The clinical Utilization of circulating cell free DNA (CCFDNA) in blood of cancer patients

International Journal of Molecular Sciences

Volumn 14, Issue 9, 2013, Pages 18925-18958

  Elshimali, Yahya I ^a   Khaddour, Husseina ^b   Sarkissyan, Marianna ^a   Wu, Yanyuan ^a,c   Vadgama, Jaydutt V ^a,c  

^a CHARLES R DREW UNIVERSITY OF MEDICINE AND SCIENCE   (United States)

^b DAMASCUS UNIVERSITY   (Syrian Arab Republic)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Circulating cell free DNA; Early diagnosis; Follow up on cancer treatment; Neoplasms; Prognosis

Indexed keywords

PHENOL; TYLOXAPOL;

ANALYTIC METHOD; AUTOMATION; BLADDER CANCER; BLOOD ANALYSIS; BLUNT END LIGATION MEDIATED WHOLE GENOME AMPLIFICATION; BRAIN CANCER; BREAST CANCER; CANCER DIAGNOSIS; CANCER PATIENT; CANCER STAGING; CAPILLARY ELECTROPHORESIS; CELL FREE SYSTEM; CIRCULATING CELL FREE DNA; CLINICAL PROTOCOL; COLORECTAL CARCINOMA; COPY NUMBER VARIATION; DNA DETERMINATION; DNA ISOLATION; DNA METHYLATION; DNA PURIFICATION; ENDOMETRIUM CANCER; ENZYME LINKED IMMUNOSORBENT ASSAY; ESOPHAGUS CARCINOMA; FOLLOW UP; GENE EXPRESSION PROFILING; GENETIC VARIABILITY; GLIOBLASTOMA; HEAD AND NECK CANCER; HEALTH CARE QUALITY; HEALTH CARE UTILIZATION; HETEROZYGOSITY LOSS; HUMAN; KIDNEY CANCER; LEUKEMIA; LIVER CELL CARCINOMA; LUNG CANCER; LUNG NON SMALL CELL CANCER; LUNG SMALL CELL CANCER; LYMPHOMA; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MELANOMA; MICROFLUIDICS; MICROSATELLITE INSTABILITY; MICROSATELLITE MARKER; MOLECULAR CLONING; NASOPHARYNX CARCINOMA; NEUROBLASTOMA; NUCLEOSPIN METHOD; OVARY CANCER; PANCREAS CARCINOMA; POLYMERASE CHAIN REACTION; PROSTATE CANCER; QIAAMP SYSTEM; QUALITATIVE RESEARCH; QUANTITATIVE STUDY; REVIEW; SENSITIVITY AND SPECIFICITY; SIGNAL PROCESSING; SINGLE NUCLEOTIDE POLYMORPHISM; SQUAMOUS CELL CARCINOMA; STOMACH CARCINOMA; TESTIS CANCER; THYROID CANCER; TRITON HEAT PHENOL PROTOCOL; UTERINE CERVIX CANCER;

DNA; DNA METHYLATION; HUMANS; LOSS OF HETEROZYGOSITY; MICROSATELLITE INSTABILITY; MULTIPLEX POLYMERASE CHAIN REACTION; NEOPLASMS;

EID: 84884199943     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms140918925     Document Type: Review

References (223)

1. Van der Vaart, M.; Pretorius, P.J. A method for characterization of total circulating DNA. Ann. N. Y. Acad. Sci. 2008, 1137, 92-97.
2. Gahan, P.B.; Swaminathan, R. Circulating nucleic acids in plasma and serum. Ann. N. Y. Acad. Sci. 2008, 1137, 1-6.
3. Swaminathan, R.; Butt, A.N. Circulating nucleic acids in plasma and serum. Ann. N. Y. Acad. Sci. 2006, 1075, 1-9.
4. Goebel, G.; Zitt, M.; Zitt, M.; Müller, H.M. Circulating nucleic acids in plasma or serum (CNAPS) as prognostic and predictive markers in patients with solid neoplasias. Dis. Markers 2005, 21, 105-120.
5. Kandel, E.S. Mutations in circulating mitochondrial DNA: Cassandra of oral cancer? Oncotarget 2012, 3, 664-665.
6. Figg, W.D.; Reid, J. Monitor tumor burden with circulating tumor DNA. Cancer Biol. Ther. 2013, 14, 697-698.
7. Jin, D.; Xie, S.; Mo, Z.; Liang, Y.; Guo, B.; Yu, M. Circulating DNA-important biomarker of cancer. J. Mol. Biomarkers Diagn. 2012, doi:10.4172/2155-9929.S2-009.
8. Schwarzenbach, H.; Hoon, D.S.; Pantel, K. Cell-free nucleic acids as biomarkers in cancer patients. Nat. Rev. Cancer 2011, 11, 426-437.
9. Perkins, G.; Yap, T.A.; Pope, L.; Cassidy, A.M.; Dukes, J.P.; Riisnaes, R.; Massard, C.; Cassier, P.A.; Miranda, S.; Clark, J., et al. Multi-purpose utility of circulating plasma DNA testing in patients with advanced cancers. PLoS One 2012, 7, e47020.
10. Chan, S.W.; Chevalier, S.; Aprikian, A.; Chen, J.Z. Simultaneous quantification of mitochondrial DNA damage and copy number in circulating blood: A sensitive approach to systemic oxidative stress. Biomed. Res. Int. 2013, 2013, doi:10.1155/2013/157547.
11. Gormally, E.; Caboux, E.; Vineis, P.; Hainaut, P. Circulating free DNA in plasma or serum as biomarker of carcinogenesis: Practical aspects and biological significance. Mutat. Res. 2007, 635, 105-117.
12. Holdenrieder, S.; Nagel, D.; Schalhorn, A.; Heinemann, V.; Wilkowski, R.; von Pawel, J.; Raith, H.; Feldmann, K.; Kremer, A.E.; Müller, S., et al. Clinical relevance of circulating nucleosomes in cancer. Ann. N. Y. Acad. Sci. 2008, 1137, 180-189.
13. Beck, J.; Urnovitz, H.B.; Riggert, J.; Clerici, M.; Schütz, E. Profile of the circulating DNA in apparently healthy individuals. Clin. Chem. 2009, 55, 607-608.
14. Giasuddin, A.S.; Jhuma, K.A.; Haq, A.M. Applications of free circulating nucleic acids in clinical medicine: Recent advances. Bangladesh Med. Res. Counc. Bull. 2008, 34, 26-32.
15. Tsang, J.C.; Lo, Y.M. Circulating nucleic acids in plasma/serum. Pathology 2007, 39, 197-207.
16. Li, J.; Harris, L.; Mamon, H.; Kulke, M.H.; Liu, W.H.; Zhu, P.; Mike Makrigiorgos, G. Whole genome amplification of plasma-circulating DNA enables expanded screening for allelic imbalance in plasma. J. Mol. Diagn. 2006, 8, 22-30.
17. Tamkovich, S.N.; Cherepanova, A.V.; Kolesnikova, E.V.; Rykova, E.Y.; Pyshnyi, D.V.; Vlassov, V.V.; Laktionov, P.P. Circulating DNA and DNase activity in human blood. Ann. N. Y. Acad. Sci. 2006, 1075, 191-196.
18. Cheng, C.; Omura-Minamisawa, M.; Kang, Y.; Hara, T.; Koike, I.; Inoue, T. Quantification of circulating cell-free DNA in the plasma of cancer patients during radiation therapy. Cancer Sci. 2009, 100, 303-309.
19. Alix-Panabières, C.; Schwarzenbach, H.; Pantel, K. Circulating tumor cells and circulating tumor DNA. Annu. Rev. Med. 2012, 63, 199-215.
20. Jung, K.; Fleischhacker, M.; Rabien, A. Cell-free DNA in the blood as a solid tumor biomarker-A critical appraisal of the literature. Clin. Chim. Acta 2010, 411, 1611-1624.
21. Rykova, E.Y.; Morozkin, E.S.; Ponomaryova, A.A.; Loseva, E.M.; Zaporozhchenko, I.A.; Cherdyntseva, N.V.; Vlassov, V.V.; Laktionov, P.P. Cell-free and cell-bound circulating nucleic acid complexes: Mechanisms of generation, concentration and content. Expert Opin. Biol. Ther. 2012, 12, S141-S153.
22. Zeerleder, S. The struggle to detect circulating DNA. Crit. Care 2006, 10, 142.
23. Board, R.E.; Williams, V.S.; Knight, L.; Shaw, J.; Greystoke, A.; Ranson, M.; Dive, C.; Blackhall, F.H.; Hughes, A. Isolation and extraction of circulating tumor DNA from patients with small cell lung cancer. Ann. N. Y. Acad. Sci. 2008, 1137, 98-107.
