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HTS AIRR-Seq data sets with minimal or no data and/or do not provide public access to the original sequence files

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#1

A list of papers with AIRR-seq data that is inaccessible, partly accessible, has broken links, etc.

  1. Agathangelidis, A. et al. High Throughput Immunoprofiling of Low Count B Lymhocytosis Reveals a Distinct T cell receptor repertoire from Chronic Lymphocytic Leukemia. Blood 2017 130:4296 (2017).
    [DOI]
    • Illumina MiSeq, mRNA
  2. Aris, M. et al. Changes in the TCR Beta Repertoire and Tumor Immune Signature From a Cutaneous Melanoma Patient Immunized with the CSF-470 Vaccine: A Case Report. Front. Immunol 9: 955 (2018).
    [PMC]
    • RNA-Seq
  3. Bashford-Rogers, R.J.M. et al. Antibody repertoire analysis in polygenic autoimmune diseases. Immunology, 155(1): 3–17 (2018).
    [DOI] [PubMed] [PMC]
    • Illumina, mRNA
  4. Bonsignori, M. et al. Analysis of a Clonal Lineage of HIV-1 Envelope V2/V3 Conformational Epitope-Specific Broadly Neutralizing Antibodies and Their Inferred Unmutated Common Ancestors. J. Virol. 85, 9998 (2011).
    [DOI]
  5. Briney. B.S. et al. Human peripheral blood antibodies with long HCDR3s are established primarily at original recombination using a limited subset of germline genes. PLoS ONE 7, e36750 (2012).
    [DOI]
    • Roche 454, mRNA
  6. Brown, S.D. et al. Profiling tissue-resident T cell repertoires RNA sequencing. Genome Med. 7,125 (2015).
    [DOI]
    • RNA-seq, mRNA
    • Used some data from TCGA
  7. Brown, S.D. et al. Defining the clonality of peripheral T cell lymphomas using RNA-Seq. Bioinformatics 8, 1111 (2016).
    [DOI] [PMC]
    • RNA-seq, mRNA
  8. Chaara, W. et al. Representativeness and robustness of TCR repertoire diversity assessment by high-throughput sequencing. BioRxiv Jan. 2 (2018).
    [DOI]
    • Abstract
  9. Chen, X. et al. Human TCR-MHC coevolution after divergencce from mice includes increased nontemplate-encoded CDR3 diversity. JEM, 214 (11): 3417 (2017).
    [DOI]
    • ImmunoSEQ, gDNA
    • Adaptive Biotechnologies
  10. Cheng, C. et al. Next generation sequencing reveals changes of the gamma-delta T cell receptor repertoires in patients with pulmonary tuberculosis. Sci Report, 8: 3956 (2018).
    [DOI] [PMC] [PubMed]
    • Illumina MiSeq, mRNA
  11. Cooper, Z.A. et al. BRAF inhibition is associated with increased clonality in tumor-infiltrating lymphocytes. Oncoimmunology 2, e26615 (2013).
    [DOI]
    • ImmunoSEQ, gDNA
    • Adaptive Biotechnologies
  12. Dewolf, S. et al. Quantifying the Size and Diversity of the Human Alloresponse Via High-Throughput T Cell Receptor Sequencing. JCI Insight, Aug 9;3(15) (2018).
    [DOI] [PMC] [PubMed]
    • ImmunoSeq, Adaptive Biotech
  13. Dickinson, G.S. et al. IL-7 Enables Antibody Responses to Bacterial Polysacharides by promoting B Cell Receptor Diversity. J Immunol, 201(4):1229-1240 (2018).
    [DOI] [PubMed]
    • Illumina, mRNA
  14. Dovedi, S.J. et al. Fractionated Radiation Therapy Stimulates Antitumor Immunity Mediated by Both Resident and Infiltrating Polyclonal T-cell Populations when Combined with PD-1 Blockade. Clinical Cancer Research, Volume 23, Issue 18 (2017).
    [DOI] [PubMed]
    • ImmunoSEQ, gDNA
    • Adaptive Biotechnologies
