Prognostic and predictive biomarkers: Tools in personalized oncology

Molecular Diagnosis and Therapy

Volumn 18, Issue 3, 2014, Pages 273-284

  Nalejska, Ewelina ^a   Mączyńska, Ewa ^a   Lewandowska, Marzena Anna ^a,b  

^a NICOLAUS COPERNICUS UNIVERSITY   (Poland)

^b Regional Oncology Centre Bydgoszcz   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

B RAF KINASE; BCR ABL PROTEIN; BIOLOGICAL MARKER; CYTOCHROME P450 2D; EPIDERMAL GROWTH FACTOR RECEPTOR; EPIDERMAL GROWTH FACTOR RECEPTOR 2; K RAS PROTEIN; MESSENGER RNA; MICRORNA; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; PLATELET DERIVED GROWTH FACTOR ALPHA RECEPTOR; PROGESTERONE RECEPTOR; PROTEIN P53; TUMOR MARKER;

BREAST CANCER; CANCER DIAGNOSIS; CANCER PATIENT; CANCER PROGNOSIS; CHROMOSOME ABERRATION; CHRONIC MYELOID LEUKEMIA; CIRCULATING TUMOR CELL; COLON CANCER; DNA METHYLATION; DNA REPAIR; ENZYME ACTIVITY; FUSION GENE; GENE AMPLIFICATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC DIFFERENCE; GERMLINE MUTATION; HUMAN; LIMIT OF DETECTION; LUNG CANCER; MELANOMA; MICROSATELLITE INSTABILITY; MOLECULAR BIOLOGY; MOLECULAR DIAGNOSTICS; NONHUMAN; ONCOGENE K RAS; ONCOLOGY; OUTCOME ASSESSMENT; OVERALL SURVIVAL; PERSONALIZED MEDICINE; POINT MUTATION; PREDICTIVE VALUE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; REVIEW; SIGNAL TRANSDUCTION; SINGLE STRAND CONFORMATION POLYMORPHISM; SOMATIC MUTATION; TANDEM REPEAT; GENETICS; METABOLISM; MOLECULAR PATHOLOGY; MOLECULARLY TARGETED THERAPY; MUTATION; NEOPLASMS; PATHOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR EMBOLISM;

DNA METHYLATION; HUMANS; INDIVIDUALIZED MEDICINE; MICRORNAS; MOLECULAR TARGETED THERAPY; MUTATION; NEOPLASMS; NEOPLASTIC CELLS, CIRCULATING; PATHOLOGY, MOLECULAR; POLYMORPHISM, SINGLE NUCLEOTIDE; TUMOR MARKERS, BIOLOGICAL;

EID: 84901514004     PISSN: 11771062     EISSN: 11792000     Source Type: Journal    
DOI: 10.1007/s40291-013-0077-9     Document Type: Review

References (106)

1. Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, Metcalf GA, Ng B, Milosavljevic A, Gonzalez-Garay ML, Osborne JR, Meyer R, Shi X, Tang Y, Koboldt DC, Lin L, Abbott R, Miner TL, Pohl C, Fewell G, Haipek C, Schmidt H, Dunford-Shore BH, Kraja A, Crosby SD, Sawyer CS, Vickery T, Sander S, Robinson J, Winckler W, Baldwin J, Chirieac LR, Dutt A, Fennell T, Hanna M, Johnson BE, Onofrio RC, Thomas RK, Tonon G, Weir BA, Zhao X, Ziaugra L, Zody MC, Giordano T, Orringer MB, Roth JA, Spitz MR, Wistuba II, Ozenberger B, Good PJ, Chang AC, Beer DG, Watson MA, Ladanyi M, Broderick S, Yoshizawa A, Travis WD, Pao W, Province MA, Weinstock GM, Varmus HE, Gabriel SB, Lander ES, Gibbs RA, Meyerson M, Wilson RK. Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008;455(7216):1069-75. doi:10.1038/nature07423.
2. Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C, Edkins S, O'Meara S, Vastrik I, Schmidt EE, Avis T, Barthorpe S, Bhamra G, Buck G, Choudhury B, Clements J, Cole J, Dicks E, Forbes S, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jenkinson A, Jones D, Menzies A, Mironenko T, Perry J, Raine K, Richardson D, Shepherd R, Small A, Tofts C, Varian J, Webb T, West S, Widaa S, Yates A, Cahill DP, Louis DN, Goldstraw P, Nicholson AG, Brasseur F, Looijenga L, Weber BL, Chiew YE, DeFazio A, Greaves MF, Green AR, Campbell P, Birney E, Easton DF, Chenevix-Trench G, Tan MH, Khoo SK, Teh BT, Yuen ST, Leung SY, Wooster R, Futreal PA, Stratton MR. Patterns of somatic mutation in human cancer genomes. Nature. 2007;446(7132):153-8. doi:10.1038/nature05610. (Pubitemid 46398669)
3. Wick W, Meisner C, Hentschel B, Platten M, Schilling A, Wiestler B, Sabel MC, Koeppen S, Ketter R, Weiler M, Tabatabai G, von Deimling A, Gramatzki D, Westphal M, Schackert G, Loeffler M, Simon M, Reifenberger G, Weller M. Prognostic or predictive value of MGMT promoter methylation in gliomas depends on IDH1 mutation. Neurology. 2013;81(17):1515-22. doi:10.1212/WNL. 0b013e3182a95680.
