Curated Studies available through the iReceptor Gateway

The goal of the iReceptor project is to facilitate sharing and comparing of AIRR-seq data sets from multiple labs and institutions. At present these studies are curated in the iReceptor Public Archive (IPA) and VDJServer, and soon other repositories will be added to this set of repositories. The following is a list of the studies whose data are presently available through the iReceptor Gateway. This includes data on immune repertoires shaped by COVID-19 and other infectious diseases, autoimmune diseases, cancer, as well as repertoires from healthy control individuals.

B-Cell AIRR-seq data from the following papers are available through the iReceptor Gateway

  • Bashford-Rogers, R.J. et al. Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations. Genome Res 23:1874–84 (2013). [DOI]
  • Boyd, S.D. et al. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci Transl Med 1:12ra23 (2009). [DOI]
  • Chang, Y.-H. et al. Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses. Sci. Rep. 6, 26556 (2016). [DOI]
  • Collins, A.M. et al. The mouse antibody heavy chain repertoire is germline-focused and highly variable between inbred strains. Philos. Trans. R. Soc. B Biol. Sci. 370, 20140236 (2015). [DOI
  • Cui, A. et al. A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput Ig Sequencing Data. J. Immunol. 197, 3566–3574 (2016). [DOI]
  • DeKosky, B.J. et al. In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire. Nature Medicine. 21(1):86-91 (2015). [DOI]
  • DeWitt, W.S. et al. A public database of memory and naive B-cell receptor sequences. PLoS ONE 11(8): e0160853 (2016). [DOI]
  • Galson, J. et al. Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures. bioRxiv (Preprint). [DOI]
  • Goel, R. et al. Distinct antibody and memory B cell responses in SARS-CoV-2 naïve and recovered individuals following mRNA vaccination, Science Immunology  15 Apr 2021: Vol. 6, Issue 58, [DOI]
  • Greiff, V. et al. Systems Analysis Reveals High Genetic and Antigen-Driven Predetermination of Antibody Repertoires throughout B Cell Development. Cell Reports, 19(17): 1467–1478 (2017). [DOI]
  • Kim, S et al. Stereotypic Neutralizing VH Clonotypes Against SARS-CoV-2 RBD in COVID-19 Patients and the Healthy Population. bioRxiv (Preprint). [DOI]
  • Michaeli, M. et al. Immunoglobulin gene repertoire diversification and selection in the stomach - from gastritis to gastric lymphomas. Front. Immunol. 5, 1–14 (2014). [DOI]
  • Mor et al. Multi-Clonal Live SARS-CoV-2 In Vitro Neutralization by Antibodies Isolated from Severe COVID-19 Convalescent Donors. PLOS Pathogens, Feb 11, 2021. [DOI].
  • Nielsen, S. et al. B cell clonal expansion and convergent antibody responses to SARS-CoV-2. Research Square (Preprint). [DOI]
  • Palanichamy, A. et al. Immunoglobulin class-switched B cells form an active immune axis between CNS and periphery in multiple sclerosis. Sci. Transl. Med. 6, 248ra106–248ra106 (2014). [DOI]
  • Snir, O. et al. Stereotyped antibody responses target posttranslationally gluten in celiac disease. JCI insight 2(17): e93961. (2017). [DOI]
  • Sokal, A. et al. Maturation and persistence of the anti-SARS-CoV-2 memory B cell response. Cell, Volume 184, Issue 5, P1201-1213.E14, March 04, 2021. [DOI]
  • Soto, C. et al. High frequency of shared clonotypes in human B cell receptor repertoires. Nature, 566, 398-402 (2019). [DOI]   
  • Stern, J.N.H. et al. B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Sci. Transl. Med. 6, 248ra107 (2014). [DOI]
  • Tipton, C.M. et al. Diversity, cellular origin and autoreactivity of antibody-secreting cell population expansions in acute systemic lupus erythematosus. Nat. Immunol. (2015). [DOI]
  • Valdes-Aleman, J. et al. Hybridization-based antibody cDNA recovery for the production of recombinant antibodies identified by repertoire sequencing. Landes Bioscience V 6:1, 493-501(2014). [DOI]
  • Vergani, S. et al. Novel Method for High-Throughput Full-Length IGHV-D-J Sequencing of the Immune Repertoire from Bulk B-Cells with Single-Cell Resolution. Front Immunol. 8: 1157 (2017). [DOI]
  • Zhou, T. et al. Multi-donor Analysis Reveal Structural Elements, Genetic Determinants, and Maturation Pathway for Effective HIV-1 Neutralization by VRC01-class Antibodies. Immunity. 39, 245-258 (2013). [DOI]
  • Zhu, J. et al. Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains. Proc. Natl. Acad. Sci. U. S. A. 110, 6470–5 (2013). [DOI]

