Abstract
Traumatic brain injury or traumatic head injury is characterized as a direct physical impact or trauma to the head, causing brain injury. It represents a major national health problem without a US Food and Drug Administration-approved therapy. The application of neuroproteomics/neurogenomics has revolutionized the characterization of protein/gene dynamics, leading to a greater understanding of post-injury biochemistry. Neuroproteomics and Neurogenomics fields have undertaken major advances in the area of neurotrauma research focusing on biomarker identification. Several candidate markers have been identified and are being evaluated for their efficacy as biological biomarkers utilizing these “omics approaches”. The identification of these differentially expressed candidate markers using these techniques is proving to be only the first step in the biomarker development process. However, to translate these findings into the clinic, data-driven development cycle incorporating data-mining steps for discovery, qualification, verification, and clinical validation is needed. Data mining steps extend beyond the collected data level into an integrated scheme of animal modeling, instrumentation, and functional data analysis. In this chapter, we provide an introductory review of data-mining/systems biology coupled approaches that have been applied to biomarker discovery and clinical validation; in addition, the need for strengthening the integral roles of these disciplines in establishing a comprehensive understanding of specific brain disorder and biomarker identification in general.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
A. Albert. On the use and computation of likelihood ratios in clinical chemistry. Clinical chemistry, 28(5):1113, 1982.
D.G. Altman. Practical statistics for medical research. Chapman & Hall/CRC, 1991.
K. Batchelder and P. Miller. A change in the marketinvesting in diagnostics. Nature biotechnology, 24(8):922–926, 2006.
Pedro Beltrao, Christina Kiel, and Luis Serrano. Structures in systems biology. Current Opinion in Structural Biology, 17(3):378 – 384, 2007.
P.M. Bossuyt, J.B. Reitsma, D.E. Bruns, C.A. Gatsonis, P.P. Glasziou, L.M. Irwig, D. Moher, D. Rennie, H.C.W. de Vet, and J.G. Lijmer. The stard statement for reporting studies of diagnostic accuracy: explanation and elaboration. Clinical Chemistry, 49(1):7, 2003.
F. Campagne, S. Neves, CW Chang, L. Skrabanek, P.T. Ram, R. Iyengar, and H. Weinstein. Quantitative information management for the biochemical computation of cellular networks. Science’s STKE: signal transduction knowledge environment, 2004(248):pl11, 2004.
S.S. Chen, W.E. Haskins, A.K. Ottens, R.L. Hayes, N. Denslow, and K.K.W. Wang. Bioinformatics for traumatic brain injury: Proteomic data mining. Data Mining in Biomedicine, pages 363–387, 2007.
A. Cornish-Bowden, PJ Hunter, AA Cuellar, ED Mjolsness, NS Juty, S. Dronov, K. Takahashi, Y. Nakayama, ED Gilles, JL Kasberger, et al. The systems biology markup language (sbml): a medium for representation and exchange of biochemical network models. Bioinformatics, 19(4):524–531, 2003.
N. Denslow, M.E. Michel, M.D. Temple, C.Y. Hsu, K. Saatman, and R.L. Hayes. Application of proteomics technology to the field of neurotrauma. Journal of neurotrauma, 20(5):401–407, 2003.
Q. Ding, Z. Wu, Y. Guo, C. Zhao, Y. Jia, F. Kong, B. Chen, H. Wang, S. Xiong, H. Que, et al. Proteome analysis of up-regulated proteins in the rat spinal cord induced by transection injury. Proteomics, 6(2):505–518, 2006.
TJ Fagan. Letter: Nomogram for bayes theorem. The New England journal of medicine, 293(5):257, 1975.
S.G.N. Grant. Systems biology in neuroscience: bridging genes to cognition. Current opinion in neurobiology, 13(5):577–582, 2003.
S.G.N. Grant and W.P. Blackstock. Proteomics in neuroscience: from protein to network. The Journal of Neuroscience, 21(21):8315, 2001.
T. Katano, T. Mabuchi, E. Okuda-Ashitaka, N. Inagaki, T. Kinumi, and S. Ito. Proteomic identification of a novel isoform of collapsin response mediator protein-2 in spinal nerves peripheral to dorsal root ganglia. Proteomics, 6(22):6085–6094, 2006.
F.H. Kobeissy, S. Sadasivan, M.W. Oli, G. Robinson, S.F. Larner, Z. Zhang, R.L. Hayes, and K.K.W. Wang. Neuroproteomics and systems biology-based discovery of protein biomarkers for traumatic brain injury and clinical validation. PROTEOMICS–Clinical Applications, 2(10–11):1467–1483, 2008.
A.I.R. Maas, N. Stocchetti, and R. Bullock. Moderate and severe traumatic brain injury in adults. The Lancet Neurology, 7(8):728–741, 2008.
