Challenges and opportunities for oncology biomarker discovery

Drug Discovery Today

Volumn 18, Issue 13-14, 2013, Pages 614-624

  Deyati, Avisek ^a,b   Younesi, Erfan ^b   Hofmann Apitius, Martin ^b   Novac, Natalia ^a  

^a Merck Serono GmbH   (Germany)

^b FRAUNHOFER INSTITUTE FOR ALGORITHMS AND SCIENTIFIC COMPUTING SCAI   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARSENIC TRIOXIDE; BRENTUXIMAB VEDOTIN; CETUXIMAB; CRIZOTINIB; DASATINIB; DENILEUKIN DIFTITOX; ERLOTINIB; EXEMESTANE; FULVESTRANT; GEFITINIB; IMATINIB; LAPATINIB; MICRORNA; PANITUMUMAB; PERTUZUMAB; TAMOXIFEN; TOSITUMOMAB; TRASTUZUMAB; TUMOR MARKER; VEMURAFENIB;

BREAST CANCER; CANCER GENETICS; CLINICAL PRACTICE; FLUORESCENCE IN SITU HYBRIDIZATION; FUSION GENE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE SEQUENCE; HUMAN; IMMUNOHISTOCHEMISTRY; KNOWLEDGE BASE; LEUKEMIA; MEDICAL TECHNOLOGY; METABOLISM; NONHUMAN; ONCOLOGY; POLYMERASE CHAIN REACTION; PROFESSIONAL KNOWLEDGE; REVIEW; WESTERN BLOTTING;

ANIMALS; BIOMEDICAL RESEARCH; DATA MINING; GENETIC MARKERS; GENOMICS; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; KNOWLEDGE BASES; MEDICAL ONCOLOGY; METABOLOMICS; NEOPLASMS; PREDICTIVE VALUE OF TESTS; PROGNOSIS; PROTEOMICS; SYSTEMS BIOLOGY; TUMOR MARKERS, BIOLOGICAL;

EID: 84879910284     PISSN: 13596446     EISSN: 18785832     Source Type: Journal    
DOI: 10.1016/j.drudis.2012.12.011     Document Type: Review

References (78)

