NCT02683876: Documentation of Clinical Trial Data and Procedures

ClinicalTrials.gov Identifier:  NCT02683876  (completed). MedRxiv publication
Principal investigators: David Wishart,  Irene Gabashvili

​Diagnostic tests:

• Direct Flow Injection Mass Spectrometry (DI-MS)  [Metabolites quantified]    [Refs]
• Quantitative NMR Spectroscopy [Metabolites quantified]    [Refs]
• Organic Acid Analysis [Metabolites quantified]     [Refs]

​Software tools:

• Chenomx NMRSuite v7.0 software (Chenomx, Edmonton, Alberta, Canada). 
• Aurametrix Software (General Availability Announcement) 
• R  (k-means and hierarchical clustering, PCA, visualization)
• VBA Excel macros (PCA, PLS, t-tests)

Downloadable Data, Blogs and Research Papers

• 900969 raw data
• 900646 raw data
• 900576 raw data
• 900874 raw data
• 900843 raw data
• 900841 raw data
• 900116 raw data
• 900365 raw data
• 900840 raw data
• 900873 raw data
• 900134 raw data
• 900126 raw data
• 900308 raw data
• 900679 raw data
• 900636 raw data
• 900970 raw data

Blogs and Research Papers

Let Those Who Never Smelled Bad Cast The First Stone
Updates on MEBO Clinical trials
​

I.S. Gabashvili "Identifying subtypes of a stigmatized medical condition"  medRxiv 19005223; doi: https://doi.org/10.1101/19005223

DI/MS

Bouatra S, Aziat F, Mandal R, Guo AC, Wilson MR, Knox C, Bjorndahl TC, Krishnamurthy R, Saleem F, Liu P, Dame ZT, Poelzer J., Huynh J, Yallou FS, Psychogios N, Dong E, Bogumil R, Roehring C, Wishart DS. The human urine metabolome. PloS one. 2013 Sep 4;8(9):e73076. PMID: 24023812

Quantitative NMR

Markley JL, Brüschweiler R, Edison AS, Eghbalnia HR, Powers R, Raftery D, Wishart DS. The future of NMR-based metabolomics. Current opinion in biotechnology. 2017 Feb 28;43:34-40.

Emwas, A.H., Roy, R., McKay, R.T., Ryan, D., Brennan, L., Tenori, L., Luchinat, C., Gao, X., Zeri, A.C., Gowda, G.A., Raftery, D., Steinbeck, C., Salek, R.M. & Wishart, D.S. Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis. J. Proteome Res. 15(2), 360-373. doi: 10.1021/acs.jproteome.5b00885 (2016) PubMed ID: 26745651

Organic Acid Analysis

Thompson JA, Markey SP. Quantitative metabolic profiling of urinary organic acids by gas chromatography-mass spectrometry. Comparison of isolation methods. Analytical chemistry. 1975 Jul 1;47(8):1313-21.

​Tsoukalas D, Alegakis A, Fragkiadaki P, Papakonstantinou E, Nikitovic D, Karataraki A, Nosyrev AE, Papadakis EG, Spandidos DA, Drakoulis N, Tsatsakis AM. Application of metabolomics: Focus on the quantification of organic acids in healthy adults. International Journal of Molecular Medicine. 2017 Jul 1;40(1):112-20.

GC-MS Sample Preparation Protocol for Organic Acids in Urine (pdf)

Amino Acid Profile

Deyl Z, Hyanek J, Horakova M. Profiling of amino acids in body fluids and tissues by means of liquid chromatography. Journal of Chromatography B: Biomedical Sciences and Applications. 1986 Jun 20;379:177-250.

Minkler PE, Hoppel CL. Quantification of carnitine and specific acylcarnitines by high-performance liquid chromatography: application to normal human urine and urine from patients with methylmalonic aciduria, isovaleric acidemia or medium-chain acyl-CoA dehydrogenase deficiency. Journal of Chromatography B: Biomedical Sciences and Applications. 1993 Apr 2;613(2):203-21.

Bouatra S, Aziat F, Mandal R, Guo AC, Wilson MR, Knox C, Bjorndahl TC, Krishnamurthy R, Saleem F, Liu P, Dame ZT. The human urine metabolome. PloS one. 2013 Sep 4;8(9):e73076.

Colorectal polyp and cancer biomarkers

Deng L, Chang D, Foshaug RR, Eisner R, Tso VK, Wishart DS, Fedorak RN. Development and Validation of a High-Throughput Mass Spectrometry Based Urine Metabolomic Test for the Detection of Colonic Adenomatous Polyps. Metabolites, June 22, 2017, 7(3), 32