As part of our longitudinal profiling of subjects in the Sound Life cohort, we administed annual flu vaccines and collected plasma samples on the day of administration (Day 0), approximately 7 days post-vaccination (Day 7), and approximately 90 days post-vaccination (Day 90) for two consecutive years per subject. For many subjects, we were also able to collect samples in the same temporal pattern, but without administration of a flu vaccine. We call these latter visits "Immune Variation" visits.
With these plasma samples, we utilized custom Meso Scale Diagnostics (MSD) multi-spot immunoassays to measure both influenza haemagglutinin (HA)-specific IgG concentration as a measure of antibody production in response to the vaccine, as well as haemagglutination inhibition (HAI) to measure functional neutralizing antibody generation. Additional details for these experiments can be found on our MSD Serology and HAI Pipeline Methods page.
Within each experiment, samples were measured in multiple technical replicates (usually 3 per sample and 2 per control). We provide results for both the raw signal from each MSD well, including all control measurements, as well as analysis-ready mean results for each sample. In addition, some samples were measured in multiple experiments, which we refer to as duplicate measures. Duplicate measures can be used to assess the consistency of results across experimental batches.
Flu Vaccine Metadata
Each year during the course of our study, all subjects were administered the same quadrivalent flu vaccine. However, which vaccine was utilized during each vaccine season varied by year. This table provides detailed information about the vaccines utilized in each year, which can be related to the serology data above based on the cohort.cohortGuid and vaccine.year columns.
Additional columns in this table are described below:
cohort.cohortGuid: The unique ID of the cohort to which the vaccine was administered (BR1: Young Adult; BR2: Older Adult)vaccine.year: The flu year during which the vaccine was administered (e.g. 2019-202)vaccine.brandName: The brand name of the vaccine administeredvaccine.antigenFullName: The full name of each antigen in the quadrivalent vaccine (e.g. A/Brisbane/02/2018 (H1N1) pdm09 (IVR-190))vaccine.doses: Number of doses administered (1 for this study)vaccine.doseSchedule: Dose schedule for vaccine administration (Single for this study)vaccine.antigenDose_ug: Dose of each antigen in the vaccine in micrograms (15 in this study)vaccine.volume_uL: Volume of the vaccine in microliters (500 in this study)vaccine.antigenName: Short antigen name based on Flu type and isolate (e.g. A/Brisbane)vaccine.antigenType: Type of flu antigen (A or B)vaccine.antigenSubtype: Subtype based on Flu isolate (H1N1 or H3N2 for type A; Victoria or Yamagata for type B)vaccine.antigenIsolate: Isolate location (e.g. Brisbane)msd.antigenName: Antigen name for the corresponding MSD assay (e.g. the B/Colorado assay for B/Maryland vaccine antigens)
Sound Life Flu Vaccine Antigen Metadata
| File Name | Description | Download Link |
|---|---|---|
| sound-life_flu-vaccine_antigen_metadata.csv | Flu Vaccine antigen information for each year of vaccine administration |
Flu-specific IgG Serology
For each vaccine administration, we measured IgG serology - that is, these measurements are not available for Immune Variation or Stand-Alone visits at which no vaccine was provided.
Flu-specific IgG serology data is provided for each antigen in our panel of 7 influenza lineages: A/Brisbane, A/Hong Kong, A/Michigan, A/Victoria, B/Colorado, B/Phuket, and B/Washington. Concentrations are reported in AU/mL based on a standard curve of reference samples.
Subject and sample metadata are included to enable analysis of serology results. Available columns in this dataset are described below:
Subject and Sample Metadata
Our serology results contain some sample-level metadata to enable connection between these results and samples used in other modalities. The sample.sampleKitGuid identifier is used across many data modalities:
Sample Identifierscohort.cohortGuid: A Globally Unique Identifier (GUID) of the Cohort the subject enrolled in for our study subject.subjectGuid: A GUID for the Subjectsample.sampleKitGuid: A GUID for the Sample Kit, representing all material collected at a visitspecimen.specimenGuid: A GUID for the plasma sample aliquot utilized in the experiment
Subject Metadata (prefix: subject)subject.biologicalSex: The biological sex of the Subjectsubject.birthYear: The Birth Year of the Subjectsubject.ageAtFirstDraw: The Age of the Subject at their first on-study sample collectionsubject.race: The self-reported Race of the Subjectsubject.ethnicity: The self-reported Ethnicity of the subjectsubject.cmv: The CMV status of the subject (Negative or Positive)
Sample Metadata (prefix: sample)sample.visitName: The name of the study visit (i.e. time point)sample.drawYear: The year of sample collection (e.g. 2021)sample.subjectAgeAtDraw: The age of the Subject in years at the time of sample collectionsample.daysSinceFirstVisit: Timing of the sample collection relative to the first visit date (Flu Year 1 Day 0)
Vaccine Metadata (prefix: vaccine)vaccine.year: The years during which the specific vaccine was administered (see the Flu Vaccine Metadata table for details)
MSD Assay Results
Data in the following columns of our table are descriptors, measurements, and results from the MSD IgG Serology assay. Columns marked with an asterix (*) are excluded from the sample-level results, as they refer to well-specific data.
Technical Metadatamsd.batchID: A unique identifier for the batch of MSD assays (multiple plates run on the same day)msd.plateID: A unique identifier for the 96-well plate of the MSD assaymsd.wellID*: The well position within the plate that was measured (e.g. A09, G10)
Assay Metadatamsd.antigenName: A short name for the antigen based on Flu type and isolate origin (e.g. A/Victoria)msd.antigenSubtype: The flu subtype for the antigen (e.g. H1N1)msd.antigenFullName: The full name of the flu strain utilized (e.g. A/Victoria/2570/2019 (H1N1) pdm09-like virus)
Dilution and Standard Concentrationsmsd.sampleDilution: Dilution applied to each sample or control (usually 10,000)msd.standardConc: Concentration value of standard control samples (only available for standard controls)
Measured Valuesmsd.signalWell*: The measured value from the MSD spot corresponding to msd.wellID and msd.antigenName.
