Acta Med. 2016, 59: 54-58

https://doi.org/10.14712/18059694.2016.54

Carrier molecules and extraction of circulating tumor DNA for next generation sequencing in colorectal cancer

Martin Beráneka,b,*, Igor Sirákc, Milan Vošmikc, Jiří Peterac, Monika Drastíkováb, Vladimír Paličkab

aDepartment of Biochemical Sciences, Charles University, Faculty of Pharmacy in Hradec Králové, Czech Republic
bInstitute of Clinical Biochemistry and Diagnostics, University Hospital Hradec Králové, Charles University, Faculty of Medicine in Hradec Králové, Czech Republic
cDepartment of Oncology, University Hospital Hradec Králové, Charles University, Faculty of Medicine in Hradec Králové, Czech Republic

Received February 10, 2016
Accepted April 18, 2016

References

1. Lo YM, Zhang J, Leung TN, Lau TK, Chang AM, Hjelm NM. Rapid clearance of fetal DNA from maternal plasma. Am J Hum Genet 1999; 64: 218–24. <https://doi.org/10.1086/302205> <PubMed>
2. Leon SA, Shapiro B, Sklaroff DM, Yaros MJ. Free DNA in the serum of cancer patients and the effect of therapy. Cancer Res 1977; 37: 646–50.
3. Lo YM, Corbetta N, Chamberlain PF, et al. Presence of fetal DNA in maternal plasma and serum. Lancet 1997; 350: 485–7. <https://doi.org/10.1016/S0140-6736(97)02174-0>
4. Wagner J. Free DNA: new potential analyte in clinical laboratory diagnostics? Biochem Med 2012; 22: 24–38. <https://doi.org/10.11613/BM.2012.004>
5. García Moreira V, Prieto García B, Baltar Martín JM, Ortega Suárez F, Alvarez FV. Cell-free DNA as a noninvasive acute rejection marker in renal transplantation. Clin Chem 2009; 55: 1958–66. <https://doi.org/10.1373/clinchem.2009.129072>
6. Saukkonen K, Lakkisto P, Pettilä V, et al. Cell-free plasma DNA as a predictor of outcome in severe sepsis and septic shock. Clin Chem 2008; 54: 1000–7. <https://doi.org/10.1373/clinchem.2007.101030>
7. Pathak AK, Bhutani M, Kumar S, Mohan A, Guleria R. Circulating cell-free DNA in plasma/serum of lung cancer patients as a potential screening and prognostic tool. Clin Chem 2006; 52: 1833–42.
8. Lecomte T, Berger A, Zinzindohoué F, et al. Detection of free-circulating tumor-associated DNA in plasma of colorectal cancer patients and its association with prognosis. Int J Cancer 2002; 100: 542–8. <https://doi.org/10.1002/ijc.10526>
9. Giacona MB, Ruben GC, Iczkowski KA, Roos TB, Porter DM, Sorenson GD. Cell-free DNA in human blood plasma: length measurements in patients with pancreatic cancer and healthy controls. Pancreas 1998; 17: 89–97. <https://doi.org/10.1097/00006676-199807000-00012>
10. Suzuki N, Kamataki A, Yamaki J, Homma Y. Characterization of circulating DNA in healthy human plasma. Clin Chim Acta 2008; 387: 55–8. <https://doi.org/10.1016/j.cca.2007.09.001>
11. Danese E, Montagnana M, Minicozzi AM, et al. Real-time polymerase chain reaction quantification of free DNA in serum of patients with polyps and colorectal cancers. Clin Chem Lab Med 2010; 48: 1665–8. <https://doi.org/10.1515/CCLM.2010.301>
12. Freidin MB, Freydina DV, Leung M, et al. Circulating tumor DNA outperforms circulating tumor cells for KRAS mutation detection in thoracic malignancies. Clin Chem 2015; 61: 1299–304. <https://doi.org/10.1373/clinchem.2015.242453>
13. Sorenson GD, Pribish DM, Valone FH, Memoli VA, Bzik DJ, Yao SL. Soluble normal and mutated DNA sequences from single-copy genes in human blood. Cancer Epidemiol Biomarkers Prev 1994; 3: 67–71.
