The impact of storage effects in biobanks on biomarker discovery in systems biology studies

Biomarkers

Volumn 15, Issue 8, 2010, Pages 677-683

  Balasubramanian, Raji ^a   Mueller, Laurin ^b   Kugler, Karl ^b   Hackl, Werner ^b   Pleyer, Lisa ^c   Dehmer, Matthias ^b   Graber, Armin ^b  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

^b UNIVERSITY FOR HEALTH SCIENCES   (Austria)

^c UNIVERSITY OF SALZBURG   (Austria)

Author keywords

Breast cancer; Computational biology; Prostate cancer

Indexed keywords

BIOLOGICAL MARKER;

ARTICLE; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; LABORATORY DIAGNOSIS; SIMULATION; STORAGE; SYSTEMS BIOLOGY;

BIOLOGICAL MARKERS; HUMANS; MODELS, THEORETICAL; SPECIMEN HANDLING; SYSTEMS BIOLOGY;

EID: 78649247310     PISSN: 1354750X     EISSN: 13665804     Source Type: Journal    
DOI: 10.3109/1354750X.2010.511265     Document Type: Article

References (27)

1. Banks RE, Stanley AJ, Cairns DA, Barrett JH, Clarke P, Tompson D, Selby PJ. (2005). Infuences of blood sample processing on low-molecular-weight proteome identified by surfaceenhanced laser desorption/ionization mass spectrometry. Clin Chem 51:1637-49.
2. Benjamini Y, Hochberg Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat SocSer B (Methodological) 57:289-300.
3. Chatterjee SK, Zetter BR. (2005). Cancer biomarkers: knowing the present and predicting the future. Future Oncol 1:37-50.
4. Diamandis EP. (2004a). Analysis of serum proteomic patterns for early cancer diagnosis: drawing attention to potential problems. J Natl Cancer Inst 96:353-6.
5. Diamandis E P. (2004b). Mass spectrometry as a diagnostic and a cancer biomarker discovery tool: opportunities and potential limitations. Mol Cell Proteomics 3:367-78.
6. Downey P, Peakman TC. (2008). Design and implementation of a high-throughput biological sample processing facility using modern manufacturing principles. Int J Epidemiol 37(Suppl. 1):i46-50.
7. Drake SK, Bowen RA, Remaley AT, Hortin GL. (2004). Potential interferences from blood collection tubes in mass spectrometric analyses of serum polypeptides. Clin Chem 50:2398-401.
8. Elliott P, Peakman TC. (2008). The UK Biobank sample handling and storage protocol for the collectionprocessing and archiving of human blood and urine. Int J Epidemiol 37:234-44.
9. Farragher SM, Tanney A, Kennedy RD, Harkin PD. (2008). RNA expression analysis from formalin fixed paraffin embedded tissues. Histochem Cell Biol 130:435-45.
10. Guo Y, Graber A, McBurney RN, Balasubramanian R. (2010). Sample size and statistical power considerations in high-dimensionality data settings: a comparative study of classification algorithms. BMC Bioinformatics under revision.
11. Hill BM, Laessig RH, Koch DD, Hassemer DJ. (1992). Comparison of plastic vs. glass evacuated serum-separator (SST) blood-drawing tubes for common clinical chemistry determinations. Clin Chem 38:1474-8.
12. Hu J, Coombes KR, Morris JS, Baggerly KA. (2005). The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales. Brief Funct Genomic Proteomic 3:322-31.
13. Kugler K., Hackl W., Müller L., Graber A. & Pfeiffer R. (2010). Quantification of Storage Effects in Biobanks and the inflicted Bias for Biomarker Discovery Studies. in preparation.
14. Liotta LA, Petricoin E F. (2008). Putting the 'Bio' back into biomarkers: orienting proteomic discovery toward biology and away from the measurement platform. Clin Chem 54:3-5.
15. Lippi G, Montagnana M, Salvagno GL, Guidi GC. (2006). Interference of blood cell lysis on routine coagulation testing. Arch Pathol Lab Med 130:181-4.
16. Lippi G, Salvagno GL, Montagnana M, Brocco G, Guidi GC. (2005). Influence of short-term venous stasis on clinical chemistry testing. Clin Chem Lab Med 43:869-75. (Pubitemid 41461164)
17. Mcburney RN, Hines WM, Von Tungeln LS, Schnackenberg LK, Beger RD, Moland CL, Han T, Fuscoe JC, Chang CW, Chen JJ, Su Z, Fan XH, Tong W, Booth SA, Balasubramanian R, Courchesne PL, Campbell JM, Graber A, Guo Y, Juhasz PJ, Li TY, Lynch MD, Morel NM, Plasterer TN, Takach EJ, Zeng C, Beland FA. (2009). The liver toxicity biomarker study: phase I design and preliminary results. ToxicolPathol 37:52-64.
18. Pepe MS, Etzioni R, Feng Z, Potter JD, Tompson ML, Tornquist M, Winget M, Yasui Y. (2001). Phases of biomarker development for early detection of cancer. J Natl Cancer Inst 93:1054-61.
19. Pilny R, Bouchal P, Borilova S, Ceskova P, Zaloudik J, Vyzula R, Vojtesek B, Valik D. (2006). Surface-enhanced laser desorption ionization/time-of-flight mass spectrometry reveals significant artifacts in serum obtained from clot activator-containing collection devices. Clin Chem 52:2115-16.
20. Rai AJ, Gelfand CA, Haywood BC, Warunek DJ, Yi J, Schuchard MD, Mehigh RJ, Cockrill SL, Scott GB, Tammen H, Schulz-Knappe P, Speicher DW, Vitzthum F, Haab BB, Siest G, Chan DW. (2005). HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics 5:3262-77.
21. Rønningen KS, Paltiel L, Meltzer HM, Nordhagen R, Lie KK, Hovengen R, Haugen M, Nystad W, Magnus P, Hoppin JA. (2006). The biobank of the Norwegian Mother and Child Cohort Study: a resource for the next 100 years. Eur J Epidemiol 21:619-25.
22. Schrohl AS, Wurtz S, Kohn E, Banks RE, Nielsen HJ, Sweep FC, Brunner N. (2008). Banking of biological fluids for studies of diseaseassociated protein biomarkers. Mol Cell Proteomics 7:2061-6.
23. Smets EM, Dijkstra-Lagemaat JE, Blankenstein MA. (2004). Influence of blood collection in plastic vs. glass evacuated serum-separator tubes on hormone and tumour marker levels. Clin Chem Lab Med 42:435-9.
24. Tibshirani R, Hastie T, Narasimhan B, Chu G. (2002). Diagnosis of multiple cancer types by shrunken centroids of gene expression. ProcNatlAcadSci U S A 99:6567-72.
25. Van der Greef J, Martin S, Juhasz P, Adourian A, Plasterer T, Verheij ER, Mcburney RN. (2007). The art and practice of systems biology in medicine: mapping patterns of relationships. J Proteome Res 6:1540-59.
26. Von Ahlfen S, Missel A, Bendrat K, Schlumpberger M. (2007). Determinants of RNA quality from FFPE samples. PLoS One 2:e1261.
27. Whiteley G. (2008). Bringing diagnostic technologies to the clinical laboratory: rigorregulationand reality. Proteomics Clin Appl 2:1378-85.