Summary of Study ST000306

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 PR000246. The data can be accessed directly via it's Project DOI: 10.21228/M8088P This work is supported by NIH grant, U2C- DK119886.

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Study IDST000306
Study TitleMetabolomics Approach to Identify Molecules and Pathways Involved in the Development of Atherosclerotic Coronary Artery Disease
Study TypeMetabolomics
Study SummaryGenetics 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
University of North Carolina
DepartmentSystems and Translational Sciences
LaboratorySumner Lab
Last NameSumner
First NameSusan
AddressEastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081
Emailsusan_sumner @unc.edu
Phone704-250-5066
Submit Date2015-12-31
Total Subjects106
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2016-12-31
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8088P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000246
Project DOI:doi: 10.21228/M8088P
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:University of North Carolina at Chapel Hill
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

Subject:

Subject ID:SU000326
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:male/female
Species Group:Human

Factors:

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

mb_sample_id local_sample_id CAD
SA013847DP2S138Elderly 1st Dx CAD
SA013848DP2S141Elderly 1st Dx CAD
SA013849DP2S129Elderly 1st Dx CAD
SA013850DP2S121Elderly 1st Dx CAD
SA013851DP2S109Elderly 1st Dx CAD
SA013852DP2S155Elderly 1st Dx CAD
SA013853DP2S159Elderly 1st Dx CAD
SA013854DP1S097Elderly 1st Dx CAD
SA013855DP2S199Elderly 1st Dx CAD
SA013856DP2S188Elderly 1st Dx CAD
SA013857DP2S172Elderly 1st Dx CAD
SA013858DP2S108Elderly 1st Dx CAD
SA013859DP2S135Elderly 1st Dx CAD
SA013860DP2S016Elderly 1st Dx CAD
SA013861DP2S029Elderly 1st Dx CAD
SA013862DP2S013Elderly 1st Dx CAD
SA013863DP2S083Elderly 1st Dx CAD
SA013864DP2S003Elderly 1st Dx CAD
SA013865DP2S005Elderly 1st Dx CAD
SA013866DP2S030Elderly 1st Dx CAD
SA013867DP2S010Elderly 1st Dx CAD
SA013868DP2S062Elderly 1st Dx CAD
SA013869DP2S031Elderly 1st Dx CAD
SA013870DP2S056Elderly 1st Dx CAD
SA013871DP2S060Elderly 1st Dx CAD
SA013872DP2S035Elderly 1st Dx CAD
SA013873DP2S168Elderly No CAD
SA013874DP2S183Elderly No CAD
SA013875DP2S164Elderly No CAD
SA013876DP2S147Elderly No CAD
SA013877DP2S197Elderly No CAD
SA013878DPTotal_Pool_4Elderly No CAD
SA013879DP2S134Elderly No CAD
SA013880DPTotal_Pool_6Elderly No CAD
SA013881DP3S008Elderly No CAD
SA013882DP2S200Elderly No CAD
SA013883DP2S001Elderly No CAD
SA013884DP2S049Elderly No CAD
SA013885DP2S042Elderly No CAD
SA013886DP2S133Elderly No CAD
SA013887DP1S081Elderly No CAD
SA013888DP2S051Elderly No CAD
SA013889DP2S033Elderly No CAD
SA013890DP2S070Elderly No CAD
SA013891DP2S102Elderly No CAD
SA013892DP2S125Elderly No CAD
SA013893DP2S086Elderly No CAD
SA013894DP2S148Mid-Age CAD
SA013895DP2S144Mid-Age CAD
SA013896DP2S171Mid-Age CAD
SA013897DP3S019Mid-Age CAD
SA013898DP2S124Mid-Age CAD
SA013899DP3S026Mid-Age CAD
SA013900DP2S191Mid-Age CAD
SA013901DP2S180Mid-Age CAD
SA013902DP2S094Mid-Age CAD
SA013903DP1S152Mid-Age CAD
SA013904DP1S142Mid-Age CAD
SA013905DP2S103Mid-Age CAD
SA013906DP1S122Mid-Age CAD
SA013907DP1S155Mid-Age CAD
SA013908DP2S050Mid-Age CAD
SA013909DP2S085Mid-Age CAD
SA013910DP2S081Mid-Age CAD
SA013911DP2S055Mid-Age CAD
SA013912DPTotal_Pool_3Total Pool
SA013913DPTotal_Pool_2Total Pool
SA013914DPTotal_Pool_1Total Pool
SA013915DP1S134Young CAD
SA013916DP1S107Young CAD
SA013917DP1S095Young CAD
SA013918DP1S135Young CAD
SA013919DP1S154Young CAD
SA013920DP3S004Young CAD
SA013921DP1S164Young CAD
SA013922DP1S090Young CAD
SA013923DP1S162Young CAD
SA013924DP1S014Young CAD
SA013925DP1S006Young CAD
SA013926DP1S080Young CAD
SA013927DP1S028Young CAD
SA013928DP1S027Young CAD
SA013929DP1S030Young CAD
SA013930DP1S059Young CAD
SA013931DP1S037Young CAD
SA013932DP1S031Young CAD
SA013933DP1S174Young No-CAD
SA013934DP1S172Young No-CAD
SA013935DP1S129Young No-CAD
SA013936DP3S011Young No-CAD
SA013937DP1S140Young No-CAD
SA013938DPTotal_Pool_5Young No-CAD
SA013939DP1S113Young No-CAD
SA013940DP3S028Young No-CAD
SA013941DP3S020Young No-CAD
SA013942DP3S018Young No-CAD
SA013943DP3S015Young No-CAD
SA013944DP1S066Young No-CAD
SA013945DP1S016Young No-CAD
SA013946DP1S020Young No-CAD
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Collection:

Collection ID:CO000320
Collection Summary:-
Sample Type:plasma
Storage Conditions:-80C

Treatment:

Treatment ID:TR000340
Treatment Summary:-

Sample Preparation:

Sampleprep ID:SP000334
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

Analysis:

Analysis ID:AN000485
Analysis Type:NMR
Num Factors:6

NMR:

NMR ID:NM000061
Analysis ID:AN000485
Instrument Name:Bruker
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)
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