14. Anker P, Lefort F, Vasioukhin V, et al. K-ras mutations are found in DNA extracted from the plasma of patients with colorectal cancer. Gastroenterology 1997; 112: 1114–20. <https://doi.org/10.1016/S0016-5085(97)70121-5>
15. 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. <https://doi.org/10.1056/NEJMoa1213261>
16. Albanese I, Scibetta AG, Migliavacca M, et al. Heterogeneity within and between primary colorectal carcinomas and matched metastases as revealed by analysis of Ki-ras and p53 mutations. Biochem Biophys Res Commun 2004; 325: 784–91. <https://doi.org/10.1016/j.bbrc.2004.10.111>
17. Baldus SE, Schaefer KL, Engers R, Hartleb D, Stoecklein NH, Gabbert HE. Prevalence and heterogeneity of KRAS, BRAF, and PIK3CA mutations in primary colorectal adenocarcinomas and their corresponding metastases. Clin Cancer Res 2010; 16: 790–9. <https://doi.org/10.1158/1078-0432.CCR-09-2446>
18. Diaz LA Jr, Williams RT, Wu J, et al. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature 2012; 486: 537–40. <https://doi.org/10.1038/nature11219> <PubMed>
19. Mouliere F, El Messaoudi S, Pang D, Dritschilo A, Thierry AR. Multi-marker analysis of circulating cell-free DNA toward personalized medicine for colorectal cancer. Mol Oncol 2014; 8: 927–41. <https://doi.org/10.1016/j.molonc.2014.02.005> <PubMed>
20. Mouliere F, Robert B, Arnau Peyrotte E, et al. High fragmentation characterizes tumour-derived circulating DNA. PLoS One 2011; 6: e23418. <https://doi.org/10.1371/journal.pone.0023418> <PubMed>
21. 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: 135–9. <https://doi.org/10.1196/annals.1448.035>
22. Shaw KJ, Thain L, Docker PT, et al. The use of carrier RNA to enhance DNA extraction from microfluidic-based silica monoliths. Anal Chim Acta 2009; 652: 231–3. <https://doi.org/10.1016/j.aca.2009.03.038>
23. Kishore R, Hardy R, Anderson VJ, Sanchez NA, Buoncristiani MR. Optimization of DNA extraction from low-yield and degraded samples using the BioRobot EZ1 and BioRobot M48. J Forensic Sci 2006; 51: 1055–61. <https://doi.org/10.1111/j.1556-4029.2006.00204.x>
24. Cheung RC, Matsui SM, Greenberg HB. Rapid and sensitive method for detection of hepatitis C virus RNA by using silica particles. J Clin Microbiol 1994; 32: 2593–7.
25. Hengen PN. Carriers for precipitating nucleic acids. Trends Biochem Sci 1996; 21: 224–5. <https://doi.org/10.1016/S0968-0004(96)30031-5>
26. Kopreski MS, Benko FA, Borys DJ, Khan A, McGarrity TJ, Gocke CD. Somatic mutation screening: identification of individuals harboring K-ras mutations with the use of plasma DNA. J Natl Cancer Inst 2000; 92: 918–23. <https://doi.org/10.1093/jnci/92.11.918>
27. Ryan BM, McManus RO, Daly JS, et al. Serum mutant K-ras in the colorectal adenoma-to-carcinoma sequence. Implications for diagnosis, postoperative follow-up, and early detection of recurrent disease. Ann N Y Acad Sci 2000; 906: 29–30. <https://doi.org/10.1111/j.1749-6632.2000.tb06586.x>
28. Andreyev HJ, Norman AR, Cunningham D, et al. Kirsten ras mutations in patients with colorectal cancer: the ‘RASCAL II’ study. Br J Cancer 2001; 85: 692–6. <https://doi.org/10.1054/bjoc.2001.1964> <PubMed>
29. 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. <https://doi.org/10.1016/S1470-2045(10)70130-3>
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