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MB Sample ID: SA305934
| Local Sample ID: | NATS-00492 |
| Subject ID: | SU002938 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 35 - 69 |
| Gender: | Male and female |
| Human Race: | Black, White, Other |
| Human Ethnicity: | Hispanic, Non-Hispanic |
| Human Smoking Status: | Yes or No |
| Human Inclusion Criteria: | positive COVID-19 diagnosis and plasma sample available |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002938 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 35 - 69 |
| Gender: | Male and female |
| Human Race: | Black, White, Other |
| Human Ethnicity: | Hispanic, Non-Hispanic |
| Human Smoking Status: | Yes or No |
| Human Inclusion Criteria: | positive COVID-19 diagnosis and plasma sample available |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| NATS-00492 | SA305934 | FL036743 | Female | Sex |
| NATS-00492 | SA305934 | FL036743 | 0 | Severity_Scale |
| NATS-00492 | SA305934 | FL036743 | Other | Race |
| NATS-00492 | SA305934 | FL036743 | Hispanic | Ethnicity |
| NATS-00492 | SA305934 | FL036743 | 0 | hasSmokingBeforeCOVID-19 |
| NATS-00492 | SA305934 | FL036743 | pre-COVID-19 | Time |
Collection:
| Collection ID: | CO002931 |
| Collection Summary: | The Mass General Brigham (MGB) Biobank contains ~100,000 banked plasma, serum, and DNA samples from >100,000 consented patients. Electronic Medical Record (EMR) data and lifestyle, environment, and family history surveys can also be linked to the banked samples. The Longitudinal EMR and Omics COVID-19 Cohort (LEOCC) consists of a subset of individuals with prospective plasma samples from the MGB Biobank. Patients with a positive COVID-19 diagnosis (defined as a COVID-19 positive infection control flag, COVID-19 presumed infection control flag, or SARS-CoV-2 RNA positive test result) and available plasma samples prior to COVID-19 (up to October 27, 2020) were included. No additional exclusion criteria were applied. Clinical data relevant to COVID-19 infection, including clinical measures, disease diagnoses, and COVID-19 severity were also extracted from EMR data for use in statistical models. This study was approved by the Brigham and Women’s Institutional Review Board (IRB: 2014P001109). A total of 940 plasma samples from 661 individuals were collected from consented patients and were stored at –80 C. These samples are categorized by the time point of collection relative to a positive COVID-19 diagnosis, including 474 pre-COVID-19 samples (date of collection < date of diagnosis), 282 during COVID-19 samples (collected within 28 days of diagnosis), and 182 post-COVID-19 samples (collected more than 28 days after COVID-19 diagnosis). For patients with multiple during and/or post-COVID-19 samples, only the sample collected at the date closest to diagnosis was retained for during-COVID-19, and only the sample collected at the date furthest from diagnosis was retained for post-COVID-19. Patients without BMI data were also excluded from the sample sets, yielding a total of n = 441 pre-COVID-19, n = 86 during COVID-19, and n = 82 post-COVID-19 samples used for analysis. |
| Sample Type: | Blood (plasma) |
Treatment:
| Treatment ID: | TR002947 |
| Treatment Summary: | The COVID-19 severity level was determined according to WHO guidelines (16) as 0 = ambulatory mild disease (no hospitalization), 1 = hospitalized moderate disease (hospitalized without ventilation), 2 = hospitalized severe disease (hospitalized with ventilation), or 3 = death. Further demographic, risk factor, and comorbidity covariables were defined before COVID-19 diagnosis for all patients as follows: age is the numerical patient age; race is categorical (black, other, white); ethnicity (Hispanic/non-Hispanic), sex (female/male), and smoking (yes/no) are binary; BMI is the numerical median body mass index (BMI) for each patient; and comorbidity level is a binary “mild” or “severe” factor based on a Charlson index < 5 or ≥ 5, respectively. |
Sample Preparation:
| Sampleprep ID: | SP002944 |
| Sampleprep Summary: | Plasma samples were sent to Metabolon for comprehensive metabolomic profiling of polar and nonpolar metabolite classes in plasma extracts. Samples were extracted and prepared according to methods published previously (19). |
Combined analysis:
| Analysis ID | AN004619 | AN004620 | AN004621 | AN004622 |
|---|---|---|---|---|
| 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 UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,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 Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE |
| Units | log transformed data | log transformed data | log transformed data | log transformed data |
Chromatography:
| Chromatography ID: | CH003475 |
| Chromatography Summary: | Low pH polar (LC/MS Pos early) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | - |
| Flow Gradient: | - |
| Flow Rate: | - |
| Solvent A: | - |
| Solvent B: | - |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003476 |
| Chromatography Summary: | Low pH Lipophilic (LC/MS Pos late) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | - |
| Flow Gradient: | - |
| Flow Rate: | - |
| Solvent A: | - |
| Solvent B: | - |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003477 |
| Chromatography Summary: | High pH (LC/MS Neg) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | - |
| Flow Gradient: | - |
| Flow Rate: | - |
| Solvent A: | - |
| Solvent B: | - |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003478 |
| Chromatography Summary: | HILIC (LC/MS Polar Neg) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) |
| Column Temperature: | - |
| Flow Gradient: | - |
| Flow Rate: | - |
| Solvent A: | - |
| Solvent B: | - |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004365 |
| Analysis ID: | AN004619 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Pos early) |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | Metabolon_Data_Filtering_and_Normalization_LEOCC.pdf |
| MS ID: | MS004366 |
| Analysis ID: | AN004620 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Pos late) |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | Metabolon_Data_Filtering_and_Normalization_LEOCC.pdf |
| MS ID: | MS004367 |
| Analysis ID: | AN004621 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Neg) |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | Metabolon_Data_Filtering_and_Normalization_LEOCC.pdf |
| MS ID: | MS004368 |
| Analysis ID: | AN004622 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Polar) |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | Metabolon_Data_Filtering_and_Normalization_LEOCC.pdf |
