A Bayesian model of NMR spectra for the deconvolution and quantification of metabolites in complex biological mixtures

Journal of the American Statistical Association

Volumn 107, Issue 500, 2012, Pages 1259-1271

  Astle, William ^a   De Iorio, Maria ^b   Richardson, Sylvia ^c   Stephens, David ^a   Ebbels, Timothy ^d  

^a MCGILL UNIVERSITY   (Canada)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Block updates; Concentration estimation; Metabolomics; Multicomponent model; Prior information

Indexed keywords

EID: 84865128266     PISSN: 01621459     EISSN: 1537274X     Source Type: Journal    
DOI: 10.1080/01621459.2012.695661     Document Type: Article

References (27)

1. Bretthorst, G. L. (1990a), "Bayesian Analysis. I. Parameter Estimation Using Quadrature NMR Models," Journal of Magnetic Resonance, 88, 533-551.
2. Bretthorst, G. L. (1990b), "Bayesian Analysis. II. Signal Detection and Model Selection," Journal of Magnetic Resonance, 88, 552-570.
3. Brindle, J., Antti, H., Holmes, E., Tranter, G., Nicholson, J., Bethell, H., Clarke, S., Schofield, P., McKilligin, E., Mosedale, D., and Grainger, D. J. (2002), "Rapid and Noninvasive Diagnosis of the Presence and Severity of Coronary Heart Disease Using1H-NMR-Based Metabonomics," Nature Medicine, 8 (12), 1439-1445.
4. Bundy, J. G., Spurgeon, D. J., Svendsen, C., Hankard, P. K., Osborn, D., Lindon, J. C., and Nicholson, J. K. (2002), "Earthworm Species of the Genus Eisenia Can Be Phenotypically Differentiated by Metabolic Profiling," FEBS Letters, 521 (1-3), 115-120.
5. Dou, L., and Hodgson, R. (1996), "Bayesian Inference and Gibbs Sampling in Spectral Analysis and Parameter Estimation: II," Inverse Problems, 12, 121-137.
6. Geyer, C. (1991), "Markov Chain Monte Carlo Maximum Likelihood," in Commputing Science and Statistics: Proceedings of the 23rd Symposium on the Interface, ed. E. Keramigas, Fairfax, VA: Fairfax: Interface Foundation, pp. 156-163.
7. Griffiths, J. R., McSheehy, P. M. J., Robinson, S. P., Troy, H., Chung, Y.-L., Leek, R. D., Williams, K. J., Stratford, I. J., Harris, A. L., and Stubbs, M. (2002), "Metabolic Changes Detected by In Vivo Magnetic Resonance Studies of HEPA-1 Wild-Type Tumors and Tumors Deficient in Hypoxia-Inducible Factor-1beta (HIF-1beta): Evidence of an Anabolic Role for the HIF-1 Pathway," Cancer Research, 62 (3), 688-695.
8. Hao, J., Astle, W., DeIorio, M., and Ebbels, T. (2012), "BATMAN-An R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model," Bioinformatics, 28 (15), 2088-2090.
9. Holmes, E., Foxall, P., Nicholson, J., Neild, G., Brown, S., Beddell, C., Sweatman, B., Rahr, E., Lindon, J., Spraul, M., and Neidig, P. (1994), "Automatic Data Reduction and Pattern Recognition Methods for Analysis of 1H Nuclear Magnetic Resonance Spectra of Human Urine From Normal and Pathological States," Analytical Biochemistry, 220 (2), 284-296.
10. Holmes, E., Loo, R. L., Stamler, J., Bictash, M., Yap, I. K. S., Chan, Q., Ebbels, T., De Iorio, M., Brown, I. J., Veselkov, K. A., Daviglus, M. L., Kesteloot, H., Ueshima, H., Zhao, L., Nicholson, J. K., and Elliott, P. (2008), "Human Metabolic Phenotype Diversity and Its Association With Diet and Blood Pressure," Nature, 453 (7193), 396-400.
11. Hore, P. (1995), Nuclear Magnetic Resonance (Vol. 32 of Oxford Chemistry Primers), Oxford: Oxford University Press.
12. Illig, T., Gieger, C., Zhai, G., Römisch-Margl, W., Wang-Sattler, R., Prehn, C., Altmaier, E., Kastenmüller, G., Kato, B. S., Mewes, H.-W., Meitinger, T., de Angelis, M. H., Kronenberg, F., Soranzo, N., Wichmann, H.-E., Spector, T. D., Adamski, J., and Suhre, K. (2010), "A Genome-Wide Perspective of Genetic Variationin Human Metabolism," Nature Genetics, 42 (2), 137-141.
13. Jasra, A., Stephens, D. A., and Holmes, C. C. (2007), "Population-Based Reversible Jump Markov Chain Monte Carlo," Biometrika, 94 (4), 787-807.