4. de Albuquerque A, Kubisch I, Stolzel U, Ernst D, Boese-Landgraf J, Breier G, Stamminger G, Fersis N, Kaul S. Prognostic and predictive value of circulating tumor cell analysis in colorectal cancer patients. J Transl Med. 2012;10:222. doi:10.1186/1479-5876-10-222.
5. Ziegler A, Koch A, Krockenberger K, Grosshennig A. Personalized medicine using DNA biomarkers: a review. Hum Genet. 2012;131(10):1627-38. doi:10.1007/s00439-012-1188-9.
6. Dias-Santagata D, Akhavanfard S, David SS, Vernovsky K, Kuhlmann G, Boisvert SL, Stubbs H, McDermott U, Settleman J, Kwak EL, Clark JW, Isakoff SJ, Sequist LV, Engelman JA, Lynch TJ, Haber DA, Louis DN, Ellisen LW, Borger DR, Iafrate AJ. Rapid targeted mutational analysis of human tumours: a clinical platform to guide personalized cancer medicine. EMBO Mol Med. 2010;2(5):146-58. doi:10.1002/emmm.201000070.
7. Banks RE, Tirukonda P, Taylor C, Hornigold N, Astuti D, Cohen D, Maher ER, Stanley AJ, Harnden P, Joyce A, Knowles M, Selby PJ. Genetic and epigenetic analysis of von Hippel-Lindau (VHL) gene alterations and relationship with clinical variables in sporadic renal cancer. Cancer Res. 2006;66(4):2000-11. doi:10.1158/0008-5472.CAN-05-3074.
8. Young AC, Craven RA, Cohen D, Taylor C, Booth C, Harnden P, Cairns DA, Astuti D, Gregory W, Maher ER, Knowles MA, Joyce A, Selby PJ, Banks RE. Analysis of VHL gene alterations and their relationship to clinical parameters in sporadic conventional renal cell carcinoma. Clin Cancer Res. 2009;15(24):7582-92. doi:10.1158/1078-0432.CCR-09-2131.
9. Nikiforov YE, Nikiforova MN. Molecular genetics and diagnosis of thyroid cancer. Nat Rev Endocrinol. 2011;7(10):569-80. doi:10.1038/nrendo.2011.142.
10. Garcia-Rostan G, Costa AM, Pereira-Castro I, Salvatore G, Hernandez R, Hermsem MJ, Herrero A, Fusco A, Cameselle-Teijeiro J, Santoro M. Mutation of the PIK3CA gene in anaplastic thyroid cancer. Cancer Res. 2005;65(22):10199-207. doi:10.1158/0008-5472.CAN-04-4259. (Pubitemid 41743711)
11. Chaiteerakij R, Addissie BD, Roberts LR. Update on biomarkers of hepatocellular carcinoma. Clin Gastroenterol Hepatol. 2013. doi:10.1016/j.cgh. 2013.10.038.
12. Lin KT, Shann YJ, Chau GY, Hsu CN, Huang CY. Identification of latent biomarkers in hepatocellular carcinoma by ultra-deep whole-transcriptome sequencing. Oncogene. 2013. doi:10.1038/onc.2013.424.
13. Yang N, Kaur S, Volinia S, Greshock J, Lassus H, Hasegawa K, Liang S, Leminen A, Deng S, Smith L, Johnstone CN, Chen XM, Liu CG, Huang Q, Katsaros D, Calin GA, Weber BL, Butzow R, Croce CM, Coukos G, Zhang L. MicroRNA microarray identifies Let-7i as a novel biomarker and therapeutic target in human epithelial ovarian cancer. Cancer Res. 2008;68(24):10307-14. doi:10.1158/0008-5472.CAN-08-1954.
14. Yang H, Kong W, He L, Zhao JJ, O'Donnell JD, Wang J, Wenham RM, Coppola D, Kruk PA, Nicosia SV, Cheng JQ. MicroRNA expression profiling in human ovarian cancer: miR-214 induces cell survival and cisplatin resistance by targeting PTEN. Cancer Res. 2008;68(2):425-33. doi:10.1158/0008-5472.CAN-07-2488. (Pubitemid 351380068)
15. Panczyk MMM. Farmakogenetyka - znaczenie w chemioterapii raka jelita grubego. Nowotwory. 2008;58(1):62-9.
16. Paduch RKJ. Markery Nowotworowe. Onkologia Polska. 2003;6(2):77-82.
17. Bates SE. Clinical applications of serum tumor markers. Ann Intern Med. 1991;115(8):623-38.
18. Cui J, Antoniou AC, Dite GS, Southey MC, Venter DJ, Easton DF, Giles GG, McCredie MR, Hopper JL. After BRCA1 and BRCA2-what next? Multifactorial segregation analyses of three-generation, population-based Australian families affected by female breast cancer. Am J Human Genet. 2001;68(2):420-31. doi:10.1086/318187. (Pubitemid 32147811)
19. Synowiec EMA, Krupa R, Woźniak K. Gene's polymorphism of DNA double-stranded repair in breast cancer. PostBiolKom. 2010;37(2):433-8.
