Opening up the "black box": Metabolic phenotyping and metabolome-wide association studies in epidemiology

Journal of Clinical Epidemiology

Volumn 63, Issue 9, 2010, Pages 970-979

  Bictash, Magda ^a   Ebbels, Timothy M ^a   Chan, Queenie ^a   Loo, Ruey Leng ^a,b   Yap, Ivan K S ^a   Brown, Ian J ^a   De Iorio, Maria ^a   Daviglus, Martha L ^c   Holmes, Elaine ^a   Stamler, Jeremiah ^c   Nicholson, Jeremy K ^a   Elliott, Paul ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b MEDWAY SCHOOL OF PHARMACY   (United Kingdom)

^c NORTHWESTERN UNIVERSITY   (United States)

Author keywords

Biomarkers; INTERMAP; INTERSALT; Metabolic phenotyping; Metabonomics; NMR spectroscopy

Indexed keywords

FALSE POSITIVE RESULT; HUMAN; METABOLITE; METABOLOME; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PHENOTYPE; PRIORITY JOURNAL; REVIEW; GENETICS; METABOLISM; METABOLOMICS; MOLECULAR EPIDEMIOLOGY; PROCEDURES; REPRODUCIBILITY; RISK ASSESSMENT; STANDARDS;

BIOLOGICAL MARKERS; HUMANS; METABOLOME; METABOLOMICS; MOLECULAR EPIDEMIOLOGY; PHENOTYPE; REPRODUCIBILITY OF RESULTS; RISK ASSESSMENT;

BIOLOGICAL MARKER;

EID: 77955655126     PISSN: 08954356     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jclinepi.2009.10.001     Document Type: Review

References (70)