1. D.J. Triggle Medicines in the 21st century OR pills, politics, potions, and profits: where is public policy? Drug Dev. Res. 59 2003 269 291
2. J. Lederberg Medicine's old battle against the bugs isn't over at all Int. Herald Tribune 1996
3. G.H. Hitchings Health care and life expectancy Science 262 1993 1632
4. B. Munos Lessons from 60 years of pharmaceutical innovation Nat. Rev. Drug Discov. 8 2009 959 968
5. J. Arrowsmith Phase II failures: 2008-2010 Nat. Rev. Drug Discov. 10 2011 328 329
6. T. Elias Why products fail in phase III In Vivo 24 2006
7. F.W. Frueh Pharmacogenomic biomarker information in drug labels approved by the United States food and drug administration: prevalence of related drug use Pharmacotherapy 28 2008 992 998
8. A.S. Ptolemy, and N. Rifai What is a biomarker? Research investments and lack of clinical integration necessitate a review of biomarker terminology and validation schema Scand. J. Clin. Lab. Invest. Suppl. 242 2010 6 14
9. I.J. Majewski, and R. Bernards Taming the dragon: genomic biomarkers to individualize the treatment of cancer Nat. Med. 17 2011 304 312
10. M.R. Trusheim Quantifying factors for the success of stratified medicine Nat. Rev. Drug Discov. 10 2011 817 833
11. C. Sawyers Targeted cancer therapy Nature 432 2004 294 297
12. J.G. Paez EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy Science 304 2004 1497 1500
13. R.J. Kreitman Immunotoxins for targeted cancer therapy AAPS 8 2006 532 551
14. M. Moroni Gene copy number for epidermal growth factor receptor (EGFR) and clinical response to antiEGFR treatment in colorectal cancer: a cohort study Lancet Oncol. 6 2005 279 286
15. A. Lièvre KRAS mutation status is predictive of response to cetuximab therapy in colorectal cancer Cancer Res. 66 2006 3992 3995
16. D.A. Eberhard Mutations in the epidermal growth factor receptor and in KRAS are predictive and prognostic indicators in patients with non-small-cell lung cancer treated with chemotherapy alone and in combination with erlotinib J. Clin. Oncol. 23 2005 5900 5909
17. R.G. Amado Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer J. Clin. Oncol. 26 2008 1626 1634
18. B.J. Druker Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia N. Engl. J. Med. 344 2001 1031 1037
19. M.C. Heinrich Kinase mutations and imatinib response in patients with metastatic gastrointestinal stromal tumor J. Clin. Oncol. 21 2003 4342 4349
20. E.L. Kwak Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer N. Engl. J. Med. 363 2010 1693 1703
21. S. Bhattacharya, and T.J. Mariani Array of hope: expression profiling identifies disease biomarkers and mechanism Biochem. Soc. Trans. 37 2009 855 862
22. L.J. van 't Veer Gene expression profiling predicts clinical outcome of breast cancer Nature 415 2002 530 536
23. S. Paik A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer N. Engl. J. Med. 351 2004 2817 2826
24. M. Moroni Somatic mutation of EGFR catalytic domain and treatment with gefitinib in colorectal cancer Ann. Oncol. 16 2005 1848 1849
25. G.D.L. Phillips Targeting HER2-positive breast cancer with trastuzumab-DM1, an antibody-cytotoxic drug conjugate Cancer Res. 68 2008 9280 9290
26. L.B. Saltz Phase II trial of cetuximab in patients with refractory colorectal cancer that expresses the epidermal growth factor receptor J. Clin. Oncol. 22 2004 1201 1208
27. U. Vanhoefer Phase I study of the humanized antiepidermal growth factor receptor monoclonal antibody EMD72000 in patients with advanced solid tumors that express the epidermal growth factor receptor J. Clin. Oncol. 22 2004 175 184
28. T.J. Lynch Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib N. Engl. J. Med. 350 2004 2129 2139
29. D.J. Freeman Activity of panitumumab alone or with chemotherapy in non-small cell lung carcinoma cell lines expressing mutant epidermal growth factor receptor Mol. Cancer Ther. 8 2009 1536 1546
30. N. Rifai Protein biomarker discovery and validation: the long and uncertain path to clinical utility Nat. Biotechnol. 24 2006 971 983
31. C.M. Niemeyer Immuno-PCR: high sensitivity detection of proteins by nucleic acid amplification Trends Biotechnol. 23 2005 208 216
32. J.E. McDermed Nucleic acid detection immunoassay for prostate-specific antigen based on immuno-PCR methodology Clin. Chem. 58 2012 732 740
33. P.S. Ward, and C.B. Thompson Metabolic reprogramming: a cancer hallmark even warburg did not anticipate Cancer Cell 21 2012 297 308
34. V.A. Krutovskikh, and Z. Herceg Oncogenic microRNAs (OncomiRs) as a new class of cancer biomarkers Bioessays 32 2010 894 904
35. L. Chang-Gong MicroRNA expression profiling using microarrays Nat. Protoc. 3 2008 563 578
36. I. Janoueix-Lerosey Somatic and germline activating mutations of the ALK kinase receptor in neuroblastoma Nature 455 2008 967 970
37. T. Bekaii-Saab A multi-institutional phase II study of the efficacy and tolerability of lapatinib in patients with advanced hepatocellular carcinomas Clin. Cancer Res. 15 2009 5895 5901
38. P.B. Chapman Improved survival with vemurafenib in melanoma with BRAF V600E mutation N. Engl. J. Med. 364 2011 2507 2516
39. M.S. Kaminski 131I-tositumomab therapy as initial treatment for follicular lymphoma N. Engl. J. Med. 352 2005 441 449
40. C. Niu Studies on treatment of acute promyelocytic leukemia with arsenic trioxide: remission induction, follow-up and molecular monitoring in 11 newly diagnosed and 47 relapsed acute promyelocytic leukemia patients Blood 94 1999 3315 3324
41. M. Hazarika Tasigna for chronic and accelerated phase Philadelphia chromosome-positive chronic myelogenous leukemia resistant to or intolerant of imatinib Clin. Cancer Res. 14 2008 5325 5331
