Summary of study ST000975

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 IDST000975
Study TitleGC6-74 metabolomics of TB vs healthy (Part 2: Serum)
Study TypeMetabolomic analysis of TB vs healthy 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:SU001014
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
SA059024MPIIB.8608case BL MAK F
SA059025MPIIB.4851case BL MAK F
SA059026MPIIB.2302case BL MAK F
SA059027MPIIB.7092case BL MAK F
SA059028MPIIB.0319case BL MAK F
SA059029MPIIB.5470case BL MAK M
SA059030MPIIB.2336case BL MAK M
SA059031MPIIB.0999case BL MAK M
SA059032MPIIB.7937case BL MAK M
SA059033MPIIB.6238case BL SUN F
SA059034MPIIB.0037case BL SUN F
SA059035MPIIB.8387case BL SUN F
SA059036MPIIB.9566case BL SUN F
SA059037MPIIB.2567case BL SUN F
SA059038MPIIB.6805case BL SUN F
SA059039MPIIB.4097case BL SUN F
SA059040MPIIB.4062case BL SUN F
SA059041MPIIB.3519case BL SUN F
SA059042MPIIB.2573case BL SUN F
SA059043MPIIB.1691case BL SUN F
SA059044MPIIB.7704case BL SUN F
SA059045MPIIB.0315case BL SUN F
SA059046MPIIB.8365case BL SUN F
SA059047MPIIB.4468case BL SUN F
SA059048MPIIB.8036case BL SUN F
SA059049MPIIB.9567case BL SUN F
SA059050MPIIB.4103case BL SUN F
SA059051MPIIB.0844case BL SUN F
SA059052MPIIB.8090case BL SUN F
SA059053MPIIB.8717case BL SUN F
SA059054MPIIB.8039case BL SUN F
SA059055MPIIB.0139case BL SUN F
SA059056MPIIB.6130case BL SUN M
SA059057MPIIB.1198case BL SUN M
SA059058MPIIB.7518case BL SUN M
SA059059MPIIB.6518case BL SUN M
SA059060MPIIB.4932case BL SUN M
SA059061MPIIB.7910case BL SUN M
SA059062MPIIB.8077case BL SUN M
SA059063MPIIB.8890case BL SUN M
SA059064MPIIB.5183case BL SUN M
SA059065MPIIB.4261case BL SUN M
SA059066MPIIB.0371case BL SUN M
SA059067MPIIB.9337case BL SUN M
SA059068MPIIB.4288case BL SUN M
SA059069MPIIB.5580case BL SUN M
SA059070MPIIB.7922case BL SUN M
SA059071MPIIB.1796case BL SUN M
SA059072MPIIB.0197case M06 SUN F
SA059073MPIIB.4272case M06 SUN F
SA059074MPIIB.1590case M06 SUN F
SA059075MPIIB.6056case M06 SUN F
SA059076MPIIB.0682case M06 SUN F
SA059077MPIIB.4041case M06 SUN F
SA059078MPIIB.1343case M06 SUN F
SA059079MPIIB.0207case M06 SUN F
SA059080MPIIB.9751case M06 SUN F
SA059081MPIIB.7467case M06 SUN F
SA059082MPIIB.2594case M06 SUN F
SA059083MPIIB.1119case M06 SUN F
SA059084MPIIB.5547case M06 SUN F
SA059085MPIIB.1585case M06 SUN M
SA059086MPIIB.0499case M06 SUN M
SA059087MPIIB.9301case M06 SUN M
SA059088MPIIB.2960case M06 SUN M
SA059089MPIIB.1144case M06 SUN M
SA059090MPIIB.7835case M06 SUN M
SA059091MPIIB.7732case M06 SUN M
SA059092MPIIB.0897case M06 SUN M
SA059093MPIIB.5911case M18 SUN F
SA059094MPIIB.6391case M18 SUN F
SA059095MPIIB.5730case M18 SUN F
SA059096MPIIB.8482case M18 SUN F
SA059097MPIIB.0304case M18 SUN F
SA059098MPIIB.4101case M18 SUN F
SA059099MPIIB.3082case M18 SUN M
SA059100MPIIB.7361case M18 SUN M
SA059101MPIIB.5221case M18 SUN M
SA059102MPIIB.2382case M18 SUN M
SA059103MPIIB.3916control BL MAK F
SA059104MPIIB.5459control BL MAK F
SA059105MPIIB.6948control BL MAK F
SA059106MPIIB.3869control BL MAK F
SA059107MPIIB.5999control BL MAK F
SA059108MPIIB.3072control BL MAK F
SA059109MPIIB.1436control BL MAK F
SA059110MPIIB.2076control BL MAK F
SA059111MPIIB.2929control BL MAK F
SA059112MPIIB.7360control BL MAK F
SA059113MPIIB.3770control BL MAK F
SA059114MPIIB.1325control BL MAK F
SA059115MPIIB.9939control BL MAK F
SA059116MPIIB.9787control BL MAK F
SA059117MPIIB.7762control BL MAK F
SA059118MPIIB.8154control BL MAK F
SA059119MPIIB.4674control BL MAK M
SA059120MPIIB.9678control BL MAK M
SA059121MPIIB.2430control BL MAK M
SA059122MPIIB.8275control BL MAK M
SA059123MPIIB.1124control BL MAK M
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Collection:

Collection ID:CO001008
Collection Summary:Collection include three different types of sample source: PLASMA, SERUM, SERUM_RMPI. In study part 2 (ID:1402) results for serum are stored.
Sample Type:Blood (serum)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001028
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP001021
Sampleprep Summary:NA

Combined analysis:

Analysis ID AN001596
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:CH001121
Instrument Name:None
Column Name:none
Chromatography Type:Unspecified

MS:

MS ID:MS001474
Analysis ID:AN001596
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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