Summary of Study ST001443
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 PR000907. The data can be accessed directly via it's Project DOI: 10.21228/M8FQ2X 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 | ST001443 |
| Study Title | Plasma metabolomic signatures of COPD |
| Study Summary | The NIH sponsored multicenter Genetic Epidemiology of COPD (COPDGene (ClinicalTrials.gov Identifier: NCT01969344) study was approved and reviewed by the institutional review board at all participating centers (1). All study participants provided written informed consent. This study enrolled 10,198 non-Hispanic white (NHW) and African American (AA) individuals from January 2008 until April 2011 (Phase 1) who were aged 45-80 with ≥10 pack-year smoking history and no exacerbations for >30 days. In addition, 465 age and gender matched healthy individuals with no history of smoking were enrolled as controls (mostly at Phase 2). From July 2013 to July 2017, 5,697 subjects returned for an in-person 5-year visit. Each in-person visit included spirometry before and after albuterol, quantitative CT imaging of the chest, and blood sampling. From two clinical centers (National Jewish Health and University of Iowa) 162 subjects at Phase 1 (all NHW) and 1,136 subjects (1,040 NHW, 96 AA) participated in an ancillary study in which they provided fresh frozen plasma collected using an 8.5 ml p100 tube (Becton Dickinson) at Phase 2. |
| Institute | National Jewish Health |
| Department | Division of Pulmonary Medicine |
| Laboratory | Bowler |
| Last Name | Bowler |
| First Name | Russell |
| Address | 1400 Jackson St. Denver, CO 80206 |
| bowlerr@njhealth.org | |
| Phone | 3032702014 |
| Submit Date | 2020-03-19 |
| Total Subjects | 162 at Phase 1, 1,136 at Phase 2 |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-09-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000907 |
| Project DOI: | doi: 10.21228/M8FQ2X |
| Project Title: | Plasma metabolomic signatures of COPD |
| Institute: | National Jewish Health |
| Department: | Division of Pulmonary Medicine |
| Last Name: | Bowler |
| First Name: | Russell |
| Address: | 1400 Jackson St. Denver, CO 80206 |
| Email: | bowlerr@njhealth.org |
| Phone: | 303 270 2014 |
| Funding Source: | NHLBI R21 HL140376, R01HL129937, R01HL 095432, R01 HL089856, R01 HL089897); and UL1 RR025680 from NCRR/HIH |
Subject:
| Subject ID: | SU001517 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Phase_study | gender | smoking_status |
|---|---|---|---|---|
| SA122414 | NJHC-01194 | 1 | F | never smoker |
| SA122415 | NJHC-01193 | 1 | F | never smoker |
| SA122416 | NJHC-01191 | 1 | F | never smoker |
| SA122417 | NJHC-01195 | 1 | F | never smoker |
| SA122418 | NJHC-01192 | 1 | F | never smoker |
| SA122419 | NJHC-01196 | 1 | F | never smoker |
| SA122420 | NJHC-01199 | 1 | F | never smoker |
| SA122421 | NJHC-01198 | 1 | F | never smoker |
| SA122422 | NJHC-01197 | 1 | F | never smoker |
| SA122423 | NJHC-01190 | 1 | F | never smoker |
| SA122424 | NJHC-01189 | 1 | F | never smoker |
| SA122425 | NJHC-01183 | 1 | F | never smoker |
| SA122426 | NJHC-01182 | 1 | F | never smoker |
| SA122427 | NJHC-01181 | 1 | F | never smoker |
| SA122428 | NJHC-01184 | 1 | F | never smoker |
| SA122429 | NJHC-01185 | 1 | F | never smoker |
| SA122430 | NJHC-01188 | 1 | F | never smoker |
| SA122431 | NJHC-01187 | 1 | F | never smoker |
| SA122432 | NJHC-01186 | 1 | F | never smoker |
| SA122433 | NJHC-01200 | 1 | F | never smoker |
| SA122434 | NJHC-01201 | 1 | F | never smoker |
| SA122435 | NJHC-01214 | 1 | F | never smoker |
| SA122436 | NJHC-01213 | 1 | F | never smoker |
| SA122437 | NJHC-01212 | 1 | F | never smoker |
| SA122438 | NJHC-01215 | 1 | F | never smoker |
| SA122439 | NJHC-01216 | 1 | F | never smoker |
| SA122440 | NJHC-01219 | 1 | F | never smoker |
| SA122441 | NJHC-01218 | 1 | F | never smoker |
| SA122442 | NJHC-01217 | 1 | F | never smoker |
| SA122443 | NJHC-01211 | 1 | F | never smoker |
| SA122444 | NJHC-01210 | 1 | F | never smoker |
| SA122445 | NJHC-01204 | 1 | F | never smoker |
| SA122446 | NJHC-01203 | 1 | F | never smoker |
