Summary of Study ST000022

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 PR000021. The data can be accessed directly via it's Project DOI: 10.21228/M8K01J This work is supported by NIH grant, U2C- DK119886.

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Study IDST000022
Study TitleBiomarker Discovery in Knee Osteoarthritis (II)
Study TypeBiomarker Discovery in Knee Osteoarthritis
Study SummaryThis metabolomics pilot and feasibility (P & F) study was conducted to provide data to be used to gain a better understanding of metabolic alterations in people with knee osteoarthritis (OA) and to discover novel biomarkers of the disease. The goal of the metabolomics study was to determine if metabolic differences, detected by a comprehensive metabolomics analysis, can be used to distinguish people who will develop symptomatic knee OA from those who will not. For this metabolomics study, individuals participating in T1 or T1* with 5-year follow-up at T2 were selected. At T2 subjects were on average 68.1(9.12) years old with an average BMI of 31.4(7.01) with 32% men and one-third African American. All had weight-bearing posterior-anterior knee films obtained with the Synaflexer positioning device at both time points and read paired for Kellgren-Lawrence grade and minimum joint space. Urine samples (second morning void) collected from 36 overweight or obese participants in the JoCo at T1 or T1* were selected from two subgroups (a group that developed radiographic osteoarthritis (n=16) and an age, race, sex, and BMI matched group that did not develop osteoarthritis (n=20). Radiographic knee OA was defined as Kellgren-Lawrence grade 2-4 at T2 in a person with Kellgren-Lawrence grade 0 or 1 at T1 or T1*.
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 Date2014-03-04
Num Groups2
Total Subjects36
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2018-08-27
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8K01J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000021
Project DOI:doi: 10.21228/M8K01J
Project Title:Johnston County Osteoarthritis Project
Project Type:Longitudinal study
Project Summary:The Johnston County Osteoarthritis Project (JoCo) is a 20+ year ongoing, population-based, prospective cohort study of knee and hip OA designed to be representative of the civilian, non-institutionalized, African American or Caucasian population aged 45 years and older, who were residents of one of 6 townships in Johnston County NC for at least 1 year, and who were physically and mentally capable of completing the studys protocol. All participants had an initial home interview, a clinic examination with radiographs, and a subsequent second home interview. Approximately 3,200 individuals were recruited into the baseline evaluation between 1991 and 1997 (T0); the first follow up visit (T1) occurred from 1999-2004, and the second follow up visit (T2) from 2006-2010. Cohort enrichment (T1*) occurred from 2003-4, allowing new participants to be enrolled; the first follow up for these individuals was at T2. At T0, the sample was approximately 38% men and one-third African American. Between T0 and T1, radiographic knee OA, defined as Kellgren-Lawrence grade 2-4, developed in 12% of knees without knee OA at T0.
Institute:University of North Carolina at Chapel Hill
Department:Thurston Arthritis Research Center, Division of Rheumatology, Allergy, and Immunology
Laboratory:Jordan Laboratory
Last Name:Jordan
First Name:Joanne
Address:3300 Thurston Bldg., CB# 7280, Chapel Hill, NC 27599-7280
Email:wpathmasiri@rti.org
Phone:1-866-827-2762
Funding Source:Center for Disease Control (CDC)

Subject:

Subject ID:SU000039
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:Average age 68.1(9.12)
Weight Or Weight Range:Average BMI of 31.4(7.01)
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 Disease Status
SA001388E0225 Cases
SA001389E0195 Cases
SA001390E0004 Cases
SA001391E0487 Cases
SA001392F0036 Cases
SA001393C0559 Cases
SA001394F0108 Cases
SA001395D2090 Cases
SA001396E0309 Cases
SA001397C0835 Cases
SA001398C0640 Cases
SA001399D1158 Cases
SA001400D0613 Cases
SA001401C0629 Cases
SA001402D0762 Cases
SA001403D1113 Cases
SA001404D2404 Control
SA001405D2111 Control
SA001406D2079 Control
SA001407D2532 Control
SA001408D2062 Control
SA001409E0607 Control
SA001410F0035 Control
SA001411E2036 Control
SA001412D2054Control
SA001413E0546 Control
SA001414A0490 Control
SA001415C0586 Control
SA001416A2003 Control
SA001417A0233 Control
SA001418C2177 Control
SA001419D0177 Control
SA001420D0945 Control
SA001421D0909 Control
SA001422D0729 Control
SA001423D1174 Control
Showing results 1 to 36 of 36