  15. Egorov, E.S. et al. The Changing Landscape of Naïve T Cell Receptor Repertoire With Human Aging. Front Immunol. 9: 1618 (2018).
    [DOI] [PMC]
    • Illumina HiSeq
  16. Emerson, R.O. et al. High-throughput sequencing of T-Cell receptors reveals a homogeneous repertoire of tumor-infiltrating lymphocytes in ovarian cancer. J. Pathol. 231(4): 433–440 (2013).
    [DOI] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  17. Fujishima, N. et al. High-Throughput Sequencing of IgG B-Cell Receptors Reveals the Frequent Usage of the Rearranged IGHV4-28//IGHJ4 Gene in Primary Immune Thrombocytopenia in Adults. Blood, 130:3582 (2017).
    [DOI]
    • Abstract
  18. Freund, N.T. et al. A New Glycan-Dependent CD4-Binding Site Neutralizing Antibody Exerts Pressure on HIV-1 In Vivo. PLoS Pathogens 11(10): e1005238 (2015).
    [DOI]
    • CDR3 in paper
  19. Gerlinger, M. et al. Ultra-deep T cell receptor sequencing reveal the complexity and intratumour heterogeneity of T cell clones in renal cell carcinomas. J. Pathol. 4, 424 (2013).
    [PMC] [DOI]
    • CDR3 in paper
    • ImmunoSEQ (Adaptive Biotech Platform)
  20. Gros, A. et al. PD-1 identifies the patient-specific CD8+ tumor-reactive repertoire infiltrating human tumors. J. Clin. Invest. 5, 2246 (2014).
    [PMC] [DOI]
    • CDR3 in paper
    • Illumina, mRNA
  21. Harris, K.E. et al. Sequence-based Discovery Demonstrates That Fixed Light Chain Human Transgenic Rats Produce a Diverse Repertoire of Antigen-Specific Antibodies. Front Immunol. 9: 889 (2018).
    [DOI] [PubMed] [PMC]
    • Illumina MiSeq
  22. Hausler, D. et al. Functional characterization of reappearing B cells after anti-CD20 treatment of CNS autoimmune disease. Proc Natl Acad Sci. 115(39):9773-9778 (2018).
    [DOI] [PubMed] [PMC]
    • Illumina MiSeq
  23. He, L. et al. Toward a more accurate view of human B-cell repertoire by next-generation sequencing, unbiased repertoire capture and single-molecule barcoding. Scientific Reports 4, 6778 (2014).
    [DOI]
    • Ion Torrent, mRNA
  24. Hirsch, C.M., et al. Surveillance of the Immune Repertoire of Aplastic Anemia Patients Using Deep Sequencing. Blood, 130:2454 (2017).
    [DOI]
    • ImmunoSeq
  25. Hosoya, T. et al. Induction of oligoclonal CD8 T cell responses against pulmonary metastatic cancer by a phospholipid-conjugated TLR7 agonist. Proc Natl Acad Sci, 115(29):E6836-E6844 (2018).
    [DOI] [PubMed]
    • Repertoire Genesis Inc.
  26. Hwang, K.K. et al. IGHV1-69 B cell chronic lymphocytic leukemia antibodies cross-react with HIV-1 and hepatitis C virus antigens as well as intestinal commensal bacteria. PLoS ONE 9(3): e90725 (2014).
    [DOI]
    • CDR3 in paper
    • From their own database
  27. Jiang, Q. et al. Patient-shared TCRB-CDR3 clonotypes correlate with favorable prognosis in chronic hepatitis B. Eur J Immunol. 48(9):1539-1549 (2018).
    [DOI] [PubMed]
    • Illumina 2500
  28. Kato, T. et al. Integrated analysis of somatic mutations and immune microenvironment of multiple regions in breast cancers. Oncotarget, 8(37):62029-62038 (2017).
    [DOI] [PubMed] [PMC]
    • Illumina MiSeq
  29. Keane, C. et al. The T-cell receptor repertoire influences the tumor mincroenvironment and is associated with survival in aggressive B-cell lymphoma. Clin. Cancer Res. 23,1820 (2017).
