Using circulating cell-free DNA to monitor personalized cancer therapy

Critical Reviews in Clinical Laboratory Sciences

Volumn 54, Issue 3, 2017, Pages 205-218

  Oellerich, Michael ^a   Schütz, Ekkehard ^b   Beck, Julia ^b   Kanzow, Philipp ^a   Plowman, Piers N ^c   Weiss, Glen J ^d   Walson, Philip D ^a  

^a UNIVERSITY MEDICAL CENTER GÖTTINGEN   (Germany)

^b Chronix Biomedical GmbH   (Germany)

^c ST BARTHOLOMEW S HOSPITAL   (United Kingdom)

^d CANCER TREATMENT CENTERS OF AMERICA   (United States)

Author keywords

cfDNA; chromosomal aberration pattern analysis; ctDNA tumor genomic profiling; Genotype directed cancer care; immunotherapy; liquid biopsy

Indexed keywords

ANDROGEN RECEPTOR; CELL FREE DNA; DNA; GEFITINIB; UNCLASSIFIED DRUG; TUMOR MARKER;

CANCER GROWTH; CANCER IMMUNOTHERAPY; CANCER RESISTANCE; CANCER THERAPY; CASTRATION RESISTANT PROSTATE CANCER; CHROMOSOME ABERRATION; CHROMOSOME LOSS; COLORECTAL CANCER; COPY NUMBER VARIATION; EGFR GENE; GENE EXPRESSION PROFILING; GENE MUTATION; GENOMIC INSTABILITY; GENOMICS; GENOTYPE; HUMAN; LIQUID BIOPSY; MELANOMA; METASTATIC BREAST CANCER; NEXT GENERATION SEQUENCING; NON SMALL CELL LUNG CANCER; ONCOGENE; ONCOGENE K RAS; PANCREAS ADENOCARCINOMA; PATIENT MONITORING; PERSONALIZED MEDICINE; POLYMERASE CHAIN REACTION; PREDICTIVE VALUE; PRIORITY JOURNAL; PROSTATE CANCER; REVIEW; TREATMENT RESPONSE; WHOLE GENOME SEQUENCING; BLOOD; CHEMISTRY; GENETICS; MALE; PROCEDURES; PROSTATE TUMOR;

BIOMARKERS, TUMOR; DNA; GENOMIC INSTABILITY; GENOMICS; HUMANS; MALE; PRECISION MEDICINE; PROSTATIC NEOPLASMS;

EID: 85019142162     PISSN: 10408363     EISSN: 1549781X     Source Type: Journal    
DOI: 10.1080/10408363.2017.1299683     Document Type: Review

References (52)

