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.
| Study ID | ST000975 |
| Study Title | GC6-74 metabolomics of TB vs healthy (Part 2: Serum) |
| Study Type | Metabolomic analysis of TB vs healthy including time to TB. |
| Study 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 |
| kaufmann@mpiib-berlin.mpg.de | |
| Phone | +49 30 28460-500 |
| Submit Date | 2018-05-15 |
| Analysis Type Detail | LC-MS |
| Release Date | 2018-11-05 |
| Release Version | 1 |
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 |
|---|---|---|---|---|---|
| SA059024 | MPIIB.8608 | case | BL | MAK | F |
| SA059025 | MPIIB.4851 | case | BL | MAK | F |
| SA059026 | MPIIB.2302 | case | BL | MAK | F |
| SA059027 | MPIIB.7092 | case | BL | MAK | F |
| SA059028 | MPIIB.0319 | case | BL | MAK | F |
| SA059029 | MPIIB.5470 | case | BL | MAK | M |
| SA059030 | MPIIB.2336 | case | BL | MAK | M |
| SA059031 | MPIIB.0999 | case | BL | MAK | M |
| SA059032 | MPIIB.7937 | case | BL | MAK | M |
| SA059033 | MPIIB.6238 | case | BL | SUN | F |
| SA059034 | MPIIB.0037 | case | BL | SUN | F |
| SA059035 | MPIIB.8387 | case | BL | SUN | F |
| SA059036 | MPIIB.9566 | case | BL | SUN | F |
| SA059037 | MPIIB.2567 | case | BL | SUN | F |
| SA059038 | MPIIB.6805 | case | BL | SUN | F |
| SA059039 | MPIIB.4097 | case | BL | SUN | F |
| SA059040 | MPIIB.4062 | case | BL | SUN | F |
| SA059041 | MPIIB.3519 | case | BL | SUN | F |
| SA059042 | MPIIB.2573 | case | BL | SUN | F |
| SA059043 | MPIIB.1691 | case | BL | SUN | F |
| SA059044 | MPIIB.7704 | case | BL | SUN | F |
| SA059045 | MPIIB.0315 | case | BL | SUN | F |
| SA059046 | MPIIB.8365 | case | BL | SUN | F |
| SA059047 | MPIIB.4468 | case | BL | SUN | F |
| SA059048 | MPIIB.8036 | case | BL | SUN | F |
| SA059049 | MPIIB.9567 | case | BL | SUN | F |
| SA059050 | MPIIB.4103 | case | BL | SUN | F |
| SA059051 | MPIIB.0844 | case | BL | SUN | F |
| SA059052 | MPIIB.8090 | case | BL | SUN | F |
| SA059053 | MPIIB.8717 | case | BL | SUN | F |
| SA059054 | MPIIB.8039 | case | BL | SUN | F |
| SA059055 | MPIIB.0139 | case | BL | SUN | F |
| SA059056 | MPIIB.6130 | case | BL | SUN | M |
| SA059057 | MPIIB.1198 | case | BL | SUN | M |
| SA059058 | MPIIB.7518 | case | BL | SUN | M |
| SA059059 | MPIIB.6518 | case | BL | SUN | M |
| SA059060 | MPIIB.4932 | case | BL | SUN | M |
| SA059061 | MPIIB.7910 | case | BL | SUN | M |
| SA059062 | MPIIB.8077 | case | BL | SUN | M |
| SA059063 | MPIIB.8890 | case | BL | SUN | M |
| SA059064 | MPIIB.5183 | case | BL | SUN | M |
| SA059065 | MPIIB.4261 | case | BL | SUN | M |
| SA059066 | MPIIB.0371 | case | BL | SUN | M |
| SA059067 | MPIIB.9337 | case | BL | SUN | M |
| SA059068 | MPIIB.4288 | case | BL | SUN | M |
| SA059069 | MPIIB.5580 | case | BL | SUN | M |