    [DOI] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  30. Khavrutskii, I.V. et al. Quantitative analysis of repertoire-scale immunoglobulin properties in vaccine-induced B-cell responses. Front Immunol, 8: 910 (2017).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  31. Kirsch, I.R. et al. TCR sequencing facilitates diagnosis and identifies mature T cells as the cell of origin in CTCL. Sci. Transl. Med. 7(308):308ra158 (2015).
    [DOI] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  32. Kirsch, I.R. et al. T-cell profiling in cancer. Molecular Oncology 9(10), 2063 (2015).
    [DOI]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  33. Koethe, J.R. et al. Adipose Tissue is Enriched for Activated and Late-Differentiated CD8+ T cells and Shows Distinct CD8+ Receptor Usage, Compared With Blood in HIV-Infected Persons. JAIDS, 77(2):e14–e21 (2018).
    [DOI] [PubMed]
    • mRNA
  34. Kolhatkar, N.S. et al. Altered BCR and TLR signals promote enhanced positive selection of autoreactive transitional B cells in Wiskott-Aldrich syndorme. JEM, 212(10):1663-77 (2015).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  35. Laubli, H. et al. The T cell repertoire in tumors overlaps with pulmonary inflammatory lesions in patients treated with checkpoint inhibitors. Oncoimmunology 7(2): e1386362 (2018).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  36. Lee DW et al. BRILIA: Integrated Tool for High-Throughput Annotation and Lineage Tree Assembly of B-Cell Repertoires. Front Immunol, 7:681 (2017)
    [PubMed] [DOI]
    • mouse, spleen, GC
    • Adaptive, gDNA
  37. Lin, Z. et al. Deep sequencing of the T cell Receptor Beta repertoire reveals signature patterns and clonal drift in atherosclerotic plaques and patients. Oncotarget, 8(59):99312-99322 (2017).
    [DOI] [PubMed] [PMC]
    • Illumina HiSeq 2000
  38. Liu, Q. et al. Direct measurement of B-cell receptor repertoire’s composition and variation in systemic lupus erythematosus. Genes Immun, 18(1):22-27 (2017).
    [DOI] [PubMed]
    • Illumina HiSeq 2000, mRNA
  39. Loges, S. et al. The Orally Available Selective Axl Inhibitor BGB324 Induces Diversification of the Immune Repertoire and Specific Changes in Plasma Biomarker Profiles. Blood, 130:1375 (2017).
    [DOI]
    • Illumina MiSeq, mRNA
  40. Looney, T. et al. Long-amplicon TCRBeta repertoire sequencing to reveal human T-cell receptor variable gene polymorphism: Implications for the prediction and interpretation of immunotherapy outcome. Journal of Clinical Oncology, Abstract 129 (2018).
    • Ion Torrent
  41. Lundgren, S. et al. Acquired Somatic Mutations in T Cells in Patients with Aplastic Anemia and Hypoplastic Myelodysplastic Syndromes. Blood, 130:1169 (2017).
    [DOI]
  42. Maldonado, L. et al. Intramuscular therapeutic vaccination targeting HPV16 induces T cell responses that localize in mucosal lesions. Sci. Transl. Med. 221ra13 (2014).
    [PMC]
    • CDR3 in paper
    • ImmunoSEQ (Adaptive Biotech Platform)
  43. Meffre, E. et al. Maturational characteristics of HIV-specific antibodies in viremic individuals. JCI insight, 1(3): e84610 (2016).
    [DOI] [PMC]
    • CDR3 in paper
  44. Mohme, M. et al. Immunophenotyping of Newly Diagnosed and Recurrent Glioblastoma Defines Distinct Immune Exhaustiond in Peripheral and Tumour-infiltrating Lymphocytes. AACR (2018).
    [DOI]
  45. Moore, P.L. et al. Evolution of an HIV glycan–dependent broadly neutralizing antibody epitope through immune escape. Nature Medicine 18, 1688 (2012).
