Summary of study ST000976

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 PR000666. The data can be accessed directly via it's Project DOI: 10.21228/M8KQ3J This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST000976
Study TitleGC6-74 matabolomic of TB (Part 3: Plasma_RPMI)
Study TypeMetabolomic analysis of TB vs heathy including time to TB.
Study SummaryWithin the GC6-74 cohorts, 4,462 HIV-negative healthy household contacts of 1,098 index TB cases were recruited from 2006 to 2012 at four African sites included in this study i.e. SUN (Stellenbosch University, South Africa), MRC (Medical Research Council Unit, The Gambia), AHRI (Armauer Hansen Research Institute, Ethiopia) and MAK (Makerere University, Uganda). The study had an exclusion period of 3 months, such that participants, who were diagnosed with active TB within 3 months of enrolment, were excluded from analysis to prevent inclusion of participants who had incipient or asymptomatic clinical TB disease at enrolment. Additional exclusion criteria were positive HIV rapid test, current or previous anti-retroviral treatment, history of TB, pregnancy, participation in drug and/or vaccine clinical trials and chronic disease diagnosis or immunosuppressive therapy within the past 6 months, and living in the study area for less than 3 months. A total of 97 individuals who developed active TB within the two year follow-up period were included in this study and matched at a ratio of 1:4 with participants who remained healthy during the 2-year follow-up period (controls); matching, by site, age class, sex, and wherever possible year of recruitment. Initial samples collected upon enrolment were termed baseline (BL) samples. Further samples were taken 6 and 18 months post-exposure, provided that the participant had remained TB free at the time of sample collection. Metabolic profiling was carried out for each study site, using either serum or plasma samples. For a small number of samples, an insufficient amount of plasma was available, so the sample was diluted using RPMI buffer.
Institute
Max Planck Institute for Infection Biology
DepartmentImmunology
Last NameKaufmann
First NameStefan
AddressCharitéplatz 1,10117 Berlin, Berlin, Deutschland
Emailkaufmann@mpiib-berlin.mpg.de
Phone+49 30 28460-500
Submit Date2018-05-15
Analysis Type DetailLC-MS
Release Date2018-11-05
Release Version1
Stefan Kaufmann Stefan Kaufmann
https://dx.doi.org/10.21228/M8KQ3J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000666
Project DOI:doi: 10.21228/M8KQ3J
Project Title:GC6-74 matabolomic of tuberculosis.
Project Type:Metabolomic analysis of TB vs heathy including time to TB.
Project Summary:Within the GC6-74 cohorts, 4,462 HIV-negative healthy household contacts of 1,098 index TB cases were recruited from 2006 to 2012 at four African sites included in this study i.e. SUN (Stellenbosch University, South Africa), MRC (Medical Research Council Unit, The Gambia), AHRI (Armauer Hansen Research Institute, Ethiopia) and MAK (Makerere University, Uganda). The study had an exclusion period of 3 months, such that participants, who were diagnosed with active TB within 3 months of enrolment, were excluded from analysis to prevent inclusion of participants who had incipient or asymptomatic clinical TB disease at enrolment. Additional exclusion criteria were positive HIV rapid test, current or previous anti-retroviral treatment, history of TB, pregnancy, participation in drug and/or vaccine clinical trials and chronic disease diagnosis or immunosuppressive therapy within the past 6 months, and living in the study area for less than 3 months. A total of 97 individuals who developed active TB within the two year follow-up period were included in this study and matched at a ratio of 1:4 with participants who remained healthy during the 2-year follow-up period (controls); matching, by site, age class, sex, and wherever possible year of recruitment. Initial samples collected upon enrolment were termed baseline (BL) samples. Further samples were taken 6 and 18 months post-exposure, provided that the participant had remained TB free at the time of sample collection. Metabolic profiling was carried out for each study site, using either serum or plasma samples. For a small number of samples, an insufficient amount of plasma was available, so the sample was diluted using RPMI buffer.
Institute:Max Planck Institute for Infection Biology
Department:Immunology
Last Name:Kaufmann
First Name:Stefan
Address:Charitéplatz 1,10117 Berlin, Berlin, Deutschland
Email:kaufmann@mpiib-berlin.mpg.de
Phone:+49 30 28460-500
Funding Source:Bill & Melinda Gates Foundation Grand Challenges in Global Health Program (BMGF GC6-74,#37772 and GC6-2013, OPP1055806)

