Challenges and prospects for biomarker research: A current perspective from the developing world

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1844, Issue 5, 2014, Pages 899-908

  Gupta, Shabarni ^a   Venkatesh, Apoorva ^a   Ray, Sandipan ^a   Srivastava, Sanjeeva ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY BOMBAY   (India)

Author keywords

Biomarker; Biorepository; Developing world; Disease heterogeneity; Funding; IP issue

Indexed keywords

BIOLOGICAL MARKER;

AWARENESS; BIOLOGICAL PHENOMENA AND FUNCTIONS CONCERNING THE ENTIRE ORGANISM; DEVELOPED COUNTRY; DEVELOPING COUNTRY; DIET; DISEASES; ECONOMIC ASPECT; EDUCATION; ENVIRONMENTAL FACTOR; ETHNICITY; EVALUATION STUDY; FINANCIAL MANAGEMENT; HUMAN; INFECTIOUS DISEASE ELISA KIT; INFORMATION PROCESSING; LIFESTYLE; MEDICAL RESEARCH; POPULATION; PRIORITY JOURNAL; PROCEDURES; PROTEIN ANALYSIS; RESEARCH ETHICS; REVIEW; RISK FACTOR; SOCIAL ASPECT; TRANSLATIONAL RESEARCH; VALIDATION STUDY;

BIOMARKER; BIOREPOSITORY; DEVELOPING WORLD; DISEASE HETEROGENEITY; FUNDING; IP ISSUE;

BIOLOGICAL MARKERS; BIOMEDICAL RESEARCH; CLINICAL MEDICINE; DEVELOPING COUNTRIES; HUMANS; PROTEINS; PROTEOMICS;

EID: 84898597608     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2013.12.020     Document Type: Review

References (99)