    [DOI]
    • ABI Sequencing
  46. Mouquet, H. et al. Memory B cell antibodies to HIV-1 gp140 cloned from individuals infected with clade A and B viruses. PLoS ONE 6(9): e24078 (2011).
    [DOI]
    • CDR3 in paper
  47. 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 29, 8272 (2016).
    [PMC] [DOI]
    • CDR3 in paper
    • Illumina MiSeq, mRNA
  48. Nakanishi, K. et al. Characterization of the T-cell receptor beta chain repertoire in tumor-infiltrating lymphocytes. Cancer Med. 9, 2513 (2016).
    [PMC] [DOI]
    • CDR3 in supplementary
    • Ion Torrent, mRNA
  49. Nogueira, R. et al. Human IgG repertoire of malaria antigen-immunized human immune system (HIS) mice. Immunol Lett. 188:46-52 (2017).
    [DOI] [PubMed]
  50. Ou, M. et al. Integrated analysis of B-cell and T-cell receptors by high-throughput sequencing reveals conserved repertoires in IgA nephropathy. Mol Med Rep, 17(5):7027-7036 (2018).
    [DOI] [PubMed] [PMC]
    • Illumina HiSeq 2000
  51. Planas, R. et al. Detailed characterization of T cell receptor repertoires in multiple sclerosis brain lesions. Front. Immunol. 9: 509 (2018).
    [DOI] [PubMed] [PMC
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  52. Reuben, A. et al. Association of the T-cell receptor landscape with survival in non-small cell lung cancer. Journal of Clinical Oncology. Abstract 140 (2018).
    [DOI]
  53. Sahin, U. et al. Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer. Nature. 547, 222 (2017).
    [DOI] [PubMed]
    • Illumina TruSeq, mRNA
    • All data are available from authors on reasonable request
  54. Sakellariou-Thompson, D. et al. Preclinical development of tumor-infiltrating lymphocyte therapy for metastatic colorectal cancer. Journal of Clinical Oncology, Vol. 36, 95 (2018).
    [DOI]
  55. Shi, B. et al. Short-term assessment of BCR repertoires of SLE patients after high dose glucocorticoid therapy with high-throughput sequencing. Springer Plus, 5:75 (2016).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ (Adaptive Biotech Platform)
  56. Simon, S. et al. TCR Analyses of Two Vast and Shared Melanoma Antigen-Specific T Cell Repertoires Common and Specific Features. Front Immunol. 9: 1962 (2018).
    [DOI] [PMC] [PubMed]
    • Illumina MiSeq, mRNA
  57. Smithey, M.J. et al. Lifelong CMV infection improves immune defense in old mice by broadening the mobilized TCR repertoire against third-party infection. Proc Natl Acad Sci, 115(29):E6817-E6825 (2018).
    [DOI] [PubMed]
    • Applied Biosystems 3730XL DNA Analyzer, mRNA
  58. Sonntag, K. et al. Immune monitoring and TCR sequencing of CD4 T cells in a long term responsive patient with metastasized pancreatic ductal carcinoma treated with individualized, neoepitope-derived multipeptide vaccines: a case report. J. Transl. Med. 16(1):23 (2018).
    [DOI] [PubMed] [PMC]
    • Big Dye Terminator
  59. Sok, D. et al. Priming HIV-1 broadly neutralizing antibody precursors in human Ig loci transgenic mice. Science 353(6307):1557 (2016).
    [DOI]
  60. Subudhi, S.K. et al. Clonal expansion of CD8 T cells in the systemic circulation precedes development of ipilimumab-induced toxicities. Proc. Natl. Acad. Sci. 42, 11919 (2016).
