Summary of study ST000978

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 PR000668. The data can be accessed directly via it's Project DOI: 10.21228/M8B69G This work is supported by NIH grant, U2C- DK119886.

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Study IDST000978
Study TitleMetabolomics biomarkers and the risk of overall mortality and ESRD in CKD: results from the Progredir Cohort.
Study Typeongoing cohort study
Study Summary454 CKD participants were originally recruited from the outpatient services from Hospital das Clinicas, Sao Paulo. Extensive baseline data and biobank were collected between 2012-2013 in the Clinical Research Center, Universitary Hospital, Sao Paulo. Participants are being actively followed for events of mortality, renal replacement therapy and CVD. Death certificates are obtained from State and National Registries. For the this uploaded data, events were determined up to May 2017 (median follow-up time of 3 y). Censoring data was considered as the last day of contact.
Institute
University of Sao Paulo
DepartmentClinical Research Center, Universitary Hospital, Sao Paulo University
LaboratoryLaboratory of Genetics and Molecular Cardiology, Heart Institute
Last NameTitan
First NameSilvia
Address255 Av Dr Eneas Carvalho Aguiar, Cerqueira César, Sao Paulo, Sp, Brazil, 05403-000
Emailsmotitan@gmail.com
Phone+1-413-362-4377
Submit Date2018-05-22
Total Subjects451
Study CommentsEvents are overall mortality, RRT, and a composite outcome of mortality and RRT. In addition, we also provided the variable for competitive data analysis (RRT considering the competing effect of death). Please see below for description of Study Design. Cox_mortality: death events (for Cox proportional hazard models) Cox_RRT: renal replacement therapy events (for Cox proportional hazard models) Cox_composite_deathRRT: death events AND renal replacement therapy events (for Cox proportional hazard models) Competitive_RRTvs death: death or renal replacement therapy events (for competitive risk analysis) Time_death: follow-up time for death events and censored-participants (for Cox models) Time_Cox_RRT: follow-up time for renal replacement therapy events and censored-participants (for Cox models) Time_composite_deathRRT: follow-up time for death AND renal replacement therapy and censored-participants (for Cox models) Time_competitive_TRSvsDeath: follow-up time for renal replacement therapy, death or censored-participants (for competitive analysis)
Analysis Type DetailGC-MS
Release Date2018-07-17
Release Version1
Silvia Titan Silvia Titan
https://dx.doi.org/10.21228/M8B69G
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000668
Project DOI:doi: 10.21228/M8B69G
Project Title:Metabolomics biomarkers and the risk of overall mortality and ESRD in CKD: results from the Progredir Cohort.
Project Type:Cohort Study
Project Summary:Prospective analysis on events of mortality, renal-replacement therapy and a composite outcome of both in a CKD cohort study evaluating metabolomics (untargeted GC-MS) biomakers.
Institute:University of Sao Paulo
Department:Clinical Research Center, Universitary Hospital, Sao Paulo University
Laboratory:Laboratory of Genetics and Molecular Cardiology, Heart Institute
Last Name:Titan
First Name:Silvia
Address:255 Av Dr Eneas Carvalho Aguiar, Cerqueira César, Sao Paulo, Sp, Brazil, 05403-000
Email:smotitan@gmail.com
Phone:+1-413-362-4377
Funding Source:FAPESP; CNPq, Brazilian Ministry of Health (Science and Technology Department); FINEP.

Subject:

Subject ID:SU001017
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:>30
Gender:Male and female
Human Inclusion Criteria:Patients from the Hospital das Clínicas Outpatient Clinics ≥30 years-old and with at least two measurements of creatinine (with a minimum interval of 3 months) ≥1.6 mg/dL for men and ≥1.4 mg/dL for women were considered potential candidates.
Human Exclusion Criteria:Patients attending oncology, psychiatry, urology, HIV/AIDS, viral hepatitis and glomerulonephritis services were excluded. The remaining candidates were then contacted by phone and invited to participate if no exclusion criteria were met (hospitalization or acute myocardial infarction in the last 6 months, autoimmune diseases, pregnancy, psychiatric diseases, ongoing chemo or immunosuppressive therapy, ongoing renal replacement therapy, glomerulonephritis, HIV/AIDS infection, hepatitis C and B, and any previous organ transplantation).

Factors:

