{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T13:14:52Z","timestamp":1780665292193,"version":"3.54.1"},"reference-count":96,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2017,6,1]],"date-time":"2017-06-01T00:00:00Z","timestamp":1496275200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2017,6,1]],"date-time":"2017-06-01T00:00:00Z","timestamp":1496275200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Autoimmunity"],"published-print":{"date-parts":[[2017,6]]},"DOI":"10.1016\/j.jaut.2017.04.002","type":"journal-article","created":{"date-parts":[[2017,4,8]],"date-time":"2017-04-08T08:18:48Z","timestamp":1491639528000},"page":"1-9","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":23,"special_numbering":"C","title":["Immune dysregulation in immunodeficiency disorders: The role of T-cell receptor sequencing"],"prefix":"10.1016","volume":"80","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4987-4051","authenticated-orcid":false,"given":"Gabriel K.","family":"Wong","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James M.","family":"Heather","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Barmettler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Cobbold","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"4","key":"10.1016\/j.jaut.2017.04.002_bib1","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1038\/nri2941","article-title":"Recombination centres and the orchestration of V(D)J recombination","volume":"11","author":"Schatz","year":"2011","journal-title":"Nat. Rev. Immunol."},{"issue":"1","key":"10.1016\/j.jaut.2017.04.002_bib2","doi-asserted-by":"crossref","first-page":"15","DOI":"10.4049\/jimmunol.173.1.15","article-title":"B\u00a0cell positive selection: road map to the primary repertoire?","volume":"173","author":"Cancro","year":"2004","journal-title":"J.\u00a0Immunol."},{"issue":"4962","key":"10.1016\/j.jaut.2017.04.002_bib3","doi-asserted-by":"crossref","first-page":"1517","DOI":"10.1126\/science.2360047","article-title":"RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination","volume":"248","author":"Oettinger","year":"1990","journal-title":"Science"},{"issue":"8\u20139","key":"10.1016\/j.jaut.2017.04.002_bib4","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1016\/j.dnarep.2004.03.015","article-title":"The mechanism of vertebrate nonhomologous DNA end joining and its role in V(D)J recombination","volume":"3","author":"Lieber","year":"2004","journal-title":"DNA Repair Amst"},{"key":"10.1016\/j.jaut.2017.04.002_bib5","doi-asserted-by":"crossref","first-page":"485","DOI":"10.3389\/fimmu.2013.00485","article-title":"Estimating the diversity, completeness, and cross-reactivity of the T cell repertoire","volume":"4","author":"Zarnitsyna","year":"2013","journal-title":"Front. Immunol."},{"key":"10.1016\/j.jaut.2017.04.002_bib6","doi-asserted-by":"crossref","first-page":"263","DOI":"10.3389\/fimmu.2013.00263","article-title":"The shape of the lymphocyte receptor repertoire: lessons from the B cell receptor","volume":"4","author":"Jackson","year":"2013","journal-title":"Front. Immunol."},{"key":"10.1016\/j.jaut.2017.04.002_bib7","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1186\/s13073-015-0243-2","article-title":"Practical guidelines for B-cell receptor repertoire sequencing analysis","volume":"7","author":"Yaari","year":"2015","journal-title":"Genome Med."},{"issue":"45","key":"10.1016\/j.jaut.2017.04.002_bib8","doi-asserted-by":"crossref","first-page":"19414","DOI":"10.1073\/pnas.1010586107","article-title":"Convergent recombination shapes the clonotypic landscape of the naive T-cell repertoire","volume":"107","author":"Quigley","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"issue":"40","key":"10.1016\/j.jaut.2017.04.002_bib9","doi-asserted-by":"crossref","first-page":"16161","DOI":"10.1073\/pnas.1212755109","article-title":"Statistical inference of the generation probability of T-cell receptors from sequence