Collection:

Collection ID:CO000022
Collection Summary:Urine samples (second morning void) collected from 36 overweight or obese participants in the JoCo at T1 or T1* were selected from two subgroups (a group that developed radiographic osteoarthritis (n=16) and an age, race, sex, and BMI matched group that did not develop osteoarthritis (n=20). Radiographic knee OA was defined as Kellgren-Lawrence grade 2-4 at T2 in a person with Kellgren-Lawrence grade 0 or 1 at T1 or T1*.
Sample Type:Urine
Storage Conditions:-80C

Treatment:

Treatment ID:TR000040

Sample Preparation:

Sampleprep ID:SP000035
Sampleprep Summary:Chenomx Internal Standard solution (70 ul) and 230 ul D20 was added to each of the 36 urine sample (400 ul), vortexed for 30s, and centrifuged at 12000 rcf for 5min. Chenomx ISTD (Chenomx, Edmonton, Alberta, Canada) contains 5mM 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS, Chemical Shift Indicator), 100 mM Imidazole (pH indicator), and 0.2% NaN3 (to inhibit bacterial growth) in D2O. 600 l aliquot of the supernatant was transferred into 5mm NMR tubes (Bruker-Biospin, Germany). Phenotypic pooled urine samples were made by combining 150 l aliquots from each of the study samples belonging to the same phenotype (cases and control). In addition, a combined phenotypic pooled sample was prepared by using 1000 l aliquot from each of the phenotypic pooled sample. Pooled NMR samples were prepared as described above and used as quality check (QC) samples.
Sampleprep Protocol Filename:Johnston_County_Procedure_March_4_2014.docx
Processing Method:Dilution using a mixture of D2O and Chenomx ISTD
Processing Storage Conditions:On ice
Extraction Method:None

Analysis:

Analysis ID:AN000041
Laboratory Name:RTI, DHMRI
Analysis Type:NMR
Acquisition Date:41527
Software Version:TopSpin 3.0
Operator Name:Wimal Pathmasiri, Kevin Knagge
Randomization Order:Yes
Detector Type:NMR
Data Format:Bruker
Chromatography ID:CH000023
Num Factors:2

NMR:

NMR ID:NM000007
Analysis ID:AN000041
Instrument Name:Bruker Avance III
Instrument Type:FT-NMR
NMR Experiment Type:1D 1H
Field Frequency Lock:Deuterium
Standard Concentration:0.5mm
Spectrometer Frequency:950 MHz
NMR Probe:5mm, Inverse ATMA
NMR Solvent:D2O
NMR Tube Size:5mm, 7 inch
Shimming Method:Topshim
Pulse Sequence:noesypr1d
Water Suppression:presat
Pulse Width:13.07 us
Power Level:12.589w
Receiver Gain:4
Offset Frequency:4468.31
Chemical Shift Ref Cpd:DSS
Temperature:298 K
Number Of Scans:64
Dummy Scans:4
Acquisition Time:1.7301503 s
Relaxation Delay:2 s
Spectral Width:18939.395 Hz, 19.93 ppm
Num Data Points Acquired:65536
Real Data Points:65536
Line Broadening:0.5
Zero Filling:Yes
Apodization:Lorentzian
Baseline Correction Method:Polynomial
Chemical Shift Ref Std:DSS
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