20. Gong M, Dong W, Shi Z, Xu Y, Ni W, An R. Genetic polymorphisms of GSTM1, GSTT1, and GSTP1 with prostate cancer risk: a meta-analysis of 57 studies. PLoS ONE. 2012;7(11):e50587. doi:10.1371/journal.pone.0050587.
21. Samzadeh M, Hasanzad M, Jamaldini SH, Haghdoost AA, Afshari M, Ziaee SA. Association of G/A polymorphism, rs266882, in AREI region of the prostate-specific antigen gene with prostate cancer risk and clinicopathological features. Urol J. 2012;9(4):691-9.
22. Plawski A, Slomski R. APC gene mutations causing familial adenomatous polyposis in Polish patients. J Appl Genet. 2008;49(4):407-14. doi:10.1007/BF03195640.
23. Xu J, Zheng SL, Isaacs SD, Wiley KE, Wiklund F, Sun J, Kader AK, Li G, Purcell LD, Kim ST, Hsu FC, Stattin P, Hugosson J, Adolfsson J, Walsh PC, Trent JM, Duggan D, Carpten J, Gronberg H, Isaacs WB. Inherited genetic variant predisposes to aggressive but not indolent prostate cancer. P Natl Acad Sci USA. 2010;107(5):2136-40. doi:10.1073/pnas.0914061107.
24. Ferlay J, Shin H, Bray F, Forman D, Mathers C, Parkin DM. GLOBOCAN 2008 v2.0, Cancer incidence and mortality worldwide: IARC CancerBase No. 10 [Internet]. International Agency for Research on Cancer, 2010; 2008.
25. Thompson IM, Pauler DK, Goodman PJ, Tangen CM, Lucia MS, Parnes HL, Minasian LM, Ford LG, Lippman SM, Crawford ED, Crowley JJ, Coltman CA Jr. Prevalence of prostate cancer among men with a prostate-specific antigen level < or =4.0 ng per milliliter. N Engl J Med. 2004;350(22):2239-46. doi:10.1056/NEJMoa031918.
26. Barry MJ. Clinical practice. Prostate-specific-antigen testing for early diagnosis of prostate cancer. N Engl J Med. 2001;344(18):1373-7. doi:10.1056/NEJM200105033441806. (Pubitemid 32378393)
27. Strittmatter F, Stieber P, Nagel D, Fullhase C, Walther S, Stief CG, Waidelich R. Detection of prostate cancer with complexed PSA and complexed/total PSA ratio - is there any advantage? Eur J Med Res. 2011;16(10):445-50.
28. Liong ML, Lim CR, Yang H, Chao S, Bong CW, Leong WS, Das PK, Loh CS, Lau BE, Yu CG, Ooi EJ, Nam RK, Allen PD, Steele GS, Wassmann K, Richie JP, Liew CC. Blood-based biomarkers of aggressive prostate cancer. PLoS ONE. 2012;7(9):e45802. doi:10.1371/journal.pone.0045802.
29. van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH. Gene expression profiling predicts clinical outcome of breast cancer. Nature. 2002;415(6871):530-36. doi:10.1038/415530a. (Pubitemid 34130608)
30. Bueno-de-Mesquita JM, Linn SC, Keijzer R, Wesseling J, Nuyten DS, van Krimpen C, Meijers C, de Graaf PW, Bos MM, Hart AA, Rutgers EJ, Peterse JL, Halfwerk H, de Groot R, Pronk A, Floore AN, Glas AM, Van't Veer LJ, van de Vijver MJ. Validation of 70-gene prognosis signature in node-negative breast cancer. Breast Cancer Res Treat. 2009;117(3):483-95. doi:10.1007/s10549-008- 0191-2.
31. Nguyen B, Cusumano PG, Deck K, Kerlin D, Garcia AA, Barone JL, Rivera E, Yao K, de Snoo FA, van den Akker J, Stork-Sloots L, Generali D. Comparison of molecular subtyping with BluePrint, MammaPrint, and TargetPrint to local clinical subtyping in breast cancer patients. Ann Surg Oncol. 2012;19(10):3257-63. doi:10.1245/s10434-012-2561-6.
32. Dabbs DJ, Klein ME, Mohsin SK, Tubbs RR, Shuai Y, Bhargava R. High false-negative rate of HER2 quantitative reverse transcription polymerase chain reaction of the Oncotype DX test: an independent quality assurance study. J Clin Oncol. 2011;29(32):4279-85. doi:10.1200/JCO.2011.34.7963.
33. Qi J, Wang J, Katayama H, Sen S, Liu SM. Circulating microRNAs (cmiRNAs) as novel potential biomarkers for hepatocellular carcinoma. Neoplasma. 2013;60(2):135-42.
34. Jones CI, Zabolotskaya MV, King AJ, Stewart HJ, Horne GA, Chevassut TJ, Newbury SF. Identification of circulating microRNAs as diagnostic biomarkers for use in multiple myeloma. Br J Cancer. 2012;107(12):1987-96. doi:10.1038/bjc.2012.525.
35. Wotschofsky Z, Busch J, Jung M, Kempkensteffen C, Weikert S, Schaser KD, Melcher I, Kilic E, Miller K, Kristiansen G, Erbersdobler A, Jung K. Diagnostic and prognostic potential of differentially expressed miRNAs between metastatic and non-metastatic renal cell carcinoma at the time of nephrectomy. Clin Chim Acta. 2013;416:5-10. doi:10.1016/j.cca.2012.11.010.
