Direct quantification of cell-free, circulating DNA from unpurified plasma

PLoS ONE

Volumn 9, Issue 3, 2014, Pages

  Breitbach, Sarah ^a   Tug, Suzan ^a   Helmig, Susanne ^a   Zahn, Daniela ^a   Kubiak, Thomas ^a   Michal, Matthias ^a   Gori, Tommaso ^a   Ehlert, Tobias ^a   Beiter, Thomas ^b   Simon, Perikles ^a  

^a JOHANNES GUTENBERG UNIVERSITY   (Germany)

^b UNIVERSITY HOSPITAL TÜBINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CHLOROFORM; DNA; DNA FRAGMENT; PHENOL CHLOROFORM ISOAMYL; UNCLASSIFIED DRUG; PRIMER DNA;

ADULT; ARTICLE; BASE PAIRING; BLOOD LEVEL; CELL FREE SYSTEM; CONCENTRATION RESPONSE; CONTROLLED STUDY; DIAGNOSTIC KIT; DNA EXTRACTION; DNA INTEGRATION; DNA PURIFICATION; ECONOMIC EVALUATION; FEMALE; HUMAN; HUMAN CELL; HUMAN TISSUE; INTERMETHOD COMPARISON; ISCHEMIC HEART DISEASE; LIMIT OF QUANTITATION; MAJOR CLINICAL STUDY; MALE; PLASMA; QUANTITATIVE STUDY; QUANTITATIVE TRAIT LOCUS; REAL TIME POLYMERASE CHAIN REACTION; SENSITIVITY ANALYSIS; BLOOD; CASE CONTROL STUDY; CORONARY ARTERY DISEASE; EXERCISE; GENETICS; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; CASE-CONTROL STUDIES; CELL-FREE SYSTEM; CORONARY DISEASE; DNA; DNA PRIMERS; EXERCISE; HUMANS; REAL-TIME POLYMERASE CHAIN REACTION;

EID: 84897076233     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0087838     Document Type: Article

References (55)