| SA122447 | NJHC-01202 | 1 | F | never smoker |
| SA122448 | NJHC-01205 | 1 | F | never smoker |
| SA122449 | NJHC-01206 | 1 | F | never smoker |
| SA122450 | NJHC-01209 | 1 | F | never smoker |
| SA122451 | NJHC-01208 | 1 | F | never smoker |
| SA122452 | NJHC-01207 | 1 | F | never smoker |
| SA122453 | NJHC-01180 | 1 | F | never smoker |
| SA122454 | NJHC-01178 | 1 | F | never smoker |
| SA122455 | NJHC-01152 | 1 | F | never smoker |
| SA122456 | NJHC-01151 | 1 | F | never smoker |
| SA122457 | NJHC-01150 | 1 | F | never smoker |
| SA122458 | NJHC-01149 | 1 | F | never smoker |
| SA122459 | NJHC-01153 | 1 | F | never smoker |
| SA122460 | NJHC-01154 | 1 | F | never smoker |
| SA122461 | NJHC-01157 | 1 | F | never smoker |
| SA122462 | NJHC-01156 | 1 | F | never smoker |
| SA122463 | NJHC-01155 | 1 | F | never smoker |
| SA122464 | NJHC-01148 | 1 | F | never smoker |
| SA122465 | NJHC-01147 | 1 | F | never smoker |
| SA122466 | NJHC-01141 | 1 | F | never smoker |
| SA122467 | NJHC-01140 | 1 | F | never smoker |
| SA122468 | NJHC-01139 | 1 | F | never smoker |
| SA122469 | NJHC-01142 | 1 | F | never smoker |
| SA122470 | NJHC-01143 | 1 | F | never smoker |
| SA122471 | NJHC-01146 | 1 | F | never smoker |
| SA122472 | NJHC-01145 | 1 | F | never smoker |
| SA122473 | NJHC-01144 | 1 | F | never smoker |
| SA122474 | NJHC-01158 | 1 | F | never smoker |
| SA122475 | NJHC-01159 | 1 | F | never smoker |
| SA122476 | NJHC-01173 | 1 | F | never smoker |
| SA122477 | NJHC-01172 | 1 | F | never smoker |
| SA122478 | NJHC-01171 | 1 | F | never smoker |
| SA122479 | NJHC-01174 | 1 | F | never smoker |
| SA122480 | NJHC-01175 | 1 | F | never smoker |
| SA122481 | NJHC-01220 | 1 | F | never smoker |
| SA122482 | NJHC-01177 | 1 | F | never smoker |
| SA122483 | NJHC-01176 | 1 | F | never smoker |
| SA122484 | NJHC-01170 | 1 | F | never smoker |
| SA122485 | NJHC-01169 | 1 | F | never smoker |
| SA122486 | NJHC-01163 | 1 | F | never smoker |
| SA122487 | NJHC-01162 | 1 | F | never smoker |
| SA122488 | NJHC-01160 | 1 | F | never smoker |
| SA122489 | NJHC-01164 | 1 | F | never smoker |
| SA122490 | NJHC-01165 | 1 | F | never smoker |
| SA122491 | NJHC-01168 | 1 | F | never smoker |
| SA122492 | NJHC-01167 | 1 | F | never smoker |
| SA122493 | NJHC-01166 | 1 | F | never smoker |
| SA122494 | NJHC-01179 | 1 | F | never smoker |
| SA122495 | NJHC-01161 | 1 | F | never smoker |
| SA122496 | NJHC-01275 | 1 | F | never smoker |
| SA122497 | NJHC-01274 | 1 | F | never smoker |
| SA122498 | NJHC-01273 | 1 | F | never smoker |
| SA122499 | NJHC-01272 | 1 | F | never smoker |
| SA122500 | NJHC-01276 | 1 | F | never smoker |
| SA122501 | NJHC-01277 | 1 | F | never smoker |
| SA122502 | NJHC-01280 | 1 | F | never smoker |
| SA122503 | NJHC-01279 | 1 | F | never smoker |
| SA122504 | NJHC-01278 | 1 | F | never smoker |
| SA122505 | NJHC-01271 | 1 | F | never smoker |
| SA122506 | NJHC-01270 | 1 | F | never smoker |
| SA122507 | NJHC-01264 | 1 | F | never smoker |
| SA122508 | NJHC-01263 | 1 | F | never smoker |
| SA122509 | NJHC-01262 | 1 | F | never smoker |
| SA122510 | NJHC-01265 | 1 | F | never smoker |
| SA122511 | NJHC-01266 | 1 | F | never smoker |
| SA122512 | NJHC-01269 | 1 | F | never smoker |
| SA122513 | NJHC-01268 | 1 | F | never smoker |
Collection:
| Collection ID: | CO001512 |
| Collection Summary: | The NIH sponsored multicenter Genetic Epidemiology of COPD (COPDGene (ClinicalTrials.gov Identifier: NCT01969344) study was approved and reviewed by the institutional review board at all participating centers (1). All study participants provided written informed consent. This study enrolled 10,198 non-Hispanic white (NHW) and African American (AA) individuals from January 2008 until April 2011 (Phase 1) who were aged 45-80 with ≥10 pack-year smoking history and no exacerbations for >30 days. In addition, 465 age and gender matched healthy individuals with no history of smoking were enrolled as controls (mostly at Phase 2). From July 2013 to July 2017, 5,697 subjects returned for an in-person 5-year visit. Each in-person visit included spirometry before and after albuterol, quantitative CT imaging of the chest, and blood sampling. From two clinical centers (National Jewish Health and University of Iowa) 162 subjects at Phase 1 (all NHW) and 1,136 subjects (1,040 NHW, 96 AA) participated in an ancillary study in which they provided fresh frozen plasma collected using an 8.5 ml p100 tube (Becton Dickinson) at Phase 2. |
