetal-derived ccfDNA for diagnostic purposes. Similarly, due to the presence of tumor-specific (somatic) variations in all cancers, the fraction of circulating cell-free plasma tumor DNA (ptDNA) in the larger pool of ccfDNA derived from normal cells can serve as extremely specific blood-based biomarkers for a patient’s cancer. In theory this “liquid biopsy” can provide a real-time assessment of molecular tumor genotype (qualitative) and existing tumor burden (quantitative). Historically, the major limitation for ptDNA as a biomarker has been related to a low detection rate; however, current and developing techniques have improved sensitivity dramatically. In this chapter, we discuss these methods, including digital polymerase chain reaction and various approaches to tagged next-generation sequencing.

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References

  1. Mandel P, Metais P (1947) Les acides nucléiques du plasma sanguin chez l’homme. C R Séances Soc Biol Fil 142:241–243

    Google Scholar 

  2. Antonatos D et al (2006) Cell-free DNA levels as a prognostic marker in acute myocardial infarction. Ann N Y Acad Sci 1075:278–281

    Article  CAS  PubMed  Google Scholar 

  3. Lam NY-L et al (2006) Plasma DNA as a prognostic marker for stroke patients with negative neuroimaging within the first 24 h of symptom onset. Resuscitation 68:71–78

    Article  CAS  PubMed  Google Scholar 

  4. Sandhu HS et al (2008) Measurement of circulating neuron-specific enolase mRNA in diabetes mellitus. Ann N Y Acad Sci 1137:258–263

    Article  CAS  PubMed  Google Scholar 

  5. Saukkonen K et al (2007) Association of cell-free plasma DNA with hospital mortality and organ dysfunction in intensive care unit patients. Intensive Care Med 33:1624–1627

    Article  CAS  PubMed  Google Scholar 

  6. Choi J-J, Reich CF, Pisetsky DS (2005) The role of macrophages in the in vitro generation of extracellular DNA from apoptotic and necrotic cells. Immunology 115(1):55–62. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1782131&tool=pmcentrez&rendertype=abstract. Accessed 22 Sept 2014

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Stroun M et al (2006) The origin and mechanism of circulating DNA. Ann N Y Acad Sci 906(1):161–168. http://doi.wiley.com/10.1111/j.1749-6632.2000.tb06608.x. Accessed 16 Sept 2013

    Article  Google Scholar 

  8. Diehl F, Schmidt K, Choti MA et al (2008) Circulating mutant DNA to assess tumor dynamics. Nat Med 14:985–990

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Jahr S et al (2001) DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells. Cancer Res 61(4):1659–1665. http://www.ncbi.nlm.nih.gov/pubmed/11245480. Accessed 1 Sept 2014

    CAS  PubMed  Google Scholar 

  10. Fleischhacker M, Schmidt B (2007) Circulating nucleic acids (CNAs) and cancer-A survey. Biochim Biophys Acta (Reviews on Cancer) 1775:181–232

    CAS  PubMed  Google Scholar 

  11. Lo YM et al (1999) Rapid clearance of fetal DNA from maternal plasma. Am J Hum Genet 64:218–224

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Chang CPY et al (2003) Elevated cell-free serum DNA detected in patients with myocardial infarction. Clin Chim Acta 327:95–101

    Article  CAS  PubMed  Google Scholar 

  13. Chiu TW et al (2006) Plasma cell-free DNA as an indicator of severity of injury in burn patients. Clin Chem Lab Med 44:13–17

    Article  CAS  PubMed  Google Scholar 

  14. Diehl F et al (2005) Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci U S A 102:16368–16373. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16258065

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Lo YM et al (2000) Plasma DNA as a prognostic marker in trauma patients. Clin Chem 46:319–323

    CAS  PubMed  Google Scholar 

  16. Rhodes A et al (2006) Plasma DNA concentration as a predictor of mortality and sepsis in critically ill patients. Crit Care (London, England) 10:R60

    Article  Google Scholar 

  17. Wimberger P et al (2011) Impact of platinum-based chemotherapy on circulating nucleic acid levels, protease activities in blood and disseminated tumor cells in bone marrow of ovarian cancer patients. Int J Cancer (J Int Cancer) 128:2572–2580