Computed Valuesmsd.signalMean: The mean of the msd.signalWell values among replicates from the same specimenmsd.signalPercentCV: The % Coefficient of Variation of msd.signalWell values among replicates from the same specimenmsd.concWell*: The computed concentration value based on the standard curve and msd.signalWell value (in AU/mL)msd.concMean: The mean of computed concentration values among replicates from the same specimen (in AU/mL)msd.concPercentCV: The % Coefficient of Variation of msd.concWell values among replicates from the same specimen
Sound Life IgG Serology MSD Data
| File Name | Description | Download Link |
|---|---|---|
| sound-life_flu_serology_duplicates.csv | Per-sample averaged IgG data for Sound Life duplicate measures (no controls) | |
| sound-life_flu_serology_duplicates_raw.csv | Raw, per-well IgG data for Sound Life duplicate measures (includes controls) | |
| sound-life_flu_serology_single.csv | Per-sample averaged IgG data for Sound Life samples (no controls) | |
| sound-life_flu_serology_single_raw.csv | Raw, per-well IgG data for Sound Life samples (includes controls) |
Haemagglutination Inhibition
We measured HAI results for each sample in the Sound Life cohort dataset. Measurements are available for all 868 samples in the Sound Life study.
HA-specific HAI results are provided for each antigen in our custom panel of 9 influenza lineages: A/Brisbane, A/Cambodia, A/Guangdong, A/HongKong, A/Kansas, A/Shanghai, A/Wisconsin, B/Phuket, and B/Washington. HAI is reported as a percent of inhibition relative to antibody-free negative control samples.
Subject and sample metadata are included to enable analysis of HAI results. Available columns in this dataset are described below:
Subject and Sample Metadata
Our serology results contain some sample-level metadata to enable connection between these results and samples used in other modalities. The sample.sampleKitGuid identifier is used across many data modalities:
Sample Identifierscohort.cohortGuid: A Globally Unique Identifier (GUID) of the Cohort the subject enrolled in for our study subject.subjectGuid: A GUID for the Subjectsample.sampleKitGuid: A GUID for the Sample Kit, representing all material collected at a visitspecimen.specimenGuid: A GUID for the plasma sample aliquot utilized in the experiment
Subject Metadata (prefix: subject)subject.biologicalSex: The biological sex of the Subjectsubject.birthYear: The Birth Year of the Subjectsubject.ageAtFirstDraw: The Age of the Subject at their first on-study sample collectionsubject.race: The self-reported Race of the Subjectsubject.ethnicity: The self-reported Ethnicity of the subjectsubject.cmv: The CMV status of the subject (Negative or Positive)
Sample Metadata (prefix: sample)sample.visitName: The name of the study visit (i.e. time point)sample.drawYear: The year of sample collection (e.g. 2021)sample.subjectAgeAtDraw: The age of the Subject in years at the time of sample collectionsample.daysSinceFirstVisit: Timing of the sample collection relative to the first visit date (Flu Year 1 Day 0)
Vaccine Metadata (prefix: vaccine)vaccine.year: The years during which the specific vaccine was administered (see the Flu Vaccine Metadata table for details)
MSD Assay Results
Data in the following columns of our table are descriptors, measurements, and results from the MSD HAI assay. Columns marked with an asterix (*) are excluded from the sample-level results, as they refer to well-specific data.
Technical Metadatamsd.batchID: A unique identifier for the batch of MSD assays (multiple plates run on the same day)msd.plateID: A unique identifier for the 96-well plate of the MSD assaymsd.wellID*: The well position within the plate that was measured (e.g. A09, G10)
Assay Metadatamsd.antigenName: A short name for the antigen based on Flu type and isolate origin (e.g. A/Victoria)msd.antigenSubtype: The flu subtype for the antigen (e.g. H1N1)msd.antigenFullName: The full name of the flu strain utilized (e.g. A/Victoria/2570/2019 (H1N1) pdm09-like virus)
Sample dilutionmsd.sampleDilution: Dilution applied to each sample or control (usually 5,000)
Measured Valuesmsd.signalWell*: The measured value from the MSD spot corresponding to msd.wellID and msd.antigenName.msd.signalBackground*: The measured value from the BSA-only MSD spot that serves as a control for background signal.
Computed Valuesmsd.signalNorm: Normalized signal from each well (msd.signalWell - msd.signalBackground)msd.signalNormMean: The mean of the msd.signalNorm values among replicates from the same specimenmsd.signalNormPercentCV: The % Coefficient of Variation of msd.signalNorm values among replicates from the same specimenmsd.blankNormMean: The mean of msd.signalNorm values among plasma-free negative control wells.msd.percentNormInhibition: The percent inhibition (100 * (1 - msd.blankNormMean/msd.signalNormMean))
Sound Life Flu HAI MSD Data
| File Name | Description | Download Link |
|---|---|---|
| sound-life_flu_hai_duplicates.csv | Per-sample averaged HAI data for Sound Life duplicate measures (no controls) | |
| sound-life_flu_hai_duplicates_raw.csv | Raw, per-well HAI data for Sound Life duplicate measures (includes controls) | |
| sound-life_flu_hai_single.csv | Per-sample averaged HAI data for Sound Life samples (no controls) | |
| sound-life_flu_hai_single_raw.csv | Raw, per-well HAI data for Sound Life samples (includes controls) |