1. Van der Vaart M, Pretorius PJ (2008) Circulating DNA. Its Origin and Fluctuation. Ann N Y Acad Sci 1137: 18-26.
2. Schwarzenbach H, Hoon DS, Pantel K (2011) Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer 11(6): 426-437.
3. Atamaniuk J, Vidotto C, Tschan H, Bachl N, Stuhlmeier KM, et al. (2004) Increased Concentrations of Cell-Free Plasma DNA after Exhaustive Exercise. Clin Chem 50(9): 1668-1670. (Pubitemid 39121238)
4. Atamaniuk J, Stuhlmeier KM, Vidotto C, Tschan H, Dossenbach-Glaninger A, et al. (2008) Effects of ultra-marathon on circulating DNA and mRNA expression of pro- and anti-apoptotic genes in mononuclear cells. Eur J Appl Physiol 104(4): 711-717.
5. Atamaniuk J, Vidotto C, Kinzlbauer M, Bachl N, Tiran B, et al. (2010) Cell-free plasma DNA and purine nucleotide degradation markers following weightlifting exercise. Eur J Physiol 110(4): 695-701.
6. Fatouros IG, Destouni A, Margonis K, Jamurtas AZ, Vrettou C, et al. (2006) Cell-Free Plasma DNA as a Novel Marker of Aseptic Inflammation Severity Related to Exercise Overtraining. Clin Chem 52(9): 1820-1824. (Pubitemid 44330721)
7. Beiter T, Fragasso A, Hudemann J, Niess AM, Simon P (2011) Short-term treadmill running as a model for studying cell-free DNA kinetics in vivo. Clin Chem 57(4): 633-636.
8. Breitbach S, Tug S, Simon P (2012) Circulating Cell-Free DNA. Sports Med 42(7): 565-586.
9. Jahr S, Hentze H, Englisch S, Hardt D, Fackelmayer FO, 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. (Pubitemid 34292602)
10. Anker P, Stroun M, Maurice PA (1975) Spontaneous release of DNA by human blood lymphocytes as shown in an in vitro system. Cancer Res 35(9): 2375-2382.
11. Stroun M, Lyautey J, Lederrey C, Olson-Sand A, Anker P (2001) About the possible origin and mechanism of circulating DNA apoptosis and active DNA release. Clin Chim Acta 313(1-2): 139-142. (Pubitemid 33016703)
12. Tamkovich SN, Cherepanova AV, Kolesnikova EV, Rykova EY, Pyshnyi DV, et al. (2006) Circulating DNA and DNase activity in human blood. Ann N Y Acad Sci 1075: 191-196. (Pubitemid 44532784)
13. Fatouros IG, Jamurtas AZ, Nickolaidis MG, Destouni A, Michailidis Y, et al. (2010) Time sampling is crucial for measurements of cell-free plasma DNA following acute aseptic inflammation induced by exercise. Clin Biochem 43(16-17): 1368-1370.
14. Loparev VN, Cartas MA, Monken CE, Velpandi A, Srinivasan A (1991) An efficient and simple method of DNA extraction from whole blood and cell lines to identify infectious agents. J Virol Methods 34(1): 105-112.
15. Huggett JF, Novak T, Garson JA, Green C, Morris-Jones SD, et al. (2008) Differential susceptibility of PCR reactions to inhibitors: an important and unrecognised phenomenon. BMC Res Notes 28(1): 70.
16. Herrera LJ, Raja S, Gooding WE, El-Hefnawy T, Kelly L, et al. (2004) Quantitative analysis of circulating plasma DNA as a tumor marker in thoracic malignancies. Clin Chem 51(1): 113-118.
17. Huang DJ, Zimmermann BG, Holzgreve W, Hahn S (2005) Use of an automated method improves the yield and quality of cell-free fetal DNA extracted from maternal plasma. Clin Chem 5(12): 2419-2420. (Pubitemid 41692604)
18. Brojer E, Zupanska B, Guz K, Orziñska A, Kaliñska A (2005) Noninvasive determination of fetal RHD status by examination of cell-free DNA in maternal plasma. Transfusion 45(9): 1473-1480. (Pubitemid 44194651)
19. Clausen FB, Krog GR, Rieneck K, Dziegiel MH (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. (Pubitemid 46144333)
20. Fong SL, Zhang JT, Lim CK, Eu KW, Liu Y (2009) Comparison of 7 methods for extracting cell-free DNA from serum samples of colorectal cancer patients. Clin Chem 55(3): 587-589.
21. Fleischhacker M, Schmidt B, Weickmann S, Fersching DM, Leszinski GS, et al. (2011) Methods for isolation of cell-free plasma DNA strongly affect DNA yield. Clin Chim Acta 412(23-24): 2085-2088.
22. Umetani N, Giuliano AE, Hiramatsu SH, Amersi F, Nakagawa T, et al. (2006) Prediction of breast tumor progression by integrity of free circulating DNA in serum. J Clin Oncol 24(26): 4270-4276. (Pubitemid 46630784)
23. Umetani N, Hiramatsu S, Hoon DS (2006) Higher amount of free circulating DNA in serum than in plasma is not mainly caused by contaminated extraneous DNA during separation. Ann N Y Acad Sci 1075: 299-307. (Pubitemid 44532797)
24. Umetani N, Kim J, Hiramatsu S, Reber HA, Hines OJ, et al. (2006) Increased Integrity of Free Circulating DNA in Sera of Patients with Colorectal or Periampullary Cancer: Direct Quantitative PCR for ALU Repeats. Clin Chem 52(6): 1062-1069. (Pubitemid 43794418)
25. Deligezer U, Eralp Y, Akisik EE, Akisik EZ, Saip P, et al. (2008) Size distribution of circulating cell-free DNA in sera of breast cancer patients in the course of adjuvant chemotherapy. Clin Chem Lab Med 46(3): 311-317. (Pubitemid 351317779)
26. Feng J, Gang F, Li X, Jin T, Houbao H, et al. (2013) Plasma cell-free DNA and its DNA integrity as biomarker to distinguish prostate cancer from benign prostatic hyperplasia in patients with increased serum prostate-specific antigen. Int Urol Nephrol 45(4): 1023-1028.
27. Lehner J, Stötzer OJ, Fersching DM, Nagel D, Holdenrieder S (2013) Plasma DNA integrity indicates response to neoadjuvant chemotherapy in patients with locally confined breast cancer. Int J Clin Pharmacol Ther 51(1): 59-62.
