Prostate cancer biomarker discovery using high performance mass spectral serum profiling

Computer Methods and Programs in Biomedicine

Volumn 96, Issue 1, 2009, Pages 33-41

  Oh, Jung Hun ^a   Lotan, Yair ^b   Gurnani, Prem ^c   Rosenblatt, Kevin P ^d   Gao, Jean ^e  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^c PERKINELMER INC   (United States)

^d University of Texas Medical Branch School of Medicine   (United States)

^e The University of Texas at Arlington   (United States)

Author keywords

Biomarker; Feature selection; Mass spectrometry; Preprocessing

Indexed keywords

EARLY DETECTION; FEATURE SELECTION; FEATURE SELECTION METHODS; MACHINE-LEARNING; MARKOV BLANKETS; MASS SPECTRA; MASS SPECTRAL; MASS SPECTROMETRY DATA; MATRIX ASSISTED LASER DESORPTION/IONIZATION; NEGATIVE PREDICTIVE VALUE; PERKINELMER; POSITIVE PREDICTIVE VALUES; PREPROCESSING; PROSTATE CANCERS; PROSTATE SPECIFIC ANTIGEN; PROSTATIC ENLARGEMENT; SELECTION ALGORITHM; SERUM SAMPLES; TIME OF FLIGHT;

BODY FLUIDS; DESORPTION; MASS SPECTROMETERS; MASS SPECTROMETRY; PEELING;

BIOMARKERS;

BIOLOGICAL MARKER; PROSTATE SPECIFIC ANTIGEN;

ADULT; ALGORITHM; ANALYTICAL EQUIPMENT; ARTICLE; BLOOD ANALYSIS; CANCER STAGING; CONTROLLED STUDY; DATA ANALYSIS; DIAGNOSTIC ACCURACY; DIFFERENTIAL DIAGNOSIS; HUMAN; MACHINE LEARNING; MAJOR CLINICAL STUDY; MALE; MASS SPECTROMETER; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PROSTATE CANCER; PROSTATE TUMOR; REFERENCE VALUE; RELIABILITY; SENSITIVITY AND SPECIFICITY; SUPPORT VECTOR MACHINE;

ALGORITHMS; HUMANS; MALE; PROSTATIC NEOPLASMS; SENSITIVITY AND SPECIFICITY; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TUMOR MARKERS, BIOLOGICAL;

EID: 67650655973     PISSN: 01692607     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cmpb.2009.04.003     Document Type: Article

References (27)