14. Kim, S. B., Wang, Z., Oraintara, S., Temiyasathit, C., andWongsawat, Y. (2008), "Feature Selection and Classification of High-Resolution NMR Spectra in the Complex Wavelet Transform Domain," Chemometrics and Intelligent Laboratory Systems, 90 (2), 161-168.
15. Liang, F., and Wong, W. (2000), "Evolutionary Monte Carlo: Applications to Cp Model Sampling and Change Point Problem," Statistica Sinica, 10, 317-342.
16. Lindon, J. C., Holmes, E., and Nicholson, J. K. (2001), "Pattern Recognition Methods and Applications in Biomedical Magnetic Resonance," Progress in Nuclear Magnetic Resonance Spectroscopy, 39 (1), 1-40.
17. Lindon, J. C., Nicholson, J. K., Holmes, E., Antti, H., Bollard, M. E., Keun, H., Beckonert, O., Ebbels, T. M., Reily, M. D., Robertson, D., Stevens, G. J., Luke, P., Breau, A. P., Cantor, G. H., Bible, R. H., Niederhauser, U., Senn, H., Schlotterbeck, G., Sidelmann, U. G., Laursen, S. M., Tymiak, A., Car, B. D., Lehman-McKeeman, L., Colet, J. M., Loukaci, A., and Thomas, C. (2003), "Contemporary Issues in Toxicology: The Role of Metabonomics in Toxicology and Its Evaluation by the COMET Project," Toxicology and Applied Pharmacology, 187 (3), 137-146.
18. Murray, I., Ghahramani, Z. and MacKay, D. J. C. (2006), "MCMC for Doubly-Intractable Distributions," in Proceedings of the 22nd Annual Conference on Uncertainty in Artificial Intelligence (UAI), eds. R. Dechter and T. S. Richardson, Corvallis, OR: AUAI Press, pp. 359-366.
19. Raamsdonk, L. M., Teusink, B., Broadhurst, D., Zhang, N., Hayes, A., Walsh, M. C., Berden, J. A., Brindle, K. M., Kell, D. B., Rowland, J. J., Westerhoff, H. V., van Dam, K., and Oliver, S. G. (2001), "A Functional Genomics Strategy That Uses Metabolome Data to Reveal the Phenotype of Silent Mutations," Nature Biotechnology, 19 (1), 45-50.
20. Roberts, G. O., and Rosenthal, J. S. (2009), "Examples of Adaptive MCMC," Journal of Computational and Graphical Statistics, 18 (2), 349-367.
21. Rubtsov, D. V., and Griffin, J. L. (2007), "Time-Domain Bayesian Detection and Estimation of Noisy Damped Sinusoidal Signals Applied to NMR Spectroscopy," Journal of Magnetic Resonance, 188 (2), 367-379.
22. Spraul, M., Neidig, P., Klauck, U., Kessler, P., Holmes, E., Nicholson, J., Sweatman, B., Salman, S., Farrant, R., Rahr, E., Beddell, C. R., and Lindon, J. C. (1994), "Automatic Reduction of NMR Spectroscopic Data for Statistical and Pattern Recognition Classification of Samples," Journal of Pharmaceutical and Biomedical Analysis, 12 (10), 1215-1225.
23. Strang, G., and Nguyen, T. (1996), Wavelets and Filter Banks, Cambridge, MA: Wellesley Cambridge Press.
24. Tredwell, G. D., Behrends, V., Geier, F. M., Liebeke, M., and Bundy, J. G. (2011), "Between-Person Comparison of Metabolite Fitting for NMR-Based Quantitative Metabolomics," Analytical Chemistry, 83 (22), 8683-8687.
25. Tredwell, G. D., Edwards-Jones, B., Leak, D. J., and Bundy, J. G. (2011), "The Development of Metabolomic Sampling Procedures for Pichiapastoris, and Baseline Metabolome Data," PLoS One, 6 (1), e16286.
26. Weljie, A. M., Newton, J., Mercier, P., Carlson, E., and Slupsky, C. M. (2006), "Targeted Profiling: Quantitative Analysis of 1H NMR Metabolomics Data," Analytical Chemistry, 78 (13), 4430-4442.
27. Wishart, D. S., Knox, C., Guo, A. C., Eisner, R., Young, N., Gautam, B., Hau, D. D., Psychogios, N., Dong, E., Bouatra, S., Mandal, R., Sinelnikov, I., Xia, J., Jia, L., Cruz, J. A., Lim, E., Sobsey, C. A., Shrivastava, S., Huang, P., Liu, P., Fang, L., Peng, J., Fradette, R., Cheng, D., Tzur, D., Clements, M., Lewis, A., De Souza, A., Zuniga, A., Dawe, M., Xiong, Y., Clive, D., Greiner, R., Nazyrova, A., Shaykhutdinov, R., Li, L., Vogel, H. J., and Forsythe, I. (2009), "HMDB: A Knowledgebase for the Human Metabolome," Nucleic Acids Research, 37 (Database issue), D603-D610.