1. S.K. Sgaier, P. Jha, P. Mony, A. Kurpad, V. Lakshmi, R. Kumar, and N.K. Ganguly Public health. Biobanks in developing countries: needs and feasibility Science 318 2007 1074 1075 (Pubitemid 350134883)
2. T. Rastogi, A. Hildesheim, and R. Sinha Opportunities for cancer epidemiology in developing countries Nat. Rev. Cancer 4 2004 909 917 (Pubitemid 39472957)
3. E. Petricoin, J. Wulfkuhle, V. Espina, and L.A. Liotta Clinical proteomics: revolutionizing disease detection and patient tailoring therapy J. Proteome Res. 3 2004 209 217 (Pubitemid 38500987)
4. S. Hanash Disease proteomics Nature 422 2003 226 232 (Pubitemid 36362760)
5. M. Kussmann, F. Raymond, and M. Affolter OMICS-driven biomarker discovery in nutrition and health J. Biotechnol. 124 2006 758 787 (Pubitemid 44088435)
6. R. Chen, and M. Snyder Promise of personalized omics to precision medicine Wiley Interdiscip. Rev. Syst. Biol. Med. 5 2013 73 82
7. R. Chen, G.I. Mias, J. Li-Pook-Than, L. Jiang, H.Y. Lam, R. Chen, E. Miriami, K.J. Karczewski, M. Hariharan, F.E. Dewey, Y. Cheng, M.J. Clark, H. Im, L. Habegger, S. Balasubramanian, M. O'Huallachain, J.T. Dudley, S. Hillenmeyer, R. Haraksingh, D. Sharon, G. Euskirchen, P. Lacroute, K. Bettinger, A.P. Boyle, M. Kasowski, F. Grubert, S. Seki, M. Garcia, M. Whirl-Carrillo, M. Gallardo, M.A. Blasco, P.L. Greenberg, P. Snyder, T.E. Klein, R.B. Altman, A.J. Butte, E.A. Ashley, M. Gerstein, K.C. Nadeau, H. Tang, and M. Snyder Personal omics profiling reveals dynamic molecular and medical phenotypes Cell 148 2012 1293 1307
8. K.R. Coombes, J.S. Morris, J. Hu, S.R. Edmonson, and K.A. Baggerly Serum proteomics profiling - a young technology begins to mature Nat. Biotechnol. 23 2005 291 292 (Pubitemid 41094414)
9. S. Ray, P.J. Reddy, R. Jain, K. Gollapalli, A. Moiyadi, and S. Srivastava Proteomic technologies for the identification of disease biomarkers in serum: advances and challenges ahead Proteomics 11 2011 2139 2161
10. A.G. Paulovich, J.R. Whiteaker, A.N. Hoofnagle, and P. Wang The interface between biomarker discovery and clinical validation: the tar pit of the protein biomarker pipeline Proteomics Clin. Appl. 2 2008 1386 1402
11. H. Mischak, J.P. Ioannidis, A. Argiles, T.K. Attwood, E. Bongcam-Rudloff, M. Broenstrup, A. Charonis, G.P. Chrousos, C. Delles, A. Dominiczak, T. Dylag, J. Ehrich, J. Egido, P. Findeisen, J. Jankowski, R.W. Johnson, B.A. Julien, T. Lankisch, H.Y. Leung, D. Maahs, F. Magni, M.P. Manns, E. Manolis, G. Mayer, G. Navis, J. Novak, A. Ortiz, F. Persson, K. Peter, H.H. Riese, P. Rossing, N. Sattar, G. Spasovski, V. Thongboonkerd, R. Vanholder, J.P. Schanstra, and A. Vlahou Implementation of proteomic biomarkers: making it work Eur. J. Clin. Invest. 42 2012 1027 1036
12. A.K. Fuzery, J. Levin, M.M. Chan, and D.W. Chan Translation of proteomic biomarkers into FDA approved cancer diagnostics: issues and challenges Clin. Proteomics 10 2013 13
13. Z. Zhang, and D.W. Chan The road from discovery to clinical diagnostics: lessons learned from the first FDA-cleared in vitro diagnostic multivariate index assay of proteomic biomarkers Cancer Epidemiol. Biomarkers Prev. 19 2010 2995 2999
14. S. Michiels, A. Kramar, and S. Koscielny Multidimensionality of microarrays: statistical challenges and (im)possible solutions Mol. Oncol. 5 2011 190 196
15. S.E. Taube, G.M. Clark, J.E. Dancey, L.M. McShane, C.C. Sigman, and S.I. Gutman A perspective on challenges and issues in biomarker development and drug and biomarker codevelopment J. Natl. Cancer Inst. 101 2009 1453 1463
