ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data

Abstract Summary An effective immune system is characterized by a diverse immune repertoire. There is a strong demand for accurate and quantitative methods to assess the diversity of the immune repertoire for various (pre-)clinical applications, including the diagnosis and prognosis of primary immune deficiencies, or to assess the response to therapy. Current strategies for immune diversity assessment generally comprise the visual inspection of the length distribution of rearranged T- and B-cell receptors. Visual inspections, however, are prone to subjective assessments and thus lead to biases. Here, we introduce ImSpectR, a unified approach to quantify immunodiversity using either spectratype, repertoire sequencing or single cell RNA sequencing data. ImSpectR scores various types of deviations from the expected length distribution and integrates these into one measure, allowing for robust quantitative comparisons of immune diversity across individuals or conditions. Availability and implementation R-package is available for download on GitHub at https://github.com/martijn-cordes/ImSpectR. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

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Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data

Nature Immunology ◽

10.1038/ni.3873 ◽

2017 ◽

Vol 18 (12) ◽

pp. 1274-1278 ◽

Cited By ~ 70

Author(s):

Florian Rubelt ◽

◽

Christian E Busse ◽

Syed Ahmad Chan Bukhari ◽

Jean-Philippe Bürckert ◽

...

Keyword(s):

Sequencing Data ◽

Immune Repertoire ◽

Immune Receptor ◽

Adaptive Immune ◽

Receptor Repertoire ◽

Repertoire Sequencing ◽

Community Recommendations

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Use of immune repertoire sequencing to resolve discordant microscopic and immunochemical findings in a case of T cell-rich large B cell lymphoma in a young dog

BMC Veterinary Research ◽

10.1186/s12917-021-02783-3 ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Gary Kwok Cheong Lee ◽

Dorothee Bienzle ◽

Stefan Matthias Keller ◽

Mei-Hua Hwang ◽

Nikos Darzentas ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

B Cell ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Immune Repertoire ◽

Large B Cell Lymphoma ◽

Repertoire Sequencing ◽

Reactive Lymphocytes ◽

Large B Cell

Abstract Background Lymphocytic neoplasms with frequent reactive lymphocytes are uncommonly reported in dogs, and can pose a diagnostic challenge. Different diagnostic modalities such as cytology, flow cytometry, histopathology, immunohistochemistry, and clonality testing, are sometimes required for a diagnosis. This report illustrates the value of using a multi-modal diagnostic approach to decipher a complex lymphocytic tumor, and introduces immune repertoire sequencing as a diagnostic adjunct. Case presentation A 10-month-old Great Dane was referred for marked ascites. Cytologic analysis of abdominal fluid and hepatic aspirates revealed a mixed lymphocyte population including numerous large lymphocytes, yielding a diagnosis of lymphoma. Flow cytometrically, abdominal fluid lymphocytes were highly positive for CD4, CD5, CD18, CD45, and MHC II, consistent with T cell lymphoma. Due to a rapidly deteriorating clinical condition, the dog was euthanized. Post mortem histologic evaluation showed effacement of the liver by aggregates of B cells surrounded by T cells, suggestive of hepatic T cell-rich large B cell lymphoma. Immune repertoire sequencing confirmed the presence of clonal B cells in the liver but not the abdominal fluid, whereas reactive T cells with shared, polyclonal immune repertoires were found in both locations. Conclusions T cell-rich large B cell lymphoma is a rare neoplasm in dogs that may be challenging to diagnose and classify due to mixed lymphocyte populations. In this case, the results of histopathology, immunohistochemistry and immune repertoire sequencing were most consistent with a hepatic B cell neoplasm and reactive T cells exfoliating into the abdominal fluid. Immune repertoire sequencing was helpful in delineating neoplastic from reactive lymphocytes and characterizing repertoire overlap in both compartments. The potential pitfalls of equating atypical cytomorphology and monotypic marker expression in neoplasia are highlighted.

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Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity

eLife ◽

10.7554/elife.38358 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 42

Author(s):

William S DeWitt ◽

Anajane Smith ◽

Gary Schoch ◽

John A Hansen ◽

Frederick A Matsen ◽

...