1. J.K. Nicholson, and I. Wilson High resolution proton magnetic resonance spectroscopy of biological fluids Prog NMR Spect 21 1989 449 501 (Pubitemid 20682955)
2. J.K. Nicholson, J.C. Lindon, and E. Holmes "Metabonomics": understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data Xenobiotica 29 1999 1181 1189
3. J.K. Nicholson, J. Connelly, J.C. Lindon, and E. Holmes Metabonomics: a platform for studying drug toxicity and gene function Nat Rev Drug Discov 1 2002 153 161
4. J.K. Nicholson, and J.C. Lindon Systems biology: metabonomics Nature 455 2008 1054 1056
5. C.L. Gavaghan McKee, E. Holmes, E. Lenz, I.D. Wilson, and J.K. Nicholson An NMR-based metabonomic approach to investigate the biochemical consequences of genetic strain differences: application to the C57BL10J and Alpk:ApfCD mouse FEBS Lett 484 2000 169 174
6. C.L. Gavaghan McKee, I.D. Wilson, and J.K. Nicholson Metabolic phenotyping of nude and normal (Alpk:ApfCD, C57BL10J) mice J Proteome Res 5 2006 378 384
7. E. Holmes, I.D. Wilson, and J.K. Nicholson Metabolic phenotyping in health and disease Cell 134 2008 714 717
8. T.A. Clayton, J.C. Lindon, J.R. Everett, C. Charuel, G. Hanton, J.L. Le Net, et al. Pharmaco-metabonomic phenotyping and personalized drug treatment Nature 440 2006 1073 1077
9. S. Rezzi, F.P. Martin, and S. Kochhar Defining personal nutrition and metabolic health through metabonomics Ernst Schering Found Symp Proc 4 2007 251 264
10. J. Stamler, P. Elliott, B. Dennis, A.R. Dyer, H. Kesteloot, K. Liu, et al. INTERMAP Research Group INTERMAP: background, aims, design, methods, and descriptive statistics (nondietary) J Hum Hypertens 17 2003 591 608
11. The INTERSALT Co-operative Research Group Sodium, potassium, body mass, alcohol and blood pressure: the INTERSALT Study J Hypertens Suppl 6 1988 S584 S586
12. M.E. Dumas, E.C. Maibaum, C. Teague, H. Ueshima, B. Zhou, J.C. Lindon, et al. Assessment of analytical reproducibility of 1H NMR spectroscopy based metabonomics for large-scale epidemiological research: the INTERMAP Study Anal Chem 78 2006 2199 2208
13. P. Jonsson, S.J. Bruce, T. Moritz, J. Trygg, M. Sjöström, R. Plumb, et al. Extraction, interpretation and validation of information for comparing samples in metabolic LC/MS data sets Analyst 130 2005 701 707
14. E. Holmes, R.L. Loo, J. Stamler, M. Bictash, I.K. Yap, Q. Chan, et al. Human metabolic phenotype diversity and its association with diet and blood pressure Nature 453 2008 396 400
15. P. Elliott, and T.C. Peakman The UK Biobank sample handling and storage protocol for the collection, processing and archiving of human blood and urine Int J Epidemiol 37 2008 234 244
16. O. Teahan, S. Gamble, E. Holmes, J. Waxman, J.K. Nicholson, C. Bevan, et al. Impact of analytical bias in metabonomic studies of human blood serum and plasma Anal Chem 78 2006 4307 4318
17. N.T. Holland, L. Pfleger, E. Berger, A. Ho, and M. Bastaki Molecular epidemiology biomarkers - sample collection and processing considerations Toxicol Appl Pharmacol 206 2005 261 268
18. N.T. Holland, M.T. Smith, B. Eskenazi, and M. Bastaki Biological sample collection and processing for molecular epidemiological studies Mutat Res 543 2003 217 234
19. C.P. Wild, C. Andersson, N.M. O'Brien, L. Wilson, and J.A. Woods A critical evaluation of the application of biomarkers in epidemiological studies on diet and health Br J Nutr 86 Suppl 1 2001 S37 S53
20. T.C. Peakman, and P. Elliott The UK Biobank sample handling and storage validation studies Int J Epidemiol 37 Suppl 1 2008 i2 i6
21. P. Elliott, and R. Stamler Manual of operations for "INTERSALT" , an international cooperative study on the relation of sodium and potassium to blood pressure Control Clin Trials 9 2 Suppl 1988 1S 117S
22. E.M. Lenz, J. Bright, I.D. Wilson, S.R. Morgan, and A.F. Nash A 1H NMR-based metabonomic study of urine and plasma samples obtained from healthy human subjects J Pharm Biomed Anal 33 2003 1103 1115
23. D.G. Robertson, M.D. Reily, R.E. Sigler, D.F. Wells, D.A. Paterson, and T.K. Braden Metabonomics: evaluation of nuclear magnetic resonance (NMR) and pattern recognition technology for rapid in vivo screening of liver and kidney toxicants Toxicol Sci 57 2000 326 337
24. S.J. Bruce, P. Jonsson, H. Antti, O. Cloarec, J. Trygg, S.L. Marklund, et al. Evaluation of a protocol for metabolic profiling studies on human blood plasma by combined ultra-performance liquid chromatography/mass spectrometry: from extraction to data analysis Anal Biochem 372 2008 237 249