repertoires","volume":"109","author":"Murugan","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"issue":"10","key":"10.1016\/j.jaut.2017.04.002_bib10","doi-asserted-by":"crossref","first-page":"2159","DOI":"10.1038\/leu.2012.246","article-title":"EuroClonality\/BIOMED-2 guidelines for interpretation and reporting of Ig\/TCR clonality testing in suspected lymphoproliferations","volume":"26","author":"Langerak","year":"2012","journal-title":"Leukemia"},{"issue":"4","key":"10.1016\/j.jaut.2017.04.002_bib11","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1038\/sj.leu.2404586","article-title":"European Study Group on, Analysis of minimal residual disease by Ig\/TCR gene rearrangements: guidelines for interpretation of real-time quantitative PCR data","volume":"21","author":"van der Velden","year":"2007","journal-title":"Leukemia"},{"issue":"3","key":"10.1016\/j.jaut.2017.04.002_bib12","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1016\/j.jaci.2010.06.015","article-title":"Transplantation of hematopoietic stem cells and long-term survival for primary immunodeficiencies in Europe: entering a new century, do we do better?","volume":"126","author":"Gennery","year":"2010","journal-title":"J.\u00a0Allergy Clin. Immunol."},{"issue":"8","key":"10.1016\/j.jaut.2017.04.002_bib13","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1007\/s10875-015-0201-1","article-title":"Primary immunodeficiency diseases: an update on the classification from the international union of immunological societies expert committee for primary immunodeficiency 2015","volume":"35","author":"Picard","year":"2015","journal-title":"J.\u00a0Clin. Immunol."},{"issue":"4","key":"10.1016\/j.jaut.2017.04.002_bib14","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1016\/j.jaci.2013.11.018","article-title":"Human syndromes of immunodeficiency and dysregulation are characterized by distinct defects in T-cell receptor repertoire development","volume":"133","author":"Yu","year":"2014","journal-title":"J.\u00a0Allergy Clin. Immunol."},{"issue":"1","key":"10.1016\/j.jaut.2017.04.002_bib15","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1111\/j.1365-2249.2011.04492.x","article-title":"Proteomics plus genomics approaches in primary immunodeficiency: the case of immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome","volume":"167","author":"Zennaro","year":"2012","journal-title":"Clin. Exp. Immunol."},{"key":"10.1016\/j.jaut.2017.04.002_bib16","first-page":"340","article-title":"Next generation sequencing reveals skewing of the T and B cell receptor repertoires in patients with wiskott-Aldrich syndrome","volume":"5","author":"O'Connell","year":"2014","journal-title":"Front. Immunol."},{"issue":"1","key":"10.1016\/j.jaut.2017.04.002_bib17","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.jaci.2015.11.004","article-title":"The crossroads of autoimmunity and immunodeficiency: lessons from polygenic traits and monogenic defects","volume":"137","author":"Grimbacher","year":"2016","journal-title":"J.\u00a0Allergy Clin. Immunol."},{"issue":"6","key":"10.1016\/j.jaut.2017.04.002_bib18","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1016\/j.jaip.2016.08.004","article-title":"Mechanism-based strategies for the management of autoimmunity and immune dysregulation in primary immunodeficiencies","volume":"4","author":"Walter","year":"2016","journal-title":"J.\u00a0Allergy Clin. Immunol. Pract."},{"issue":"12","key":"10.1016\/j.jaut.2017.04.002_bib19","doi-asserted-by":"crossref","first-page":"2257","DOI":"10.1038\/sj.leu.2403202","article-title":"Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936","volume":"17","author":"van Dongen","year":"2003","journal-title":"Leukemia"},{"issue":"1","key":"10.1016\/j.jaut.2017.04.002_bib20","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1046\/j.1365-2141.2003.04036.x","article-title":"Assessing diversity: immune reconstitution and T-cell receptor BV spectratype analysis following stem cell transplantation","volume":"120","author":"Peggs","year":"2003","journal-title":"Br. J. Haematol."