Summary of study ST000974

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 IDST000974
Study TitleGC6-74 matabolomic of TB (Part 1: Plasma)
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 Date2018-05-04
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:SU001013
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
SA058658MPIIB.4622case BL AHRI F
SA058659MPIIB.9335case BL AHRI F
SA058660MPIIB.2102case BL AHRI F
SA058661MPIIB.2425case BL AHRI F
SA058662MPIIB.8032case BL AHRI F
SA058663MPIIB.9274case BL AHRI F
SA058664MPIIB.3511case BL AHRI F
SA058665MPIIB.2003case BL AHRI M
SA058666MPIIB.9204case BL AHRI M
SA058667MPIIB.1512case BL AHRI M
SA058668MPIIB.4615case BL AHRI M
SA058669MPIIB.4924case BL MRC F
SA058670MPIIB.9617case BL MRC F
SA058671MPIIB.4562case BL MRC F
SA058672MPIIB.7245case BL MRC F
SA058673MPIIB.8728case BL MRC F
SA058674MPIIB.5965case BL MRC F
SA058675MPIIB.8760case BL MRC F
SA058676MPIIB.6456case BL MRC F
SA058677MPIIB.7600case BL MRC F
SA058678MPIIB.1840case BL MRC F
SA058679MPIIB.4523case BL MRC F
SA058680MPIIB.6236case BL MRC F
SA058681MPIIB.7569case BL MRC F
SA058682MPIIB.9479case BL MRC F
SA058683MPIIB.8196case BL MRC F
SA058684MPIIB.3741case BL MRC F
SA058685MPIIB.2677case BL MRC F
SA058686MPIIB.4719case BL MRC F
SA058687MPIIB.2916case BL MRC F
SA058688MPIIB.4869case BL MRC M
SA058689MPIIB.3967case BL MRC M
SA058690MPIIB.9357case BL MRC M
SA058691MPIIB.9278case BL MRC M
SA058692MPIIB.9227case BL MRC M
SA058693MPIIB.3274case BL MRC M
SA058694MPIIB.4458case BL MRC M
SA058695MPIIB.2288case BL MRC M
SA058696MPIIB.8968case BL MRC M
SA058697MPIIB.1514case BL MRC M
SA058698MPIIB.1415case BL MRC M
SA058699MPIIB.6436case BL MRC M
SA058700MPIIB.9046case BL MRC M
SA058701MPIIB.3625case BL MRC M
SA058702MPIIB.9655case BL MRC M
SA058703MPIIB.5094case BL SUN F
SA058704MPIIB.2389case BL SUN F
SA058705MPIIB.6451case BL SUN F
SA058706MPIIB.7324case BL SUN F
SA058707MPIIB.0316case BL SUN F
SA058708MPIIB.1327case BL SUN F
SA058709MPIIB.4227case BL SUN F
SA058710MPIIB.3267case BL SUN M
SA058711MPIIB.9690case BL SUN M
SA058712MPIIB.3626case BL SUN M
SA058713MPIIB.8928case BL SUN M
SA058714MPIIB.8613case M06 AHRI F
SA058715MPIIB.1844case M06 AHRI F
SA058716MPIIB.0829case M06 AHRI F
SA058717MPIIB.8120case M06 AHRI F
SA058718MPIIB.8620case M06 AHRI F
SA058719MPIIB.7831case M06 AHRI M
SA058720MPIIB.5900case M06 AHRI M
SA058721MPIIB.2508case M06 MRC F
SA058722MPIIB.2726case M06 MRC F
SA058723MPIIB.3897case M06 MRC F
SA058724MPIIB.8570case M06 MRC F
SA058725MPIIB.0146case M06 MRC F
SA058726MPIIB.2388case M06 MRC F
SA058727MPIIB.5857case M06 MRC F
SA058728MPIIB.9583case M06 MRC F
SA058729MPIIB.1022case M06 MRC F
SA058730MPIIB.1548case M06 MRC F
SA058731MPIIB.8376case M06 MRC F
SA058732MPIIB.9608case M06 MRC M
SA058733MPIIB.6090case M06 MRC M
SA058734MPIIB.4094case M06 MRC M
SA058735MPIIB.1253case M06 MRC M
SA058736MPIIB.3331case M06 MRC M
SA058737MPIIB.5715case M06 MRC M
SA058738MPIIB.8581case M06 MRC M
SA058739MPIIB.1897case M06 MRC M
SA058740MPIIB.5872case M18 AHRI M
SA058741MPIIB.2491case M18 AHRI M
SA058742MPIIB.1016case M18 MRC F
SA058743MPIIB.6652case M18 MRC F
SA058744MPIIB.6281case M18 MRC F
SA058745MPIIB.0644case M18 MRC M
SA058746MPIIB.9882case M18 MRC M
SA058747MPIIB.7834case M18 MRC M
SA058748MPIIB.4277case M18 MRC M
SA058749MPIIB.1502case M18 MRC M
SA058750MPIIB.9129control BL AHRI F
SA058751MPIIB.4420control BL AHRI F
SA058752MPIIB.1881control BL AHRI F
SA058753MPIIB.0136control BL AHRI F
SA058754MPIIB.4670control BL AHRI F
SA058755MPIIB.4027control BL AHRI F
SA058756MPIIB.5539control BL AHRI F
SA058757MPIIB.8823control BL AHRI F
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Collection:

Collection ID:CO001007
Collection Summary:Whol study collection include three different types of sample source: PLASMA, SERUM, SERUM_RMPI. In study part 1 (ID:1398) results for plasma are stored.
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001027
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP001020
Sampleprep Summary:NA

Combined analysis:

Analysis ID AN001595
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:CH001120
Instrument Name:None
Column Name:none
Chromatography Type:Unspecified

MS:

MS ID:MS001473
Analysis ID:AN001595
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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