25. K.K. Pasikanti, P.C. Ho, and E.C. Chan Development and validation of a gas chromatography/mass spectrometry metabonomic platform for the global profiling of urinary metabolites Rapid Commun Mass Spectrom 22 2008 2984 2992
26. E.J. Want, B.F. Cravatt, and G. Siuzdak The expanding role of mass spectrometry in metabolite profiling and characterization Chembiochem 6 2005 1941 1951
27. M. Lauridsen, S.H. Hansen, J.W. Jaroszewski, and C. Cornett Human urine as test material in 1H NMR-based metabonomics: recommendations for sample preparation and storage Anal Chem 79 2007 1181 1186
28. A.D. Maher, S.F. Zirah, E. Holmes, and J.K. Nicholson Experimental and analytical variation in human urine in 1H NMR spectroscopy-based metabolic phenotyping studies Anal Chem 79 2007 5204 5211
29. W.B. Dunn, D. Broadhurst, D.I. Ellis, M. Brown, A. Halsall, S. O'Hagan, et al. A GC-TOF-MS study of the stability of serum and urine metabolomes during the UK Biobank sample collection and preparation protocols Int J Epidemiol 37 Suppl 1 2008 i23 i30
30. R.H. Barton, J.K. Nicholson, P. Elliott, and E. Holmes High-throughput 1H NMR-based metabolic analysis of human serum and urine for large-scale epidemiological studies: validation study Int J Epidemiol 37 Suppl 1 2008 i31 i40
31. J.C. Lindon, J.K. Nicholson, E. Holmes, H.C. Keun, A. Craig, J.T. Pearce, et al. Summary recommendations for standardization and reporting of metabolic analyses Nat Biotechnol 23 2005 833 838
32. S.A. Sansone, T. Fan, R. Goodacre, J.L. Griffin, N.W. Hardy, R. Kaddurah-Daouk, et al. The metabolomics standards initiative Nat Biotechnol 25 2007 846 848
33. D.J. Crockford, E. Holmes, J.C. Lindon, R.S. Plumb, S. Zirah, S.J. Bruce, et al. Statistical heterospectroscopy, an approach to the integrated analysis of NMR and UPLC-MS data sets: application in metabonomic toxicology studies Anal Chem 78 2006 363 371
34. S. Wagner, K. Scholz, M. Sieber, M. Kellert, and W. Voelkel Tools in metabonomics: an integrated validation approach for LC-MS metabolic profiling of mercapturic acids in human urine Anal Chem 79 2007 2918 2926
35. G. Zurek, M. Godejohann, H. Schafer, C. Fischer, P. Neidig, D. Han, et al. P119-M combined analysis of urine samples using NMR and LC/MS J Biomol Tech 18 2007 42
36. H.C. Keun, T.M. Ebbels, H. Antti, M.E. Bollard, O. Beckonert, G. Schlotterbeck, et al. Analytical reproducibility in (1)H NMR-based metabonomic urinalysis Chem Res Toxicol 15 2002 1380 1386
37. O. Fiehn, J. Kopka, P. Dörmann, T. Altmann, R.N. Trethewey, and L. Willmitzer Metabolite profiling for plant functional genomics Nat Biotechnol 18 2000 1157 1161
38. H.G. Gika, G.A. Theodoridis, J.E. Wingate, and I.D. Wilson Within-day reproducibility of an HPLC-MS-based method for metabonomic analysis: application to human urine J Proteome Res 6 2007 3291 3303
39. T. Sangster, H. Major, R. Plumb, A.J. Wilson, and I.D. Wilson A pragmatic and readily implemented quality control strategy for HPLC-MS and GC-MS-based metabonomic analysis Analyst 131 2006 1075 1078
40. S. Kochhar, D.M. Jacobs, Z. Ramadan, F. Berruex, A. Fuerholz, and L.B. Fay Probing gender-specific metabolism differences in humans by nuclear magnetic resonance-based metabonomics Anal Biochem 352 2006 274 281
41. N.G. Psihogios, I.F. Gazi, M.S. Elisaf, K.I. Seferiadis, and E.T. Bairaktari Gender-related and age-related urinalysis of healthy subjects by NMR-based metabonomics NMR Biomed 21 2008 195 207
42. C.M. Slupsky, K.N. Rankin, J. Wagner, H. Fu, D. Chang, A.M. Weljie, et al. Investigations of the effects of gender, diurnal variation, and age in human urinary metabolomic profiles Anal Chem 79 2007 6995 7004
43. E.M. Lenz, J. Bright, I.D. Wilson, A. Hughes, J. Morrisson, H. Lindberg, et al. Metabonomics, dietary influences and cultural differences: a 1H NMR-based study of urine samples obtained from healthy British and Swedish subjects J Pharm Biomed Anal 36 2004 841 849
44. M. Assfalg, I. Bertini, D. Colangiuli, C. Luchinat, H. Schäfer, B. Schütz, et al. Evidence of different metabolic phenotypes in humans Proc Natl Acad Sci U S A 105 2008 1420 1424
45. S. Rezzi, Z. Ramadan, F.P. Martin, L.B. Fay, P. van Bladeren, J.C. Lindon, et al. Human metabolic phenotypes link directly to specific dietary preferences in healthy individuals J Proteome Res 6 2007 4469 4477
46. C. Stella, B. Beckwith-Hall, O. Cloarec, E. Holmes, J.C. Lindon, J. Powell, et al. Susceptibility of human metabolic phenotypes to dietary modulation J Proteome Res 5 2006 2780 2788