1. Ashida A, Sakaizawa K, Mikoshiba A, Uhara H, Okuyama R. 2016. Quantitative analysis of the BRAF V600E mutation in circulating tumor-derived DNA in melanoma patients using competitive allele-specific TaqMan PCR. Int J Clin Oncol. 21:981–988.
2. Azad AA, Volik SV, Wyatt AW, Haegert A, Le Bihan S, Bell RH, Anderson SA, McConeghy B, Shukin R, Bazov J, et al. 2015. Androgen receptor gene aberrations in circulating cell-free DNA:biomarkers of therapeutic resistance in castration-resistant prostate cancer. Clin Cancer Res. 21:2315–2324.
3. Baccarani M, Cortes J, Pane F, Niederwieser D, Saglio G, Apperley J, Cervantes F, Deininger M, Gratwohl A, Guilhot F, et al. 2009. Chronic myeloid leukemia:an update of concepts and management recommendations of European LeukemiaNet. J Clin Oncol. 27:6041–6051.
4. Beck J, Urnovitz HB, Mitchell WM, Schütz E. 2010. Next generation sequencing of serum circulating nucleic acids from patients with invasive ductal breast cancer reveals differences to healthy and nonmalignant controls. Mol Cancer Res. 8:335–342.
5. Beck J, Urnovitz HB, Riggert J, Clerici M, Schütz E. 2009. Profile of the circulating DNA in apparently healthy individuals. Clin Chem. 55:730–738.
6. Chan KC, Jiang P, Zheng YW, Liao GJ, Sun H, Wong J, Siu SS, Chan WC, Chan SL, Chan AT, et al. 2013. Cancer genome scanning in plasma:detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clin Chem. 59:211–224.
7. Coe TM, Fero KE, Fanta PT, Mallory RJ, Tang CM, Murphy JD, Sicklick JK. 2016. Population-based epidemiology and mortality of small malignant gastrointestinal stromal tumors in the USA. J Gastrointest Surg. 20:1132–1140.
8. Dawson SJ, Tsui DW, Murtaza M, Biggs H, Rueda OM, Chin SF, Dunning MJ, Gale D, Forshew T, Mahler-Araujo B, et al. 2013. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med. 368:1199–1209.
9. Del Re M, Biasco E, Crucitta S, Derosa L, Rofi E, Orlandini C, Miccoli M, Galli L, Falcone A, Jenster GW, et al. 2017. The detection of androgen receptor splice variant 7 in plasma-derived exosomal RNA strongly predicts resistance to hormonal therapy in metastatic prostate cancer patients. Eur Urol. 71:680–687.
10. Diehl F, Li M, Dressman D, He Y, Shen D, Szabo S, Diaz LA Jr, Goodman SN, David KA, Juhl H, et al. 2005. Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci USA. 102:16368–16373.
11. Eisenhauer EA, Therasse P, Bogaerts J, Schwartz LH, Sargent D, Ford R, Dancey J, Arbuck S, Gwyther S, Mooney M, et al. 2009. New response evaluation criteria in solid tumours:revised RECIST guideline (version 1.1). Eur J Cancer. 45:228–247.
12. FDA. Table of Pharmacogenomic Biomarkers in Drug Labeling [Internet]. Silver Spring (MD):U.S. Food and Drug Administration [cited 2016 Nov 22]. Available from:http://www.fda.gov/Drugs/ScienceResearch/ResearchAreas/Pharmacogenetics/ucm083378.htm
13. Freidin MB, Freydina DV, Leung M, Montero Fernandez A, Nicholson AG, Lim E. 2015. Circulating tumor DNA outperforms circulating tumor cells for KRAS mutation detection in thoracic malignancies. Clin Chem. 61:1299–1304.
14. Gagan J, Van Allen EM., 2015. Next-generation sequencing to guide cancer therapy. Genome Med. 7:80.
15. Gao B, Sun Y, Zhang J, Ren Y, Fang R, Han X, Shen L, Liu XY, Pao W, Chen H. 2010. Spectrum of LKB1, EGFR, and KRAS mutations in Chinese lung adenocarcinomas. J Thorac Oncol. 5:1130–1135.
16. Garcia-Murillas I, Schiavon G, Weigelt B, Ng C, Hrebien S, Cutts RJ, Cheang M, Osin P, Nerurkar A, Kozarewa I, et al. 2015. Mutation tracking in circulating tumor DNA predicts relapse in early breast cancer. Sci Transl Med. 7:302ra133.
17. Grade M, Difilippantonio MJ, Camps J., 2015. Patterns of chromosomal aberrations in solid tumors. Recent Results Cancer Res. 200:115–142.