24. Umetani, N.; Kim, J.; Hiramatsu, S.; Reber, H.A.; Hines, O.J.; Bilchik, A.J.; Hoon, D.S. Increased integrity of free circulating DNA in sera of patients with colorectal or periampullary cancer: Direct quantitative PCR for ALU repeats. Clin. Chem. 2006, 52, 1062-1069.
25. Kolesnikova, E.V.; Tamkovich, S.N.; Bryzgunova, O.E.; Shelestyuk, P.I.; Permyakova, V.I.; Vlassov, V.V.; Tuzikov, A.S.; Laktionov, P.P.; Rykova, E.Y. Circulating DNA in the blood of gastric cancer patients. Ann. N. Y. Acad. Sci. 2008, 1137, 226-231.
26. Circulating nucleic acids-RNA-DNA-microRNA-small RNAs (1). Available online: http://cna.gene-quantification.info/ (accessed on 2 September 2013).
27. Agostini, M.; Enzo, M.V.; Bedin, C.; Belardinelli, V.; Goldin, E.; del Bianco, P.; Maschietto, E.; D'Angelo, E.; Izzi, L.; Saccani, A., et al. Circulating cell-free DNA: A promising marker of regional lymphonode metastasis in breast cancer patients. Cancer Biomarkers 2012, 11, 89-98.
28. Stroun, M.; Lyautey, J.; Lederrey, C.; Olson-Sand, A.; Anker, P. About the possible origin and mechanism of circulating DNA apoptosis and active DNA release. Clin. Chim. Acta 2001, 313, 139-142.
29. Widschwendter, M.; Menon, U. Circulating methylated DNA: A new generation of tumor markers. Clin. Cancer Res. 2006, 12, 7205-7208.
30. Alves, G.; Kawamura, M.T.; Nascimento, P.; Maciel, C.; Oliveira, J.A.; Teixeira, A.; Carvalho Mda, G. DNA release by line-1 (L1) retrotransposon. Could it be possible? Ann. N. Y. Acad. Sci. 2000, 906, 129-133.
31. Van der Vaart, M.; Pretorius, P.J. Characterization of circulating DNA in healthy human plasma. Clin. Chim. Acta 2008, 395, 186.
32. Bryzgunova, O.E.; Skvortsova, T.E.; Kolesnikova, E.V.; Starikov, A.V.; Rykova, E.Y.; Vlassov, V.V.; Laktionov, P.P. Isolation and comparative study of cell-free nucleic acids from human urine. Ann. N. Y. Acad. Sci. 2006, 1075, 334-340.
33. El Messaoudi, S.; Rolet, F.; Mouliere, F.; Thierry, A.R. Circulating cell free DNA: Preanalytical considerations. Clin. Chim. Acta 2013, 424, 222-230.
34. QIAampSystem. Available online: http://www.ebiotrade.com/buyf/productsf/qiagen/QIAamp_system.htm (accessed on 2 September 2013).
35. QIAamp® DNA Mini Kit and QIAamp DNA Blood Mini Kit Handbook. Available online: http://www.calpoly.edu/~bio/ubl/protocols_files/qiaalu.pdf (accessed on 2 September 2013).
36. Xie, G.S.; Hou, A.R.; Li, L.Y.; Gao, Y.N.; Cheng, S.J. Quantification of plasma DNA as a screening tool for lung cancer. Chin. Med. J. 2004, 117, 1485-1488.
37. Xue, X.; Teare, M.D.; Holen, I.; Zhu, Y.M.; Woll, P.J. Optimizing the yield and utility of circulating cell-free DNA from plasma and serum. Clin. Chim. Acta 2009, 404, 100-104.
38. Hufnagl, C.; Stocher, M.; Moik, M.; Geisberger, R.; Greil, R. A modified Phenol-chloroform extraction method for isolating circulating cell free DNA of tumor patients. J. Nucleic Acids Invest. 2013, doi:10.4081/jnai.2013.e1.
39. Kirsch, C.; Weickmann, S.; Schmidt, B.; Fleischhacker, M. An improved method for the isolation of free-circulating plasma DNA and cell-free DNA from other body fluids. Ann. N. Y. Acad. Sci. 2008, 1137, 135-139.
40. Fleischhacker, M.; Schmidt, B. Circulating nucleic acids (CNAs) and cancer-A survey. Biochim. Biophys. Acta 2007, 1775, 181-232.
41. Mouliere, F.; Robert, B.; Arnau Peyrotte, E.; del Rio, M.; Ychou, M.; Molina, F.; Gongora, C.; Thierry, A.R. High fragmentation characterizes tumour-derived circulating DNA. PLoS One 2011, 6, e23418.
42. Korabecna, M.; Opatrna, S.; Wirth, J.; Rulcova, K.; Eiselt, J.; Sefrna, F.; Horinek, A. Cell-free plasma DNA during peritoneal dialysis and hemodialysis and in patients with chronic kidney disease. Ann. N. Y. Acad. Sci. 2008, 1137, 296-301.
43. An, Q.; Liu, Y.; Gao, Y.; Huang, J.; Fong, X.; Li, L.; Zhang, D.; Cheng, S. Detection of p16 hypermethylation in circulating plasma DNA of non-small cell lung cancer patients. Cancer Lett. 2002, 188, 109-114.
44. Liu, Y.; An, Q.; Li, L.; Zhang, D.; Huang, J.; Feng, X.; Cheng, S.; Gao, Y. Hypermethylation of p16INK4a in Chinese lung cancer patients: Biological and clinical implications. Real-time PCR for hypermethylated genes. Carcinogenesis 2003, 24, 1897-1901.
45. Nakayama, G.; Hibi, K.; Nakayama, H.; Kodera, Y.; Ito, K.; Akiyama, S.; Nakao, A. A highly sensitive method for the detection of p16 methylation in the serum of colorectal cancer patients. Anticancer Res. 2007, 27, 1459-1463.
46. Zachariah, R.R.; Schmid, S.; Buerki, N.; Radpour, R.; Holzgreve, W.; Zhong, X. Levels of circulating cell-free nuclear and mitochondrial DNA in benign and malignant ovarian tumors. Obstet. Gynecol. 2008, 112, 843-850.
47. Tani, N.; Ichikawa, D.; Ikoma, D.; Ikoma, H.; Sai, S.; Tomita, H.; Okamoto, K.; Kikuchi, S.; Fujiwara, H.; Ochiai, T., et al. An early detection of recurrence using reverse transcriptase-polymerase chain reaction (RT-PCR) and methylation-specific polymerase chain reaction (MSP) from peripheral blood in patients after gastrectomy. Gan To Kagaku Ryoho 2006, 33, 1720-1722.
48. Ikoma, D.; Ichikawa, D.; Ueda, Y.; Tani, N.; Tomita, H.; Sai, S.; Kikuchi, S.; Fujiwara, H.; Otsuji, E.; Yamagishi, H. Circulating tumor cells and aberrant methylation as tumor markers in patients with esophageal cancer. Anticancer Res. 2007, 27, 535-539.
49. Goldshtein, H.; Hausmann, M.J.; Douvdevani, A. A rapid direct fluorescent assay for cell-free DNA quantification in biological fluids. Ann. Clin. Biochem. 2009, 46, 488-494.
50. Nakamura, T.; Sunami, E.; Nguyen, T.; Hoon, D.S. Analysis of loss of heterozygosity in circulating DNA. Methods Mol. Biol. 2009, 520, 221-229.
51. Forshew, T.; Murtaza, M.; Parkinson, C.; Gale, D.; Tsui, D.W.; Kaper, F.; Dawson, S.J.; Piskorz, A.M.; Jimenez-Linan, M.; Bentley, D., et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci. Transl. Med. 2012, doi:10.1126/scitranslmed.3003726.
52. Cooke, S.; Campbell, P. Circulating DNA and next-generation sequencing. Recent Results Cancer Res. 2012, 195, 143-149.
53. Vaissière, T.; Cuenin, C.; Paliwal, A.; Vineis, P.; Hoek, G.; Krzyzanowski, M.; Airoldi, L.; Dunning, A.; Garte, S.; Hainaut, P., et al. Quantitative analysis of DNA methylation after whole bisulfitome amplification of a minute amount of DNA from body fluids. Epigenetics 2009, 4, 221-230.
54. Lofton-Day, C.; Model, F.; Devos, T.; Tetzner, R.; Distler, J.; Schuster, M.; Song, X.; Lesche, R.; Liebenberg, V.; Ebert, M., et al. DNA methylation biomarkers for blood-based colorectal cancer screening. Clin. Chem. 2008, 54, 414-423.
55. Keeley, B.; Stark, A.; Pisanic, T.R., II; Kwak, R.; Zhang, Y.; Wrangle, J.; Baylin, S.; Herman, J.; Ahuja, N.; Wang, J. Extraction and processing of circulating DNA from large sample volumes using methylation on beads for the detection of rare epigenetic events. Clin. Chim. Acta 2013, 425C, 169-175.