Keyword(s):

T Cell ◽

T Cell Receptor ◽

Genetic Background ◽

Cell Receptor ◽

Sequencing Data ◽

Human T Cell ◽

Disease Associations ◽

Repertoire Sequencing ◽

Mhc Polymorphism ◽

Occurrence Patterns

The T cell receptor (TCR) repertoire encodes immune exposure history through the dynamic formation of immunological memory. Statistical analysis of repertoire sequencing data has the potential to decode disease associations from large cohorts with measured phenotypes. However, the repertoire perturbation induced by a given immunological challenge is conditioned on genetic background via major histocompatibility complex (MHC) polymorphism. We explore associations between MHC alleles, immune exposures, and shared TCRs in a large human cohort. Using a previously published repertoire sequencing dataset augmented with high-resolution MHC genotyping, our analysis reveals rich structure: striking imprints of common pathogens, clusters of co-occurring TCRs that may represent markers of shared immune exposures, and substantial variations in TCR-MHC association strength across MHC loci. Guided by atomic contacts in solved TCR:peptide-MHC structures, we identify sequence covariation between TCR and MHC. These insights and our analysis framework lay the groundwork for further explorations into TCR diversity.

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Ligation-anchored PCR unveils immune repertoire of TCR-beta from whole blood

10.1101/007062 ◽

2014 ◽

Author(s):

Fan Gao ◽

Kai Wang

Keyword(s):

High Throughput Sequencing ◽

Read Length ◽

Integrative Approach ◽

Sequencing Data ◽

Immune Repertoire ◽

Universal Primer ◽

Illumina Hiseq ◽

Variable Regions ◽

Anchored Pcr ◽

Pcr Method

Background As one of the genetic mechanisms for adaptive immunity, V(D)J recombination generates an enormous repertoire of T-cell receptors (TCRs). With the development of high-throughput sequencing techniques, systematic exploration of V(D)J recombination becomes possible. Multiplex PCR method has been previously developed to assay immune repertoire, however the usage of primer pools has inherent bias in target amplification. In our study, we developed a ligation-anchored PCR method to unbiasedly amplify the repertoire. Results By utilizing a universal primer paired with a single primer targeting the conserved constant region, we amplified TCR-beta (TRB) variable regions from total RNA extracted from blood. Next-generation sequencing libraries were then prepared for Illumina HiSeq 2500 sequencer, which provided 151 bp read length to cover the entire V(D)J recombination region. We evaluated this approach on blood samples from patients with malignant and benign meningiomas. Mapping of sequencing data showed 64% to 91% of mapped TCRV-containing reads belong to TRB subtype. An increased usage of TRBV29-1 was observed in malignant meningiomas. Also distinct signatures were identified from CDR3 sequence logos, with predominant subset as 42 nt for benign and 45 nt for malignant samples, respectively. Conclusions In summary, we report an integrative approach to monitor immune repertoire in a systematic manner.

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PIRD: Pan Immune Repertoire Database

Bioinformatics ◽

10.1093/bioinformatics/btz614 ◽

2019 ◽

Cited By ~ 1

Author(s):

Wei Zhang ◽

Longlong Wang ◽

Ke Liu ◽

Xiaofeng Wei ◽

Kai Yang ◽

...

Keyword(s):

Data Storage ◽

High Throughput Sequencing ◽

Homo Sapiens ◽

Adaptive Immune System ◽

B Cell Receptors ◽

Sequencing Data ◽

Immune Repertoire ◽

Adaptive Immune ◽

Potential Applications ◽

Antibody Drug

Abstract Motivation T and B cell receptors (TCRs and BCRs) play a pivotal role in the adaptive immune system by recognizing an enormous variety of external and internal antigens. Understanding these receptors is critical for exploring the process of immunoreaction and exploiting potential applications in immunotherapy and antibody drug design. Although a large number of samples have had their TCR and BCR repertoires sequenced using high-throughput sequencing in recent years, very few databases have been constructed to store these kinds of data. To resolve this issue, we developed a database. Results We developed a database, the Pan Immune Repertoire Database (PIRD), located in China National GeneBank (CNGBdb), to collect and store annotated TCR and BCR sequencing data, including from Homo sapiens and other species. In addition to data storage, PIRD also provides functions of data visualization and interactive online analysis. Additionally, a manually curated database of TCRs and BCRs targeting known antigens (TBAdb) was also deposited in PIRD. Availability and implementation PIRD can be freely accessed at https://db.cngb.org/pird.

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