18. Heitzer E, Auer M, Hoffmann EM, Pichler M, Gasch C, Ulz P, Lax S, Waldispuehl-Geigl J, Mauermann O, Mohan S, et al. 2013. Establishment of tumor-specific copy number alterations from plasma DNA of patients with cancer. Int J Cancer. 133:346–356.
19. Heitzer E, Ulz P, Belic J, Gutschi S, Quehenberger F, Fischereder K, Benezeder T, Auer M, Pischler C, Mannweiler S, et al. 2013. Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing. Genome Med. 5:30.
20. ICGC. ICGC Cancer Genome Projects [Internet]. Ontario (ON):International Cancer Genome Consortium [cited 2016 Nov 10]. Available from:https://icgc.org/
21. Janku F, Huang HJ, Claes B, Falchook GS, Fu S, Hong D, Ramzanali NM, Nitti G, Cabrilo G, Tsimberidou AM, et al. 2016. BRAF mutation testing in Cell-Free DNA from the plasma of patients with advanced cancers using a rapid, automated molecular diagnostics system. Mol Cancer Ther. 15:1397–1404.
22. Jorde LB, Carey JC, Bamshad MJ., 2010. Medical genetics. 4th ed. Philadelphia (PA):Mosby Elsevier.
23. Koshiyama DB, Capra ME, Paskulin GA, Rosa RF, Oliveira CA, Vanelli T, Fogliatto LM, Zen PR. 2013. Cytogenetic response to imatinib treatment in Southern Brazilian patients with chronic myelogenous leukemia and variant Philadelphia chromosome. Ann Hematol. 92:185–189.
24. Kris MG, Johnson BE, Berry LD, Kwiatkowski DJ, Iafrate AJ, Wistuba II, Varella-Garcia M, Franklin WA, Aronson SL, Su PF, et al. 2014. Using multiplexed assays of oncogenic drivers in lung cancers to select targeted drugs. Jama. 311:1998–2006.
25. Kuderer NM, Burton KA, Blau S, Rose AL, Parker S, Lyman GH, Blau CA. 2016. Comparison of 2 commercially available next-generation sequencing platforms in oncology. JAMA Oncol. DOI:10.1001/jamaoncol.2016.4983
26. Lo YM, Zhang J, Leung TN, Lau TK, Chang AM, Hjelm NM. 1999. Rapid clearance of fetal DNA from maternal plasma. Am J Hum Genet. 64:218–224.
27. López SO, García-Olmo DC, García-Arranz M, Guadalajara H, Pastor C, García-Olmo D. 2016. KRAS G12V mutation detection by droplet digital PCR in circulating cell-free DNA of colorectal cancer patients. Int J Mol Sci. 17:484.
28. Machado MP, Tomaz JP, Lorand-Metze I, de Souza CA, Vigorito AC, Delamain MT, Bendit I, Pereira NF, Pagnano KB. 2011. Monitoring of BCR-ABL levels in chronic myeloid leukemia patients treated with imatinib in the chronic phase–the importance of a major molecular response. Rev Bras Hematol Hemoter. 33:211–215.
29. Mao C, Yuan JQ, Yang ZY, Fu XH, Wu XY, Tang JL. 2015. Blood as a substitute for tumor tissue in detecting EGFR mutations for guiding EGFR TKIs treatment of nonsmall cell lung cancer:a systematic review and meta-analysis. Medicine (Baltimore). 94:e775.
30. Maus MV, Grupp SA, Porter DL, June CH. 2014. Antibody-modified T cells:CARs take the front seat for hematologic malignancies. Blood. 123:2625–2635.
31. McDermott U, Downing JR, Stratton MR., 2011. Genomics and the continuum of cancer care. N Engl J Med. 364:340–350.
32. Mouliere F, El Messaoudi S, Gongora C, Guedj AS, Robert B, Del Rio M, Molina F, Lamy PJ, Lopez-Crapez E, Mathonnet M, et al. 2013. Circulating cell-free DNA from colorectal cancer patients may reveal high KRAS or BRAF mutation load. Transl Oncol. 6:319–328.
33. Murtaza M, Dawson SJ, Tsui DW, Gale D, Forshew T, Piskorz AM, Parkinson C, Chin SF, Kingsbury Z, Wong AS, et al. 2013. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature. 497:108–112.
34. National Cancer Institute. The NCI dictionary of cancer terms [Internet]. Rockville (MD):National Cancer Institute at the National Institutes of Health [cited 2016 Nov 10]. Available from:www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=561717
35. Oxnard GR, Paweletz CP, Kuang Y, Mach SL, O'Connell A, Messineo MM, Luke JJ, Butaney M, Kirschmeier P, Jackman DM, et al. 2014. Noninvasive detection of response and resistance in EGFR-mutant lung cancer using quantitative next-generation genotyping of cell-free plasma DNA. Clin Cancer Res. 20:1698–1705.
