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"PROJECT":{"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":"Department of Medicine, 4126A Katz Group Centre for Pharmacy & Health, University of Alberta, Edmonton, AB T6G 2E1, Canada.","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"},
"STUDY":{"STUDY_TITLE":"1H-NMR urinary metabolomic profiling for diagnosis of gastric cancer (part II)","STUDY_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":"Department of Medicine, 4126A Katz Group Centre for Pharmacy & Health, University of Alberta, Edmonton, AB T6G 2E1, Canada.","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"},
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"Sample ID":"sample_110",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"110","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"111",
"Sample ID":"sample_111",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"111","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"112",
"Sample ID":"sample_112",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"112","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"113",
"Sample ID":"sample_113",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"113","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"114",
"Sample ID":"sample_114",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"114","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"115",
"Sample ID":"sample_115",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"115","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"116",
"Sample ID":"sample_116",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"116","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"117",
"Sample ID":"sample_117",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"117","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"118",
"Sample ID":"sample_118",
"Factors":{"Sample_Type":"QC"},
"Additional sample data":{"QC":"1","Batch":"4","Order":"118","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"119",
"Sample ID":"sample_119",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"119","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"120",
"Sample ID":"sample_120",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"120","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"121",
"Sample ID":"sample_121",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"121","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"122",
"Sample ID":"sample_122",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"122","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"123",
"Sample ID":"sample_123",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"123","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"124",
"Sample ID":"sample_124",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"124","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"125",
"Sample ID":"sample_125",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"125","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"126",
"Sample ID":"sample_126",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"126","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"127",
"Sample ID":"sample_127",
"Factors":{"Sample_Type":"QC"},
"Additional sample data":{"QC":"1","Batch":"4","Order":"127","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"128",
"Sample ID":"sample_128",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"128","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"129",
"Sample ID":"sample_129",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"129","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"130",
"Sample ID":"sample_130",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"130","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"131",
"Sample ID":"sample_131",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"131","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"132",
"Sample ID":"sample_132",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"132","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"133",
"Sample ID":"sample_133",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"133","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"134",
"Sample ID":"sample_134",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"134","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"135",
"Sample ID":"sample_135",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"135","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"136",
"Sample ID":"sample_136",
"Factors":{"Sample_Type":"QC"},
"Additional sample data":{"QC":"1","Batch":"4","Order":"136","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"137",
"Sample ID":"sample_137",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"137","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"138",
"Sample ID":"sample_138",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"138","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"139",
"Sample ID":"sample_139",
"Factors":{"Sample_Type":"Sample"},
"Additional sample data":{"QC":"-","Batch":"4","Order":"139","Day of Expt":"18/Dec/14"}
},
{
"Subject ID":"140",
"Sample ID":"sample_140",
"Factors":{"Sample_Type":"QC"},
"Additional sample data":{"QC":"1","Batch":"4","Order":"140","Day of Expt":"18/Dec/14"}
}
],
"COLLECTION":{"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_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."},
"SAMPLEPREP":{"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."},
"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"-","INSTRUMENT_NAME":"-","COLUMN_NAME":"-"},
"ANALYSIS":{"ANALYSIS_TYPE":"NMR"},
"NM":{"INSTRUMENT_NAME":"600 MHz Varian Inova spectrometer","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"1D-1H","SPECTROMETER_FREQUENCY":"600 MHz"},
"NMR_METABOLITE_DATA":{
"Units":"area",
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acid adenine dinucleotide","Idx":"97","Name":"M97"},{"Metabolite":"O-Acetylcarnitine","Idx":"98","Name":"M98"},{"Metabolite":"O-Phosphocholine","Idx":"99","Name":"M99"},{"Metabolite":"Oxypurinol","Idx":"100","Name":"M100"},{"Metabolite":"Pantothenate","Idx":"101","Name":"M101"},{"Metabolite":"Phenylacetate","Idx":"102","Name":"M102"},{"Metabolite":"Phenylalanine","Idx":"103","Name":"M103"},{"Metabolite":"Proline","Idx":"104","Name":"M104"},{"Metabolite":"Propylene glycol","Idx":"105","Name":"M105"},{"Metabolite":"Pyridoxine","Idx":"106","Name":"M106"},{"Metabolite":"Pyroglutamate","Idx":"107","Name":"M107"},{"Metabolite":"Pyruvate","Idx":"108","Name":"M108"},{"Metabolite":"Sarcosine","Idx":"109","Name":"M109"},{"Metabolite":"Serotonin","Idx":"110","Name":"M110"},{"Metabolite":"Succinate","Idx":"111","Name":"M111"},{"Metabolite":"Sucrose","Idx":"112","Name":"M112"},{"Metabolite":"Taurine","Idx":"113","Name":"M113"},{"Metabolite":"Threonine","Idx":"114","Name":"M114"},{"Metabolite":"Trigonelline","Idx":"115","Name":"M115"},{"Metabolite":"Trimethylamine","Idx":"116","Name":"M116"},{"Metabolite":"Trimethylamine N-oxide","Idx":"117","Name":"M117"},{"Metabolite":"Tropate","Idx":"118","Name":"M118"},{"Metabolite":"Tryptophan","Idx":"119","Name":"M119"},{"Metabolite":"Tyrosine","Idx":"120","Name":"M120"},{"Metabolite":"Urocanate","Idx":"121","Name":"M121"},{"Metabolite":"Valine","Idx":"122","Name":"M122"},{"Metabolite":"Xanthine","Idx":"123","Name":"M123"},{"Metabolite":"Xylose","Idx":"124","Name":"M124"},{"Metabolite":"cis-Aconitate","Idx":"125","Name":"M125"},{"Metabolite":"trans-Aconitate","Idx":"126","Name":"M126"},{"Metabolite":"β-Alanine","Idx":"147","Name":"M127"},{"Metabolite":"π-Methylhistidine","Idx":"148","Name":"M128"},{"Metabolite":"τ-Methylhistidine","Idx":"149","Name":"M129"}]
}
}