},{"issue":"9","key":"10.1016\/j.jaut.2017.04.002_bib21","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1002\/cyto.a.20767","article-title":"Efficient characterization of the TCR repertoire in lymph nodes by flow cytometry","volume":"75","author":"Salameire","year":"2009","journal-title":"Cytom. A"},{"issue":"4","key":"10.1016\/j.jaut.2017.04.002_bib22","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1002\/1097-0320(20000801)40:4<336::AID-CYTO9>3.0.CO;2-0","article-title":"Flow cytometric analysis of the Vbeta repertoire in healthy controls","volume":"40","author":"van den Beemd","year":"2000","journal-title":"Cytometry"},{"issue":"19","key":"10.1016\/j.jaut.2017.04.002_bib23","doi-asserted-by":"crossref","first-page":"4099","DOI":"10.1182\/blood-2009-04-217604","article-title":"Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells","volume":"114","author":"Robins","year":"2009","journal-title":"Blood"},{"issue":"10","key":"10.1016\/j.jaut.2017.04.002_bib24","doi-asserted-by":"crossref","first-page":"1817","DOI":"10.1101\/gr.092924.109","article-title":"Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing","volume":"19","author":"Freeman","year":"2009","journal-title":"Genome Res."},{"issue":"12","key":"10.1016\/j.jaut.2017.04.002_bib25","doi-asserted-by":"crossref","first-page":"12ra23","DOI":"10.1126\/scitranslmed.3000540","article-title":"Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing","volume":"1","author":"Boyd","year":"2009","journal-title":"Sci. Transl. Med."},{"issue":"7","key":"10.1016\/j.jaut.2017.04.002_bib26","doi-asserted-by":"crossref","first-page":"4285","DOI":"10.4049\/jimmunol.1003898","article-title":"A\u00a0mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing","volume":"186","author":"Venturi","year":"2011","journal-title":"J.\u00a0Immunol."},{"issue":"3","key":"10.1016\/j.jaut.2017.04.002_bib27","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1038\/nri2260","article-title":"The molecular basis for public T-cell responses?","volume":"8","author":"Venturi","year":"2008","journal-title":"Nat. Rev. Immunol."},{"issue":"6","key":"10.1016\/j.jaut.2017.04.002_bib28","doi-asserted-by":"crossref","first-page":"2689","DOI":"10.4049\/jimmunol.1302064","article-title":"Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling","volume":"192","author":"Britanova","year":"2014","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.jaut.2017.04.002_bib29","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1007\/978-1-61779-842-9_32","article-title":"IMGT((R)) tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT\/V-QUEST and IMGT\/HighV-QUEST for NGS","volume":"882","author":"Alamyar","year":"2012","journal-title":"Methods Mol. Biol."},{"issue":"5","key":"10.1016\/j.jaut.2017.04.002_bib30","doi-asserted-by":"crossref","first-page":"1642","DOI":"10.4049\/jimmunol.1600526","article-title":"Accelerated loss of TCR repertoire diversity in common variable immunodeficiency","volume":"197","author":"Wong","year":"2016","journal-title":"J.\u00a0Immunol."},{"issue":"1\u20132","key":"10.1016\/j.jaut.2017.04.002_bib31","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/S0022-0981(00)00178-7","article-title":"The measurement of marine species diversity, with an application to the benthic fauna of the Norwegian continental shelf","volume":"250","author":"Gray","year":"2000","journal-title":"J.\u00a0Exp. Mar. Bio Ecol."},{"key":"10.1016\/j.jaut.2017.04.002_bib32","article-title":"Clonal and constricted T cell repertoire in common variable immune deficiency","author":"Ramesh","year":"2015","journal-title":"Clin. Immunol."},{"key":"10.1016\/j.jaut.2017.04.002_bib33","doi-asserted-by":"crossref","first-page":"456","DOI":"10.3389\/fimmu.2013.00456","article-title":"Preparing unbiased T-cell receptor and antibody cDNA libraries for the deep next generation sequencing profiling","volume":"4","author":"Mamedov","year":"2013","journal-title":"Front. Immunol."},{"key":"10.1016\/j.jaut.2017.04.002_bib34","doi-asserted-by":"crossref","first-page":"2680","DOI":"10.1038\/ncomms3680","article-title":"Using synthetic templates to design an unbiased multiplex PCR assay","volume":"4","author":"Carlson","year":"2013","journal-title":"Nat. Commun."