36. Picard S, Titier K, Etienne G, Teilhet E, Ducint D, Bernard MA, Lassalle R, Marit G, Reiffers J, Begaud B, et al. 2007. Trough imatinib plasma levels are associated with both cytogenetic and molecular responses to standard-dose imatinib in chronic myeloid leukemia. Blood. 109:3496–3499.
37. Reck M, Hagiwara K, Han B, Tjulandin S, Grohe C, Yokoi T, Morabito A, Novello S, Arriola E, Molinier O, et al. 2016. ctDNA determination of EGFR mutation status in European and Japanese patients with advanced NSCLC:the assess study. J Thorac Oncol. 11:1682–1689.
38. Sandelin M, Berglund A, Sundström M, Micke P, Ekman S, Bergqvist M, Bergström S, Koyi H, Brandén E, Janson C, et al. 2015. Patients with non-small cell lung cancer analyzed for EGFR:adherence to guidelines, prevalence and outcome. Anticancer Res. 35:3979–3985.
39. Santiago-Walker A, Gagnon R, Mazumdar J, Casey M, Long GV, Schadendorf D, Flaherty K, Kefford R, Hauschild A, Hwu P, et al. 2016. Correlation of BRAF mutation status in circulating-free DNA and tumor and association with clinical outcome across four BRAFi and MEKi clinical trials. Clin Cancer Res. 22:567–574.
40. Schiavon G, Hrebien S, Garcia-Murillas I, Cutts RJ, Pearson A, Tarazona N, Fenwick K, Kozarewa I, Lopez-Knowles E, Ribas R, et al. 2015. Analysis of ESR1 mutation in circulating tumor DNA demonstrates evolution during therapy for metastatic breast cancer. Sci Transl Med. 7:313ra182.
41. Schütz E, Akbari MR, Beck J, Urnovitz H, Zhang WW, Bornemann-Kolatzki K, Mitchell WM, Nam RK, Narod SA. 2015. Chromosomal instability in cell-free DNA is a serum biomarker for prostate cancer. Clin Chem. 61:239–248.
42. Schütz E, Gummert J, Mohr F, Oellerich M. 1993. Azathioprine-induced myelosuppression in thiopurine methyltransferase deficient heart transplant recipient. Lancet. 341:436.
43. Sun K, Jiang P, Chan KC, Wong J, Cheng YK, Liang RH, Chan WK, Ma ES, Chan SL, Cheng SH, et al. 2015. Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments. Proc Natl Acad Sci USA. 112:E5503–E5512.
44. Tannock IF, Hickman JA., 2016. Limits to personalized cancer medicine. N Engl J Med. 375:1289–1294.
45. Thress KS, Paweletz CP, Felip E, Cho BC, Stetson D, Dougherty B, Lai Z, Markovets A, Vivancos A, Kuang Y, et al. 2015. Acquired EGFR C797S mutation mediates resistance to AZD9291 in non-small cell lung cancer harboring EGFR T790M. Nat Med. 21:560–562.
46. Tie J, Gibbs P., 2016. Sequencing circulating cell-free DNA:the potential to refine precision cancer medicine. Clin Chem. 62:796–798.
47. Wang L, McLeod HL, Weinshilboum RM., 2011. Genomics and drug response. N Engl J Med. 364:1144–1153.
48. Weiss GJ, Beck J, Braun DP, Bornemann-Kolatzki K, Barilla H, Cubello R, Sangal A, Whitehead RP, Kundranda M, Khemka V, et al. 2016. Abstract 3138:changes in tumor cell-free DNA copy number instability (CNI) predict therapeutic response in metastatic cancers [abstract]. Cancer Res. 76:abstr 3138.
49. Weiss GJ, Beck J, Braun DP, Bornemann-Kolatzki K, Barilla H, Cubello R, Quan W, Waypa J, Sangal A, Khemka V, et al. 2016. Tumor cell-free DNA copy number instability (CNI) to predict therapeutic response to immunotherapy prior to cycle 2 [abstract]. J Clin Oncol. 34:abstr 3027.
50. Widmer N, Bardin C, Chatelut E, Paci A, Beijnen J, Levêque D, Veal G, Astier A. 2014. Review of therapeutic drug monitoring of anticancer drugs part two-targeted therapies. Eur J Cancer. 50:2020–2036.
51. Zill OA, Greene C, Sebisanovic D, Siew LM, Leng J, Vu M, Hendifar AE, Wang Z, Atreya CE, Kelley RK, et al. 2015. Cell-free DNA next-generation sequencing in pancreatobiliary carcinomas. Cancer Discov. 5:1040–1048.
52. Zugazagoitia J, Guedes C, Ponce S, Ferrer I, Molina-Pinelo S, Paz-Ares L. 2016. Current challenges in cancer treatment. Clin Ther. 38:1551–1566.