36. Han ZB, Chen HY, Fan JW, Wu JY, Tang HM, Peng ZH. Up-regulation of microRNA-155 promotes cancer cell invasion and predicts poor survival of hepatocellular carcinoma following liver transplantation. J Cancer Res Clin Oncol. 2012;138(1):153-61. doi:10.1007/s00432-011-1076-z.
37. Lotte Christensen L, Tobiasen H, Holm A, Schepeler T, Ostenfeld MS, Thorsen K, Rasmussen MH, Birkenkamp-Demtroeder K, Sieber OM, Gibbs P, Lubinski J, Lamy P, Laurberg S, Oster B, Hansen KQ, Hagemann-Madsen R, Byskov K, Orntoft TF, Andersen CL. MiRNA-362-3p induces cell cycle arrest through targeting of E2F1, USF2 and PTPN1 and is associated with recurrence of colorectal cancer. Int J Cancer. 2012. doi:10.1002/ijc.28010.
38. Decock A, Ongenaert M, Hoebeeck J, De Preter K, Van Peer G, Van Criekinge W, Ladenstein R, Schulte JH, Noguera R, Stallings RL, Van Damme A, Laureys G, Vermeulen J, Van Maerken T, Speleman F, Vandesompele J. Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers. Genome Biol. 2012;13(10):R95. doi:10.1186/gb-2012-13-10-r95.
39. Xu J, Shetty PB, Feng W, Chenault C, Bast RC Jr, Issa JP, Hilsenbeck SG, Yu Y. Methylation of HIN-1, RASSF1A, RIL and CDH13 in breast cancer is associated with clinical characteristics, but only RASSF1A methylation is associated with outcome. BMC Cancer. 2012;12:243. doi:10.1186/1471-2407-12-243.
40. Vasiljevic N, Ahmad AS, Beesley C, Thorat MA, Fisher G, Berney DM, Moller H, Yu Y, Lu YJ, Cuzick J, Foster CS, Lorincz AT. Association between DNA methylation of HSPB1 and death in low Gleason score prostate cancer. Prostate Cancer Prostatic Dis. 2012. doi:10.1038/pcan.2012.47.
41. Warren JD, Xiong W, Bunker AM, Vaughn CP, Furtado LV, Roberts WL, Fang JC, Samowitz WS, Heichman KA. Septin 9 methylated DNA is a sensitive and specific blood test for colorectal cancer. BMC Med. 2011;9:133. doi:10.1186/1741-7015-9-133.
42. Hunter KW, Crawford NP, Alsarraj J. Mechanisms of metastasis. Breast Cancer Res. 2008;10(Suppl 1):S2. doi:10.1186/bcr1988.
43. Chang YS, di Tomaso E, McDonald DM, Jones R, Jain RK, Munn LL. Mosaic blood vessels in tumors: frequency of cancer cells in contact with flowing blood. Proc Natl Acad Sci USA. 2000;97(26):14608-13. doi:10.1073/pnas.97.26. 14608. (Pubitemid 32016623)
44. Magnowski P, Bochynski H, Nowak-Markwitz E, Zabel M, Spaczynski M. Circulating tumor cells (CTCs) - clinical significance in patients with ovarian cancer. Ginekol Pol. 2012;83(4):291-4.
45. Muller V, Riethdorf S, Rack B, Janni W, Fasching PA, Solomayer E, Aktas B, Kasimir-Bauer S, Pantel K, Fehm T. Prognostic impact of circulating tumor cells assessed with the Cell Search System and AdnaTest Breast in metastatic breast cancer patients: the DETECT study. Breast Cancer Res. 2012;14(4):R118. doi:10.1186/bcr3243.
46. Lucci A, Hall CS, Lodhi AK, Bhattacharyya A, Anderson AE, Xiao L, Bedrosian I, Kuerer HM, Krishnamurthy S. Circulating tumour cells in non-metastatic breast cancer: a prospective study. Lancet Oncol. 2012;13(7):688-95. doi:10.1016/S1470-2045(12)70209-7.
47. Kołacińska APM, Morawiec Z. Novel diagnostic tests for breast cancer. Oncol Clin Pract. 2007;3(2):56-8.
48. Wang FB, Yang XQ, Yang S, Wang BC, Feng MH, Tu JC. A higher number of circulating tumor cells (CTC) in peripheral blood indicates poor prognosis in prostate cancer patients - a meta-analysis. Asian Pac J Cancer Prev. 2011;12(10):2629-35.
49. Walther A, Johnstone E, Swanton C, Midgley R, Tomlinson I, Kerr D. Genetic prognostic and predictive markers in colorectal cancer. Nat Rev Cancer. 2009;9(7):489-99. doi:10.1038/nrc2645.
50. Voon PJ, Kong HL. Tumour genetics and genomics to personalise cancer treatment. Ann Acad Med Singap. 2011;40(8):362-8.
51. Vogelstein B, Fearon ER, Hamilton SR, Kern SE, Preisinger AC, Leppert M, Nakamura Y, White R, Smits AM, Bos JL. Genetic alterations during colorectal-tumor development. N Engl J Med. 1988;319(9):525-32. doi:10.1056/NEJM198809013190901.