Subject:

Subject ID:SU001015
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:8-60
Gender:Male and female
Human Smoking Status:YES

Factors:

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

mb_sample_id local_sample_id GROUP TIMEPOINT REGION GENDER
SA059364MPIIB.7138case BL MAK F
SA059365MPIIB.2949case BL MAK F
SA059366MPIIB.7424case BL MAK M
SA059367MPIIB.4132case BL MAK M
SA059368MPIIB.3660case BL MAK M
SA059369MPIIB.2072case BL MAK M
SA059370MPIIB.3365case BL MAK M
SA059371MPIIB.4138case M06 MAK F
SA059372MPIIB.0898case M06 MAK M
SA059373MPIIB.9763case M06 MAK M
SA059374MPIIB.7717control BL MAK F
SA059375MPIIB.2304control BL MAK F
SA059376MPIIB.2872control BL MAK F
SA059377MPIIB.4755control BL MAK F
SA059378MPIIB.3319control BL MAK F
SA059379MPIIB.3768control BL MAK F
SA059380MPIIB.2902control BL MAK M
SA059381MPIIB.2981control BL MAK M
SA059382MPIIB.3772control BL MAK M
SA059383MPIIB.7816control BL MAK M
SA059384MPIIB.9322control BL MAK M
SA059385MPIIB.9798control BL MAK M
SA059386MPIIB.8308control BL MAK M
SA059387MPIIB.6606control BL MAK M
SA059388MPIIB.5431control BL MAK M
SA059389MPIIB.6114control BL MAK M
SA059390MPIIB.5074control BL MAK M
SA059391MPIIB.8510control BL MAK M
SA059392MPIIB.0560control BL MAK M
SA059393MPIIB.7468control BL MAK M
SA059394MPIIB.4380control BL MAK M
SA059395MPIIB.6037control BL MAK M
SA059396MPIIB.5969control BL MAK M
SA059397MPIIB.8814control BL MAK M
SA059398MPIIB.7374control BL MAK M
SA059399MPIIB.4312control M06 MAK F
SA059400MPIIB.0523control M06 MAK F
SA059401MPIIB.4981control M06 MAK F
SA059402MPIIB.9818control M06 MAK F
SA059403MPIIB.4243control M06 MAK M
SA059404MPIIB.7049control M06 MAK M
SA059405MPIIB.8512control M06 MAK M
SA059406MPIIB.0240control M06 MAK M
SA059407MPIIB.3787control M06 MAK M
SA059408MPIIB.6068control M06 MAK M
Showing results 1 to 45 of 45

Collection:

Collection ID:CO001009
Collection Summary:Collection include three different types of sample source: PLASMA, SERUM, SERUM_RMPI. In study part 2 (ID:1403) results for serum_rmpi are stored.
Sample Type:Blood (serum)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001029
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP001022
Sampleprep Summary:NA

Combined analysis:

Analysis ID AN001597
Analysis type MS
Chromatography type Unspecified
Chromatography system None
Column none
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units scaled units

Chromatography:

Chromatography ID:CH001122
Instrument Name:None
Column Name:none
Chromatography Type:Unspecified

MS:

MS ID:MS001475
Analysis ID:AN001597
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The formulas were provided by Metabolon, Inc. who did the compound identification. The asterisks indicate the level of certainty about compound identification from mass spectroscopy: * indicates that a compound that has not been confirmed based on a standard, but we are confident in its identity; ** implies that a compound for which a standard is not available, but we are reasonably confident in its identity or the information provided. Basically, there is no standard available to confirm its identity.
Ion Mode:UNSPECIFIED
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