56. Chiminqgi, M.; Moutereau, S.; Pernet, P.; Conti, M.; Barbu, V.; Lemant, J.; Sacko, M.; Vaubourdolle, M.; Loric, S. Specific real-time PCR vs. fluorescent dyes for serum free DNA quantification. Clin. Chem. Lab. Med. 2007, 45, 993-995.
57. Sharma, V.K.; Vouros, P.; Glick, J. Mass spectrometric based analysis, characterization and applications of circulating cell free DNA isolated from human body fluids. Int. J. Mass. Spectrom. 2011, 304, 172-183.
58. Cell free fetal DNA. Available online: http://en.wikipedia.org/wiki/Cell-free_fetal_DNA (accessed on 2 September 2013).
59. Holmberg, R.C.; Gindlesperger, A.; Stokes, T.; Lopez, D.; Hyman, L.; Freed, M.; Belgrader, P.; Harvey, J.; Li, Z. Akonni TruTip® and Qiagen® methods for extraction of fetal circulating DNA-evaluation by real-time and digital PCR. PLoS One 2013, 8, e73068.
60. Taly, V.; Pekin, D.; Benhaim, L.; Kotsopoulos, S.K.; le Corre, D.; Li, X.; Atochin, I.; Link, D.R.; Griffiths, A.D.; Pallier, K., et al. Multiplex picodroplet digital PCR to detect KRAS mutations in circulating DNA from the plasma of colorectal cancer patients. Clin. Chem. 2013, doi:10.1373/clinchem.2013.206359.
61. Gevensleben, H.; Garcia-Murillas, I.; Graeser, M.K.; Schiavon, G.; Osin, P.; Parton, M.; Smith, I.E.; Ashworth, A.; Turner, N.C. Noninvasive detection of HER2 amplification with plasma DNA digital PCR. Clin. Cancer Res. 2013, 19, 3276-3284.
62. Müller, H.M.; Widschwendter, A.; Fiegl, H.; Ivarsson, L.; Goebel, G.; Perkmann, E.; Marth, C.; Widschwendter, M. DNA methylation in serum of breast cancer patients: An independent prognostic marker. Cancer Res. 2003, 63, 7641-7645.
63. De Sario, A. Clinical and molecular overview of inherited disorders resulting from epigenomic dysregulation. Eur. J. Med. Genet. 2009, 52, 363-372.
64. Hodges, E.; Smith, A.D.; Kendall, J.; Xuan, Z.; Ravi, K.; Rooks, M.; Zhang, M.Q.; Ye, K.; Bhattacharjee, A.; Brizuela, L., et al. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res. 2009, 19, 1593-1605.
65. Herman, J.G. Circulating methylated DNA. Ann. N. Y. Acad. Sci. 2004, 1022, 33-39.
66. Patel, A.; Groopman, J.D.; Umar, A. DNA methylation as a cancer-specific biomarker: From molecules to populations. Ann. N. Y. Acad. Sci. 2003, 983, 286-297.
67. Li, L.; Choi, J.Y.; Lee, K.M.; Sung, H.; Park, S.K.; Oze, I.; Pan, K.F.; You, W.C.; Chen, Y.X.; Fang, J.Y., et al. DNA methylation in peripheral blood: A potential biomarker for cancer molecular epidemiology. J. Epidemiol. 2012, 22, 384-394.
68. Wong, I.H.; Lo, Y.M.; Johnson, P.J. Epigenetic tumor markers in plasma and serum: Biology and applications to molecular diagnosis and disease monitoring. Ann. N. Y. Acad. Sci. 2001, 945, 36-50.
69. Sunami, E.; Vu, A.T.; Nguyen, S.L.; Hoon, D.S. Analysis of methylated circulating DNA in cancer patients' blood. Methods Mol. Biol. 2009, 507, 349-356.
70. Kim, J.C.; Mirkin, S.M. The balancing act of DNA repeat expansions. Curr. Opin. Genet. Dev. 2013, 23, 280-288.
71. Markovic, S.; Antic, J.; Dimitrijevic, I.; Zogovic, B.; Bojic, D.; Svorcan, P.; Markovic, V.; Krivokapic, Z. Microsatellite instability affecting the T17 repeats in intron 8 of HSP110, as well as five mononucleotide repeats in patients with colorectal carcinoma. Biomarkers Med. 2013, 7, 613-621.
72. Carpagnano, G.E.; Costantino, E.; Palladino, G.P.; Lacedonia, D.; Martinelli, D.; Orlando, S.; Foschino-Barbaro, M.P. Microsatellite alterations and cell-free DNA analysis: Could they increase the cytology sensitivity in the diagnosis of malignant pleural effusion? Rejuvenation Res. 2012, 15, 265-273.
73. Lu, Y.; Soong, T.D.; Elemento, O. A novel approach for characterizing microsatellite instability in cancer cells. PLoS One 2013, 8, e63056.
74. Zauber, P.; Huang, J.; Sabbath-Solitare, M.; Marotta, S. Similarities of molecular genetic changes in synchronous and metachronous colorectal cancers are limited and related to the cancers' proximities to each other. J. Mol. Diagn. 2013, 15, 652-660.
75. Heyn, H.; Moran, S.; Hernando-Herraez, I.; Sayols, S.; Gomez, A.; Sandoval, J.; Monk, D.; Hata, K.; Marques-Bonet, T.; Wang, L., et al. DNA methylation contributes to natural human variation. Genome Res. 2013, 23, 1363-1372.
76. Genetic variation. Available online: http://www.biology-online.org/dictionary/Genetic_variation (accessed on 2 September 2013).
77. Palumbo, E.; Tosoni, E.; Matricardi, L.; Russo, A. Genetic instability of the tumor suppressor gene FHIT in normal human cells. Genes Chromosomes Cancer 2013, 52, 832-844.
78. Wang, E.; Zou, J.; Zaman, N.; Beitel, L.K.; Trifiro, M.; Paliouras, M. Cancer systems biology in the genome sequencing era: Part 1, dissecting and modeling of tumor clones and their networks. Semin. Cancer Biol. 2013, 23, 279-285.
79. Wrzeszczynski, K.O.; Varadan, V.; Kamalakaran, S.; Levine, D.A.; Dimitrova, N.; Lucito, R. Integrative prediction of gene function and platinum-free survival from genomic and epigenetic features in ovarian cancer. Methods Mol. Biol. 2013, 1049, 35-51.
80. Heitzer, E.; Auer, M.; Hoffmann, E.M.; Pichler, M.; Gasch, C.; Ulz, P.; Lax, S.; Waldispuehl-Geigl, J.; Mauermann, O.; Mohan, S., et al. Establishment of tumor-specific copy number alterations from plasma DNA of patients with cancer. Int. J. Cancer 2013, 133, 346-356.
81. Long, X.D.; Zhao, D.; Wang, C.; Huang, X.Y.; Yao, J.G.; Ma, Y.; Wei, Z.H.; Liu, M.; Zeng, L.X.; Mo, X.Q., et al. Genetic polymorphisms in DNA repair genes XRCC4 and XRCC5 and aflatoxin B1-related hepatocellular carcinoma. Epidemiology 2013, 24, 671-681.
82. Dorjgochoo, T.; Zheng, Y.; Gao, Y.T.; Ma, X.; Long, J.; Bao, P.; Zhang, B.; Wen, W.; Lu, W.; Zheng, W., et al. No association between genetic variants in angiogenesis and inflammation pathway genes and breast cancer survival among Chinese women. Cancer Epidemiol. 2013, doi:10.1016/j.canep.2013.06.005.
83. Bhayal, A.C.; Krishnaveni, D.; Rangarao, K.P.; Bogadi, V.; Suman, C.; Jyothy, A.; Nallari, P.; Venkateshwari, A. Role of tumor necrosis factor-α-308 G/A promoter polymorphism in gastric cancer. Saudi J. Gastroenterol. 2013, 19, 182-186.
84. Duell, E.J.; Holly, E.A.; Kelsey, K.T.; Bracci, P.M. Genetic variation in CYP17A1 and pancreatic cancer in a population-based case-control study in the San Francisco Bay area, California. Int. J. Cancer 2010, 126, 790-795.
85. Landmark-Høyvik, H.; Dumeaux, V.; Nebdal, D.; Lund, E.; Tost, J.; Kamatani, Y.; Renault, V.; Børresen-Dale, A.L.; Kristensen, V.; Edvardsen, H. Genome-wide association study in breast cancer survivors reveals SNPs associated with gene expression of genes belonging to MHC class I and II. Genomics 2013, doi:10.1016/j.ygeno.2013.07.006.
86. Kivistö, K.T.; Kroemer, H.K.; Eichelbaum, M. The role of human cytochrome P450 enzymes in the metabolism of anticancer agents: Implications for drug interactions. Br. J. Clin. Pharmacol. 1995, 40, 523-530.