    [Supp]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  61. Suessmuth, Y. et al. CMV reactivation drives posttransplant T-cell reconstitution and results in defects in the underlying TCR beta repertoire. Blood, 125(25): 3835–3850 (2015).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  62. Sui, W. et al. Composition and variation analysis of the TCR β-chain CDR3 repertoire in systemic lupus erythematosus using high-throughput sequencing. Mol. Immun. 67(2):455 (2015).
    [DOI]
    • Illumina HiSeq, mRNA
  63. Thorne, J.J. et al. Longterm maintenance of human naïve T cells through in situ homeostasis in lymphoid tissue sites. Sci. Immunol. 1(6) (2016).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  64. Tobin, J. et al. The Tumor Microenvironment is Independently Prognostic of Conventional and Clinicogenetic Risk Models in Follicular Lymphoma. ASH. Vol. 130, Pg 728 (2017).
    [DOI]
    • Abstract only
  65. Tsuda, S. et al. Clonally Expanded Decidual Effector Regulatory T Cells Increase in Late Gestation of Normal Pregnancy, but Not in Preeclampsia, in Humans. Front. Immunol 9:1934 (2018).
    [DOI] [PubMed] [PMC]
  66. Walker, L.M. et al. Broad neutralization coverage of HIV by multiple highly potent antibodies. Nature, 477(7365): 466–470 (2012).
    [DOI] [PMC]
  67. Williams, W. B. et al. Diversification of HIV-1 vaccine-induced immunity by gp41-microbiota cross-reactive antibodies. Science, 349(6249): aab1253 (2015).
    [DOI] [PMC]
    • Illumina, mRNA
  68. Willis, J.R. et al. Long antibody HCDR3s from HIV-naïve donors presented on a PG9 neutralizing antibody background mediate HIV neutralization. Proc Natl Acad Sci U S A. 113, 4446 (2016).
    [DOI] [PMC]
    • Illumina HiSeq, mRNA
  69. Wong, H.S. et al. V-J combinations of T-cell receptor predict responses to erythropoietin in end-stage renal disease patients. J. Biomed Sci, 24(1):43 (2017).
    [DOI] [PubMed] [PMC]
    • Illumina MiSeq, mRNA
  70. Xiao, M. et al. Deep sequencing and circos analyses of antibody libraries reveal antigen-drien selection of Ig Vh genes during HIV-1 infection. Exp Mol Pathol. 95, 357 (2013).
    [DOI] [PMC]
    • Roche 454, mRNA
  71. Zhang, W. et al. Characterization of the B Cell Receptor Repertoire in the Intestinal Mucosa and of Tumor-Infiltrating Lymphocytes in Colorectal Adenoma and Carcinoma. J Immunol. 198, 3719 (2017).
    [DOI] [PubMed]
    • Illumina HiSeq 2500, mRNA
  72. Zhao, D.T. et al. Characteristics of IgH-CDR3 repertoire of peripheral B cells in a patient with primary biliary cholangitis: a preliminary study using high-throughput sequencing. Zhonghua Gan Zang Bing Za Zhi. 25(11):847-851 (2017).
    [DOI] [PubMed]
    • Qualcomm sequencing
  73. Zhu, J. et al. Immune surveillance by CD8aa+ skin-resident T cells in human herpes virus infection. Nature, 497(7450):494-7 (2013).
    [DOI] [PubMed] [PMC]
    • Illumina HiSeq, mRNA
    • ImmunoSEQ Analyzer, Adaptive Biotechnologies
3 Likes
#2

This one should be public according to @laserson

#3

Hi, just wanted to clarify:

  1. Gomez-Tourino, I. et al. T cell receptor Beta-chains display abnormal shortening and repertoire sharing in type 1 diabetes. Nature Communications, 8;1792 (2017).
    [DOI]
  • ImmunoSEQ, mRNA
  • Adaptive Biotechnologies

Adaptive-processed data has been available from OSF: DOI 10.17605/OSF.IO/72XSZ

#4

Thank you Ania! I’ve relocated the record to the Publicly available AIRR-seq data sets: T cells page. Please let us know if you see any other records that need correcting.