Genotyping cell-free tumor DNA in the blood to detect residual disease and drug resistance

Genome Biology

Volumn 15, Issue 8, 2014, Pages

  Siravegna, Giulia ^a,b,c   Bardelli, Alberto ^a,b  

^a UNIVERSITY OF TURIN   (Italy)

^b CANDIOLO CANCER INSTITUTE   (Italy)

^c FIRC INSTITUTE OF MOLECULAR ONCOLOGY   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; GENOMIC DNA; DNA;

BLOOD ANALYSIS; CANCER GENETICS; CANCER RESISTANCE; CANCER STAGING; DNA DETERMINATION; EXOME; EXOSOME; GENE MUTATION; GENETIC CODE; GENOTYPING TECHNIQUE; HUMAN; LIQUID BIOPSY; MINIMAL RESIDUAL DISEASE; MOLECULAR EVOLUTION; PATIENT MONITORING; REVIEW; SOLID TUMOR; TUMOR BIOPSY; TUMOR LOCALIZATION; BLOOD; CELL FREE SYSTEM; DRUG RESISTANCE; GENETICS; GENOTYPE; NEOPLASM; NEOPLASM, RESIDUAL; PATHOLOGY;

CELL-FREE SYSTEM; DNA, NEOPLASM; DRUG RESISTANCE, NEOPLASM; GENOTYPE; HUMANS; NEOPLASM, RESIDUAL; NEOPLASMS;

EID: 84964314311     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-014-0449-4     Document Type: Review

References (52)