1. Jemal A., Siegel R., Ward E., Hao Y., Xu J., Murray T., and Thun M.J. Cancer statistics. CA Cancer J. Clin. 58 2 (2008) 71-96
2. Catalona W.J., and Smith D.S. Comparison of different serum prostate specific antigen measures for early prostate cancer detection. Cancer 74 (1994) 1516-1518
3. Catalona W.J., Richie J.P., Ahmann F.R., Hudson M.A., Scardino P.T., Flanigan R.C., et al. Comparison of digital rectal examination and serum prostate specific antigen in the early detection of prostate cancer: results of a multicenter clinical trial of 6630 men. J. Urol. 151 (1994) 1283-1290
4. Jacobsen S.J., Katusic S.K., Bergstralh E.J., Oesterling J.E., Ohrt D., Klee G.G., et al. Incidence of prostate cancer diagnosis in the eras before and after serum prostate-specific antigen testing. JAMA 274 (1995) 1445-1449
5. Keetch D.W., Catalona W.J., and Smith D.S. Serial prostatic biopsies in men with persistently elevated serum prostate specific antigen values. J. Urol. 151 (1994) 1571-1574
6. Thompson I.M., Pauler D.K., Goodman P.J., Tangen C.M., Lucia M.S., Parnes H.L., et al. Prevalence of prostate cancer among men with a prostate-specific antigen level < or =4.0 ng per millilitre. N. Engl. J. Med. 350 (2004) 2239-2246
7. Canto E.I., Singh H., Shariat S.F., Lamb D.J., Mikolajczyk S.D., Linton H.J., et al. Serum BPSA outperforms both total PSA and free PSA as a predictor of prostatic enlargement in men without prostate cancer. Urology 63 (2004) 905-910
8. Gretzer M.B., and Partin A.W. PSA markers in prostate cancer detection. Urol. Clin. North Am. 30 (2003) 677-686
9. Mikolajczyk S.D., and Rittenhouse H.G. Pro PSA: a more cancer specific form of prostate specific antigen for the early detection of prostate cancer. Keio J. Med. 52 (2003) 86-91
10. Merchant M., and Weinberger S.R. Recent advancements in surface-enhanced laser desorption/ionization-time-of-flight-mass spectrometry. Electrophoresis 21 (2000) 1164-1177
11. Petricoin III E.F., Ornstein D.K., Paweletz C.P., Ardekani A., Hackett P.S., Hitt B.A., et al. Serum proteomic patterns for detection of prostate cancer. J. Natl. Cancer Inst. 94 (2002) 1576-1578
12. Adam B.L., Qu Y., Davis J.W., Ward M.D., Clements M.A., Cazares L.H., et al. Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res. 62 (2002) 3609-3614
13. Qu Y., Adam B.L., Yasui Y., Ward M.D., Cazares L.H., Schellhammer P.F., et al. Boosted decision tree analysis of surface-enhanced laser desorption/ionization mass spectral serum profiles discriminates prostate cancer from noncancer patients. Clin. Chem. 48 (2002) 1835-1843
14. Banez L.L., Prasanna P., Sun L., Ali A., Zou Z., Adam B.L., et al. Diagnostic potential of serum proteomic patterns in prostate cancer. J. Urol. 170 (2003) 442-446
15. Lehrer S., Roboz J., Ding H., Zhao S., Diamond E.J., Holland J.F., et al. Putative protein markers in the sera of men with prostatic neoplasms. BJU Int. 92 (2003) 223-225
16. Diamandis E.P. Analysis of serum proteomic patterns for early cancer diagnosis: drawing attention to potential problems. J. Natl. Cancer Inst. 96 5 (2004) 353-356
17. Villanueva J., Philip J., Chaparro C.A., Li Y., Toledo-Crow R., DeNoyer L., Fleisher M., Robbins R.J., and Tempst P. Correcting common errors in identifying cancer-specific serum peptide signatures. J. Proteome Res. 4 4 (2005) 1060-1072
18. Fisher W.G., Rosenblatt K.P., Fishman D.A., Whiteley G.R., Mikulskis A., Kuzdzal S.A., et al. A robust biomarker discovery pipeline for high-performance mass spectrometry data. J. Bioinform. Comput. Biol. 5 (2007) 1023-1045
19. Burges C.J.C. A tutorial on support vector machines for pattern recognition. Data Min. Knowl. Discov. 2 (1998) 121-167
20. German D.C., Gurnani P., Nandi A., Garner H.R., Fisher W., Diaz-Arrastia R., et al. Serum biomarkers for Alzheimer's disease: proteomic discovery. Biomed. Pharmacother. 61 (2007) 383-389
21. Lopez M.F., Mikulskis A., Kuzdzal S., Bennett D.A., Kelly J., Golenko E., et al. High-resolution serum proteomic profiling of Alzheimer disease samples reveals disease-specific, carrier-protein-bound mass signatures. Clin. Chem. 51 (2005) 1946-1954
22. Donegan M., Tomlinson A., Nair H., and Juhasz P. Controlling matrix suppression for matrix-assisted laser desorption/ionization analysis of small molecules. Rapid Commun. Mass Spectrom. 18 (2004) 1885-1888
23. Bafna V., and Edwards N. SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. Bioinformatics 17 (2001) S13-S21
24. Clauser B.T., Baker P.R., and Burlingame A.L. Role of accurate mass measurement (±10 ppm) in protein identification strategies employing MS or MS/MS. Anal. Chem. 71 (1999) 2871-2882
25. Kolibal J., and Howard D. Novel algorithm for MALDI-TOF baseline drift removal. Proceedings of IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (2005) 400-405
26. Koller D., and Sahami M. Toward optimal feature selection. Proceedings of the Thirteenth International Conference on Machine Learning (1996) 284-292
27. Oh J.H., Kim Y.B., Gurnani P., Rosenblatt K.P., and Gao J. Biomarker selection for predicting Alzheimer disease using high-resolution MALDI-TOF data. Proceedings of IEEE International Conference on Bioinformatics and Bioengineering (2007) 464-471