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

mb_sample_id local_sample_id Cox_Mortality Cox_RRT Cox_Composite_DeathRRT Competitive_RRTvsDeath
SA059449279. . . .
SA059450141N . . .
SA059451242N . . .
SA05945247N . . .
SA059453296N . . .
SA059454357N . . .
SA059455280N N N N
SA059456281N N N N
SA059457283N N N N
SA059458286N N N N
SA059459285N N N N
SA059460284N N N N
SA059461282N N N N
SA059462276N N N N
SA059463271N N N N
SA059464268N N N N
SA059465267N N N N
SA059466265N N N N
SA059467272N N N N
SA059468273N N N N
SA059469277N N N N
SA059470287N N N N
SA059471275N N N N
SA059472274N N N N
SA059473278N N N N
SA059474289N N N N
SA059475309N N N N
SA059476308N N N N
SA059477307N N N N
SA059478306N N N N
SA059479310N N N N
SA059480312N N N N
SA059481317N N N N
SA059482316N N N N
SA059483315N N N N
SA059484314N N N N
SA059485305N N N N
SA059486304N N N N
SA059487293N N N N
SA059488292N N N N
SA059489291N N N N
SA059490263N N N N
SA059491294N N N N
SA059492295N N N N
SA059493303N N N N
SA059494302N N N N
SA059495298N N N N
SA059496297N N N N
SA059497288N N N N
SA059498261N N N N
SA059499223N N N N
SA059500222N N N N
SA059501219N N N N
SA059502218N N N N
SA059503224N N N N
SA059504225N N N N
SA059505231N N N N
SA059506229N N N N
SA0595071N N N N
SA059508227N N N N
SA059509217N N N N
SA059510216N N N N
SA059511200N N N N
SA059512199N N N N
SA059513197N N N N
SA059514196N N N N
SA059515203N N N N
SA059516205N N N N
SA059517212N N N N
SA059518211N N N N
SA059519210N N N N
SA059520206N N N N
SA059521232N N N N
SA059522233N N N N
SA059523254N N N N
SA059524251N N N N
SA059525250N N N N
SA059526249N N N N
SA059527255N N N N
SA059528256N N N N
SA059529319N N N N
SA059530260N N N N
SA059531259N N N N
SA059532258N N N N
SA059533248N N N N
SA059534247N N N N
SA059535240N N N N
SA059536237N N N N
SA059537236N N N N
SA059538235N N N N
SA059539241N N N N
SA059540243N N N N
SA059541246N N N N
SA059542245N N N N
SA059543244N N N N
SA059544262N N N N
SA059545321N N N N
SA059546399N N N N
SA059547398N N N N
SA059548397N N N N
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Collection:

Collection ID:CO001011
Collection Summary:Storage conditions: Liquid nitrogen, Time of collection: Morning fasting.
Sample Type:Blood (serum)
Collection Method:Morning - fasting
Volumeoramount Collected:0.5 ml
Storage Conditions:Described in summary
Collection Vials:Straws
Collection Tube Temp:Room temperature

Treatment:

Treatment ID:TR001031
Treatment Summary:None

Sample Preparation:

Sampleprep ID:SP001024
Sampleprep Summary:70uL os serum was thawed on ice and added 300uL of acetronile, isopropanol and water solution (3:3:2 v/v) followed by spike of 5uL of d27 myristic acid (3mg/ml) as internal standard. Samples were vortexed and centrifuged to 15800xg during 15 minutes at 4C. 320uL of supernatante were transferred to a new tube and dried in speedvac during 18 hours. Residues were suspended in 50µL methoxyamine in pyridine solution (40mg/mL), 3µL of FAME (Fatty acid methyl ester ) was added, and the mixture was vortexed for 3 min. This methoximation reaction was performed at room temperature for 16h, followed by trimethylsilylation for 1h adding 100µL MSTFA (N-methyl-N-trimethylsilyltrifluoroacetamine) with 1% TMCS (trimethylchlorosilane) (Sigma-Aldrich). After derivatization, 1µL of this derivative was used for Gas Chromatography Mass Spectrometry (GC/MS) analysis. Storage condition: Desiccator at 4 degree
Processing Method:Protein Precipitation followed by metabolite extraction
Processing Storage Conditions:On ice
Extraction Method:Acetonitrile:Isopropanol: water(3:3:2 v/v)
Extract Storage:Described in summary
Sample Resuspension:Methoxyamine in pyridine
Sample Derivatization:MSTFA + 1% TMCS
Sample Spiking:5uL of d27 Myristic Acid (3mg/mL) and FAME

Combined analysis:

Analysis ID AN001602
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890B
Column DB5-MS + 10m Duraguard capillary column (Agilent 122-5532G)
MS Type EI
MS instrument type Single quadrupole
MS instrument name Agilent 5975C
Ion Mode POSITIVE
Units peak height

Chromatography:

Chromatography ID:CH001124
Instrument Name:Agilent 7890B
Column Name:DB5-MS + 10m Duraguard capillary column (Agilent 122-5532G)
Column Temperature:60°C for 1 min, and then increased to 310°C at a rate of 10°C/min
Flow Rate:0.736ml/min
Injection Temperature:250C
Sample Injection:1uL
Analytical Time:37 minutes
Capillary Voltage:70eV
Oven Temperature:60°C for 1 min, and then increased to 310°C at a rate of 10°C/min
Weak Wash Solvent Name:Methanol
Weak Wash Volume:3x 5uL
Strong Wash Solvent Name:Isopropanol
Strong Wash Volume:3x 5uL
Sample Syringe Size:10uL
Chromatography Type:GC

MS:

MS ID:MS001480
Analysis ID:AN001602
Instrument Name:Agilent 5975C
Instrument Type:Single quadrupole
MS Type:EI
Ion Mode:POSITIVE
Helium Flow:0.736ml/min
Ionization Energy:70ev
Reagent Gas:Helium
Scan Range Moverz:50 to500m/z
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