52. Loupakis F, Ruzzo A, Cremolini C, Vincenzi B, Salvatore L, Santini D, Masi G, Stasi I, Canestrari E, Rulli E, Floriani I, Bencardino K, Galluccio N, Catalano V, Tonini G, Magnani M, Fontanini G, Basolo F, Falcone A, Graziano F. KRAS codon 61, 146 and BRAF mutations predict resistance to cetuximab plus irinotecan in KRAS codon 12 and 13 wild-type metastatic colorectal cancer. Br J Cancer. 2009;101(4):715-21. doi:10.1038/sj.bjc.6605177.
53. Lewandowska MA, Jóźwicki W, Starzynski J, Kowalewski J. Analysis of EGFR mutation frequency and coexistence of KRAS and EGFR mutations using RT-PCR in lung adenocarcinoma: may a clinical and pathological model of a patient's qualification for targeted therapy have an impact on time to obtain genetic results? Pol J Cardio Thorac Surg. 2012;9(4):443-51.
54. Lewandowska MA, Żurawski B, Jozwicki W. KRAS and BRAF mutation analysis in colorectal adenocarcinoma specimens with a low percentage of tumor cells. Mol Diagn Ther. 2013;17(3):193-203. doi:10.1007/s40291-013-0025-8.
55. Sartore-Bianchi A, Martini M, Molinari F, Veronese S, Nichelatti M, Artale S, Di Nicolantonio F, Saletti P, De Dosso S, Mazzucchelli L, Frattini M, Siena S, Bardelli A. PIK3CA mutations in colorectal cancer are associated with clinical resistance to EGFR-targeted monoclonal antibodies. Cancer Res. 2009;69(5):1851-7. doi:10.1158/0008-5472.CAN-08-2466.
56. Jiang WQ, Fu FF, Li YX, Wang WB, Wang HH, Jiang HP, Teng LS. Molecular biomarkers of colorectal cancer: prognostic and predictive tools for clinical practice. J Zhejiang Univ Sci B. 2012;13(9):663-75. doi:10.1631/jzus.B1100340.
57. Gross E, Busse B, Riemenschneider M, Neubauer S, Seck K, Klein HG, Kiechle M, Lordick F, Meindl A. Strong association of a common dihydropyrimidine dehydrogenase gene polymorphism with fluoropyrimidine-related toxicity in cancer patients. PLoS ONE. 2008;3(12):e4003. doi:10.1371/journal.pone.0004003.
58. Wei X, McLeod HL, McMurrough J, Gonzalez FJ, Fernandez-Salguero P. Molecular basis of the human dihydropyrimidine dehydrogenase deficiency and 5-fluorouracil toxicity. J Clin Invest. 1996;98(3):610-5. doi:10.1172/JCI118830. (Pubitemid 26349163)
59. Raida M, Schwabe W, Hausler P, Van Kuilenburg AB, Van Gennip AH, Behnke D, Hoffken K. Prevalence of a common point mutation in the dihydropyrimidine dehydrogenase (DPD) gene within the 5'-splice donor site of intron 14 in patients with severe 5-fluorouracil (5-FU)-related toxicity compared with controls. Clin Cancer Res. 2001;7(9):2832-9. (Pubitemid 32911393)
60. Van Kuilenburg AB, Meinsma R, Zoetekouw L, Van Gennip AH. Increased risk of grade IV neutropenia after administration of 5-fluorouracil due to a dihydropyrimidine dehydrogenase deficiency: high prevalence of the IVS14+1g>a mutation. Int J Cancer. 2002;101(3):253-8. doi:10.1002/ijc.10599. (Pubitemid 34970893)
61. Ribic CM, Sargent DJ, Moore MJ, Thibodeau SN, French AJ, Goldberg RM, Hamilton SR, Laurent-Puig P, Gryfe R, Shepherd LE, Tu D, Redston M, Gallinger S. Tumor microsatellite-instability status as a predictor of benefit from fluorouracil-based adjuvant chemotherapy for colon cancer. N Engl J Med. 2003;349(3):247-57. doi:10.1056/NEJMoa022289. (Pubitemid 36859476)
62. Bras-Goncalves RA, Rosty C, Laurent-Puig P, Soulie P, Dutrillaux B, Poupon MF. Sensitivity to CPT-11 of xenografted human colorectal cancers as a function of microsatellite instability and p53 status. Br J Cancer. 2000;82(4):913-23. doi:10.1054/bjoc.1999.1019. (Pubitemid 30085246)
63. Riely GJ, Pao W, Pham D, Li AR, Rizvi N, Venkatraman ES, Zakowski MF, Kris MG, Ladanyi M, Miller VA. Clinical course of patients with non-small cell lung cancer and epidermal growth factor receptor exon 19 and exon 21 mutations treated with gefitinib or erlotinib. Clin Cancer Res. 2006;12(3 Pt 1):839-44. doi:10.1158/1078-0432.CCR-05-1846. (Pubitemid 43259866)
64. Krawczyk P, Ramlau R, Powrózek T, Wojas-Krawczyk K, Sura S, Jarosz B, Walczyna B, Pankowski J, Szumiło J, Dyszkiewicz W, Woźniak A, Milanowski J. Wykrywalność mutacji w genie EGFR u chorych na niedrobnokomórkowego raka płuca w wybranych ośrodkach w Polsce zaangażowanych w diagnostykȩ molekularna̧. Pol J Cardio Thorac Surg. 2012;9(4):431-8. doi:10.5114/kitp.2012.32680.