87. Slattery, M.L.; John, E.M.; Stern, M.C.; Herrick, J.; Lundgreen, A.; Giuliano, A.R.; Hines, L.; Baumgartner, K.B.; Torres-Mejia, G.; Wolff, R.K. Associations with growth factor genes (FGF1, FGF2, PDGFB, FGFR2, NRG2, EGF, ERBB2) with breast cancer risk and survival: The breast cancer health disparities study. Breast Cancer Res. Treat. 2013, 140, 587-601.
88. Zardavas, D.; Pugliano, L.; Piccart, M. Personalized therapy for breast cancer: A dream or a reality? Future Oncol. 2013, 9, 1105-1119.
89. Horvath, A.; Pakala, S.B.; Mudvari, P.; Reddy, S.D.; Ohshiro, K.; Casimiro, S.; Pires, R.; Fuqua, S.A.; Toi, M.; Costa, L., et al. Novel insights into breast cancer genetic variance through RNA sequencing. Sci. Rep. 2013, 3, doi:10.1038/srep02256.
90. Hyland, P.L.; Lin, S.W.; Hu, N.; Zhang, H.; Wang, L.; Su, H.; Wang, C.; Ding, T.; Tang, Z.Z.; Fan, J.H., et al. Genetic variants in fas signaling pathway genes and risk of gastric cancer. Int. J. Cancer 2013, doi:10.1002/ijc.28415.
91. Thongbai, C.; Sa-Nguanmoo, P.; Kranokpiruk, P.; Poovorawan, K.; Poovorawan, Y.; Tangkijvanich, P. Hepatitis B virus genetic variation and TP53 R249S mutation in patients with hepatocellular carcinoma in Thailand. Asian Pac. J. Cancer Prev. 2013, 14, 3555-3559.
92. Breitbach, S.; Tug, S.; Simon, P. Circulating cell-free DNA: An up-coming molecular marker in exercise physiology. Sports Med. 2012, 42, 565-586.
93. Ilhan-Mutlu, A.; Wagner, L.; Preusser, M. Circulating biomarkers of CNS tumors: An update Biomarkers Med. 2013, 7, 267-285.
94. Combaret, V.; Audoynaud, C.; Iacono, I.; Favrot, M.C.; Schell, M.; Bergeron, C.; Puisieux, A. Circulating MYCN DNA as a tumor-specific marker in neuroblastoma patients. Cancer Res. 2002, 62, 3646-3648.
95. Yagyu, S.; Gotoh, T.; Iehara, T.; Miyachi, M.; Katsumi, Y.; Tsubai-Shimizu, S.; Kikuchi, K.; Tamura, S.; Tsuchiya, K.; Imamura, T., et al. Circulating methylated-DCR2 gene in serum as an indicator of prognosis and therapeutic efficacy in patients with MYCN nonamplified neuroblastoma. Clin. Cancer Res. 2008, 14, 7011-7019.
96. Misawa, A.; Tanaka, S.; Yagyu, S.; Tsuchiya, K.; Iehara, T.; Sugimoto, T.; Hosoi, H. RASSF1A hypermethylation in pretreatment serum DNA of neuroblastoma patients: A prognostic marker. Br. J. Cancer 2009, 100, 399-404.
97. Weaver, K.D.; Grossman, S.A.; Herman, J.G. Methylated tumor-specific DNA as a plasma biomarker in patients with glioma. Cancer Invest. 2006, 24, 35-40.
98. Lavon, I.; Refael, M.; Zelikovitch, B.; Shalom, E.; Siegal, T. Serum DNA can define tumor-specific genetic and epigenetic markers in gliomas of various grades. Neuro Oncol. 2010, 12, 173-180.
99. Salkeni, M.A.; Zarzour, A.; Ansay, T.Y.; McPherson, C.M.; Warnick, R.E.; Rixe, O.; Bahassi, E.M. Detection of EGFRvIII mutant DNA in the peripheral blood of brain tumor patients. J. Neurooncol. 2013, doi:10.1007/s11060-013-1209-0.
100. Majchrzak-Celińska, A.; Paluszczak, J.; Kleszcz, R.; Magiera, M.; Barciszewska, A.M.; Nowak, S.; Baer-Dubowska, W. Detection of MGMT, RASSF1A, p15INK4B, and p14ARF promoter methylation incirculating tumor-derived DNA of central nervous system cancer patients. J. Appl. Genet. 2013, 54, 335-344.
101. Catarino, R.; Ferreira, M.M.; Rodrigues, H.; Coelho, A.; Nogal, A.; Sousa, A.; Medeiros, R. Quantification of free circulating tumor DNA as a diagnostic marker for breast cancer. DNA Cell Biol. 2008, 27, 415-421.
102. Zanetti-Dällenbach, R.A.; Schmid, S.; Wight, E.; Holzgreve, W.; Ladewing, A.; Hahn, S.; Zhong, X.Y. Levels of circulating cell-free serum DNA in benign and malignant breast lesions. Int. J. Biol. Markers 2007, 22, 95-99.
103. Zanetti-Dällenbach, R.; Wight, E.; Fan, A.X.; Lapaire, O.; Hahn, S.; Holzgreve, W.; Zhong, X.Y. Positive correlation of cell-free DNA in plasma/serum in patients with malignant and benign breast disease. Anticancer Res. 2008, 28, 921-925.
104. Hashad, D.; Sorour, A.; Ghazal, A.; Talaat, I. Free circulating tumor DNA as a diagnostic marker for breast cancer. J. Clin. Lab. Anal. 2012, 26, 467-472.
105. Schwarzenbach, H.; Eichelser, C.; Kropidlowski, J.; Janni, W.; Rack, B.; Pantel, K. Loss of heterozygosity at tumor suppressor genes detectable on fractionated circulating cell-free tumor DNA as indicator of breast cancer progression. Clin. Cancer Res. 2012, 18, 5719-5730.
106. Weiss, L.; Hufnagl, C.; Greil, R. Circulating tumor DNA to monitor metastatic breast cancer. N. Engl. J. Med. 2013, 369, 93.
107. Page, K.; Hava, N.; Ward, B.; Brown, J.; Guttery, D.S.; Ruangpratheep, C.; Blighe, K.; Sharma, A.; Walker, R.A.; Coombes, R.C., et al. Detection of HER2 amplification in circulating free DNA in patients with breast cancer. Br. J. Cancer 2011, 104, 1342-1348.
108. Shaw, J.A.; Page, K.; Blighe, K.; Hava, N.; Guttery, D.; Ward, B.; Brown, J.; Ruangpratheep, C.; Stebbing, J.; Payne, R., et al. Genomic analysis of circulating cell-free DNA infers breast cancer dormancy. Genome Res. 2012, 22, 220-231.
109. Van der Auwera, I.; Elst, H.J.; van Laere, S.J.; Maes, H.; Huget, P.; van Dam, P.; van Marck, E.A.; Vermeulen, P.B.; Dirix, L.Y. The presence of circulating total DNA and methylated genes is associated with circulating tumour cells in blood from breast cancer patients. Br. J. Cancer 2009, 100, 1277-1286.
110. Umetani, N.; Giuliano, A.E.; Hiramatsu, S.H.; Amersi, F.; Nakagawa, T.; Martino, S.; Hoon, D.S. Prediction of breast tumor progression by integrity of free circulating DNA in serum. J. Clin. Oncol. 2006, 24, 4270-4276.
111. Mirza, S.; Sharma, G.; Parshad, R.; Srivastava, A.; Gupta, S.D.; Ralhan, R. Clinical significance of promoter hypermethylation of ERβ and RARβ2 in tumor and serum DNA in Indian breast cancer patients. Ann. Surg. Oncol. 2012, 19, 3107-3115.
112. Rykova, E.; Skvortsova, T.E.; Hoffmann, A.L.; Tamkovich, S.N.; Starikov, A.V.; Bryzgunova, O.E.; Permiakova, V.I.; Warnecke, J.M.; Sczakiel, G.; Vlasov, V.V., et al. Breast cancer diagnostics based on extracellular DNA and RNA circulating in blood. Biomed. Khim. 2008, 54, 94-103.
113. Zurita, M.; Lara, P.C.; del Moral, R.; Torres, B.; Linares-Fernández, J.L.; Arrabal, S.R.; Martínez-Galán, J.; Oliver, F.J.; Ruiz de Almodóvar, J.M. Hypermethylated 14-3-3-sigma and ESR1 gene promoters in serum as candidate biomarkers for the diagnosis and treatment efficacy of breast cancer metastasis. BMC Cancer 2010, 10, 217.
114. Hu, X.C.; Wong, I.H.; Chow, L.W. Tumor-derived aberrant methylation in plasma of invasive ductal breast cancer patients: Clinical implications. Oncol. Rep. 2003, 10, 1811-1815.