},{"issue":"4","key":"10.1016\/j.jaut.2017.04.002_bib35","doi-asserted-by":"crossref","first-page":"1518","DOI":"10.1073\/pnas.0913939107","article-title":"High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets","volume":"107","author":"Wang","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jaut.2017.04.002_bib36","first-page":"644","article-title":"Dynamic perturbations of the T-cell receptor repertoire in chronic HIV infection and following antiretroviral therapy","volume":"6","author":"Heather","year":"2015","journal-title":"Front. Immunol."},{"issue":"16","key":"10.1016\/j.jaut.2017.04.002_bib37","doi-asserted-by":"crossref","first-page":"5980","DOI":"10.1073\/pnas.1319389111","article-title":"Distinctive properties of identical twins' TCR repertoires revealed by high-throughput sequencing","volume":"111","author":"Zvyagin","year":"2014","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jaut.2017.04.002_bib38","doi-asserted-by":"crossref","first-page":"339","DOI":"10.3389\/fimmu.2016.00339","article-title":"IMGT\/StatClonotype for pairwise evaluation and visualization of NGS IG and TR IMGT clonotype (AA) diversity or expression from IMGT\/HighV-QUEST","volume":"7","author":"Aouinti","year":"2016","journal-title":"Front. Immunol."},{"issue":"11","key":"10.1016\/j.jaut.2017.04.002_bib39","doi-asserted-by":"crossref","first-page":"e0142353","DOI":"10.1371\/journal.pone.0142353","article-title":"IMGT\/HighV-QUEST Statistical Significance of IMGT Clonotype (AA) Diversity per Gene for Standardized Comparisons of Next Generation Sequencing Immunoprofiles of Immunoglobulins and T Cell Receptors","volume":"10","author":"Aouinti","year":"2015","journal-title":"PLoS One"},{"issue":"11","key":"10.1016\/j.jaut.2017.04.002_bib40","doi-asserted-by":"crossref","first-page":"e1004503","DOI":"10.1371\/journal.pcbi.1004503","article-title":"VDJtools: unifying post-analysis of T cell receptor repertoires","volume":"11","author":"Shugay","year":"2015","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.jaut.2017.04.002_bib41","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1186\/s12859-015-0613-1","article-title":"tcR: an R package for T cell receptor repertoire advanced data analysis","volume":"16","author":"Nazarov","year":"2015","journal-title":"BMC Bioinforma."},{"issue":"4","key":"10.1016\/j.jaut.2017.04.002_bib42","doi-asserted-by":"crossref","first-page":"e31","DOI":"10.1093\/nar\/gkv1016","article-title":"LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins","volume":"44","author":"Yu","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jaut.2017.04.002_bib43","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbw138","article-title":"High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities","author":"Heather","year":"2017","journal-title":"Brief. Bioinform"},{"issue":"3","key":"10.1016\/j.jaut.2017.04.002_bib44","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1016\/j.jaci.2012.10.040","article-title":"Thymic function in MHC class II-deficient patients","volume":"131","author":"Lev","year":"2013","journal-title":"J.\u00a0Allergy Clin. Immunol."},{"issue":"5","key":"10.1016\/j.jaut.2017.04.002_bib45","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1016\/j.jaci.2012.07.029","article-title":"Primary T-cell immunodeficiency with immunodysregulation caused by autosomal recessive LCK deficiency","volume":"130","author":"Hauck","year":"2012","journal-title":"J.\u00a0Allergy Clin. Immunol."},{"issue":"6","key":"10.1016\/j.jaut.2017.04.002_bib46","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1182\/blood-2015-10-676304","article-title":"Modeling altered T-cell development with induced pluripotent stem cells from patients with RAG1-dependent immune deficiencies","volume":"128","author":"Brauer","year":"2016","journal-title":"Blood"},{"issue":"1","key":"10.1016\/j.jaut.2017.04.002_bib47","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/S0165-2478(02)00291-2","article-title":"Impaired thymic output and restricted T-cell repertoire in two infants with immunodeficiency and early-onset generalized dermatitis","volume":"86","author":"Pirovano","year":"2003","journal-title":"Immunol. Lett."