| SA059070 | MPIIB.7922 | case | BL | SUN | M |
| SA059071 | MPIIB.1796 | case | BL | SUN | M |
| SA059072 | MPIIB.0197 | case | M06 | SUN | F |
| SA059073 | MPIIB.4272 | case | M06 | SUN | F |
| SA059074 | MPIIB.1590 | case | M06 | SUN | F |
| SA059075 | MPIIB.6056 | case | M06 | SUN | F |
| SA059076 | MPIIB.0682 | case | M06 | SUN | F |
| SA059077 | MPIIB.4041 | case | M06 | SUN | F |
| SA059078 | MPIIB.1343 | case | M06 | SUN | F |
| SA059079 | MPIIB.0207 | case | M06 | SUN | F |
| SA059080 | MPIIB.9751 | case | M06 | SUN | F |
| SA059081 | MPIIB.7467 | case | M06 | SUN | F |
| SA059082 | MPIIB.2594 | case | M06 | SUN | F |
| SA059083 | MPIIB.1119 | case | M06 | SUN | F |
| SA059084 | MPIIB.5547 | case | M06 | SUN | F |
| SA059085 | MPIIB.1585 | case | M06 | SUN | M |
| SA059086 | MPIIB.0499 | case | M06 | SUN | M |
| SA059087 | MPIIB.9301 | case | M06 | SUN | M |
| SA059088 | MPIIB.2960 | case | M06 | SUN | M |
| SA059089 | MPIIB.1144 | case | M06 | SUN | M |
| SA059090 | MPIIB.7835 | case | M06 | SUN | M |
| SA059091 | MPIIB.7732 | case | M06 | SUN | M |
| SA059092 | MPIIB.0897 | case | M06 | SUN | M |
| SA059093 | MPIIB.5911 | case | M18 | SUN | F |
| SA059094 | MPIIB.6391 | case | M18 | SUN | F |
| SA059095 | MPIIB.5730 | case | M18 | SUN | F |
| SA059096 | MPIIB.8482 | case | M18 | SUN | F |
| SA059097 | MPIIB.0304 | case | M18 | SUN | F |
| SA059098 | MPIIB.4101 | case | M18 | SUN | F |
| SA059099 | MPIIB.3082 | case | M18 | SUN | M |
| SA059100 | MPIIB.7361 | case | M18 | SUN | M |
| SA059101 | MPIIB.5221 | case | M18 | SUN | M |
| SA059102 | MPIIB.2382 | case | M18 | SUN | M |
| SA059103 | MPIIB.3916 | control | BL | MAK | F |
| SA059104 | MPIIB.5459 | control | BL | MAK | F |
| SA059105 | MPIIB.6948 | control | BL | MAK | F |
| SA059106 | MPIIB.3869 | control | BL | MAK | F |
| SA059107 | MPIIB.5999 | control | BL | MAK | F |
| SA059108 | MPIIB.3072 | control | BL | MAK | F |
| SA059109 | MPIIB.1436 | control | BL | MAK | F |
| SA059110 | MPIIB.2076 | control | BL | MAK | F |
| SA059111 | MPIIB.2929 | control | BL | MAK | F |
| SA059112 | MPIIB.7360 | control | BL | MAK | F |
| SA059113 | MPIIB.3770 | control | BL | MAK | F |
| SA059114 | MPIIB.1325 | control | BL | MAK | F |
| SA059115 | MPIIB.9939 | control | BL | MAK | F |
| SA059116 | MPIIB.9787 | control | BL | MAK | F |
| SA059117 | MPIIB.7762 | control | BL | MAK | F |
| SA059118 | MPIIB.8154 | control | BL | MAK | F |
| SA059119 | MPIIB.4674 | control | BL | MAK | M |
| SA059120 | MPIIB.9678 | control | BL | MAK | M |
| SA059121 | MPIIB.2430 | control | BL | MAK | M |
| SA059122 | MPIIB.8275 | control | BL | MAK | M |
| SA059123 | MPIIB.1124 | control | BL | MAK | M |
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 |