16. B. Domon, and R. Aebersold Challenges and opportunities in proteomics data analysis Mol. Cell. Proteomics 5 2006 1921 1926 (Pubitemid 44688200)
17. J. Listgarten, and A. Emili Practical proteomic biomarker discovery: taking a step back to leap forward Drug Discov. Today 10 2005 1697 1702 (Pubitemid 41817620)
18. M.W. Qoronfleh Role and challenges of proteomics in pharma and biotech: technical, scientific and commercial perspective Expert Rev. Proteomics 3 2006 179 195 (Pubitemid 43987846)
19. D.M. Potter, L.H. Butterfield, S.J. Divito, C.A. Sander, and J.M. Kirkwood Pitfalls in retrospective analyses of biomarkers: a case study with metastatic melanoma patients J. Immunol. Methods 376 2012 108 112
20. J.D. Brooks Translational genomics: the challenge of developing cancer biomarkers Genome Res. 22 2012 183 187
21. K.A. Phillips, B.S. Van, and A.M. Issa Diagnostics and biomarker development: priming the pipeline Nat. Rev. Drug Discov. 5 2006 463 469 (Pubitemid 44136958)
22. Z. Feng, R. Prentice, and S. Srivastava Research issues and strategies for genomic and proteomic biomarker discovery and validation: a statistical perspective Pharmacogenomics 5 2004 709 719 (Pubitemid 39236584)
23. J. Tosoian, and S. Loeb PSA and beyond: the past, present, and future of investigative biomarkers for prostate cancer Sci. World J. 10 2010 1919 1931
24. J.S. Ross, J.A. Fletcher, G.P. Linette, J. Stec, E. Clark, M. Ayers, W.F. Symmans, L. Pusztai, and K.J. Bloom The Her-2/neu gene and protein in breast cancer 2003: biomarker and target of therapy Oncologist 8 2003 307 325 (Pubitemid 36929717)
25. E.T. Fung A recipe for proteomics diagnostic test development: the OVA1 test, from biomarker discovery to FDA clearance Clin. Chem. 56 2010 327 329
26. N. Pearce Epidemiology in a changing world: variation, causation and ubiquitous risk factors Int. J. Epidemiol. 40 2011 503 512
27. D. Mabey, R.W. Peeling, A. Ustianowski, and M.D. Perkins Diagnostics for the developing world Nat. Rev. Microbiol. 2 2004 231 240 (Pubitemid 39490084)
28. R.W. Peeling, and D. Mabey Point-of-care tests for diagnosing infections in the developing world Clin. Microbiol. Infect. 16 2010 1062 1069
29. World Health Organization. World Health Statistics 2013.
30. Global disease study reveals successes, challenges; Global Health Matters Jan/Feb 2013 Retrieved from website www.fic.nih.gov
31. M.Y. Osei-Atweneboana, S. Lustigman, R.K. Prichard, B.A. Boatin, and M.G. Basanez A research agenda for helminth diseases of humans: health research and capacity building in disease-endemic countries for helminthiases control PLoS Negl. Trop. Dis. 6 2012 e1602
32. I.N. Hakyemez, G. Aktas, H. Savli, A. Kucukbayrak, S. Gurel, and T. Tas A fascioliasis case: a not rare cause of hypereosinophilia in developing countries, present in developed too Mediterr. J. Hematol. Infect. Dis. 4 2012 e2012029
33. S. Ebrahim, N. Pearce, L. Smeeth, J.P. Casas, S. Jaffar, and P. Piot Tackling non-communicable diseases in low- and middle-income countries: is the evidence from high-income countries all we need? PLoS Med. 10 2013 e1001377
34. R. Shidhaye, E. Mendenhall, K. Sumathipala, A. Sumathipala, and V. Patel Association of somatoform disorders with anxiety and depression in women in low and middle income countries: a systematic review Int. Rev. Psychiatry 25 2013 65 76
35. F. Young, J.A. Critchley, L.K. Johnstone, and N.C. Unwin A review of co-morbidity between infectious and chronic disease in Sub Saharan Africa: TB and diabetes mellitus, HIV and metabolic syndrome, and the impact of globalization Glob. Health 5 2009 9