},{"issue":"3","key":"10.1016\/j.jaut.2017.04.002_bib48","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1111\/j.1365-2249.2007.03378.x","article-title":"Clonotypic analysis of T cell reconstitution after haematopoietic stem cell transplantation (HSCT) in patients with severe combined immunodeficiency","volume":"148","author":"Okamoto","year":"2007","journal-title":"Clin. Exp. Immunol."},{"issue":"3","key":"10.1016\/j.jaut.2017.04.002_bib49","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1111\/cei.12273","article-title":"Co-existence of clonal expanded autologous and transplacental-acquired maternal T cells in recombination activating gene-deficient severe combined immunodeficiency","volume":"176","author":"Lev","year":"2014","journal-title":"Clin. Exp. Immunol."},{"issue":"6","key":"10.1016\/j.jaut.2017.04.002_bib50","doi-asserted-by":"crossref","first-page":"4124","DOI":"10.4049\/jimmunol.181.6.4124","article-title":"A\u00a0RAG1 mutation found in Omenn syndrome causes coding flank hypersensitivity: a novel mechanism for antigen receptor repertoire restriction","volume":"181","author":"Wong","year":"2008","journal-title":"J.\u00a0Immunol."},{"issue":"7","key":"10.1016\/j.jaut.2017.04.002_bib51","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1038\/nri2336","article-title":"Unravelling the association of partial T-cell immunodeficiency and immune dysregulation","volume":"8","author":"Liston","year":"2008","journal-title":"Nat. Rev. Immunol."},{"issue":"1","key":"10.1016\/j.jaut.2017.04.002_bib52","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1111\/imr.12112","article-title":"Wiskott-Aldrich syndrome protein\u2013dynamic regulation of actin homeostasis: from activation through function and signal termination in T lymphocytes","volume":"256","author":"Matalon","year":"2013","journal-title":"Immunol. Rev."},{"issue":"12","key":"10.1016\/j.jaut.2017.04.002_bib53","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1182\/blood-2005-06-2336","article-title":"Analysis of T-cell repertoire diversity in Wiskott-Aldrich syndrome","volume":"106","author":"Wada","year":"2005","journal-title":"Blood"},{"issue":"1","key":"10.1016\/j.jaut.2017.04.002_bib54","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/j.jaci.2014.06.025","article-title":"T-cell receptor diversity is selectively skewed in T-cell populations of patients with Wiskott-Aldrich syndrome","volume":"135","author":"Wu","year":"2015","journal-title":"J.\u00a0Allergy Clin. Immunol."},{"issue":"227","key":"10.1016\/j.jaut.2017.04.002_bib55","doi-asserted-by":"crossref","first-page":"227ra33","DOI":"10.1126\/scitranslmed.3007280","article-title":"Gene therapy for Wiskott-Aldrich syndrome\u2013long-term efficacy and genotoxicity","volume":"6","author":"Braun","year":"2014","journal-title":"Sci. Transl. Med."},{"issue":"1","key":"10.1016\/j.jaut.2017.04.002_bib56","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1111\/j.1365-2249.2004.02409.x","article-title":"Early deficit of lymphocytes in Wiskott-Aldrich syndrome: possible role of WASP in human lymphocyte maturation","volume":"136","author":"Park","year":"2004","journal-title":"Clin. Exp. Immunol."},{"issue":"2","key":"10.1016\/j.jaut.2017.04.002_bib57","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1073\/pnas.0610289104","article-title":"Lymphopenic mice reconstituted with limited repertoire T cells develop severe, multiorgan, Th2-associated inflammatory disease","volume":"104","author":"Milner","year":"2007","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"issue":"8","key":"10.1016\/j.jaut.2017.04.002_bib58","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1136\/jclinpath-2015-203351","article-title":"T-cell abnormalities in common variable immunodeficiency: the hidden defect","volume":"69","author":"Wong","year":"2016","journal-title":"J.\u00a0Clin. Pathol."