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Data from immunocompromised individuals vaccinated with SARS-CoV2 vaccines: antibody titers, B cell receptor repertoire sequencing, and B cell immunophenotyping

https://doi.org/10.48723/bbag-t656
The dataset contains B cell receptor (BCR) sequencing data. Two types of data are included: Antigen-specific BCR sequences obtained by sorting B cells (CD19+, CD20+, IgG+, IgM-, Spike+) followed by PCR and Sanger sequencing for SARS-CoV-2. Sequences are provided per individual and also as a combined dataset. Bulk BCR repertoire sequencing for IgM and IgG, with one FASTQ file per individual and sample. All sequences are provided as FASTQ or FASTA files. Users will need to realign and re-annotate VDJ segments using their preferred reference database and software. More details on the experimental design and sorting strategy can be found in the published paper: DOI 10.1002/cti2.70077 No direct identifiers are included; sample IDs are pseudonymized. The size of the dataset is approximately 30 GB.
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Citation and access

Data access level:

Creator/​Principal investigator(s):

Research principal:

Data contains personal data:

Yes

Type of personal data:

The dataset contains pseudonymized genetic data from BCR sequencing. No direct identifiers are included. Indirect identifiers include coded sample IDs and health-related groupings (e.g., GVHD+ vs GVHD-). Risk of re-identification is very low, so data can be shared under controlled access.

Code key exists:

Yes

Sensitive personal data:

Yes

Citation:

Language:

Method and outcome

Unit of analysis:

Population:

The dataset includes samples from participants of the COVAXID clinical trial (EudraCT 2021-000175-37; NCT04780659), a prospective study of SARS-CoV-2 mRNA vaccination in alloHCT recipients. Both male and female participants were included. Participants who had pre-existing immunity, a positive PCR at baseline, or COVID-19 infection between Day 0 and Day 35 were excluded from analyses of vaccine-induced responses, except for one participant included in overall IGH repertoire analysis. Subgroups for BCR sequencing were selected based on cGVHD status (cGVHD+ vs cGVHD-) and sample availability. Sex distribution was reasonably balanced, although not always exactly 50-50 due to sample selection.

Time method:

Study design:

  • Experimental study
  • Non-randomised trial

Sampling procedure:

Description of sampling:

Samples were collected from participants at Day 0 and Day 35 after two mRNA SARS-CoV-2 vaccinations. PBMCs were isolated and cryopreserved, and B cell receptor sequences were obtained either from antigen-specific B cells or bulk IgM/IgG repertoires. FASTQ/FASTA files are provided per sample. Detailed sampling and processing procedures are described in Hellgren et al. (DOI: 10.1002/cti2.70077).

Time period(s) investigated:

Number of individuals/​objects:

20

Data format/​data structure:

Samples/material Collected from scientific collection/biobank

Name:

The data are derived from human PBMC and B cell samples collected in the COVAXID clinical trial. Samples were specifically collected for this study and cryopreserved for later immunological analysis

Type(s) of sample:

Peripheral blood samples.

Geographic coverage

Geographic location:

Lowest geographic unit:

Country

Highest geographic unit:

Country

Administrative information

Responsible department/​unit:

Department of Medicine, Solna [K2]

Contributor(s):

Ethics Review:

Swedish Ethical Review Authority - 2021-00451

Funding

Funding agency:

Award number:

2021-04779_VR

Award title:

Covid-19 vaccination in immunocompromised individuals: An interdisciplinary framework to gain clinical and mechanistic insight into durable immunity to SARS-CoV-2 infection

Funding information:

There is a clear knowledge gap of whether patients with immunosuppressive disorders can generate durable immunity and protection after Covid-19 vaccination. To address this question, we here assemble a interdisciplinary team of Covid-19 clinicians and researchers in four county councils. Aim 1. We aim to define the effect of Covid-19 by evaluating presence and persistence of antibody and cell- mediated immune responses, and assess safety in Covid-19 vaccinated patients with primary and secondary immunodeficiencies compared to healthy controls. Also, through linkage of national registers, protective effect for severe Covid-19 will be evaluated on a nationwide level in immunocompromised persons. Aim 2. We aim to define correlates of an effective vaccine response (high neutralization capacity) from studies on patients with different immunological profiles/deficiencies. Also, emergence of new variants in immunocompromised patients after vaccination will be examined. Collection of unique samples from 1040 individuals from two phase 4 clinical trials, together with the use of cutting-edge immunological, single-cell technologies and usage of national registers will be the central tenets of this project proposal, where we hypothesize that most patients, despite their immunological status, will generate some type of immune response and thereby gain from vaccination. This information will have implications for future vaccination guidelines in this frail population.

Funding agency:

Award number:

2021-0017

Funding agency:

  • Cancerfonden

Award number:

21 1728 Pj

Topic and keywords

CESSDA Topic Classification:

Standard för svensk indelning av forskningsämnen 2025:

Keywords:

Publications

Citation:

Hellgren F, Arcoverde Cerveira R, Lindgren G, Chen P, Lenart K, Ols S, Cagigi A, Valentini D, Rocavert Barranco M, Shaloom Vitus E, Corcoran M, Gwon Y-D, Forsell MNE, Evander M, COVAXID study group, Bergman P, Buggert M, Ljunggren H-G, Aleman S, Karlsson Hedestam GB, Björklund A, Nordlander A, Ljungman P, Mielke S*, Loré K*. The Impact of B Cell Reconstitution on mRNA Vaccine Responses in Allogeneic Stem Cell Transplant Recipients. Clinical & Translational Immunology. 2026.

Contact

Metadata

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