Summary of Study ST001047

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000699. The data can be accessed directly via it's Project DOI: 10.21228/M8B10B This work is supported by NIH grant, U2C- DK119886.

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Study IDST001047
Study Title1H-NMR urinary metabolomic profiling for diagnosis of gastric cancer.
Study SummaryBackground: Metabolomics has shown promise in gastric cancer (GC) detection. This research sought to identify whether GC has a unique urinary metabolomic profile compared with benign gastric disease (BN) and healthy (HE) patients. Methods: Urine from 43 GC, 40 BN, and 40 matched HE patients was analysed using 1H nuclear magnetic resonance (1H-NMR) spectroscopy, generating 77 reproducible metabolites (QC-RSD <25%). Univariate and multivariate (MVA) statistics were employed. A parsimonious biomarker profile of GC vs HE was investigated using LASSO regularised logistic regression (LASSO-LR). Model performance was assessed using Receiver Operating Characteristic (ROC) curves. Results: GC displayed a clear discriminatory biomarker profile; the BN profile overlapped with GC and HE. LASSO-LR identified three discriminatory metabolites: 2-hydroxyisobutyrate, 3-indoxylsulfate, and alanine, which produced a discriminatory model with an area under the ROC of 0.95. Conclusions: GC patients have a distinct urinary metabolite profile. This study shows clinical potential for metabolic profiling for early GC diagnosis.
Institute
University of Alberta
Last NameBroadhurst
First NameDavid
AddressDepartment of Medicine, 4126A Katz Group Centre for Pharmacy & Health, University of Alberta, Edmonton, AB T6G 2E1, Canada.
Emaild.broadhurst@ecu.edu.au
Phone+61 8 6304 2705
Submit Date2018-09-03
PublicationsChan, A. W., Mercier, P., Schiller, D., Bailey, R., Robbins, S., Eurich, D. T., Sawyer, M. B., Broadhurst, D. (2016). 1H-NMR urinary metabolomic profiling for diagnosis of gastric cancer. British Journal of Cancer, 114(1), 59-62. doi:10.1038/bjc.2015.414
Raw Data File Type(s)d
Analysis Type DetailNMR
Release Date2018-10-10
Release Version1
David Broadhurst David Broadhurst
https://dx.doi.org/10.21228/M8B10B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000699
Project DOI:doi: 10.21228/M8B10B
Project Title:1H-NMR urinary metabolomic profiling for diagnosis of gastric cancer
Project Summary:Background: Metabolomics has shown promise in gastric cancer (GC) detection. This research sought to identify whether GC has a unique urinary metabolomic profile compared with benign gastric disease (BN) and healthy (HE) patients. Methods: Urine from 43 GC, 40 BN, and 40 matched HE patients was analysed using 1H nuclear magnetic resonance (1H-NMR) spectroscopy, generating 77 reproducible metabolites (QC-RSD <25%). Univariate and multivariate (MVA) statistics were employed. A parsimonious biomarker profile of GC vs HE was investigated using LASSO regularised logistic regression (LASSO-LR). Model performance was assessed using Receiver Operating Characteristic (ROC) curves. Results: GC displayed a clear discriminatory biomarker profile; the BN profile overlapped with GC and HE. LASSO-LR identified three discriminatory metabolites: 2-hydroxyisobutyrate, 3-indoxylsulfate, and alanine, which produced a discriminatory model with an area under the ROC of 0.95. Conclusions: GC patients have a distinct urinary metabolite profile. This study shows clinical potential for metabolic profiling for early GC diagnosis.
Institute:University of Alberta
Last Name:Broadhurst
First Name:David
Address:270 Joondalup Drive, Joondalup, WA 6027, AUSTRALIA
Email:d.broadhurst@ecu.edu.au
Phone:+61 8 6304 2705
Publications:Chan, A. W., Mercier, P., Schiller, D., Bailey, R., Robbins, S., Eurich, D. T., Sawyer, M. B., Broadhurst, D. (2016). 1H-NMR urinary metabolomic profiling for diagnosis of gastric cancer. British Journal of Cancer, 114(1), 59-62. doi:10.1038/bjc.2015.414

Subject:

Subject ID:SU001087
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Sample_Type
SA070432sample_37QC
SA070433sample_46QC
SA070434sample_28QC
SA070435sample_118QC
SA070436sample_19QC
SA070437sample_100QC
SA070438sample_91QC
SA070439sample_1QC
SA070440sample_73QC
SA070441sample_82QC
SA070442sample_64QC
SA070443sample_127QC
SA070444sample_55QC
SA070445sample_109QC
SA070446sample_136QC
SA070447sample_10QC
SA070448sample_140QC
SA070449sample_135Sample
SA070450sample_93Sample
SA070451sample_92Sample
SA070452sample_90Sample
SA070453sample_94Sample
SA070454sample_96Sample
SA070455sample_134Sample
SA070456sample_101Sample
SA070457sample_99Sample
SA070458sample_98Sample
SA070459sample_89Sample
SA070460sample_97Sample
SA070461sample_95Sample
SA070462sample_87Sample
SA070463sample_139Sample
SA070464sample_80Sample
SA070465sample_79Sample
SA070466sample_78Sample
SA070467sample_77Sample
SA070468sample_81Sample
SA070469sample_138Sample
SA070470sample_137Sample
SA070471sample_86Sample
SA070472sample_85Sample
SA070473sample_84Sample
SA070474sample_83Sample
SA070475sample_88Sample
SA070476sample_102Sample
SA070477sample_120Sample
SA070478sample_121Sample
SA070479sample_119Sample
SA070480sample_131Sample
SA070481sample_117Sample
SA070482sample_132Sample
SA070483sample_122Sample
SA070484sample_123Sample
SA070485sample_126Sample
SA070486sample_129Sample
SA070487sample_130Sample
SA070488sample_125Sample
SA070489sample_124Sample
SA070490sample_116Sample
SA070491sample_115Sample
SA070492sample_107Sample
SA070493sample_108Sample
SA070494sample_106Sample
SA070495sample_105Sample
SA070496sample_103Sample
SA070497sample_104Sample
SA070498sample_76Sample
SA070499sample_133Sample
SA070500sample_113Sample
SA070501sample_114Sample
SA070502sample_112Sample
SA070503sample_111Sample
SA070504sample_110Sample
SA070505sample_128Sample
SA070506sample_71Sample
SA070507sample_24Sample
SA070508sample_25Sample
SA070509sample_26Sample
SA070510sample_23Sample
SA070511sample_22Sample
SA070512sample_20Sample
SA070513sample_21Sample
SA070514sample_27Sample
SA070515sample_29Sample
SA070516sample_34Sample
SA070517sample_35Sample
SA070518sample_33Sample
SA070519sample_32Sample
SA070520sample_30Sample
SA070521sample_31Sample
SA070522sample_18Sample
SA070523sample_17Sample
SA070524sample_6Sample
SA070525sample_7Sample
SA070526sample_5Sample
SA070527sample_4Sample
SA070528sample_2Sample
SA070529sample_3Sample
SA070530sample_8Sample
SA070531sample_9Sample
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Collection:

Collection ID:CO001081
Collection Summary:Midstream urine samples were collected from 43 GC, 40 BN, and 40 HE patients from January 2009 to December 2014 from three hospitals in Edmonton, Canada. GC samples were collected prior to chemoradiotherapy and surgery. All patients provided written informed consent. Ethics approval was obtained from the Health Research Ethics Board at the University of Alberta. Inclusion criteria for cancer patients were: biopsy-confirmed diagnosis of GC, age >=18 years, and no metastases on their staging computed tomography scans. BN patients had to experience gastrointestinal symptoms (such as haematemesis or epigastric discomfort) and must have endoscopic evidence within the past 6 months of consent that symptoms were not due to a malignant cause. BN patients had the following conditions: gastritis, gastro- oesophageal reflux disease (GORD), portal hypertensive gastro- pathy, varices, gastritis, ulcers, and polyps. HE controls had no declared history of cancer and no gastrointestinal symptoms. Groups were matched on age, gender, and BMI. Exclusion criteria included: breastfeeding, pregnancy, significant cardiac disease with New York Heart Association XClass II, systemic infection, prior cancer, and glomerular filtration rate 30 ml min ^-1.
Sample Type:Urine

Treatment:

Treatment ID:TR001101
Treatment Summary:Within 2h of collection, one ml aliquots of urine mixed with 50ml of 0.42% sodium azide preservative were prepared and biobanked at -80 °C.

Sample Preparation:

Sampleprep ID:SP001094
Sampleprep Summary:Urine aliquots were thawed and prepared by adding 75 μL of a chemical shift standard (Chenomx Inc., Edmonton, Alberta, Canada) containing 4.6 mM 2,2-dimethyl-2-silapentane-5-sulfonate-d6 sodium salt (DSS-D6), 0.20% w/v NaN3 and 98.0% v/v D2O, to 675 μL of urine. Samples were titrated to a final pH of 6.75 ± 0.05 using small volumes of sodium hydroxide (NaOH) and hydrochloric acid (HCl). Samples were centrifuged for 10 minutes at 10000 x g at 4 °C to remove particulate matter. Next, 700 μL of supernatant was transferred to a 4” long, 5 mm diameter NMR tube (Wilmad, Nuena, NJ, USA 505-PS-4) immediately prior to NMR acquisition.

Analysis:

Analysis ID:AN001711
Analysis Type:NMR
Num Factors:2
Num Metabolites:129
Units:area

NMR:

NMR ID:NM000127
Analysis ID:AN001711
Instrument Name:600 MHz Varian Inova spectrometer
Instrument Type:FT-NMR
NMR Experiment Type:1D 1H
Spectrometer Frequency:600 MHz
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