S. Mondello, S.A. Robicsek, A. Gabrielli, G.M. Brophy, L. Papa, J. Tepas III, C. Robertson, A. Buki, D. Scharf, M. Jixiang, et al. αii-spectrin breakdown products (sbdps): Diagnosis and outcome in severe traumatic brain injury patients. Journal of Neurotrauma, 27(7):1203–1213, 2010.
G.D. Murray, D. Barer, S. Choi, H. Fernandes, B. Gregson, K.R. Lees, A.I.R. Maas, A. Marmarou, A.D. Mendelow, E.W. Steyerberg, et al. Design and analysis of phase iii trials with ordered outcome scales: the concept of the sliding dichotomy. Journal of neurotrauma, 22(5):511–517, 2005.
D. Nickerson and P. Hunter. Using cellml in computational models of multiscale physiology. In Engineering in Medicine and Biology Society, 2005. IEEE-EMBS 2005. 27th Annual International Conference of the, pages 6096–6099. IEEE, 2005.
N. Nogoy. Neuroproteomics: the hunt for biomarkers of neurotrauma. andrew ottens talks to nicole nogoy. Expert review of proteomics, 4(3):343, 2007.
N.A. Obuchowski, M.L. Lieber, and F.H. Wians Jr. Roc curves in clinical chemistry: uses, misuses, and possible solutions. Clinical chemistry, 50(7):1118, 2004.
S. Okie. Traumatic brain injury in the war zone. N Engl J Med, 352(20):2043–2047, 2005.
A.K. Ottens, F.H. Kobeissy, B.F. Fuller, M. Chen Liu, M.W. Oli, R.L. Hayes, and K.K.W. Wang. Novel neuroproteomic approaches to studying traumatic brain injury. Progress in Brain Research, 161:401–418, 2007.
A.K. Ottens, F.H. Kobeissy, E.C. Golden, Z. Zhang, W.E. Haskins, S.S. Chen, R.L. Hayes, KK Wang, and N.D. Denslow. Neuroproteomics in neurotrauma. Mass spectrometry reviews, 25(3):380–408, 2006.
V. Ozdemir, B. Williams-Jones, S.J. Glatt, M.T. Tsuang, J.B. Lohr, and C. Reist. Shifting emphasis from pharmacogenomics to theragnostics. Nature, 200:6.
J.A. Pineda, S.B. Lewis, A.B. Valadka, L. Papa, H.J. Hannay, S.C. Heaton, J.A. Demery, M.C. Liu, J.M. Aikman, V. Akle, et al. Clinical significance of α ii-spectrin breakdown products in cerebrospinal fluid after severe traumatic brain injury. Journal of neurotrauma, 24(2):354–366, 2007.
J.B. Redell, Y. Liu, and P.K. Dash. Traumatic brain injury alters expression of hippocampal micrornas: potential regulators of multiple pathophysiological processes. Journal of neuroscience research, 87(6):1435–1448, 2009.
N. Rifai, M.A. Gillette, and S.A. Carr. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nature biotechnology, 24(8):971–983, 2006.
K.E. Saatman, A.C. Duhaime, R. Bullock, A.I.R. Maas, A. Valadka, and G.T. Manley. Classification of traumatic brain injury for targeted therapies. Journal of neurotrauma, 25(7):719–738, 2008.
JA Wagner, SA Williams, and CJ Webster. Biomarkers and surrogate end points for fit-for-purpose development and regulatory evaluation of new drugs. Clinical Pharmacology & Therapeutics, 81(1):104–107, 2007.
K.K.W. Wang, S.F. Larner, G. Robinson, and R.L. Hayes. Neuroprotection targets after traumatic brain injury. Current opinion in neurology, 19(6):514, 2006.
K.K.W. Wang, A.K. Ottens, M.C. Liu, S.B. Lewis, C. Meegan, M.W. Oli, F.C. Tortella, and R.L. Hayes. Proteomic identification of biomarkers of traumatic brain injury. Expert review of proteomics, 2(4):603–614, 2005.
G. Zoroya. Scientists: brain injuries from war worse than thought. USA Today, 2007.
M.H. Zweig and G. Campbell. Receiver-operating characteristic (roc) plots: a fundamental evaluation tool in clinical medicine. Clin Chem, 39(4):561–577, 1993.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Mondello, S., Kobeissy, F., Fingers, I., Zhang, Z., Hayes, R.L., Wang, K.K.W. (2012). Data Mining Strategies Applied in Brain Injury Models. In: Pardalos, P., Xanthopoulos, P., Zervakis, M. (eds) Data Mining for Biomarker Discovery. Springer Optimization and Its Applications(), vol 65. Springer, Boston, MA. https://doi.org/10.1007/978-1-4614-2107-8_1
Download citation
DOI: https://doi.org/10.1007/978-1-4614-2107-8_1
Published:
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4614-2106-1
Online ISBN: 978-1-4614-2107-8
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)