36. K.H. Wagner, and H. Brath A global view on the development of non communicable diseases Prev. Med. 54 2012 S38 S41 (Suppl.)
37. T.A. Gaziano, A. Bitton, S. Anand, S. Abrahams-Gessel, and A. Murphy Growing epidemic of coronary heart disease in low- and middle-income countries Curr. Probl. Cardiol. 35 2010 72 115
38. C. Are, S. Rajaram, M. Are, H. Raj, B.O. Anderson, S.R. Chaluvarya, M. Vijayakumar, T. Song, M. Pandey, J.A. Edney, and E.L. Cazap A review of global cancer burden: trends, challenges, strategies, and a role for surgeons J. Surg. Oncol. 107 2013 221 226
39. World Health Organization. International Agency for Research on Cancer. GLOBOCAN 2008.
40. J. Ferlay, H.R. Shin, F. Bray, D. Forman, C. Mathers, and D.M. Parkin Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008 Int. J. Cancer 127 2010 2893 2917
41. A. Jemal, F. Bray, M.M. Center, J. Ferlay, E. Ward, and D. Forman Global cancer statistics CA Cancer J. Clin. 61 2011 69 90
42. C. de Martel, J. Ferlay, S. Franceschi, J. Vignat, F. Bray, D. Forman, and M. Plummer Global burden of cancers attributable to infections in 2008: a review and synthetic analysis Lancet Oncol. 13 2012 607 615
43. D. Stuckler Population causes and consequences of leading chronic diseases: a comparative analysis of prevailing explanations Milbank Q. 86 2008 273 326
44. R. Nugent Chronic diseases in developing countries: health and economic burdens Ann. N. Y. Acad. Sci. 1136 2008 70 79 (Pubitemid 351862178)
45. J.N. Nkengasong, T. Mesele, S. Orloff, Y. Kebede, P.N. Fonjungo, R. Timperi, and D. Birx Critical role of developing national strategic plans as a guide to strengthen laboratory health systems in resource-poor settings Am. J. Clin. Pathol. 131 2009 852 857
46. L. Warnich, B.I. Drogemoller, M.S. Pepper, C. Dandara, and G.E. Wright Pharmacogenomic research in South Africa: lessons learned and future opportunities in the rainbow nation Curr. Pharmacogenomics Pers. Med. 9 2011 191 207
47. D.C. Hay Burgess, J. Wasserman, and C.A. Dahl Global health diagnostics Nature 444 Suppl. 1 2006 1 2
48. C.A. Petti, C.R. Polage, T.C. Quinn, A.R. Ronald, and M.A. Sande Laboratory medicine in Africa: a barrier to effective health care Clin. Infect. Dis. 42 2006 377 382 (Pubitemid 43122314)
49. World Health Organization Regulation of in vitro diagnostics: a global perspective Diagnostics for Tuberculosis: Global Demand and Market Potential 2006 194 203 (Geneva)
50. P.J. Hotez, J.H. Remme, P. Buss, G. Alleyne, C. Morel, and J.G. Breman Combating tropical infectious diseases: report of the Disease Control Priorities in Developing Countries Project Clin. Infect. Dis. 38 2004 871 878 (Pubitemid 38387237)
51. I. Rudan, A. Marusic, and H. Campbell Developing biobanks in developing countries J. Glob. Health 1 2011 2 4
52. S. Ray, A. Moiyadi, and S. Srivastava Epidemiology: biorepositories for cancer research in developing countries Nat. Rev. Clin. Oncol. 10 2013 434 436
53. GBI Research Biobanks - 2012 Year Book [online] http://www.gbiresearch. com/Report.aspx?ID=Biobanks-2012-Year-Book 2012
54. N.K. Ganguly Indian Biobanks: Concepts and Prospects [Power-Point Slides] Retrieved from web-site: http://www.euindiacoop.org/2009/downloads/nk-ganguly. pdf 2009
55. Consolidated Report of Hospital Based Cancer Registries 2007-2011.
56. Three-Year Report of Population Based Cancer Registries 2009-2011.
57. NCRP An Overview, National Cancer Registry Programme 2005-2006 2008 ICMR Bangalore
58. G. Poste Biospecimens, biomarkers, and burgeoning data: the imperative for more rigorous research standards Trends Mol. Med. 18 2012 717 722