65. Pao W, Miller VA, Politi KA, Riely GJ, Somwar R, Zakowski MF, Kris MG, Varmus H. Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the EGFR kinase domain. PLoS Med. 2005;2(3):e73. doi:10.1371/journal.pmed.0020073.
66. Yun CH, Mengwasser KE, Toms AV, Woo MS, Greulich H, Wong KK, Meyerson M, Eck MJ. The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP. Proc Natl Acad Sci USA. 2008;105(6):2070-5. doi:10.1073/pnas.0709662105. (Pubitemid 351439466)
67. Bean J, Brennan C, Shih JY, Riely G, Viale A, Wang L, Chitale D, Motoi N, Szoke J, Broderick S, Balak M, Chang WC, Yu CJ, Gazdar A, Pass H, Rusch V, Gerald W, Huang SF, Yang PC, Miller V, Ladanyi M, Yang CH, Pao W. MET amplification occurs with or without T790M mutations in EGFR mutant lung tumors with acquired resistance to gefitinib or erlotinib. Proc Natl Acad Sci USA. 2007;104(52):20932-7. doi:10.1073/pnas.0710370104.
68. Soda M, Choi YL, Enomoto M, Takada S, Yamashita Y, Ishikawa S, Fujiwara S, Watanabe H, Kurashina K, Hatanaka H, Bando M, Ohno S, Ishikawa Y, Aburatani H, Niki T, Sohara Y, Sugiyama Y, Mano H. Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature. 2007;448(7153):561- 6. doi:10.1038/nature05945. (Pubitemid 47206930)
69. Wong DW, Leung EL, So KK, Tam IY, Sihoe AD, Cheng LC, Ho KK, Au JS, Chung LP, Pik Wong M. The EML4-ALK fusion gene is involved in various histologic types of lung cancers from nonsmokers with wild-type EGFR and KRAS. Cancer. 2009;115(8):1723-33. doi:10.1002/cncr.24181.
70. Soda M, Takada S, Takeuchi K, Choi YL, Enomoto M, Ueno T, Haruta H, Hamada T, Yamashita Y, Ishikawa Y, Sugiyama Y, Mano H. A mouse model for EML4-ALK-positive lung cancer. Proc Natl Acad Sci USA. 2008;105(50):19893-7. doi:10.1073/pnas.0805381105.
71. Soda M, Isobe K, Inoue A, Maemondo M, Oizumi S, Fujita Y, Gemma A, Yamashita Y, Ueno T, Takeuchi K, Choi YL, Miyazawa H, Tanaka T, Hagiwara K, Mano H. A prospective PCR-based screening for the EML4-ALK oncogene in non-small cell lung cancer. Clin Cancer Res. 2012;18(20):5682-9. doi:10.1158/1078-0432. CCR-11-2947.
72. Druker BJ, Guilhot F, O'Brien SG, Gathmann I, Kantarjian H, Gattermann N, Deininger MW, Silver RT, Goldman JM, Stone RM, Cervantes F, Hochhaus A, Powell BL, Gabrilove JL, Rousselot P, Reiffers J, Cornelissen JJ, Hughes T, Agis H, Fischer T, Verhoef G, Shepherd J, Saglio G, Gratwohl A, Nielsen JL, Radich JP, Simonsson B, Taylor K, Baccarani M, So C, Letvak L, Larson RA. Five-year follow-up of patients receiving imatinib for chronic myeloid leukemia. N Engl J Med. 2006;355(23):2408-17. doi:10.1056/NEJMoa062867. (Pubitemid 44903745)
73. Chapman PB, Einhorn LH, Meyers ML, Saxman S, Destro AN, Panageas KS, Begg CB, Agarwala SS, Schuchter LM, Ernstoff MS, Houghton AN, Kirkwood JM. Phase III multicenter randomized trial of the Dartmouth regimen versus dacarbazine in patients with metastatic melanoma. J Clin Oncol. 1999;17(9):2745-51. (Pubitemid 29415231)
74. Davies H, Bignell GR, Cox C, Stephens P, Edkins S, Clegg S, Teague J, Woffendin H, Garnett MJ, Bottomley W, Davis N, Dicks E, Ewing R, Floyd Y, Gray K, Hall S, Hawes R, Hughes J, Kosmidou V, Menzies A, Mould C, Parker A, Stevens C, Watt S, Hooper S, Wilson R, Jayatilake H, Gusterson BA, Cooper C, Shipley J, Hargrave D, Pritchard-Jones K, Maitland N, Chenevix-Trench G, Riggins GJ, Bigner DD, Palmieri G, Cossu A, Flanagan A, Nicholson A, Ho JW, Leung SY, Yuen ST, Weber BL, Seigler HF, Darrow TL, Paterson H, Marais R, Marshall CJ, Wooster R, Stratton MR, Futreal PA. Mutations of the BRAF gene in human cancer. Nature. 2002;417(6892):949-54. doi:10.1038/nature00766. (Pubitemid 34716871)
75. Chapman PB, Hauschild A, Robert C, Haanen JB, Ascierto P, Larkin J, Dummer R, Garbe C, Testori A, Maio M, Hogg D, Lorigan P, Lebbe C, Jouary T, Schadendorf D, Ribas A, O'Day SJ, Sosman JA, Kirkwood JM, Eggermont AM, Dreno B, Nolop K, Li J, Nelson B, Hou J, Lee RJ, Flaherty KT, McArthur GA. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med. 2011;364(26):2507-16. doi:10.1056/NEJMoa1103782.
