{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000306","ANALYSIS_ID":"AN000485","VERSION":"1","CREATED_ON":"January 1, 2016, 5:37 pm"},

"PROJECT":{"PROJECT_TITLE":"Metabolomics Approach to Identify Molecules and Pathways Involved in the Development of Atherosclerotic Coronary Artery Disease","PROJECT_SUMMARY":"Genetics play major roles in the development of atherosclerotic coronary artery disease (CAD). Despite tremendous efforts worldwide invested to decipher the genetic components controlling the development of CAD, the genetic architecture of CAD remains largely unclear. As part of an on-going effort to identify molecules and pathways involved in the development of atherosclerotic CAD, we propose to use rigorous angiographic criteria to define CAD phenotype for genomics and metabolomics study. We identified two extreme groups, namely “young CAD” group, who are very young individuals (age <= 40 years) proven to have severe CAD required revascularization, and “CAD-free elderly”, who are at very advanced age (Age >= 80 years) but have no angiographically apparent CAD. Phenotypically, these two groups are in sharp contrary. Conventional risk factors account for small portion of different phenotypes. We hypothesize that there are genetically programmed pathways and molecules accelerating atherosclerotic pathogenesis, in the “young CAD” patients and preventing the development of CAD in the “CAD-free elderly” patients. We sought to combine genomics and metabolomics approaches to profile and identify these pathways and molecules. Both plasma and urine samples from patients in these two groups, and their age matched control groups, will undergo unbiased metabolomics profiling with high throughput quantitative nuclear magnetic resonance (NMR) and mass spectrometry (MS) technology in RTI metabolomics core facility. Comprehensive statistic and multi-variant analytic approaches will be used to identify pathways and molecules significance to the pathogenesis of atherosclerosis. These data will be integrated with genomics data from next generation sequencing of genetic materials from the same groups of patients to further explore the molecular mechanisms underlying atherosclerosis and CAD.","INSTITUTE":"UNC Chapel Hill School of Medicine","DEPARTMENT":"Heart & Vascular Center","LAST_NAME":"Dai","FIRST_NAME":"Xuming","ADDRESS":"BW Building, CB 7075, 160 Dental Circle, Chapel Hill, NC 27599","EMAIL":"xdai@unch.unc.edu","PHONE":"919-966-5956"},

"STUDY":{"STUDY_TITLE":"Metabolomics Approach to Identify Molecules and Pathways Involved in the Development of Atherosclerotic Coronary Artery Disease","STUDY_TYPE":"Metabolomics","STUDY_SUMMARY":"Genetics play major roles in the development of atherosclerotic coronary artery disease (CAD). Despite tremendous efforts worldwide invested to decipher the genetic components controlling the development of CAD, the genetic architecture of CAD remains largely unclear. As part of an on-going effort to identify molecules and pathways involved in the development of atherosclerotic CAD, we propose to use rigorous angiographic criteria to define CAD phenotype for genomics and metabolomics study. We identified two extreme groups, namely “young CAD” group, who are very young individuals (age <= 40 years) proven to have severe CAD required revascularization, and “CAD-free elderly”, who are at very advanced age (Age >= 80 years) but have no angiographically apparent CAD. Phenotypically, these two groups are in sharp contrary. Conventional risk factors account for small portion of different phenotypes. We hypothesize that there are genetically programmed pathways and molecules accelerating atherosclerotic pathogenesis, in the “young CAD” patients and preventing the development of CAD in the “CAD-free elderly” patients. We sought to combine genomics and metabolomics approaches to profile and identify these pathways and molecules. Both plasma and urine samples from patients in these two groups, and their age matched control groups, will undergo unbiased metabolomics profiling with high throughput quantitative nuclear magnetic resonance (NMR) and mass spectrometry (MS) technology in RTI metabolomics core facility. Comprehensive statistic and multi-variant analytic approaches will be used to identify pathways and molecules significance to the pathogenesis of atherosclerosis. These data will be integrated with genomics data from next generation sequencing of genetic materials from the same groups of patients to further explore the molecular mechanisms underlying atherosclerosis and CAD.","INSTITUTE":"RTI International","DEPARTMENT":"Systems and Translational Sciences","LABORATORY":"NIH Eastern Regional Comphrehensive Metabolomics Resource Core","LAST_NAME":"Sumner","FIRST_NAME":"Susan","ADDRESS":"3040 E. Cornwallis Road","EMAIL":"ssumner@rti.org","PHONE":"919-541-7479","TOTAL_SUBJECTS":"106"},