1. Diaz LA, Bardelli A: Liquid biopsies: genotyping circulating tumor DNA. J Clin Oncol 2014, 32:579-586.
2. Pantel K, Alix-Panabières C: Real-time liquid biopsy in cancer patients: fact or fiction? Cancer Res 2013, 73:6384-6388.
3. Pantel K, Diaz LA, Polyak K: Tracking tumor resistance using 'liquid biopsies'. Nat Med 2013, 19:676-677.
4. Mandel P, Metais P: Les acides nucleiques du plasma sanguin chez l'homme. C R Seances Soc Biol Fil 1948, 142:241-243.
5. Leon SA, Shapiro B, Sklaroff DM, Yaros MJ: Free DNA in the serum of cancer patients and the effect of therapy. Cancer Res 1977, 37:646-650.
6. Stroun M, Anker P, Maurice P, Lyautey J, Lederrey C, Beljanski M: Neoplastic characteristics of the DNA found in the plasma of cancer patients. Oncology 1989, 46:318-322.
7. Vasioukhin V, Anker P, Maurice P, Lyautey J, Lederrey C, Stroun M: 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, 86:774-779.
8. 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.
9. Nawroz H, Koch W, Anker P, Stroun M, Sidransky D: Microsatellite alterations in serum DNA of head and neck cancer patients. Nat Med 1996, 2:1035-1037.
10. Chen XQ, Stroun M, Magnenat JL, Nicod LP, Kurt AM, Lyautey J, Lederrey C, Anker P: Microsatellite alterations in plasma DNA of small cell lung cancer patients. Nat Med 1996, 2:1033-1035.
11. Anker P, Lefort F, Vasioukhin V, Lyautey J, Lederrey C, Chen XQ, Stroun M, Mulcahy HE, Farthing MJ: K-ras mutations are found in DNA extracted from the plasma of patients with colorectal cancer. Gastroenterology 1997, 112:1114-1120.
12. Silva JM, Dominguez G, Villanueva MJ, Gonzalez R, Garcia JM, Corbacho C, Provencio M, España P, Bonilla F: Aberrant DNA methylation of the p16INK4a gene in plasma DNA of breast cancer patients. Br J Cancer 1999, 80:1262-1264.
13. Silva JM, Gonzalez R, Dominguez G, Garcia JM, España P, Bonilla F: TP53 gene mutations in plasma DNA of cancer patients. Genes Chromosomes Cancer 1999, 24:160-161.
14. Murtaza M, Dawson SJ, Tsui DW, Gale D, Forshew T, Piskorz AM, Parkinson C, Chin SF, Kingsbury Z, Wong AS, Marass F, Humphray S, Hadfield J, Bentley D, Chin TM, Brenton JD, Caldas C, Rosenfeld N: Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 2013, 497:108-112.
15. Jen J, Wu L, Sidransky D: An overview on the isolation and analysis of circulating tumor DNA in plasma and serum. Ann N Y Acad Sci 2000, 906:8-12.
16. Thijssen MA, Swinkels DW, Ruers TJ, de Kok JB: Difference between free circulating plasma and serum DNA in patients with colorectal liver metastases. Anticancer Res 2002, 22:421-425.
17. Lee TH, Montalvo L, Chrebtow V, Busch MP: Quantitation of genomic DNA in plasma and serum samples: higher concentrations of genomic DNA found in serum than in plasma. Transfusion 2001, 41:276-282.
18. Steinman CR: Free DNA in serum and plasma from normal adults. J Clin Invest 1975, 56:512-515.
19. Chan KC, Yeung SW, Lui WB, Rainer TH, Lo YM: Effects of preanalytical factors on the molecular size of cell-free DNA in blood. Clin Chem 2005, 51:781-784.
20. Jung M, Klotzek S, Lewandowski M, Fleischhacker M, Jung K: Changes in concentration of DNA in serum and plasma during storage of blood samples. Clin Chem 2003, 49:1028-1029.
21. Thierry AR, Mouliere F, Gongora C, Ollier J, Robert B, Ychou M, Del Rio M, Molina F: Origin and quantification of circulating DNA in mice with human colorectal cancer xenografts. Nucleic Acids Res 2010, 38:6159-6175.
22. El Messaoudi S, Rolet F, Mouliere F, Thierry AR: Circulating cell free DNA: Preanalytical considerations. Clin Chim Acta 2013, 424:222-230.
23. Fleischhacker M, Schmidt B: Circulating nucleic acids (CNAs) and cancer-a survey. Biochim Biophys Acta 2007, 1775:181-232.
24. Stroun M, Maurice P, Vasioukhin V, Lyautey J, Lederrey C, Lefort F, Rossier A, Chen XQ, Anker P: The origin and mechanism of circulating DNA. Ann N Y Acad Sci 2000, 906:161-168.
25. Gahan PB, Swaminathan R: Circulating nucleic acids in plasma and serum. Recent developments. Ann N Y Acad Sci 2008, 1137:1-6.
26. 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.
27. Properzi F, Logozzi M, Fais S: Exosomes: the future of biomarkers in medicine. Biomark Med 2013, 7:769-778.
28. Muller L, Hong CS, Stolz DB, Watkins SC, Whiteside TL: Isolation of biologically-active exosomes from human plasma. J Immunol Methods 2014. doi:10.1016/j.jim.2014.06.007.
29. Thakur BK, Zhang H, Becker A, Matei I, Huang Y, Costa-Silva B, Zheng Y, Hoshino A, Brazier H, Xiang J, Williams C, Rodriguez-Barrueco R, Silva JM, Zhang W, Hearn S, Elemento O, Paknejad N, Manova-Todorova K, Welte K, Bromberg J, Peinado H, Lyden D: Double-stranded DNA in exosomes: a novel biomarker in cancer detection. Cell Res 2014, 24:766-769.
30. Diehl F, Li M, Dressman D, He Y, Shen D, Szabo S, Diaz LA, Goodman SN, David KA, Juhl H, Kinzler KW, Vogelstein B: Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci U S A 2005, 102:16368-16373.