T-Cell AIRR-seq data from the following papers are available through the iReceptor Gateway

  • Chen, Z. et al. T cell receptor b-chain repertoire analysis reveals intratumour heterogeneity of tumour-infiltrating lymphocytes in oesophageal squamous cell carcinoma. J. Pathol. 4, 450 (2016). [DOI]
  • DeWitt, W.S. et al. Dynamics of the cytotoxic T cell response to a model of acute viral infection. J. Virol. 89(8):4517-26 (2015). [DOI]
  • Emerson, R. et al. Immunosequencing Identifies Signatures of Cytomegalovirus Exposure History and HLA-mediated Effects on the T Cell Repertoire. Nature Genetics 49: 659–665 (2017). [DOI]
  • Feng, L. et al. Heterogeneity of tumor-infiltrating lymphocytes ascribed to local immune status rather than neoantigens by multi-omics analysis of glioblastoma multiforme. Scientific Reports, 7, 6968 (2017). [DOI]
  • Jia, Q. et al. Local mutational diversity drives intratumoral immune heterogeneity in non-small cell lung cancer. Nat. Commun. 9(1) (2018). [DOI]
  • Lang-Kuhs, K.A. et al. T cell receptor repertoire among women who cleared and failed to clear cervical human papillomavirus infection: An exploratory proof-of-principle study. PLoS ONE 13(1): e0178167 (2018). [DOI]
  • Liao, M. et al. Single-cell Landscape of Bronchoalveolar Immune Cells in Patients With COVID-19, Nature Medicine, 26, 842-844, 2020. [DOI]
  • Minervina, A. et al. Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection. bioRxiv (Preprint). [DOI]
  • Munson, D.J. et al. Identification of shared TCR sequences from T cells in human breast cancer using emulson RT-PCR. Proc. Natl. Acad. Sci USA 113(29): 8272–8277 (2016). [DOI]
  • Ostmeyer, J. et al. Biophysicochemical motifs in T cell receptor sequences as a potential biomarker for high-grade serous ovarian carcinoma. PLoS One. Mar 5;15(3):e0229569 (2020). [DOI]
  • Pogorelyy, M.V. et al. Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins. Proc. Natl. Acad. Sci. USA 115(50) (2018). [DOI]
  • Putintseva, E. V et al. Mother and child T cell receptor repertoires: deep profiling study. Front. Immunol. 4, 463 (2013). [DOI]
  • Sims, J.S. et al. Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire. proc. Natl. Acad. Sci. USA 113(25) (2016). [DOI]
  • Shi, L. et al. Multi-omics study revealing the complexity and spatial heterogeneity of tumor-infiltrating lymphocytes in primary liver carcinoma. Oncotarget, 8(21):34844-34857 (2017). [DOI]
  • Tanno, H. et al. Determinants Governing T Cell Receptor α/β-chain Pairing in Repertoire Formation of Identical Twins. PNAS 2020 Jan 7;117(1):532-540. [DOI]
  • Theil, A. et al. T cell receptor repertoires after adoptive transfer of expanded allogeneic regulatory T cells. Clin Exp Immunol. 187(2):316-324 (2017). [DOI]
  • Wang, T. et al. The different T-cell receptor repertoires in breast cancer tumors, draining lymph nodes, and adjacent tissues. Cancer Immunol Res., 5(2): 148-156 (2017). [DOI]
  • Zvyagin, I.V. et al. Tracking T-cell immune reconstitution after TCRαβ/CD19-depleted hematopoietic cells transplantation in children. Leukemia. 5, 1145-53 (2017). [DOI]

Both B- and T-Cell AIRR-seq data from the following papers are available through the iReceptor Gateway

  • Rubelt, F. et al. Individual heritable differences result in unique Lymphocyte receptor repertoires of naïve and antigen-experienced cells. Nat. Commun. 7: 1112 (2016). [DOI]
  • Schultheiß ., C. et al. Next Generation Sequencing of T and B cell receptor repertoires from COVID-19 patients showed signatures associated with severity of disease, Immunity (2020). [DOI]
  • Wen et al. Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing, Cell Discovery, 6, 31 (2020). [DOI]