59. N. Lopez-Bigas, M. Cline, B. Broom, A. Margolin, L. Omberg, J. Weinstein, and M. Axton Thread 4: data discovery, transparency and visualization Nat. Genet. 45 2013
60. Sandra Orchard Data standardization and sharing - the work of the HUPO-PSI Biochim. Biophys. Acta, Proteins Proteomics 1844 1 2013 82 87
61. N. del-Toro, M. Dumousseau, S. Orchard, R.C. Jimenez, E. Galeota, G. Launay, J. Goll, K. Breuer, K. Ono, L. Salwinski, and H. Hermjakob A new reference implementation of the PSICQUIC web service Nucleic Acids Res. 41 2013 W601 W606
62. C.F. Taylor, N.W. Paton, K.S. Lilley, P.A. Binz, R.K. Julian Jr., A.R. Jones, W. Zhu, R. Apweiler, R. Aebersold, E.W. Deutsch, M.J. Dunn, A.J. Heck, A. Leitner, M. Macht, M. Mann, L. Martens, T.A. Neubert, S.D. Patterson, P. Ping, S.L. Seymour, P. Souda, A. Tsugita, J. Vandekerckhove, T.M. Vondriska, J.P. Whitelegge, M.R. Wilkins, I. Xenarios, J.R. Yates III, and H. Hermjakob The minimum information about a proteomics experiment (MIAPE) Nat. Biotechnol. 25 2007 887 893 (Pubitemid 47236919)
63. A. Costello, and A. Zumla Moving to research partnerships in developing countries BMJ 321 2000 827 829
64. S. Eckhouse, G. Lewison, and R. Sullivan Trends in the global funding and activity of cancer research Mol. Oncol. 2 2008 20 32
65. J.M. Fernandez, R.M. Stein, and A.W. Lo Commercializing biomedical research through securitization techniques Nat. Biotechnol. 30 2012 964 975
66. M.H. Cheng Cancer research funding in Asia Mol. Oncol. 1 2007 135 137
67. B. Orelli Biotech crowdfunding paves way for angels Nat. Biotechnol. 30 2012 1020
68. Data-Enabled Life Sciences Alliances International (DELSA Global) Workshop Flyer Retrieved from: http://www.amritabioquest.org/workshop/delsa/ images/delsa.pdf
69. Y.L. Chen, and K.H. Yang Avoidable waste in the production and reporting of evidence Lancet 374 2009 786
70. P. Mortensen, J.W. Gouw, J.V. Olsen, S.E. Ong, K.T. Rigbolt, J. Bunkenborg, J. Cox, L.J. Foster, A.J. Heck, B. Blagoev, J.S. Andersen, and M. Mann MSQuant, an open source platform for mass spectrometry-based quantitative proteomics J. Proteome Res. 9 2010 393 403
71. K.C. Leptos, D.A. Sarracino, J.D. Jaffe, B. Krastins, and G.M. Church MapQuant: open-source software for large-scale protein quantification Proteomics 6 2006 1770 1782
72. S. Ray, N.R. Koshy, P.J. Reddy, and S. Srivastava Virtual Labs in proteomics: new E-learning tools J. Proteomics 75 2012 2515 2525
73. S. Srivastava, V. Ozdemir, S. Ray, J.R. Panga, S. Noronha, B. Nair, and S. Diwakar Online education: E-learning booster in developing world Nature 501 2013 316
74. E.J. Emanuel, D. Wendler, J. Killen, and C. Grady What makes clinical research in developing countries ethical? The benchmarks of ethical research J. Infect. Dis. 189 2004 930 937 (Pubitemid 38328195)
75. L. London Ethical oversight of public health research: can rules and IRBs make a difference in developing countries? Am. J. Public Health 92 2002 1079 1084 (Pubitemid 34700967)
76. A. Cambon-Thomsen The social and ethical issues of post-genomic human biobanks Nat. Rev. Genet. 5 2004 866 873 (Pubitemid 39457502)
77. F. Eisner, Robin, Reddy, T. Srinivasa, Biomarkers for early detection of ovarian cancer. European patent specification. EP 2 199 801 B1 (2013).
78. ORBAN, and A. Tihamer Diabetes biomarkers 2013 World Intellectual Property Organization. International Bureau WO (2013/177505 A1)
79. A. Rushdy, G. Michael, and C. Steven Methods and devices for tuberculosis diagnosis using biomarker profiles 2013 World Intellectual Property Organization. International Bureau WO (2013/177502 A1)