42. H. Takei Multicenter phase II trial of neoadjuvant exemestane for postmenopausal patients with hormone receptor-positive, operable breast cancer: Saitama Breast Cancer Clinical Study Group (SBCCSG-03) Breast Cancer Res. Treat. 107 2008 87 94
43. M.S. Tsao Erlotinib in lung cancer - molecular and clinical predictors of outcome N. Engl. J. Med. 353 2005 133 144
44. S. Addo A phase I trial to assess the pharmacology of the new oestrogen receptor antagonist fulvestrant on the endometrium in healthy postmenopausal volunteers Br. J. Cancer 87 2002 1354 1359
45. A. Hochhaus Dasatinib induces durable cytogenetic responses in patients with chronic myelogenous leukemia in chronic phase with resistance or intolerance to imatinib Leukemia 22 2008 1200 1206
46. N.H. Dang Phase II trial of denileukin diftitox for relapsed/refractory T-cell non-Hodgkin lymphoma Br. J. Haematol. 136 2007 439 447
47. D.J. Slamon Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2 N. Engl. J. Med. 344 2001 783 792
48. S.A. Jagarlapudi, and K.V. Kishan Database systems for knowledge-based discovery Methods Mol. Biol. 575 2009 159 172
49. T.A. Brentnall Proteins that underlie neoplastic progression of ulcerative colitis Proteomics Clin. Appl. 3 2009 1326 1339
50. R. Chen Quantitative proteomics analysis reveals that proteins differentially expressed in chronic pancreatitis are also frequently involved in pancreatic cancer Mol. Cell Proteomics 6 2007 1331 1342
51. I. Fichtner Establishment of patient-derived non-small cell lung cancer xenografts as models for the identification of predictive biomarkers Clin. Cancer Res. 14 2008 6456 6468
52. J.N. Andersen Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors Sci. Transl. Med. 2 2010 43 55
53. H. Chang Effect of neoadjuvant ixabepilone (ixa) on cell cycle genes and tumor-initiating cell (TIC) signature in breast cancer (BC) J. Clin. Oncol. 2011 29
54. P.W. Faber Potential non-synonymous single nucleotide polymorphisms (nsSNPs) associated with toxicity in metastatic clear cell renal cell carcinoma (MCCRCC) patients (pts) treated with sunitinib J. Clin. Oncol. 2008 26
55. Y.F. Wong Identification of molecular markers and signaling pathway in endometrial cancer in Hong Kong Chinese women by genome-wide gene expression profiling Oncogene 26 2007 1971 1982
56. L. Ruan Analysis of EGFR signaling pathway in nasopharyngeal carcinoma cells by quantitative phosphoproteomics Proteome Sci. 2011 10.1186/1477-5956-9- 35
57. Z. Fu Metastasis suppressor gene Raf kinase inhibitor protein (RKIP) is a novel prognostic marker in prostate cancer Prostate 66 2006 248 256
58. D.R. Rhodes Multiplex biomarker approach for determining risk of prostate-specific antigen-defined recurrence of prostate cancer J. Natl. Cancer Inst. 95 2003 661 668
59. V. Walia Loss of breast epithelial marker hCLCA2 promotes epithelial-to-mesenchymal transition and indicates higher risk of metastasis Oncogene 31 2012 2237 2246
60. D. Laifenfeld Early patient stratification and predictive biomarkers in drug discovery and development: a case study of ulcerative colitis anti-TNF therapy Adv. Exp. Med. Biol. 736 2012 645 653
61. S. Szalma Effective knowledge management in translational medicine J. Transl. Med. 2010 10.1186/1479-5876-8-68
62. M. Mal Metabotyping of human colorectal cancer using two-dimensional gas chromatography mass spectrometry Anal. Bioanal. Chem. 403 2012 483 493
63. E. Shmelkov Assessing quality and completeness of human transcriptional regulatory pathways on a genome-wide scale Biol. Direct 6 2011 15
64. C.A. Altar A prototypical process for creating evidentiary standards for biomarkers and diagnostics Clin. Pharmacol. Ther. 83 2008 368 371
65. H.C. Harsha A compendium of potential biomarkers of pancreatic cancer PLoS Med. 2009 10.1371/journal.pmed.1000046
66. J.L. Pennings Discovery of novel serum biomarkers for prenatal Down syndrome screening by integrative data mining PLoS One 2009 10.1371/journal. pone.0008010
67. X. Deng Link test - a statistical method for finding prostate cancer biomarkers Comput. Biol. Chem. 30 2006 425 433
68. M. Bundschus Extraction of semantic biomedical relations from text using conditional random fields BMC Bioinformatics 2008 10.1186/1471-2105-9-207
69. P.L. Elkin BioProspecting: novel marker discovery obtained by mining the bibleome BMC Bioinformatics 2009 10.1186/1471-2105-10-S2-S9
70. M.T. Islam Biomarker Information Extraction Tool (BIET) development using natural language processing and machine learning Proceedings of the International Conference and Workshop on Emerging Trends in Technology 2010 ACM 121 126
71. W. Jessen Mining PubMed for biomarker-disease associations to guide discovery Nat. Proc. 2012 10.1038/npre.2012.6941.1
72. M. Ongenaert PubMeth: a cancer methylation database combining text mining and expert annotation Nucleic Acids Res. 36 2008 D842 D846
73. E. Younesi Mining biomarker information in biomedical literature BMC Med. Inform. Decis. Making 12 2012 148
74. E.C. Butcher Systems biology in drug discovery Nat. Biotechnol. 22 2004 1253 1259
75. P. Khatri Ten years of pathway analysis: current approaches and outstanding challenges PLoS Comput. Biol. 2012 10.1371/journal.pcbi.1002375
76. P.K. Kreeger, and D.A. Lauffenburger Cancer systems biology: a network modeling perspective Carcinogenesis 31 2010 2 8
77. D. Sahoo The power of boolean implication networks Front Physiol. 2012 10.3389/fphys.2012.00276
78. F. Martin Assessment of network perturbation amplitude by applying high throughput data to causal biological networks BMC Syst. Biol. 2012 10.1186/1752-0509-6-54