115. Divella, R.; Tommasi, S.; Lacalamita, R.; Daniele, A.; Abbate, I.; Garrisi, V.M.; Savino, E.; Coviello, M.; Rubini, V.; Simone, G., et al. Circulating hTERT DNA in early breast cancer. Anticancer Res. 2009, 29, 2845-2849
116. Zmetakova, I.; Danihel, L.; Smolkova, B.; Mego, M.; Kajabova, V.; Rusnak, T.K.; Rychly, B.; Danis, D.; Repiska, V., et al. Evaluation of protein expression and DNA methylation profiles detected by pyrosequencing in invasive breast cancer. Neoplasma. 2013, doi:10.4149/neo_2013_082.
117. Chimonidou, M.; Tzitzira, A.; Strati, A.; Sotiropoulou, G.; Sfikas, C.; Malamos, N.; Georgoulias, V.; Lianidou, E. CST6 promoter methylation in circulating cell-free DNA of breast cancer patients. Clin. Biochem. 2013, 46, 235-240.
118. Deligezer, U.; Eralp, Y.; Akisik, E.Z.; Akisik, E.E.; Saip, P.; Topuz, E.; Dalay, N. Effect of adjuvant chemotherapy on integrity of free serum DNA in patients with breast cancer. Ann. N. Y. Acad. Sci. 2008, 1137, 175-179.
119. Nicolini, C.; Ens, C.; Cerutti, T.; Roehe, A.V.; Agnes, G.; Damin, A.P.; Alexandre, C.O. Elevated level of cell-free plasma DNA is associated with advanced-stage breast cancer and metastasis. Clin. Chem. Lab. Med. 2013, 27, 1-2.
120. Liggett, T.E.; Melnikov, A.A.; Marks, J.R.; Levenson, V.V. Methylation patterns in cell-free plasma DNA reflect removal of the primary tumor and drug treatment of breast cancer patients. Int. J. Cancer 2011, 128, 492-499.
121. Sharma, G.; Mirza, S.; Parshad, R.; Gupta, S.D.; Ralhan, R. DNA methylation of circulating DNA: A marker for monitoring efficacy of neoadjuvant chemotherapy in breast cancer patients. Tumour Biol. 2012, 33, 1837-1843.
122. Lehner, J.; Stötzer, O.J.; Fersching, D.; Nagel, D.; Holdenrieder, S. Circulating plasma DNA and DNA integrity in breast cancer patients undergoing neoadjuvant chemotherapy. Clin. Chim. Acta 2013, 425C, 206-211.
123. El Tarhouny, S.; Seefeld, M.; Fan, A.X.; Hahn, S.; Holzgreve, W.; Zhong, X.Y. Comparison of serum VEGF and its soluble receptor sVEGFR1 with serum cell-free DNA in patients with breast tumor. Cytokine 2008, 44, 65-69.
124. Dawson, S.J.; Tsui, D.W.; Murtaza, M.; Biggs, H.; Rueda, O.M.; Chin, S.F.; Dunning, M.J.; Gale, D.; Forshew, T.; Mahler-Araujo, B.; Rajan S., et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N. Engl. J. Med. 2013, 368, 1199-1209.
125. Tanaka, H.; Tsuda, H.; Nishimura, S.; Nomura, H.; Kataoka, F.; Chiyoda, T.; Tanaka, K.; Iguchi, Y.; Susumu, N.; Aoki, D. Role of circulating free alu DNA in endometrial cancer. Int. J. Gynecol. Cancer 2012, 22, 82-86.
126. Zachariah, R.; Schmid, S.; Radpour, R.; Buerki, N.; Fan, A.X.; Hahn, S.; Holzgreve, W.; Zhong, X.Y. Circulating cell-free DNA as a potential biomarker for minimal and mild endometriosis. Reprod. Biomed. Online 2009, 18, 407-411.
127. Wang, B.G.; Huang, H.Y.; Chen, Y.C.; Bristow, R.E.; Kassauei, K.; Cheng, C.C.; Roden, R.; Sokoll, L.J.; Chan, D.W.; Shih, I.M. Increased plasma DNA integrity in cancer patients. Cancer Res. 2003, 63, 3966-3968.
128. Domenyuk, V.P.; Litovkin, K.V.; Verbitskaya, T.G.; Dubinina, V.G.; Bubnov, V.V. Identification of new DNA markers of endometrial cancer in patients from the Ukrainian population. Exp. Oncol. 2007, 29, 152-155.
129. Pölcher, M.; Ellinger, J.; Willems, S.; El-Maarri, O.; Höller, T.; Amann, C.; Wolfgarten, M.; Rudlowski, C.; Kuhn, W.; Braun, M. Impact of the menstrual cycle on circulating cell-free DNA. Anticancer Res. 2010, 30, 2235-2240.
130. Dobrzycka, B.; Terlikowski, S.J.; Mazurek, A.; Kowalczuk, O.; Niklinska, W.; Chyczewski, L.; Kulikowski, M. Circulating free DNA, p53 antibody and mutations of KRAS gene in endometrial cancer. Int. J. Cancer 2010, 127, 612-621.
131. Guan, T.; Guo, X.Y.; Ye, C.L.; Jiang, Y.H. Analysis of circulating DNA level in the plasma of cervical cancer patients. Nan Fang Yi Ke Da Xue Xue Bao 2008, 28, 1663-1667.
132. Widschwendter, A.; Müller, H.M.; Fiegl, H.; Ivarsson, L.; Wiedemair, A.; Müller-Holzner, E.; Goebel, G.; Marth, C.; Widschwendter, M. DNA methylation in serum and tumors of cervical cancer patients. Clin. Cancer Res. 2004, 10, 565-571.
133. Widschwendter, A.; Ivarsson, L.; Blassnig, A.; Müller, H.M.; Fiegl, H.; Wiedemair, A.; Müller-Holzner, E.; Goebel, G.; Marth, C.; Widschwendter, M. CDH1 and CDH13 methylation in serum is an independent prognostic marker in cervical cancer patients. Int. J. Cancer 2004, 109, 163-166.
134. Ma, L.; Liu, F.R.; Zhang, S.L. Detection of circulating hypermethylated tumor-specific RASSF1A DNA in ovarian cancer patients. Zhonghua Bing Li Xue Za Zhi 2005, 34, 785-787.
135. Kamat, A.A.; Bischoff, F.Z.; Dang, D.; Baldwin, M.F.; Han, L.Y.; Lin, Y.G.; Merritt, W.M.; Landen, C.N., Jr.; Lu, C.; Gershenson, D.M., et al. Circulating cell-free DNA: A novel biomarker for response to therapy in ovarian carcinoma. Cancer Biol. Ther. 2006, 5, 1369-1374.
136. Dobrzycka, B.; Terlikowski, S.J.; Kinalski, M.; Kowalczuk, O.; Niklinska, W.; Chyczewski, L. Circulating free DNA and p53 antibodies in plasma of patients with ovarian epithelial cancers. Ann. Oncol. 2011, 22, 1133-1140.
137. Kuhlmann, J.D.; Schwarzenbach, H.; Wimberger, P.; Poetsch, M.; Kimmig, R.; Kasimir-Bauer, S. LOH at 6q and 10q in fractionated circulating DNA of ovarian cancer patients is predictive for tumor cell spread and overall survival. BMC Cancer 2012, 12, 325.
138. Ren, N.; Ye, Q.H.; Qin, L.X.; Zhang, B.H.; Liu, Y.K.; Tang, Z.Y. Circulating DNA level is negatively associated with the long-term survival of hepatocellular carcinoma patients. World J. Gastroenterol. 2006, 12, 3911-3914.
139. Iizuka, N.; Sakaida, I.; Moribe, T.; Fujita, N.; Miura, T.; Stark, M.; Tamatsukuri, S.; Ishitsuka, H.; Uchida, K.; Terai, S., et al. Elevated levels of circulating cell-free DNA in the blood of patients with hepatitis C virus-associated hepatocellular carcinoma. Anticancer Res. 2006, 26, 4713-4719.
140. Tangkijvanich, P.; Hourpai, N.; Rattanatanyong, P.; Wisedopas, N.; Mahachai, V.; Mutirangura, A. Serum LINE-1 hypomethylation as a potential prognostic marker for hepatocellular carcinoma. Clin. Chim. Acta 2007, 379, 127-133.
141. Iida, M.; Iizuka, N.; Sakaida, I.; Moribe, T.; Fujita, N.; Miura, T.; Tamatsukuri, S.; Ishitsuka, H.; Uchida, K.; Terai, S., et al. Relation between serum levels of cell-free DNA and inflammation status in hepatitis C virus-related hepatocellular carcinoma. Oncol. Rep. 2008, 20, 761-765.
142. Hosny, G.; Farahat, N.; Tayel, H.; Hainaut, P. Ser-249 TP53 and CTNNB1 mutations in circulating free DNA of Egyptian patients with hepatocellular carcinoma versus chronic liver diseases. Cancer Lett. 2008, 264, 201-208.