47. C.A. Smith, E.J. Want, G. O'Maille, R. Abagyan, and G. Siuzdak XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification Anal Chem 78 2006 779 787
48. M. Katajamaa, J. Miettinen, and M. Oresic MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data Bioinformatics 22 2006 634 636
49. R. Baran, H. Kochi, N. Saito, M. Suematsu, T. Soga, T. Nishioka, et al. MathDAMP: a package for differential analysis of metabolite profiles BMC Bioinform 7 2006 530
50. C.D. Broeckling, I.R. Reddy, A.L. Duran, X. Zhao, and L.W. Sumner MET-IDEA: data extraction tool for mass spectrometry-based metabolomics Anal Chem 78 2006 4334 4341
51. A.M. Weljie, J. Newton, P. Mercier, E. Carlson, and C.M. Slupsky Targeted profiling: quantitative analysis of 1H NMR metabolomics data Anal Chem 78 2006 4430 4442
52. D.J. Crockford, H.C. Keun, L.M. Smith, E. Holmes, and J.K. Nicholson Curve-fitting method for direct quantitation of compounds in complex biological mixtures using 1H NMR: application in metabonomic toxicology studies Anal Chem 77 2005 4556 4562
53. I.A. Lewis, S.C. Schommer, B. Hodis, K.A. Robb, M. Tonelli, W.M. Westler, et al. Method for determining molar concentrations of metabolites in complex solutions from two-dimensional 1H-13C NMR spectra Anal Chem 79 2007 9385 9390
54. E. Holmes, F.W. Bonner, B.C. Sweatman, J.C. Lindon, C.R. Beddell, E. Rahr, et al. Nuclear magnetic resonance spectroscopy and pattern recognition analysis of the biochemical processes associated with the progression of and recovery from nephrotoxic lesions in the rat induced by mercury(II) chloride and 2-bromoethanamine Mol Pharmacol 42 1992 922 930
55. H. Hotelling The generalization of the Student's ratio Ann Math Stat 2 1931 360 378
56. J. Trygg, and S. Wold Orthogonal projections to latent structures (O-PLS) J Chemometr 16 2002 119 128
57. J. Trygg, and S. Wold O2-PLS, a two-block (X-Y) latent variable regression (LVR) method with an integral OSC filter J Chemometr 17 2003 53 64
58. S.B. Pounds Estimation and control of multiple testing error rates for microarray studies Brief Bioinform 7 2006 25 36
59. H. Martens, and M. Martens Modified Jack-knife estimation of parameter uncertainty in bilinear modelling by partial least squares regression (PLSR) Food Qual Pref 11 2000 5 16
60. I. Pe'er, R. Yelensky, D. Altshuler, and M.J. Daly Estimation of the multiple testing burden for genomewide association studies of nearly all common variants Genet Epidemiol 32 2008 381 385
61. S.B.L. Akoka, and M. Trierweiler Concentration measurement by proton NMR using the ERETIC method Anal Chem 71 1999 2254 2557
62. T. Kohonen The self-organizing map Proc IEEE 78 1990 1464
63. K.P. Gartland, C.R. Beddell, J.C. Lindon, and J.K. Nicholson Application of pattern recognition methods to the analysis and classification of toxicological data derived from proton nuclear magnetic resonance spectroscopy of urine Mol Pharmacol 39 1991 629 642
64. O. Cloarec, M.E. Dumas, A. Craig, R.H. Barton, J. Trygg, J. Hudson, et al. Statistical total correlation spectroscopy: an exploratory approach for latent biomarker identification from metabolic 1H NMR data sets Anal Chem 77 2005 1282 1289
65. J.L. Griffin, S.A. Bonney, C. Mann, A.M. Hebbachi, G.F. Gibbons, J.K. Nicholson, et al. An integrated reverse functional genomic and metabolic approach to understanding orotic acid-induced fatty liver Physiol Genomics 17 2004 140 149
66. T.G. Kleno, B. Kiehr, D. Baunsgaard, and U.G. Sidelmann Combination of "omics" data to investigate the mechanism(s) of hydrazine-induced hepatotoxicity in rats and to identify potential biomarkers Biomarkers 9 2004 116 138
67. A. Craig, J. Sidaway, E. Holmes, T. Orton, D. Jackson, R. Rowlinson, et al. Systems toxicology: integrated genomic, proteomic and metabonomic analysis of methapyrilene induced hepatotoxicity in the rat J Proteome Res 5 2006 1586 1601
68. M. Rantalainen, O. Cloarec, O. Beckonert, I.D. Wilson, D. Jackson, R. Tonge, et al. Statistically integrated metabonomic-proteomic studies on a human prostate cancer xenograft model in mice J Proteome Res 5 2006 2642 2655
69. A. Vilasi, P.R. Cutillas, A.D. Maher, S.F. Zirah, G. Capasso, A.W. Norden, et al. Combined proteomic and metabonomic studies in three genetic forms of the renal Fanconi syndrome Am J Physiol Renal Physiol 293 2007 F456 F467
70. M.P. van Iersel, T. Kelder, A.R. Pico, K. Hanspers, S. Coort, B.R. Conklin, and C. Evelo Presenting and exploring biological pathways with PathVisio Bioinformatics 9 2008 399