| Sample Type: | Blood (plasma) |
Treatment:
| Treatment ID: | TR001532 |
| Treatment Summary: | The NIH sponsored multicenter Genetic Epidemiology of COPD (COPDGene (ClinicalTrials.gov Identifier: NCT01969344) study was approved and reviewed by the institutional review board at all participating centers (1). All study participants provided written informed consent. This study enrolled 10,198 non-Hispanic white (NHW) and African American (AA) individuals from January 2008 until April 2011 (Phase 1) who were aged 45-80 with ≥10 pack-year smoking history and no exacerbations for >30 days. In addition, 465 age and gender matched healthy individuals with no history of smoking were enrolled as controls (mostly at Phase 2). From July 2013 to July 2017, 5,697 subjects returned for an in-person 5-year visit. Each in-person visit included spirometry before and after albuterol, quantitative CT imaging of the chest, and blood sampling. |
Sample Preparation:
| Sampleprep ID: | SP001525 |
| Sampleprep Summary: | P100 plasma was profiled using the Metabolon (Durham, USA) Global Metabolomics Platform, as described (2-4). Briefly, samples were extracted with methanol under vigorous shaking for two minutes (Glen Mills GenoGrinder 2000) followed by centrifugation to remove protein, dissociate small molecules bound to protein or trapped in the precipitated protein matrix, and to recover chemically diverse metabolites. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase/ultrahigh performance liquid chromatography/tandem mass spectrometry (RP/UPLC-MS/MS) methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by hydrophilic interaction chromatography (HILIC)/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup. |
Combined analysis:
| Analysis ID | AN002411 | AN002412 | AN002413 | AN002414 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | Reversed phase | HILIC |
| Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity | Waters Acquity |
| Column | Waters Acquity BEH C18 (100 x 2mm,1.7um) | Waters Acquity BEH C18 (100 x 2mm,1.7um) | Waters Acquity BEH C18 (100 x 2mm,1.7um) | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo LTQ | Thermo LTQ | Thermo LTQ | Thermo LTQ |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE |
| Units | AU | AU | AU | AU |
Chromatography:
| Chromatography ID: | CH001772 |
| Chromatography Summary: | Low pH polar |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm,1.7um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001773 |
| Chromatography Summary: | Low pH Lipophilic |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm,1.7um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001774 |
| Chromatography Summary: | High pH |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm,1.7um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001775 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS002252 |
| Analysis ID: | AN002411 |
| Instrument Name: | Thermo LTQ |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Proprietary analytical software for integration and peak picking |
| Ion Mode: | POSITIVE |
| MS ID: | MS002253 |
| Analysis ID: | AN002412 |
| Instrument Name: | Thermo LTQ |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Proprietary analytical software for integration and peak picking |
| Ion Mode: | POSITIVE |
| MS ID: | MS002254 |
| Analysis ID: | AN002413 |
| Instrument Name: | Thermo LTQ |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Proprietary analytical software for integration and peak picking |
| Ion Mode: | NEGATIVE |
| MS ID: | MS002255 |
| Analysis ID: | AN002414 |
| Instrument Name: | Thermo LTQ |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Proprietary analytical software for integration and peak picking |
| Ion Mode: | NEGATIVE |