143. Wong, I.H.; Lo, Y.M.; Zhang, J.; Liew, C.T.; Ng, M.H.; Wong, N.; Lai, P.B.; Lau, W.Y.; Hjelm, N.M.; Johnson, P.J. Detection of aberrant p16 methylation in the plasma and serum of liver cancer patients. Cancer Res. 1999, 59, 71-73.
144. Chan, K.C.; Lai, P.B.; Mok, T.S.; Chan, H.L.; Ding, C.; Yeung, S.W.; Lo, Y.M. Quantitative analysis of circulating methylated DNA as a biomarker for hepatocellular carcinoma. Clin. Chem. 2008, 54, 1528-1536.
145. Pang, J.Z.; Qin, L.X.; Ren, N.; Ye, Q.H.; Ying, W.D.; Liu, Y.K.; Tang, Z.Y. Microsatellite alterations of circulating DNA in the plasma of patients with hepatocellular carcinoma. Zhonghua Yi Xue Za Zhi 2006, 86, 1662-1665.
146. Pang, J.Z.; Qin, L.X.; Wang, Q.Q.; Ren, N.; Sun, B.S.; Lin, G.L.; Ye, Q.H.; Liu, Y.K.; Tang, Z.Y. Loss of heterozygosity of plasma circulating DNA from hepatocellular carcinoma patients and its clinical significance. Zhonghua Gan Zang Bing Za Zhi 2007, 15, 906-909.
147. Zhou, J.; Shi, Y.H.; Fan, J. Circulating cell-free nucleic acids: Promising biomarkers of hepatocellular carcinoma. Semin. Oncol. 2012, 39, 440-448.
148. Melnikov, A.A.; Scholtens, D.; Talamonti, M.S.; Bentrem, D.J.; Levenson, V.V. Methylation profile of circulating plasma DNA in patients with pancreatic cancer. J. Surg. Oncol. 2009, 99, 119-122.
149. Gornik, I.; Wagner, J.; Gasparović, V.; Lauc, G.; Gornik, O. Free serum DNA is an early predictor of severity in acute pancreatitis. Clin. Biochem. 2009, 42, 38-43.
150. Sawabu, N.; Watanabe, H.; Yamaguchi, Y.; Ohtsubo, K.; Motoo, Y. Serum tumor markers and molecular biological diagnosis in pancreatic cancer. Pancreas 2004, 28, 263-267.
151. Liggett, T.; Melnikov, A.; Yi, Q.L.; Replogle, C.; Brand, R.; Kaul, K.; Talamonti, M.; Abrams, R.A.; Levenson, V. Differential methylation of cell-free circulating DNA among patients with pancreatic cancer versus chronic pancreatitis. Cancer 2010, 116, 1674-1680.
152. Tomita, H.; Ichikawa, D.; Ikoma, D.; Sai, S.; Tani, N.; Ikoma, H.; Fujiwara, H.; Kikuchi, S.; Okamoto, K.; Ochiai, T., et al. Quantification of circulating plasma DNA fragments as tumor markers in patients with esophageal cancer. Anticancer Res. 2007, 27, 2737-2741.
153. Tomita, H.; Ichikawa, D.; Sai, S.; Morimura, R.; Murayama, Y.; Komatsu, S.; Ikoma, D.; Tani, N.; Ikoma, H.; Fujiwara, H., et al. Quantification of circulating plasma DNA fragments as tumor markers in patients with esophageal and gastric cancer. Gan To Kagaku Ryoho 2007, 34, 1908-1910.
154. Hoffmann, A.C.; Vallböhmer, D.; Prenzel, K.; Metzger, R.; Heitmann, M.; Neiss, S.; Ling, F.; Hölscher, A.H.; Schneider, P.M.; Brabender, J. Methylated DAPK and APC promoter DNA detection in peripheral blood is significantly associated with apparent residual tumor and outcome. J. Cancer Res. Clin. Oncol. 2009, 135, 1231-1237.
155. Sai, S.; Ichikawa, D.; Tomita, H.; Ikoma, D.; Tani, N.; Ikoma, H.; Kikuchi, S.; Fujiwara, H.; Ueda, Y.; Otsuji, E. Quantification of plasma cell-free DNA in patients with gastric cancer. Anticancer Res. 2007, 27, 2747-2751.
156. Sakakura, C.; Hamada, T.; Miyagawa, K.; Nishio, M.; Miyashita, A.; Nagata, H.; Ida, H.; Yazumi, S.; Otsuji, E.; Chiba, T., et al. Quantitative analysis of tumor-derived methylated RUNX3 sequences in the serum of gastric cancer patients. Anticancer Res. 2009, 29, 2619-2625.
157. Schwarzenbach, H.; Stoehlmacher, J.; Pantel, K.; Goekkurt, E. Detection and monitoring of cell-free DNA in blood of patients with colorectal cancer. Ann. N. Y. Acad. Sci. 2008, 1137, 190-196.
158. Frattini, M.; Gallino, G.; Signoroni, S.; Balestra, D.; Battaglia, L.; Sozzi, G.; Leo, E.; Pilotti, S.; Pierotti, M.A. Quantitative analysis of plasma DNA in colorectal cancer patients: A novel prognostic tool. Ann. N. Y. Acad. Sci. 2006, 1075, 185-190.
159. Schmidt, K.; Diehl, F. A blood-based DNA test for colorectal cancer screening. Discov. Med. 2007, 7, 7-12.
160. Taback, B.; Saha, S.; Hoon, D.S. Comparative analysis of mesenteric and peripheral blood circulating tumor DNA in colorectal cancer patients. Ann. N. Y. Acad. Sci. 2006, 1075, 197-203.
161. Flamini, E.; Mercatali, L.; Nanni, O.; Calistri, D.; Nunziatini, R.; Zoli, W.; Rosetti, P.; Gardini, N.; Lattuneddu, A.; Verdecchia, G.M., et al. Free DNA and carcinoembryonic antigen serum levels: An important combination for diagnosis of colorectal cancer. Clin. Cancer Res. 2006, 12, 6985-6988.
162. Kin, C.; Kidess, E.; Poultsides, G.A.; Visser, B.C.; Jeffrey, S.S. Colorectal cancer diagnostics: Biomarkers, cell-free DNA, circulating tumor cells and defining heterogeneous populations by single-cell analysis. Expert Rev. Mol. Diagn. 2013, 13, 581-599.
163. Da Silva Filho, B.F.; Gurgel, A.P.; Neto, M.Á.; de Azevedo, D.A.; de Freitas, A.C.; Silva Neto Jda, C.; Silva, L.A. Circulating cell-free DNA in serum as a biomarker of colorectal cancer. J. Clin. Pathol. 2013, 66, 775-778.
164. Tóth, K.; Galamb, O.; Spisák, S.; Wichmann, B.; Sipos, F.; Leiszter, K.; Molnár, J.; Molnár, B.; Tulassay, Z. Free circulating DNA based colorectal cancer screening from peripheral blood: The possibility of the methylated septin 9 gene marker. Orv. Hetil. 2009, 150, 969-977.
165. Tóth, K.; Sipos, F.; Kalmár, A.; Patai, A.V.; Wichmann, B.; Stoehr, R.; Golcher, H.; Schellerer, V.; Tulassay, Z.; Molnár, B. Detection of methylated SEPT9 in plasma is a reliable screening method for both left- and right-sided colon cancers. PLoS One 2012, 7, e46000.
166. DeVos, T.; Tetzner, R.; Model, F.; Weiss, G.; Schuster, M.; Distler, J.; Steiger, K.V.; Grützmann, R.; Pilarsky, C.; Habermann, J.K., et al. Circulating methylated SEPT9 DNA in plasma is a biomarker for colorectal cancer. Clin. Chem. 2009, 55, 1337-1346.
167. Wallner, M.; Herbst, A.; Behrens, A.; Crispin, A.; Stieber, P.; Göke, B.; Lamerz, R.; Kolligs, F.T. Methylation of serum DNA is an independent prognostic marker in colorectal cancer. Clin. Cancer Res. 2006, 12, 7347-7352.
168. Herbst, A.; Wallner, M.; Rahmig, K.; Stieber, P.; Crispin, A.; Lamerz, R.; Kolligs, F.T. Methylation of helicase-like transcription factor in serum of patients with colorectal cancer is an independent predictor of disease recurrence. Eur. J. Gastroenterol. Hepatol. 2009, 21, 565-569.
169. Misale, S.; Yaeger, R.; Hobor, S.; Scala, E.; Janakiraman, M.; Liska, D.; Valtorta, E.; Schiavo, R.; Buscarino, M.; Siravegna, G., et al. Emergence of KRAS mutations and acquired resistance to anti-EGFR therapy in colorectal cancer. Nature 2012, 486, 532-536.