    Article  CAS  PubMed  Google Scholar 

  18. Dennis Lo YM, Chiu RWK (2007) Prenatal diagnosis: progress through plasma nucleic acids. Nat Rev Genet 8:71–77

    Article  Google Scholar 

  19. Dennis Lo YM et al (1997) Presence of fetal DNA in maternal plasma and serum. Lancet 350:485–487

    Article  Google Scholar 

  20. Herzenberg L (1979) Fetal cells in the blood of pregnant women: detection and enrichment by fluorescence-activated cell sorting. Proc Natl Acad Sci U S A 76:1453–1455. http://www.pnas.org/content/76/3/1453.short

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Li Y et al (2006) Cell-free DNA in maternal plasma: is it all a question of size? Ann N Y Acad Sci 1075:81–87

    Article  CAS  PubMed  Google Scholar 

  22. Lo YM et al (1998) Quantitative analysis of fetal DNA in maternal plasma and serum: implications for noninvasive prenatal diagnosis. Am J Hum Genet 62:768–775

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Lun FMF et al (2008) Microfluidics digital PCR reveals a higher than expected fraction of fetal DNA in maternal plasma. Clin Chem 54:1664–1672

    Article  CAS  PubMed  Google Scholar 

  24. Chiu RWK, Lo YMD (2013) Clinical applications of maternal plasma fetal DNA analysis: translating the fruits of 15 years of research. Clin Chem Lab Med: CCLM/FESCC 51:197–204. http://www.ncbi.nlm.nih.gov/pubmed/23072857

    CAS  Google Scholar 

  25. Chiu RWK et al (2008) Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Nat Acad Sci U S A 105:20458–20463

    Article  CAS  Google Scholar 

  26. Li Y et al (2005) Detection of paternally inherited fetal point mutations for beta-thalassemia using size-fractionated cell-free DNA in maternal plasma. JAMA 293(7):843–849. http://jama.jamanetwork.com/article.aspx?articleid=200371. Accessed 7 Oct 2014

    Article  CAS  PubMed  Google Scholar 

  27. Lo YM (1999) Fetal RhD genotyping from maternal plasma. Ann Med 31:308–312

    Article  CAS  PubMed  Google Scholar 

  28. Leon SA et al (1977) Free DNA in the serum of cancer patients and the effect of therapy. Cancer Res 37(3):646–650. http://www.ncbi.nlm.nih.gov/pubmed/837366. Accessed 7 Oct 2014

    CAS  PubMed  Google Scholar 

  29. Allen D et al (2004) Role of cell-free plasma DNA as a diagnostic marker for prostate cancer. Ann N Y Acad Sci 1022:76–80

    Article  CAS  PubMed  Google Scholar 

  30. Chun FKH et al (2006) Circulating tumour-associated plasma DNA represents an independent and informative predictor of prostate cancer. BJU Int 98:544–548

    Article  CAS  PubMed  Google Scholar 

  31. Schwarzenbach H et al (2008) Detection and monitoring of cell-free DNA in blood of patients with colorectal cancer. Ann N Y Acad Sci 1137:190–196

    Article  CAS  PubMed  Google Scholar 

  32. Giacona MB et al (1998) Cell-free DNA in human blood plasma: length measurements in patients with pancreatic cancer and healthy controls. Pancreas 17:89–97

    Article  CAS  PubMed  Google Scholar 

  33. Chen XQ et al (1999) Detecting tumor-related alterations in plasma or serum DNA of patients diagnosed with breast cancer. Clin Cancer Res 5:2297–2303

    CAS  PubMed  Google Scholar 

  34. Garcia JN et al (2006) Extracellular tumor DNA in plasma and overall survival in breast cancer patients. Genes Chromosomes Cancer 45:692–701

    Article  CAS  PubMed  Google Scholar 

  35. Shinozaki M et al (2007) Utility of circulating B-RAF DNA mutation in serum for monitoring melanoma patients receiving biochemotherapy. Clin Cancer Res 13:2068–2074

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Castells A et al (1999) K-ras mutations in DNA extracted from the plasma of patients with pancreatic carcinoma: diagnostic utility and prognostic significance. J Clin Oncol: Off J Am Soc Clin Oncol 17:578–584

    CAS  Google Scholar 

  37. Dianxu F et al (2002) A prospective study of detection of pancreatic carcinoma by combined plasma K-ras mutations and serum CA19-9 analysis. Pancreas 25:336–341