28. Pavlícek A, Jabbari K, Paces J, Paces V, Hejnar JV, et al. (2001) Similar integration but different stability of Alus and LINEs in the human genome. Gene 3;276(1-2): 39-45.
29. Buzdin A, Ustyugova S, Gogvadze E, Lebedev Y, Hunsmann G, et al. (2003) Genome-wide targeted search for human specific and polymorphic L1 integrations. Hum Genet 112(5-6): 527-533. (Pubitemid 36869046)
30. Beck J, Urnovitz HB, Riggert J, Clerici M, Schütz E (2009) Profile of the circulating DNA in apparently healthy individuals. Clin Chem 55(4): 730-738.
31. Cui M, Jing R, Fan M, Zhu J, Ju S (2013) The Relationship between Cell-Free Circulating DNA and Inflammation in Acute Coronary Syndrome. Cardiology 126(2): 124-125.
32. Chang CPY, Chia RH, Wu TL, Tsao KC, Sun CF, et al. (2003) Elevated cell-free serum DNA detected in patients with myocardial infarction. Clin Chim 327(1): 95-101.
33. Antonatos D, Patsilinakos S, Spanodimos S, Korkonikitas P, Tsigas D (2006) Cell-Free DNA Levels as a Prognostic Marker in Acute Myocardial Infarction. Ann N Y Acadf Sci 1075(1): 278-281. (Pubitemid 44532794)
34. Destouni A, Vrettou C, Antonatos D, Chouliaras G, Traeger-Synodinos J, et al. (2009) Cell-free DNA levels in acute myocardial infarction patients during hospitalization. Acta Cardiol 64(1): 51-57.
35. Chiu RW, Poon LL, Lau TK, Leung TN, Wong EM, et al. (2001) Effects of blood-processing protocols on fetal and total DNA quantification in maternal plasma. Clin Chem 47(9): 1607-1613. (Pubitemid 32781573)
36. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Meth Mol Biol 132: 365-386.
37. Sai S, Ichikawa D, Tomita H, Ikoma D, Tani N, et al. (2007) Quantification of plasma cell-free DNA in patients with gastric cancer. Anticancer Res 27(4C): 2747-2751. (Pubitemid 47227992)
38. Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 3(6): 1101-1108. (Pubitemid 351818697)
39. Mygind T, Birkelund S, Birkebaek NH, Østergaard L, Jensen JS, et al. (2002) Determination of PCR efficiency in chelex-100 purified clinical samples and comparison of real-time quantitative PCR and conventional PCR for detection of Chlamydia pneumoniae. BMC Microbiol 9(2): 17.
40. Cordaux R, Batzer MA (2009) The impact of retrotransposons on human genome evolution. Nature Reviews Genetics 10: 691-703.
41. Puszyk WM, Crea F, Old RW (2008) Unequal representation of different unique genomic DNA sequences in the cell-free plasma DNA of individual donors. Clin Biochem 42(7-8): 736-738.
42. Tangkijvanich P, Hourpai N, Rattanatanyong P, Wisedopas N, Mahachai V, et al. (2007) Serum LINE-1 hypomethylation as a potential prognostic marker for hepatocellular carcinoma. Clin Chim Acta 379(1): 127-133. (Pubitemid 46389509)
43. Esser KH, Marx WH, Lisowsky T (2006) maxXbond: first regeneration system for DNA binding silica matrices. New solutions allow multiple reuse of valuable material. Nat Met 3: i-ii. (Pubitemid 43135353)
44. Schmidt B, Weickmann S, Witt C, Fleischhacker M (2005) Improved method for isolating cell-free DNA. Clin Chem 51(8): 1561-1563. (Pubitemid 41060908)
45. Boom RCJA, Sol CJ, Salimans MM, Jansen CL, Wertheim-van Dillen PM, et al. (1990) Rapid and simple method for purification of nucleic acids. J Clin Microbiol 28(3): 495-503. (Pubitemid 20078123)
46. Parida SK, Dash S, Patel S, Mishra BK (2006) Adsorption of organic molecules on silica surface. Adv Colloid Interface Sci 121(1): 77-110. (Pubitemid 44278748)
47. Mamon H, Hader C, Li J, Wang L, Kulke M, et al. (2008) Preferential amplification of apoptotic DNA from plasma: potential for enhancing detection of minor DNA alterations in circulating DNA. Clin Chem 54(9): 1582-1584.
48. Heitzer E, Auer M, Hoffmann EM, Pichler M, Gasch C, et al. (2013) Establishment of tumor-specific copy number alterations from plasma DNA of patients with cancer. Int J Cancer 133: 346-357.
49. Chan KC, Leung SF, Yeung SW, Chan AT, Lo YM (2008) Persistent aberrations in circulating DNA integrity after radiotherapy are associated with poor prognosis in nasopharyngeal carcinoma patients. Clin Cancer Res 14(13): 4141-4145.
50. Salvianti F, Pinzani P, Verderio P, Ciniselli CM, Massi D, et al. (2012) Multiparametric analysis of cell-free DNA in melanoma patients. PLoS One 7(11): e49843. doi: 10.1371/journal.pone.0049843
51. Yun DD, Alpert JS (1997) Acute coronary syndromes. Cardiology 88(3): 223-237 (Pubitemid 27153608)
52. Lee YJ, Yoon KA, Han JY, Kim HT, Yun T, et al. (2011) Circulating cell-free DNA in plasma of never smokers with advanced lung adenocarcinoma receiving gefitinib or standard chemotherapy as first-line therapy. Clin Cancer Res 17(15): 5179-5187.
53. Macher H, Egea-Guerrero JJ, Revuelto-Rey J, Gordillo-Escobar E, Enamorado-Enamorado J, et al. (2012) Role of early cell-free DNA levels decrease as a predictive marker of fatal outcome after severe traumatic brain injury. Clin Chim Acta 414:12-7.
54. Balta S, Demirkol S, Cakar M, Karaman M, Ay SA, et al. (2013) Cell-Free Circulating DNA as a Novel Biomarker in Patients with the Acute Coronary Syndrome. Cardiology 126(2): 122-123.
55. Jensen MK, Wang Y, Rimm EB, Townsend MK, Willett W, et al. (2013) Fluorescent Oxidation Products and Risk of Coronary Heart Disease: A Prospective Study in Women. J Am Heart Assoc 2:e000195: 1-7.