31. Jahr S, Hentze H, Englisch S, Hardt D, Fackelmayer FO, Hesch RD, Knippers R: DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells. Cancer Res 2001, 61:1659-1665.
32. Chun FK, Müller I, Lange I, Friedrich MG, Erbersdobler A, Karakiewicz PI, 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.
33. Allen D, Butt A, Cahill D, Wheeler M, Popert R, Swaminathan R: Role of cell-free plasma DNA as a diagnostic marker for prostate cancer. Ann N Y Acad Sci 2004, 1022:76-80.
34. 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.
35. Sunami E, Vu AT, Nguyen SL, Giuliano AE, Hoon DS: Quantification of LINE1 in circulating DNA as a molecular biomarker of breast cancer. Ann N Y Acad Sci 2008, 1137:171-174.
36. Raptis L, Menard HA: Quantitation and characterization of plasma DNA in normals and patients with systemic lupus erythematosus. J Clin Invest 1980, 66:1391-1399.
37. Shapiro B, Chakrabarty M, Cohn EM, Leon SA: Determination of circulating DNA levels in patients with benign or malignant gastrointestinal disease. Cancer 1983, 51:2116-2120.
38. Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, Agrawal N, Bartlett BR, Wang H, Luber B, Alani RM, Antonarakis ES, Azad NS, Bardelli A, Brem H, Cameron JL, Lee CC, Fecher LA, Gallia GL, Gibbs P, Le D, Giuntoli RL, Goggins M, Hogarty MD, Holdhoff M, Hong SM, Jiao Y, Juhl HH, Kim JJ, Siravegna G, Laheru DA, et al: Detection of circulating tumor DNA in early-and late-stage human malignancies. Sci Transl Med 2014, 6:224ra224.
39. Holdhoff M, Schmidt K, Donehower R, Diaz LA: Analysis of circulating tumor DNA to confirm somatic KRAS mutations. J Natl Cancer Inst 2009, 101:1284-1285.
40. Diehl F, Schmidt K, Choti MA, Romans K, Goodman S, Li M, Thornton K, Agrawal N, Sokoll L, Szabo SA, Kinzler KW, Vogelstein B, Diaz LA Jr: Circulating mutant DNA to assess tumor dynamics. Nat Med 2008, 14:985-990.
41. Bardelli A, Corso S, Bertotti A, Hobor S, Valtorta E, Siravegna G, Sartore-Bianchi A, Scala E, Cassingena A, Zecchin D, Apicella M, Migliardi G, Galimi F, Lauricella C, Zanon C, Perera T, Veronese S, Corti G, Amatu A, Gambacorta M, Diaz LA Jr, Sausen M, Velculescu VE, Comoglio P, Trusolino L, Di Nicolantonio F, Giordano S, Siena S: Amplification of the MET receptor drives resistance to anti-EGFR therapies in colorectal cancer. Cancer Discov 2013, 3:658-673.
42. Leary RJ, Sausen M, Diaz LA, Velculescu VE: Cancer detection using whole-genome sequencing of cell free DNA. Oncotarget 2013, 4:1119-1120.
43. Diaz LA, Sausen M, Fisher GA, Velculescu VE: Insights into therapeutic resistance from whole-genome analyses of circulating tumor DNA. Oncotarget 2013, 4:1856-1857.
44. Mohan S, Heitzer E, Ulz P, Lafer I, Lax S, Auer M, Pichler M, Gerger A, Eisner F, Hoefler G, Bauernhofer T, Geigl JB, Speicher MR: Changes in colorectal carcinoma genomes under anti-EGFR therapy identified by whole-genome plasma DNA sequencing. PLoS Genet 2014, 10:e1004271.
45. Wimberger P, Roth C, Pantel K, Kasimir-Bauer S, Kimmig R, Schwarzenbach H: 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 2011, 128:2572-2580.
46. Beaver JA, Jelovac D, Balukrishna S, Cochran RL, Croessmann S, Zabransky DJ, Wong HY, Valda Toro P, Cidado J, Blair BG, Chu D, Burns T, Higgins MJ, Stearns V, Jacobs L, Habibi M, Lange J, Hurley PJ, Lauring J, VanDenBerg DA, Kessler J, Jeter S, Samuels ML, Maar D, Cope L, Cimino-Mathews A, Argani P, Wolff AC, Park BH: Detection of cancer DNA in plasma of early stage breast cancer patients. Clin Cancer Res 2014, 20:2643-2650.
47. Martini M, Vecchione L, Siena S, Tejpar S, Bardelli A: Targeted therapies: how personal should we go? Nat Rev Clin Oncol 2012, 9:87-97.
48. Dawson SJ, Tsui DW, Murtaza M, Biggs H, Rueda OM, Chin SF, Dunning MJ, Gale D, Forshew T, Mahler-Araujo B, Rajan S, Humphray S, Becq J, Halsall D, Wallis M, Bentley D, Caldas C, Rosenfeld N: Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med 2013, 368:1199-1209.
49. Dawson SJ, Rosenfeld N, Caldas C: Circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med 2013, 369:93-94.
50. Diaz LA, Williams RT, Wu J, Kinde I, Hecht JR, Berlin J, Allen B, Bozic I, Reiter JG, Nowak MA, Kinzler KW, Oliner KS, Vogelstein B: The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature 2012, 486:537-540.
51. Kuang Y, Rogers A, Yeap BY, Wang L, Makrigiorgos M, Vetrand K, Thiede S, Distel RJ, Jänne PA: Noninvasive detection of EGFR T790M in gefitinib or erlotinib resistant non-small cell lung cancer. Clin Cancer Res 2009, 15:2630-2636.
52. Misale S, Yaeger R, Hobor S, Scala E, Janakiraman M, Liska D, Valtorta E, Schiavo R, Buscarino M, Siravegna G, Bencardino K, Cercek A, Chen CT, Veronese S, Zanon C, Sartore-Bianchi A, Gambacorta M, Gallicchio M, Vakiani E, Boscaro V, Medico E, Weiser M, Siena S, Di Nicolantonio F, Solit D, Bardelli A: Emergence of KRAS mutations and acquired resistance to anti-EGFR therapy in colorectal cancer. Nature 2012, 486:532-536.