    Article  PubMed  Google Scholar 

  38. Kopreski MS et al (2000) Somatic mutation screening: identification of individuals harboring K-ras mutations with the use of plasma DNA. J Natl Cancer Inst 92:918–923. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10841827

    Article  CAS  PubMed  Google Scholar 

  39. Taniguchi K et al (2011) Quantitative detection of EGFR mutations in circulating tumor DNA derived from lung adenocarcinomas. Clin Cancer Res 17:7808–7815

    Article  CAS  PubMed  Google Scholar 

  40. Diaz LA Jr et al (2012) The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature 486:537–540

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Misale S et al (2012) Emergence of KRAS mutations and acquired resistance to anti-EGFR therapy in colorectal cancer. Nature 486:532–536

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Branford S (2007) Chronic myeloid leukemia: molecular monitoring in clinical practice. ASH Education Program Book, pp 376–383. http://asheducationbook.hematologylibrary.org/content/2007/1/376\nhttp://asheducationbook.hematologylibrary.org/content/2007/1/376.full.pdf

  43. Yu M et al (2013) Circulating breast tumor cells exhibit dynamic changes in epithelial and mesenchymal composition. Science 339:580–584. http://www.sciencemag.org/content/339/6119/580.abstract

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Campbell PJ et al (2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 40:722–729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Stephens PJ et al (2009) Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462:1005–1010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Leary RJ et al (2010) Development of personalized tumor biomarkers using massively parallel sequencing. Sci Transl Med 2:20ra14

    Article  PubMed  PubMed Central  Google Scholar 

  47. McBride DJ et al (2010) Use of cancer-specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors. Genes Chromosomes Cancer 49:1062–1069

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Leary RJ et al (2012) Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med 4:162ra154. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3641759&tool=pmcentrez&rendertype=abstract

    Article  PubMed  PubMed Central  Google Scholar 

  49. Ryan BM et al (2003) A prospective study of circulating mutant KRAS2 in the serum of patients with colorectal neoplasia: strong prognostic indicator in postoperative follow up. Gut 52:101–108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Wang S et al (2010) Potential clinical significance of a plasma-based KRAS mutation analysis in patients with advanced non-small cell lung cancer. Clin Cancer Res: Off J Am Assoc Cancer Res 16:1324–1330

    Article  CAS  Google Scholar 

  51. Boddy JL et al (2005) Prospective study of quantitation of plasma DNA levels in the diagnosis of malignant versus benign prostate disease. Clin Cancer Res 11:1394–1399

    Article  CAS  PubMed  Google Scholar 

  52. Schwarzenbach H, Alix-Panabières C et al (2009) Cell-free tumor DNA in blood plasma as a marker for circulating tumor cells in prostate cancer. Clin Cancer Res 15:1032–1038

    Article  CAS  PubMed  Google Scholar 

  53. Schwarzenbach H, Pantel K et al (2009) Comparative evaluation of cell-free tumor DNA in blood and disseminated tumor cells in bone marrow of patients with primary breast cancer. Breast Cancer Res 11:R71

    Article  PubMed  PubMed Central  Google Scholar 

  54. Diehl F, Schmidt K, Durkee KH et al (2008) Analysis of mutations in DNA isolated from plasma and stool of colorectal cancer patients. Gastroenterology 135:489–498

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Ellinger J et al (2008) CpG island hypermethylation in cell-free serum DNA identifies patients with localized prostate cancer. Prostate 68:42–49

    Article  CAS  PubMed  Google Scholar 

  56. Taback B, Saha S, Hoon DSB (2006) Comparative analysis of mesenteric and peripheral blood circulating tumor DNA in colorectal cancer patients. Ann N Y Acad Sci 1075:197–203

    Article  CAS  PubMed  Google Scholar 

  57. Beaver JA et al (2014) Detection of cancer DNA in plasma of patients with early-stage breast cancer. Clin Cancer Res: Off J Am Assoc Cancer Res 20(10):2643–2650. http://www.ncbi.nlm.nih.gov/pubmed/24504125. Accessed 9 July 2014

    Article  CAS  Google Scholar 

  58. Higgins MJ et al (2012) Detection of tumor PIK3CA status in metastatic breast cancer using peripheral blood. Clin Cancer Res: Off J Am Assoc Cancer Res 18(12):3462–3469. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3533370&tool=pmcentrez&rendertype=abstract. Accessed 18 Oct 2013

