Prostate cancer region prediction by fusing results from MALDI spectra-processing and texture analysis

Simulation

Volumn 88, Issue 10, 2012, Pages 1247-1259

  Chuang, Shao Hui ^a   Li, Jiang ^a   Sun, Xiaoyan ^a   Vadlamudi, Ayyappa ^a   Sun, Bo ^b   Cazares, Lisa ^c   Nyalwidhe, Julius ^c   Troyer, Dean ^c   Semmes, John ^c   McKenzie, Frederic D ^a  

^a 231 Kaufman Hall ^*  (United States)

^b LINCOLN UNIVERSITY   (United States)

^c EASTERN VIRGINIA MEDICAL SCHOOL   (United States)

Author keywords

biomarker identification; imaging biomarker; MALDI mass spectra; prostate cancer

Indexed keywords

BIOMARKER IDENTIFICATION; BIOPSY TISSUES; MALDI-MS; MASS SPECTRA; MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY; OPTICAL IMAGE; PREDICTION MODEL; PREDICTION-BASED; PROSTATE CANCERS; TEXTURE ANALYSIS; TISSUE SLICE;

DATA PROCESSING; DISEASES; FORECASTING; GEOMETRICAL OPTICS; IMAGE PROCESSING; MASS SPECTROMETRY; TEXTURES; TISSUE;

MOLECULAR IMAGING;

EID: 84867340253     PISSN: 00375497     EISSN: 17413133     Source Type: Journal    
DOI: 10.1177/0037549712441522     Document Type: Article

References (34)

1. Jemal A, Siegel R, Ward E, et al. Cancer statistics, 2008. CA Cancer J Clin. 2008 ; 58: 71-96
2. Department of Health and Human Services, National Institutes of Health (NIH), National Cancer Institute (NCI). Fact sheet on proteomics and cancer. 2009 ;:
3. Catalona WJ, Smith DS, Ratliff TL, Dodds KM, et al. Measurement of prostate-specific antigen in serum as a screening test for prostate cancer. N. Engl. J. Med. 1991 ; 324: 1156-1161
4. Drake RR, Cazares L, Semmes OJ. Mining the low molecular weight proteome of blood. Proteomics Clin. Appl.. 2007 ; 1: 758-768
5. Li J, Manry MT, Narasimha PL, et al. Feature selection using a piecewise linear network. IEEE Transaction on Networks. 2006 2006 ; 17: 1101-1115
6. Li J, Manry MT, Liu LM, et al. Iterative improvement of neural classifiers. FLAIRS. 2004 ;: 700-705
7. Wun-Jae Kim SP, Kim YJ. Biomarkers in bladder cancer: present status and perspectives. Biomarker Insights. 2007 ; 2: 95-105
8. Semmes OJ, Feng Z, Adam B, et al. Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer. Clin. Chem. 2005 ; 51: 102-112
9. Van 't Veer LJ, Dai H, Van de Vijver MJ, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature. 2002 ; 415: 530-536
10. Pritzker KP. Cancer biomarkers: easier said than done. Clin. Chem. 2002 ; 48: 1147-1150
11. Duffy MJ, Esteva FJ, Harbeck N, et al. National Academy of Clinical Biochemistry guidelines for the use of tumor markers in breast cancer. NACB: Practice Guidelines and Recommendations for Use of Tumor Markers in the Clinic. 2006 ;:
12. Gast MC, Schellens JH, Beijnen JH. Clinical proteomics in breast cancer: a review. Breast Cancer Res Treat. 2009 ; 116: 17-29
13. Caprioli RM, Farmer TB, Gile J. Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. Anal. Chem. 1997 ; 69: 4751-4760
14. Chaurand P, Cornett DS, Caprioli RM. Molecular imaging of thin mammalian tissue sections by mass spectrometry. Curr. Opin. Biotechnol. 2006 ; 17: 431-436
15. Caldwell RL, Caprioli RM. Tissue profiling by mass spectrometry: a review of methodology and applications. Mol. Cell. Proteomics. 2005 ; 4: 394-401
16. Chaurand P, Sanders ME, Jensen RA, et al. Proteomics in diagnostic pathology: profiling and imaging proteins directly in tissue sections. Am. J. Pathol. 2004 ; 165: 1057-1068
17. Tabesh A, Teverovskiy M, Pang H, et al. Multifeature prostate cancer diagnosis and gleason grading of histological images. IEEE Trans. on Medical Imaging. 2007 ; 26: 1366-1378
18. Huang P, Hsiung C. Automatic classification for pathological prostate images based on fractal analysis. IEEE Trans. on Medical Imaging. 2009 ; 28: 1037-1050
19. Tahir MA, Bouridane A, Kurugollu F. An FPGA-based coprocessor for GLCM and Haralick texture features and their application in prostate cancer classification. Analog Integrated Circuits Signal Process. 2005 ; 43: 205-215
20. Galloway MM. Texture analysis using gray level run lengths. Computer Graphics and Image Processing. 1975 ; 4: 172-179
21. Chaurand P, Stoeckli M, Caprioli RM. Direct profiling of proteins in biological tissue sections by MALDI mass spectrometry. Anal. Chem. 1999 ; 71: 5263-5270
22. Caldwell RL, Caprioli RM. Tissue profiling by mass spectrometry: a review of methodology and applications. Mol. Cell. Proteomics. 2005 ; 4: 394-401
23. RauschM. MSI additions by Markus Stoeckli.software-BioMap: www.maldi.msi.orgAccessed: January2008; Novartis.
24. Vapnik V The Nature of Statistical Learning Theory. Berlin: Springer-Verlag ; 1995 :
25. Mantena V, Jiang W, Li J, et al. Prostate cancer biomarker identification using MALDI-MS data: initial results. IEEE/NIH LiSSA. 2009 ;: 116-119
26. Myers SR, Ali Y. Determination of tobacco specific hemoglobin adducts in smoking mothers and new born babies by mass spectrometry. Biomarker Insights. 2007 ; 2: 269-282
27. Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, et al. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteo-mics. 2005 ; 4: 1487-1502
28. Jordan KW, He W, Halpern EF, et al. Evaluation of tissue metabolites with high-resolution magic angle spinning MR spectroscopy human prostate samples after three-year storage at -80°C. Biomarker Insights. 2007 ; 2: 147-154
29. Biomarkers and surrogate endpoints: preferred definitions and conceptual framework. Clin. Pharmacol. Ther. 2001 ; 69: 89-95
30. Gewin V. Missing the mark. Nature. 2007 ; 449: 770-771
31. McLerran D, Grizzle WE, Semmes OJ, et al. Analytical validation of serum proteomic profiling for diagnosis of prostate cancer: sources of sample bias. Clin. Chem. 2008 2008 ; 54: 44-52
32. McLerran D, Grizzle WE, Feng Z, et al. SELDI-TOF MS whole serum proteomic profiling with IMAC surface does not reliably detect prostate cancer. Clin. Chem. 2008 ; 54: 53-60
33. Tracy MB, Chen H, Weaver DM, et al. Precision enhancement of MALDI-TOF MS using high-resolution peak detection and label-free alignment. Proteomics. 2008 ; 8: 1530-1538
34. Li J, Vadlamudi A, Chuang S, et al. Combining prostate cancer region predictions from MALDI spectra processing and texture analysis. IEEE International Conference on Bioinformatics and Bioengineering (BIBE) ; 2010 Philadelphia, PA ; 2010. 73.