80. K. Bensalah, F. Montorsi, and S.F. Shariat Challenges of cancer biomarker profiling Eur. Urol. 52 2007 1601 1609 (Pubitemid 350052431)
81. M.M. Hopkins, and S. Hogarth Biomarker patents for diagnostics: problem or solution? Nat. Biotechnol. 30 2012 498 500
82. T.A. Caulfield, and E.R. Gold Genetic testing, ethical concerns, and the role of patent law Clin. Genet. 57 2000 370 375 (Pubitemid 30245823)
83. S. Benowitz European groups oppose Myriad's latest patent on BRCA1 J. Natl. Cancer Inst. 95 2003 8 9 (Pubitemid 36124286)
84. Biomarkers unbound Nat. Biotechnol. 30 2012 372
85. G. Wallstrom, K.S. Anderson, and J. LaBaer Biomarker discovery for heterogeneous diseases Cancer Epidemiol. Biomarkers Prev. 22 2013 747 755
86. R.R. Gullapalli, K.V. Desai, L. Santana-Santos, J.A. Kant, and M.J. Becich Next generation sequencing in clinical medicine: challenges and lessons for pathology and biomedical informatics J. Pathol. Inform. 3 2012 40
87. A.L. McGuire, T. Caulfield, and M.K. Cho Research ethics and the challenge of whole-genome sequencing Nat. Rev. Genet. 9 2008 152 156 (Pubitemid 351147709)
88. A.J. Rai, and F. Vitzthum Effects of preanalytical variables on peptide and protein measurements in human serum and plasma: implications for clinical proteomics Expert Rev. Proteomics 3 2006 409 426 (Pubitemid 44231984)
89. J. Yi, D. Craft, and C.A. Gelfand Minimizing preanalytical variation of plasma samples by proper blood collection and handling Methods Mol. Biol. 728 2011 137 149
90. S. Orchard, H. Hermjakob, and R. Apweiler The proteomics standards initiative Proteomics 3 2003 1374 1376 (Pubitemid 36929559)
91. H. Hermjakob, L. Montecchi-Palazzi, G. Bader, J. Wojcik, L. Salwinski, A. Ceol, S. Moore, S. Orchard, U. Sarkans, C. von Mering, B. Roechert, S. Poux, E. Jung, H. Mersch, P. Kersey, M. Lappe, Y. Li, R. Zeng, D. Rana, M. Nikolski, H. Husi, C. Brun, K. Shanker, S.G. Grant, C. Sander, P. Bork, W. Zhu, A. Pandey, A. Brazma, B. Jacq, M. Vidal, D. Sherman, P. Legrain, G. Cesareni, I. Xenarios, D. Eisenberg, B. Steipe, C. Hogue, and R. Apweiler The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data Nat. Biotechnol. 22 2004 177 183 (Pubitemid 38160532)
92. D.A. Cairns, J.H. Barrett, L.J. Billingham, A.J. Stanley, G. Xinarianos, J.K. Field, P.J. Johnson, P.J. Selby, and R.E. Banks Sample size determination in clinical proteomic profiling experiments using mass spectrometry for class comparison Proteomics 9 2009 74 86
93. P.L. Bedard, A.R. Hansen, M.J. Ratain, and L.L. Siu Tumour heterogeneity in the clinic Nature 501 2013 355 364
94. S.D. Patterson Data analysis - the Achilles heel of proteomics Nat. Biotechnol. 21 2003 221 222 (Pubitemid 36314795)
95. I.E. deVera, J.E. Katz, and D.B. Agus Clinical proteomics: the promises and challenges of mass spectrometry-based biomarker discovery Clin. Adv. Hematol. Oncol. 4 2006 541 549 (Pubitemid 44251583)
96. R. Aebersold, A.L. Burlingame, and R.A. Bradshaw Western blots versus selected reaction monitoring assays: time to turn the tables? Mol. Cell. Proteomics 12 2013 2381 2382
97. N.F. Marko The cancer megafund: determinants of success Nat. Biotechnol. 31 2013 492 494
98. C. Olivier, B. Williams-Jones, B. Godard, B. Mikalson, and V. Ozdemir Personalized medicine, bioethics and social responsibilities: re-thinking the pharmaceutical industry to remedy inequities in patient care and international health Curr. Pharmacogenomics Pers. Med. Former Curr. Pharmacog. 6 2008 108 120
99. S. Ray, N.R. Koshy, S. Diwakar, B. Nair, and S. Srivastava Sakshat Labs: India's virtual proteomics initiative PLoS Biol. 10 2012 e1001353