170. Zitt, M.; Müller, H.M.; Rochel, M.; Schwendinger, V.; Zitt, M.; Goebel, G.; Devries, A.; Margreiter, R.; Oberwalder, M.; Zeillinger, R., et al. Circulating cell-free DNA in plasma of locally advanced rectal cancer patients undergoing preoperative chemoradiation: A potential diagnostic tool for therapy monitoring. Dis. Markers 2008, 25, 159-165.
171. Diaz, L.A., Jr.; Williams, R.T.; Wu, J.; Kinde, I.; Hecht, J.R.; Berlin, J.; Allen, B.; Bozic, I.; Reiter, J.G.; Nowak, M.A., et al. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature 2012, 486, 537-540.
172. Morgan, S.R.; Whiteley, J.; Donald, E.; Smith, J.; Eisenberg, M.T.; Kallam, E.; Kam-Morgan, L. Comparison of KRAS mutation assessment in tumor DNA and circulating free DNA in plasma and serum samples. Clin. Med. Insights Pathol. 2012, 5, 15-22.
173. Trevisiol, C.; di Fabio, F.; Nascimbeni, R.; Peloso, L.; Salbe, C.; Ferruzzi, E.; Salerni, B.; Gion, M. Prognostic value of circulating KRAS2 gene mutations in colorectal cancer with distant metastases. Int. J. Biol. Markers 2006, 21, 223-228.
174. Mouliere, F.; El Messaoudi, S.; Gongora, C.; Guedj, A.S.; Robert, B.; del Rio, M.; Molina, F.; Lamy, P.J.; Lopez-Crapez, E.; Mathonnet, M., et al. Circulating cell-free DNA from colorectal cancer patients may reveal high KRAS or BRAF mutation load. Transl. Oncol. 2013, 6, 319-328.
175. Chan, K.C.; Leung, S.F.; Yeung, S.W.; Chan, A.T.; Lo, Y.M. Persistent aberrations in circulating DNA integrity after radiotherapy are associated with poor prognosis in nasopharyngeal carcinoma patients. Clin. Cancer Res. 2008, 14, 4141-4145.
176. Jiang, W.W.; Zahurak, M.; Goldenberg, D.; Milman, Y.; Park, H.L.; Westra, W.H.; Koch, W.; Sidransky, D.; Califano, J. Increased plasma DNA integrity index in head and neck cancer patients. Int. J. Cancer 2006, 119, 2673-2676.
177. Chan, S.L.; Hui, E.P.; Leung, S.F.; Chan, A.T.; Ma, B.B. Radiological, pathological and DNA remission in recurrent metastatic nasopharyngeal carcinoma. BMC Cancer 2006, 6, 259.
178. Chan, K.C.; Lo, Y.M. Circulating EBV DNA as a tumor marker for nasopharyngeal carcinoma. Semin. Cancer Biol. 2002, 12, 489-496.
179. Chuang, T.C.; Chuang, A.Y.; Poeta, L.; Koch, W.M.; Califano, J.A.; Tufano, R.P. Detectable BRAF mutation in serum DNA samples from patients with papillary thyroid carcinomas. Head Neck 2010, 32, 229-234.
180. Hohaus, S.; Giachelia, M.; Massini, G.; Mansueto, G.; Vannata, B.; Bozzoli, V.; Criscuolo, M.; D'Alò, F.; Martini, M.; Larocca, L.M., et al. Cell-free circulating DNA in Hodgkin's and non-Hodgkin's lymphomas. Ann. Oncol. 2009, 20, 1408-1413.
181. Hosny, G.; Farahat, N.; Hainaut, P. TP53 mutations in circulating free DNA from Egyptian patients with non-Hodgkin's lymphoma. Cancer Lett. 2009, 275, 234-239.
182. Mussolin, L.; Burnelli, R.; Pillon, M.; Carraro, E.; Farruggia, P.; Todesco, A.; Mascarin, M.; Rosolen, A. Plasma cell-free DNA in paediatric lymphomas. J. Cancer 2013, 4, 323-329.
183. Jiang, Y.; Pan, S.Y.; Xia, W.Y.; Chen, D.; Wang, H.; Zhang, L.X.; Xu, J.; Peng, Y.; Qiu, H.R.; Miao, K.R., et al. Dynamic monitoring of plasma circulating DNA in patients with acute myeloid leukemia and its clinical. Zhongguo Shiyan Xueyexue Zazhi 2012, 20, 53-56.
184. Yoon, K.A.; Park, S.; Lee, S.H.; Kim, J.H.; Lee, J.S. Comparison of circulating plasma DNA levels between lung cancer patients and healthy controls. J. Mol. Diagn. 2009, 11, 182-185.
185. Xue, X.; Zhu, Y.M.; Woll, P.J. Circulating DNA and lung cancer. Ann. N. Y. Acad. Sci. 2006, 1075, 154-164.
186. Van der Drift, M.A.; Hol, B.E.; Klaassen, C.H.; Prinsen, C.F.; van Aarssen, Y.A.; Donders, R.; van der Stappen, J.W.; Dekhuijzen, P.N.; van der Heijden, H.F.; Thunnissen, F.B. Circulating DNA is a non-invasive prognostic factor for survival in non-small cell lung cancer. Lung Cancer 2010, 68, 283-287.
187. Lee, S.M.; Park, J.Y.; Kim, D.S. Methylation of TMEFF2 gene in tissue and serum DNA from patients with non-small cell lung cancer. Mol. Cells 2012, 34, 171-176.
188. Paci, M.; Maramotti, S.; Bellesia, E.; Formisano, D.; Albertazzi, L.; Ricchetti, T.; Ferrari, G.; Annessi, V.; Lasagni, D.; Carbonelli, C., et al. Circulating plasma DNA as diagnostic biomarker in non-small cell lung cancer. Lung Cancer 2009, 64, 92-97.
189. Sánchez-Céspedes, M.; Monzó, M.; Rosell, R.; Pifarré, A.; Calvo, R.; López-Cabrerizo, M.P.; Astudillo, J. Detection of chromosome 3p alterations in serum DNA of non-small-cell lung cancer patients. Ann. Oncol. 1998, 9, 113-116.
190. Bruhn, N.; Beinert, T.; Oehm, C.; Jandrig, B.; Petersen, I.; Chen, X.Q.; Possinger, K.; Fleischhacker, M. Detection of microsatellite alterations in the DNA isolated from tumor cells and from plasma DNA of patients with lung cancer. Ann. N. Y. Acad. Sci. 2000, 906, 72-82.
191. Ramirez, J.L.; Rosell, R.; Taron, M.; Sanchez-Ronco, M.; Alberola, V.; de Las Peñas, R.; Sanchez, J.M.; Moran, T.; Camps, C.; Massuti, B., et al. 14-3-3sigma methylation in pretreatment serum circulating DNA of cisplatin-plus-gemcitabine-treated advanced non-small-cell lung cancer patients predicts survival. J. Clin. Oncol. 2005, 23, 9105-9112.
192. Fischer, J.R.; Ohnmacht, U.; Rieger, N.; Zemaitis, M.; Stoffregen, C.; Manegold, C.; Lahm, H. Prognostic significance of RASSF1A promoter methylation on survival of non-small cell lung cancer patients treated with gemcitabine. Lung Cancer 2007, 56, 115-123.
193. Usadel, H.; Brabender, J.; Danenberg, K.D.; Jerónimo, C.; Harden, S.; Engles, J.; Danenberg, P.V.; Yang, S.; Sidransky, D. Quantitative adenomatous polyposis coli promoter methylation analysis in tumor tissue, serum, and plasma DNA of patients with lung cancer. Cancer Res. 2002, 62, 371-375.
194. Kimura, T.; Holland, W.S.; Kawaguchi, T.; Williamson, S.K.; Chansky, K.; Crowley, J.J.; Doroshow, J.H.; Lenz, H.J.; Gandara, D.R.; Gumerlock, P.H. Mutant DNA in plasma of lung cancer patients: Potential for monitoring response to therapy. Ann. N. Y. Acad. Sci. 2004, 1022, 55-60.
195. Ng, C.S.; Zhang, J.; Wan, S.; Lee, T.W.; Arifi, A.A.; Mok, T.; Lo, D.Y.; Yim, A.P. Tumor p16M is a possible marker of advanced stage in non-small cell lung cancer. J. Surg. Oncol. 2002, 79, 101-106.
196. Ponomaryova, A.A.; Rykova, E.Y.; Cherdyntseva, N.V.; Skvortsova, T.E.; Dobrodeev, A.Y.; Zav'yalov, A.A.; Bryzgalov, L.O.; Tuzikov, S.A.; Vlassov, V.V.; Laktionov, P.P. Potentialities of aberrantly methylated circulating DNA for diagnostics and post-treatment follow-up of lung cancer patients. Lung Cancer 2013, 81, 397-403.