76. Spittle C, Ward MR, Nathanson KL, Gimotty PA, Rappaport E, Brose MS, Medina A, Letrero R, Herlyn M, Edwards RH. Application of a BRAF pyrosequencing assay for mutation detection and copy number analysis in malignant melanoma. J Mol Diagn. 2007;9(4):464-71. doi:10.2353/jmoldx.2007.060191. (Pubitemid 47434113)
77. Montagut C, Sharma SV, Shioda T, McDermott U, Ulman M, Ulkus LE, Dias-Santagata D, Stubbs H, Lee DY, Singh A, Drew L, Haber DA, Settleman J. Elevated CRAF as a potential mechanism of acquired resistance to BRAF inhibition in melanoma. Cancer Res. 2008;68(12):4853-61. doi:10.1158/0008-5472.CAN-07- 6787.
78. Emery CM, Vijayendran KG, Zipser MC, Sawyer AM, Niu L, Kim JJ, Hatton C, Chopra R, Oberholzer PA, Karpova MB, MacConaill LE, Zhang J, Gray NS, Sellers WR, Dummer R, Garraway LA. MEK1 mutations confer resistance to MEK and B-RAF inhibition. Proc Natl Acad Sci USA. 2009;106(48):20411-6. doi:10.1073/pnas. 0905833106.
79. Curtin JA, Busam K, Pinkel D, Bastian BC. Somatic activation of KIT in distinct subtypes of melanoma. J Clin Oncol. 2006;24(26):4340-6. doi:10.1200/JCO.2006.06.2984. (Pubitemid 46630793)
80. Lim JS, Chen XA, Singh O, Yap YS, Ng RC, Wong NS, Wong M, Lee EJ, Chowbay B. Impact of CYP2D6, CYP3A5, CYP2C9 and CYP2C19 polymorphisms on tamoxifen pharmacokinetics in Asian breast cancer patients. Br J Clin Pharmacol. 2011;71(5):737-50. doi:10.1111/j.1365-2125.2011.03905.x.
81. Lim HS, Ju Lee H, Seok Lee K, Sook Lee E, Jang IJ, Ro J. Clinical implications of CYP2D6 genotypes predictive of tamoxifen pharmacokinetics in metastatic breast cancer. J Clin Oncol. 2007;25(25):3837-45. doi:10.1200/JCO.2007.11.4850. (Pubitemid 47477258)
82. Xu Y, Sun Y, Yao L, Shi L, Wu Y, Ouyang T, Li J, Wang T, Fan Z, Fan T, Lin B, He L, Li P, Xie Y. Association between CYP2D6 &z.ast;10 genotype and survival of breast cancer patients receiving tamoxifen treatment. Ann Oncol. 2008;19(8):1423-9. doi:10.1093/annonc/mdn155.
83. Abraham JE, Maranian MJ, Driver KE, Platte R, Kalmyrzaev B, Baynes C, Luccarini C, Shah M, Ingle S, Greenberg D, Earl HM, Dunning AM, Pharoah PD, Caldas C. CYP2D6 gene variants: association with breast cancer specific survival in a cohort of breast cancer patients from the United Kingdom treated with adjuvant tamoxifen. Breast Cancer Res. 2010;12(4):R64. doi:10.1186/bcr2629.
84. Toyama T, Yamashita H, Sugiura H, Kondo N, Iwase H, Fujii Y. No association between CYP2D6&z.ast;10 genotype and survival of node-negative Japanese breast cancer patients receiving adjuvant tamoxifen treatment. Jpn J Clin Oncol. 2009;39(10):651-6. doi:10.1093/jjco/hyp076.
85. Mitra D, Brumlik MJ, Okamgba SU, Zhu Y, Duplessis TT, Parvani JG, Lesko SM, Brogi E, Jones FE. An oncogenic isoform of HER2 associated with locally disseminated breast cancer and trastuzumab resistance. Mol Cancer Ther. 2009;8(8):2152-62. doi:10.1158/1535-7163.MCT-09-0295.
86. Bassullu N, Turkmen I, Dayangac M, Yagiz Korkmaz P, Yasar R, Akyildiz M, Yaprak O, Tokat Y, Yuzer Y, Bulbul Dogusoy G. The predictive and prognostic significance of c-erb-B2, EGFR, PTEN, mTOR, PI3K, p27, and ERCC1 expression in hepatocellular carcinoma. Hepat Mon. 2012;12(10 HCC):e7492. doi:10.5812/ hepatmon.7492.
87. Cittelly DM, Das PM, Spoelstra NS, Edgerton SM, Richer JK, Thor AD, Jones FE. Downregulation of miR-342 is associated with tamoxifen resistant breast tumors. Mol Cancer. 2010;9:317. doi:10.1186/1476-4598-9-317.
88. Nordentoft I, Birkenkamp-Demtroder K, Agerbaek M, Theodorescu D, Ostenfeld MS, Hartmann A, Borre M, Orntoft TF, Dyrskjot L. miRNAs associated with chemo-sensitivity in cell lines and in advanced bladder cancer. BMC Med Genomics. 2012;5:40. doi:10.1186/1755-8794-5-40.
