Abstract
Properly performed, biomarker discovery can lead to effective candidates that can ultimately serve as predictors of disease, medical condition, define therapeutic parameters, and many other applications in medicine. Preferably, biomarkers comprise a panel of indicators, e.g. proteins and/or peptides that can be predictive or diagnostic of the medical condition of interest. Emphasis here is placed on “panel,” as single candidates are rarely sufficient to provide the necessary sensitivity and specificity. To develop an effective panel that survives the development process described in Chap. 19, proper experimental design and attention to important statistical parameters are critical to ensure success. Errors in discovery can lead to an inefficient use of expensive resources, as these may not be uncovered until the latter stages in biomarker development. Hence, accuracy, precision, and an estimate of the power of the proposed analyses are critical in the discovery of the panel of candidate biomarkers by proteomic methods, as is the selection of statistical approaches to refine and appropriately reduce the dataset for subsequent confirmatory assays.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Glanz SA (2005) Primer of biostatistics. McGraw-Hill, New York
(2005) Special issue: exploring the human plasma proteome. The HUPO Plasma Proteome Project (HPPP). Proteomics 5:3223–3549
Richter R, Schulz-Knappe P, Schrader M, Standker L, Jurgens M, Tammen H, Forssmann W-G (1999) Composition of the peptide fraction in human blood plasma: database of circulating human peptides. J Chromatogr B Biomed Sci Appl 726:25–35
Villanueva J, Martorella AJ, Lawlor K, Philip J, Fleisher M, Robbins RJ, Tempst P (2006) Serum peptidome patterns that distinguish metastatic thyroid carcinoma from cancer-free controls are unbiased by gender and age. Mol Cell Proteomics 5:1840–1852
Pretzer E, Wiktorowicz JE (2008) Saturation fluorescence labeling of proteins for proteomic analyses. Anal Biochem 374:250–262
Tyagarajan K, Pretzer EL, Wiktorowicz JE (2003) Thiol-reactive dyes for fluorescence labeling of proteomic samples. Electrophoresis 24:2348–2358
Miseta A, Csutora P (2000) Relationship between the occurrence of cysteine in proteins and the complexity of organisms. Mol Biol Evol 17:1232–1239
Wiktorowicz JE, Stafford S, Rea H, Urvil P, Soman K, Kurosky A, Perez-Polo JR, Savidge TC (2011) Quantification of cysteinyl S-nitrosylation by fluorescence in unbiased proteomic studies. Biochemistry 50:5601–5614
Yao X, Freas A, Ramirez J, Demirev PA, Fenselau C (2001) Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal Chem 73:2836–2842
Miyagi M, Rao KCS (2007) Proteolytic 18O-labeling strategies for quantitative proteomics. Mass Spectrom Rev 26:121–136
Khedr A, Hegazy M, Kamal A, Shehata MA (2015) Profiling of esterified fatty acids as biomarkers in the blood of dengue fever patients using a microliter-scale extraction followed by gas chromatography and mass spectrometry. J Sep Sci 38:316–324
Poole-Smith BK, Gilbert A, Gonzalez AL, Beltran M, Tomashek KM, Ward BJ, Hunsperger EA, Ndao M (2014) Discovery and characterization of potential prognostic biomarkers for dengue hemorrhagic fever. Am J Trop Med Hyg 91:1218–1226
Thayan R, Huat TL, See LL, Tan CP, Khairullah NS, Yusof R, Devi S (2009) The use of two-dimension electrophoresis to identify serum biomarkers from patients with dengue haemorrhagic fever. Trans R Soc Trop Med Hyg 103:413–419
Lee CY, Seet RC, Huang SH, Long LH, Halliwell B (2009) Different patterns of oxidized lipid products in plasma and urine of dengue fever, stroke, and Parkinson’s disease patients: cautions in the use of biomarkers of oxidative stress. Antioxid Redox Signal 11:407–420
Brasier AR, Garcia J, Wiktorowicz JE, Spratt HM, Comach G, Ju H, Recinos A 3rd, Soman K, Forshey BM, Halsey ES, Blair PJ, Rocha C, Bazan I, Victor SS, Wu Z, Stafford S, Watts D, Morrison AC, Scott TW, Kochel TJ (2012) Discovery proteomics and nonparametric modeling pipeline in the development of a candidate biomarker panel for dengue hemorrhagic fever. Clin Transl Sci 5:8–20
Brasier AR, Zhao Y, Wiktorowicz JE, Spratt HM, Nascimento EJM, Cordeiro MT, Soman KV, Ju H, Recinos A, Stafford S, Wu Z, Marques ETA, Vasilakis N (2015) Molecular classification of outcomes from dengue virus −3 infections. J Clin Virol 64:97–106
WHO (2002) Control of chagas’ disease. Second report of the WHO Expert Committee. WHO Tech Rep Ser 905:1–109, Geneva
Duran-Rehbein GA, Vargas-Zambrano JC, Cuellar A, Puerta CJ, Gonzalez JM (2014) Mammalian cellular culture models of Trypanosoma cruzi infection: a review of the published literature. Parasite 21:38
Wen JJ, Dhiman M, Whorton EB, Garg NJ (2008) Tissue-specific oxidative imbalance and mitochondrial dysfunction during Trypanosoma cruzi infection in mice. Microbes Infect 10:1201–1209
Gupta S, Wen JJ, Garg NJ (2009) Oxidative stress in chagas disease. Interdiscip Perspect Infect Dis 190354
Savidge TC, Urvil P, Oezguen N, Ali K, Choudhury A, Acharya V, Pinchuk I, Torres AG, English RD, Wiktorowicz JE, Loeffelholz M, Kumar R, Shi L, Nie W, Braun W, Herman B, Hausladen A, Feng H, Stamler JS, Pothoulakis C (2011) Host S-nitrosylation inhibits clostridial small molecule-activated glucosylating toxins. Nat Med 17:1136–1141
Sheffield-Moore M, Wiktorowicz JE, Soman KV, Danesi CP, Kinsky MP, Dillon EL, Randolph KM, Casperson SL, Gore DC, Horstman AM, Lynch JP, Doucet BM, Mettler JA, Ryder JW, Ploutz-Snyder LL, Hsu JW, Jahoor F, Jennings K, White GR, McCammon SD, Durham WJ (2013) Sildenafil increases muscle protein synthesis and reduces muscle fatigue. Clin Transl Sci 6:463–468
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Wiktorowicz, J.E., Soman, K.V. (2016). Discovery of Candidate Biomarkers. In: Mirzaei, H., Carrasco, M. (eds) Modern Proteomics – Sample Preparation, Analysis and Practical Applications. Advances in Experimental Medicine and Biology, vol 919. Springer, Cham. https://doi.org/10.1007/978-3-319-41448-5_21
Download citation
DOI: https://doi.org/10.1007/978-3-319-41448-5_21
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-41446-1
Online ISBN: 978-3-319-41448-5
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)