    Article  CAS  Google Scholar 

  59. Gerlinger M et al (2012) Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 366:883–892

    Article  CAS  PubMed  Google Scholar 

  60. Rothé F et al (2014) Plasma circulating tumor DNA as an alternative to metastatic biopsies for mutational analysis in breast cancer. Ann Oncol: Off J Eur Soc Med Oncol/ESMO 25(10):1959–1965. http://www.ncbi.nlm.nih.gov/pubmed/25185240. Accessed 29 Sept 2014

    Article  Google Scholar 

  61. Clausen FB et al (2007) Improvement in fetal DNA extraction from maternal plasma. Evaluation of the NucliSens magnetic extraction system and the QIAamp DSP virus kit in comparison with the QIAamp DNA blood mini kit. Prenat Diagn 27(1):6–10. http://www.ncbi.nlm.nih.gov/pubmed/17154236. Accessed 7 Oct 2014

    Article  CAS  PubMed  Google Scholar 

  62. Legler TJ et al (2008) Fetal DNA: strategies for optimal recovery. Methods Mol Biol 444:209–218

    Article  CAS  PubMed  Google Scholar 

  63. Rodríguez de Alba M et al (2012) Noninvasive prenatal diagnosis of monogenic disorders. Expert Opin Biol Ther 12:S171–S179

    Article  Google Scholar 

  64. Sykes PJ et al (1992) Quantitation of targets for PCR by use of limiting dilution. BioTechniques 13(3):444–449. http://www.ncbi.nlm.nih.gov/pubmed/1389177. Accessed 1 Oct 2014

    CAS  PubMed  Google Scholar 

  65. Vogelstein B, Kinzler KW (1999) Digital PCR. Proc Natl Acad Sci U S A 96(16):9236–9241. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=17763&tool=pmcentrez&rendertype=abstract. Accessed 24 Sept 2014

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Diehl F et al (2006) BEAMing: single-molecule PCR on microparticles in water-in-oil emulsions. Nat Methods 3:551–559

    Article  CAS  PubMed  Google Scholar 

  67. Dressman D et al (2003) Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Nat Acad Sci U S A 100:8817–8822

    Article  CAS  Google Scholar 

  68. Li M et al (2006) BEAMing up for detection and quantification of rare sequence variants. Nat Methods 3:95–97

    Article  CAS  PubMed  Google Scholar 

  69. Forshew T et al (2012) Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med 4(136):136ra68. http://stm.sciencemag.org/content/4/136/136ra68.full. Accessed 10 July 2014

    Article  PubMed  Google Scholar 

  70. Kinde I et al (2011) Detection and quantification of rare mutations with massively parallel sequencing. Proc Nat Acad Sci U S A 108(23):9530–9535. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3111315&tool=pmcentrez&rendertype=abstract. Accessed 17 Sept 2013

    Article  Google Scholar 

  71. Schmitt MW et al (2012) From the cover: detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci 109:14508–14513

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Itsara LS et al (2014) Oxidative stress is not a major contributor to somatic mitochondrial DNA mutations. PLoS Genet 10(2):e1003974. http://dx.plos.org/10.1371/journal.pgen.1003974. Accessed 13 Aug 2014 (DM Turnbull ed.)

    Article  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Bunting and Blaustein Building, 1650 Orleans Street, Room 151, 21287, Baltimore, MD, USA

    Heather A. Parsons, Julia A. Beaver & Ben H. Park M.D., PhD

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  1. Heather A. Parsons
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  2. Julia A. Beaver
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  3. Ben H. Park M.D., PhD
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Corresponding author

Correspondence to Ben H. Park M.D., PhD .

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Editors and Affiliations

  1. Johns Hopkins University, Sidney Kimmel Comprehensive Cancer Ctr., BALTIMORE, Maryland, USA

    Vered Stearns

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© 2016 Breast Cancer Research Foundation

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Parsons, H., Beaver, J., Park, B. (2016). Circulating Plasma Tumor DNA. In: Stearns, V. (eds) Novel Biomarkers in the Continuum of Breast Cancer. Advances in Experimental Medicine and Biology(), vol 882. Springer, Cham. https://doi.org/10.1007/978-3-319-22909-6_11

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