89. Bleeker FE, Molenaar RJ, Leenstra S. Recent advances in the molecular understanding of glioblastoma. J Neurooncol. 2012;108(1):11-27. doi:10.1007/s11060-011-0793-0.
90. van den Bent MJ, Hegi ME, Stupp R. Recent developments in the use of chemotherapy in brain tumours. Eur J Cancer. 2006;42(5):582-8. doi:10.1016/j.ejca.2005.06.031. (Pubitemid 43343679)
91. Hegi ME, Diserens AC, Godard S, Dietrich PY, Regli L, Ostermann S, Otten P, Van Melle G, de Tribolet N, Stupp R. Clinical trial substantiates the predictive value of O-6-methylguanine-DNA methyltransferase promoter methylation in glioblastoma patients treated with temozolomide. Clin Cancer Res. 2004;10(6):1871-4. (Pubitemid 38375541)
92. Hegi ME, Diserens AC, Gorlia T, Hamou MF, de Tribolet N, Weller M, Kros JM, Hainfellner JA, Mason W, Mariani L, Bromberg JE, Hau P, Mirimanoff RO, Cairncross JG, Janzer RC, Stupp R. MGMT gene silencing and benefit from temozolomide in glioblastoma. N Engl J Med. 2005;352(10):997-1003. doi:10.1056/NEJMoa043331. (Pubitemid 40349502)
93. Esteller M, Garcia-Foncillas J, Andion E, Goodman SN, Hidalgo OF, Vanaclocha V, Baylin SB, Herman JG. Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. N Engl J Med. 2000;343(19):1350-4. doi:10.1056/NEJM200011093431901.
94. Zawlik I, Vaccarella S, Kita D, Mittelbronn M, Franceschi S, Ohgaki H. Promoter methylation and polymorphisms of the MGMT gene in glioblastomas: a population-based study. Neuroepidemiology. 2009;32(1):21-9. doi:10.1159/ 000170088.
95. Watts GS, Pieper RO, Costello JF, Peng YM, Dalton WS, Futscher BW. Methylation of discrete regions of the O6-methylguanine DNA methyltransferase (MGMT) CpG island is associated with heterochromatinization of the MGMT transcription start site and silencing of the gene. Mol Cell Biol. 1997;17(9):5612-9. (Pubitemid 27357657)
96. Patel SA, Graunke DM, Pieper RO. Aberrant silencing of the CpG island-containing human O6-methylguanine DNA methyltransferase gene is associated with the loss of nucleosome-like positioning. Mol Cell Biol. 1997;17(10):5813-22. (Pubitemid 27411088)
97. Pieper RO, Patel S, Ting SA, Futscher BW, Costello JF. Methylation of CpG island transcription factor binding sites is unnecessary for aberrant silencing of the human MGMT gene. J Biol Chem. 1996;271(23):13916-24. (Pubitemid 26185440)
98. Esteller M, Hamilton SR, Burger PC, Baylin SB, Herman JG. Inactivation of the DNA repair gene O6-methylguanine-DNA methyltransferase by promoter hypermethylation is a common event in primary human neoplasia. Cancer Res. 1999;59(4):793-7. (Pubitemid 29086728)
99. Nakada M, Furuta T, Hayashi Y, Minamoto T, Hamada J. The strategy for enhancing temozolomide against malignant glioma. Front Oncol. 2012;2:98. doi:10.3389/fonc.2012.00098.
100. Karakousis G, Yang R, Xu X. Circulating melanoma cells as a predictive biomarker. J Invest Dermatol. 2013;133(6):1460-2. doi:10.1038/jid.2013.34.
101. Magbanua MJ, Sosa EV, Scott JH, Simko J, Collins C, Pinkel D, Ryan CJ, Park JW. Isolation and genomic analysis of circulating tumor cells from castration resistant metastatic prostate cancer. BMC Cancer. 2012;12:78. doi:10.1186/1471-2407-12-78.
102. Reinholz MM, Kitzmann KA, Tenner K, Hillman D, Dueck AC, Hobday TJ, Northfelt DW, Moreno-Aspitia A, Roy V, LaPlant B, Allred JB, Stella PJ, Lingle WL, Perez EA. Cytokeratin-19 and mammaglobin gene expression in circulating tumor cells from metastatic breast cancer patients enrolled in North Central Cancer Treatment Group trials, N0234/336/436/437. Clin Cancer Res. 2011;17(22):7183-93. doi:10.1158/1078-0432.CCR-11-0981.
103. Lewandowski R, Roszkowski K, Lewandowska MA. Personalized medicine in oncology: vision or realistic concept? Contemp Oncol. 2011;15(1):1-6.
104. Poznanski M, Lewandowska MA. Application of high-throughput technologies in cancer molecular diagnostics. Oncol Clin Pract. 2013;9(2):70-7.
105. The Cancer Genome Atlas (TCGA) Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008;455(7216):1061-68. doi:10.1038/nature07385.
106. Lewandowska MA, Furtak J, Szylberg T, Roszkowski K, Windorbska W, Rytlewska J, Jozwicki W. An analysis of the prognostic value of IDH1 (isocitrate dehydrogenase 1) mutation in polish glioma patients. Mol Diagn Ther. 2013 Aug 10. doi:10.1007/s40291-013-0050-7.