197. Nakamura, T.; Sueoka-Aragane, N.; Iwanaga, K.; Sato, A.; Komiya, K.; Kobayashi, N.; Hayashi, S.; Hosomi, T.; Hirai, M.; Sueoka, E., et al. Application of a highly sensitive detection system for epidermal growth factor receptor mutations in plasma DNA. J. Thorac. Oncol. 2012, 7, 1369-1381.
198. Tamkovich, S.N.; Litviakov, N.V.; Bryzgunova, O.E.; Dobrodeev, A.Y.; Rykova, E.Y.; Tuzikov, S.A.; Zav'ialov, A.A.; Vlassov, V.V.; Cherdyntseva, N.V.; Laktionov, P.P. Cell-surface-bound circulating DNA as a prognostic factor in lung cancer. Ann. N. Y. Acad. Sci. 2008, 1137, 214-217.
199. Ellinger, J.; Wittkamp, V.; Albers, P.; Perabo, F.G.; Mueller, S.C.; von Ruecker, A.; Bastian, P.J. Cell-free circulating DNA: Diagnostic value in patients with testicular germ cell cancer. J. Urol. 2009, 181, 363-371.
200. Ellinger, J.; Albers, P.; Müller, S.C.; von Ruecker, A.; Bastian, P.J. Circulating mitochondrial DNA in the serum of patients with testicular germ cell cancer as a novel noninvasive diagnostic biomarker. BJU Int. 2009, 104, 48-52.
201. Ellinger, J.; Albers, P.; Perabo, F.G.; Müller, S.C.; von Ruecker, A.; Bastian, P.J. CpG island hypermethylation of cell-free circulating serum DNA in patients with testicular cancer. J. Urol. 2009, 182, 324-329.
202. Goessl, C.; Müller, M.; Straub, B.; Miller, K. DNA alterations in body fluids as molecular tumor markers for urological malignancies. Eur. Urol. 2002, 41, 668-676.
203. Cairns, P. Detection of promoter hypermethylation of tumor suppressor genes in urine from kidney cancer patients. Ann. N. Y. Acad. Sci. 2004, 1022, 40-43.
204. Delgado, P.O.; Alves, B.C.; Gehrke Fde, S.; Kuniyoshi, R.K.; Wroclavski, M.L.; del Giglio, A.; Fonseca, F.L. Characterization of cell-free circulating DNA in plasma in patients with prostate cancer. Tumour Biol. 2013, 34, 983-986.
205. Schwarzenbach, H.; Alix-Panabières, C.; Müller, I.; Letang, N.; Vendrell, J.P.; Rebillard, X.; Pantel, K. Cell-free tumor DNA in blood plasma as a marker for circulating tumor cells in prostate cancer. Clin. Cancer Res. 2009, 15, 1032-1038.
206. Sunami, E.; Shinozaki, M.; Higano, C.S.; Wollman, R.; Dorff, T.B.; Tucker, S.J.; Martinez, S.R.; Mizuno, R.; Singer, F.R.; Hoon, D.S. Multimarker circulating DNA assay for assessing blood of prostate cancer patients. Clin. Chem. 2009, 55, 559-567.
207. Bryzgunova, O.E.; Morozkin, E.S.; Yarmoschuk, S.V.; Vlassov, V.V.; Laktionov, P.P. Methylation-specific sequencing of GSTP1 gene promoter in circulating/extracellular DNA from blood and urine of healthy donors and prostate cancer patients. Ann. N. Y. Acad. Sci. 2008, 1137, 222-225.
208. Ellinger, J.; Haan, K.; Heukamp, L.C.; Kahl, P.; Büttner, R.; Müller, S.C.; von Ruecker, A.; Bastian, P.J. CpG island hypermethylation in cell-free serum DNA identifies patients with localized prostate cancer. Prostate 2008, 68, 42-49.
209. Chun, F.K.; Müller, I.; Lange, I.; Friedrich, M.G.; Erbersdobler, A.; Karakiewicz, P.I.; Graefen, M.; Pantel, K.; Huland, H.; Schwarzenbach, H. Circulating tumour-associated plasma DNA represents an independent and informative predictor of prostate cancer. BJU Int. 2006, 98, 544-548.
210. Cherepanova, A.V.; Tamkovich, S.N.; Bryzgunova, O.E.; Vlassov, V.V.; Laktionov, P.P. Deoxyribonuclease activity and circulating DNA concentration in blood plasma of patients with prostate tumors. Ann. N. Y. Acad. Sci. 2008, 1137, 218-221.
211. Altimari, A.; Grigioni, A.D.; Benedettini, E.; Gabusi, E.; Schiavina, R.; Martinelli, A.; Morselli-Labate, A.M.; Martorana, G.; Grigioni, W.F.; Fiorentino, M. Diagnostic role of circulating free plasma DNA detection in patients with localized prostate cancer. Am. J. Clin. Pathol. 2008, 129, 756-762.
212. Papadopoulou, E.; Davilas, E.; Sotiriou, V.; Georgakopoulos, E.; Georgakopoulou, S.; Koliopanos, A.; Aggelakis, F.; Dardoufas, K.; Agnanti, N.J.; Karydas, I., et al. Cell-free DNA and RNA in plasma as a new molecular marker for prostate and breast cancer. Ann. N. Y. Acad. Sci. 2006, 1075, 235-243.
213. Bastian, P.J.; Palapattu, G.S.; Yegnasubramanian, S.; Lin, X.; Rogers, C.G.; Mangold, L.A.; Trock, B.; Eisenberger, M.; Partin, A.W.; Nelson, W.G. Prognostic value of preoperative serum cell-free circulating DNA in men with prostate cancer undergoing radical prostatectomy. Clin. Cancer Res. 2007, 13, 5361-5367.
214. Ellinger, J.; Müller, S.C.; Wernert, N.; von Ruecker, A.; Bastian, P.J. Mitochondrial DNA in serum of patients with prostate cancer: A predictor of biochemical recurrence after prostatectomy. BJU Int. 2008, 102, 628-632.
215. Ellinger, J.; Bastian, P.J.; Haan, K.I.; Heukamp, L.C.; Buettner, R.; Fimmers, R.; Mueller, S.C.; von Ruecker, A. Noncancerous PTGS2 DNA fragments of apoptotic origin in sera of prostate cancer patients qualify as diagnostic and prognostic indicators. Int. J. Cancer 2008, 122, 138-143.
216. Müller, I.; Beeger, C.; Alix-Panabières, C.; Rebillard, X.; Pantel, K.; Schwarzenbach, H. Identification of loss of heterozygosity on circulating free DNA in peripheral blood of prostate cancer patients: Potential and technical improvements. Clin. Chem. 2008, 54, 688-696.
217. Kwee, S.; Song, M.A.; Cheng, I.; Loo, L.; Tiirikainen, M. Measurement of circulating cell-free DNA in relation to 18F-fluorocholine PET/CT imaging in chemotherapy-treated advanced prostate cancer. Clin. Transl. Sci. 2012, 5, 65-70.
218. Cortese, R.; Kwan, A.; Lalonde, E.; Bryzgunova, O.; Bondar, A.; Wu, Y.; Gordevicius, J.; Park, M.; Oh, G.; Kaminsky, Z., et al. Epigenetic markers of prostate cancer in plasma circulating DNA. Hum. Mol. Genet. 2012, 21, 3619-3631.
219. Daniotti, M.; Vallacchi, V.; Rivoltini, L.; Patuzzo, R.; Santinami, M.; Arienti, F.; Cutolo, G.; Pierotti, M.A.; Parmiani, G.; Rodolfo, M. Detection of mutated BRAFV600E variant in circulating DNA of stage III-IV melanoma patients. Int. J. Cancer 2007, 120, 2439-2444.
220. Nakamoto, D.; Yamamoto, N.; Takagi, R.; Katakura, A.; Mizoe, J.E.; Shibahara, T. Detection of microsatellite alterations in plasma DNA of malignant mucosal melanoma using whole genome amplification. Bull. Tokyo Dent. Coll. 2008, 49, 77-87.
221. Takagi, R.; Nakamoto, D.; Mizoe, J.E.; Tsujii, H. LOH analysis of free DNA in the plasma of patients with mucosal malignant melanoma in the head and neck. Int. J. Clin. Oncol. 2007, 12, 199-204.
222. Lo Nigro, C.; Wang, H.; McHugh, A.; Lattanzio, L.; Matin, R.; Harwood, C.; Syed, N.; Hatzimichael, E.; Briasoulis, E.; Merlano, M., et al. Methylated tissue factor pathway inhibitor 2 (TFPI2) DNA in serum is a biomarker of metastatic melanoma. J. Invest. Dermatol. 2013, 133, 1278-1285.
223. Kakimoto, Y.; Yamamoto, N.; Shibahara, T. Microsatellite analysis of serum DNA in patients with oral squamous cell carcinoma. Oncol. Rep. 2008, 20, 1195-1200.