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"Sample ID":"DP3S008",
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{
"Subject ID":"-",
"Sample ID":"DPTotal_Pool_4",
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"Sample ID":"DPTotal_Pool_6",
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"Subject ID":"-",
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"Factors":{"CAD":"Mid-Age CAD"}
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"Sample ID":"DP3S026",
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{
"Subject ID":"-",
"Sample ID":"DPTotal_Pool_1",
"Factors":{"CAD":"Total Pool"}
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{
"Subject ID":"-",
"Sample ID":"DPTotal_Pool_2",
"Factors":{"CAD":"Total Pool"}
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"Subject ID":"-",
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"Factors":{"CAD":"Young CAD"}
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"Subject ID":"-",
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"Factors":{"CAD":"Young CAD"}
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"Subject ID":"-",
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"Subject ID":"-",
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"Subject ID":"-",
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"Factors":{"CAD":"Young CAD"}
},
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"Subject ID":"-",
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"Factors":{"CAD":"Young CAD"}
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"Subject ID":"-",
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"Factors":{"CAD":"Young CAD"}
},
{
"Subject ID":"-",
"Sample ID":"DP1S162",
"Factors":{"CAD":"Young CAD"}
},
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"Subject ID":"-",
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"Factors":{"CAD":"Young CAD"}
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{
"Subject ID":"-",
"Sample ID":"DP3S004",
"Factors":{"CAD":"Young CAD"}
},
{
"Subject ID":"-",
"Sample ID":"DP1S005",
"Factors":{"CAD":"Young No-CAD"}
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"Subject ID":"-",
"Sample ID":"DP1S009",
"Factors":{"CAD":"Young No-CAD"}
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"Subject ID":"-",
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"Subject ID":"-",
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"Subject ID":"-",
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},
{
"Subject ID":"-",
"Sample ID":"DP1S113",
"Factors":{"CAD":"Young No-CAD"}
},
{
"Subject ID":"-",
"Sample ID":"DP1S129",
"Factors":{"CAD":"Young No-CAD"}
},
{
"Subject ID":"-",
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},
{
"Subject ID":"-",
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{
"Subject ID":"-",
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{
"Subject ID":"-",
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"Factors":{"CAD":"Young No-CAD"}
},
{
"Subject ID":"-",
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"Factors":{"CAD":"Young No-CAD"}
},
{
"Subject ID":"-",
"Sample ID":"DP3S018",
"Factors":{"CAD":"Young No-CAD"}
},
{
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"Factors":{"CAD":"Young No-CAD"}
},
{
"Subject ID":"-",
"Sample ID":"DP3S028",
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},
{
"Subject ID":"-",
"Sample ID":"DPTotal_Pool_5",
"Factors":{"CAD":"Young No-CAD"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"-","SAMPLE_TYPE":"plasma","STORAGE_CONDITIONS":"-80C"},

"TREATMENT":{"TREATMENT_SUMMARY":"-"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Plasma samples were transferred to labeled tubes. A total of 219 study samples were thawed on ice for sample preparation200 uL of plasma sample were thawed and transferred to labeled tubes on ice where they were mixed with 50 uL Saline master mix (5mM Formate). Analytical quality control (QC) phenotypic pooled samples were generated by transferring a 25 µL of each sample of each respective phenotypical experimental sample into different 1.5 mL tubes. Whole study (total) pools were generated by transferring 200 uL of plasma from each Pool sample into a 2.0 mL tube. The tubes were vortexed for 4 min on a multi-tube vortexer and centrifuged at 16,000 rcf for 4 min. A 200 µl aliquot of the supernatant was transferred into pre-labeled 3mm NMR tubes for data acquisition on a 700 MHz spectrometer.","SAMPLEPREP_PROTOCOL_FILENAME":"CAD_Metabolomics_Procedures.docx"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"-","INSTRUMENT_NAME":"-","COLUMN_NAME":"-"},

"ANALYSIS":{"ANALYSIS_TYPE":"NMR"},

"NM":{"INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"Other","FIELD_FREQUENCY_LOCK":"Deuterium","STANDARD_CONCENTRATION":"0.5 mM","SPECTROMETER_FREQUENCY":"700 MHz","NMR_PROBE":"5 mm ATMA Cryoprobe","NMR_SOLVENT":"D2O","NMR_TUBE_SIZE":"5 mm","SHIMMING_METHOD":"Topshim","PULSE_SEQUENCE":"noesypr1d","WATER_SUPPRESSION":"yes","RECEIVER_GAIN":"4.5","OFFSET_FREQUENCY":"3299.5","CHEMICAL_SHIFT_REF_CPD":"DSS","TEMPERATURE":"298.1 K","NUMBER_OF_SCANS":"128","DUMMY_SCANS":"4","ACQUISITION_TIME":"3.893","SPECTRAL_WIDTH":"12.0227 ppm, 8.417 Hz","NUM_DATA_POINTS_ACQUIRED":"65536","REAL_DATA_POINTS":"65536","LINE_BROADENING":"0.5 Hz","ZERO_FILLING":"yes","APODIZATION":"Lorentzian","BASELINE_CORRECTION_METHOD":"Polynomial","CHEMICAL_SHIFT_REF_STD":"DSS-D6","BINNED_DATA_EXCLUDED_RANGE":"water (4.60 – 5.10 ppm) EDTA (2.53 – 2.59 ppm, 2.67 -2.72 ppm, 3.06 – 3.15 ppm, 3.22 - 3.28 and 3.56 – 3.65ppm) noise regions (5.50-5.70 ppm, 5.90-6.80 ppm, 7.85-10.786 ppm)","INSTRUMENT_NAME":"Bruker 700MHz"},

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