},{"issue":"3","key":"10.1016\/j.jaut.2017.04.002_bib59","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1006\/clim.2000.4941","article-title":"Characterization of the T cell receptor repertoire in patients with common variable immunodeficiency: oligoclonal expansion of CD8(+) T cells","volume":"97","author":"Serrano","year":"2000","journal-title":"Clin. Immunol."},{"issue":"6","key":"10.1016\/j.jaut.2017.04.002_bib60","doi-asserted-by":"crossref","first-page":"3932","DOI":"10.4049\/jimmunol.178.6.3932","article-title":"Unravelling the complexity of T cell abnormalities in common variable immunodeficiency","volume":"178","author":"Giovannetti","year":"2007","journal-title":"J.\u00a0Immunol."},{"issue":"2","key":"10.1016\/j.jaut.2017.04.002_bib61","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/j.clim.2015.09.002","article-title":"High-throughput sequencing reveals an altered T cell repertoire in X-linked agammaglobulinemia","volume":"161","author":"Ramesh","year":"2015","journal-title":"Clin. Immunol."},{"issue":"5","key":"10.1016\/j.jaut.2017.04.002_bib62","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1182\/blood-2016-02-701029","article-title":"XLF deficiency results in reduced N-nucleotide addition during V(D)J recombination","volume":"128","author":"IJspeert","year":"2016","journal-title":"Blood"},{"issue":"4","key":"10.1016\/j.jaut.2017.04.002_bib63","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1128\/MCB.01057-12","article-title":"Cernunnos deficiency reduces thymocyte life span and alters the T cell repertoire in mice and humans","volume":"33","author":"Vera","year":"2013","journal-title":"Mol. Cell Biol."},{"key":"10.1016\/j.jaut.2017.04.002_bib64","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1111\/j.0105-2896.2004.00155.x","article-title":"Enforcing order within a complex locus: current perspectives on the control of V(D)J recombination at the murine T-cell receptor alpha\/delta locus","volume":"200","author":"Krangel","year":"2004","journal-title":"Immunol. Rev."},{"issue":"97","key":"10.1016\/j.jaut.2017.04.002_bib65","doi-asserted-by":"crossref","first-page":"97ra79","DOI":"10.1126\/scitranslmed.3002715","article-title":"Long-term persistence of a polyclonal T cell repertoire after gene therapy for X-linked severe combined immunodeficiency","volume":"3","author":"Gaspar","year":"2011","journal-title":"Sci. Transl. Med."},{"issue":"6","key":"10.1016\/j.jaut.2017.04.002_bib66","doi-asserted-by":"crossref","first-page":"e1000396","DOI":"10.1371\/journal.pcbi.1000396","article-title":"The dynamics of T-cell receptor repertoire diversity following thymus transplantation for DiGeorge anomaly","volume":"5","author":"Ciupe","year":"2009","journal-title":"PLoS Comput. Biol."},{"issue":"34","key":"10.1016\/j.jaut.2017.04.002_bib67","doi-asserted-by":"crossref","first-page":"36577","DOI":"10.18632\/oncotarget.5369","article-title":"Good syndrome presenting with CD8(+) T-Cell large granular lymphocyte leukemia","volume":"6","author":"Caperton","year":"2015","journal-title":"Oncotarget"},{"issue":"2","key":"10.1016\/j.jaut.2017.04.002_bib68","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1038\/nbt.2783","article-title":"Beyond model antigens: high-dimensional methods for the analysis of antigen-specific T cells","volume":"32","author":"Newell","year":"2014","journal-title":"Nat. Biotechnol."},{"issue":"5","key":"10.1016\/j.jaut.2017.04.002_bib69","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1016\/j.cell.2014.03.047","article-title":"Deconstructing the peptide-MHC specificity of T cell recognition","volume":"157","author":"Birnbaum","year":"2014","journal-title":"Cell"},{"issue":"3","key":"10.1016\/j.jaut.2017.04.002_bib70","doi-asserted-by":"crossref","first-page":"931","DOI":"10.4049\/jimmunol.1202466","article-title":"CD8+ TCR repertoire formation is guided primarily by the peptide component of the antigenic complex","volume":"190","author":"Koning","year":"2013","journal-title":"J.\u00a0Immunol."},{"issue":"47","key":"10.1016\/j.jaut.2017.04.002_bib71","doi-asserted-by":"crossref","first-page":"47ra64","DOI":"10.1126\/scitranslmed.3001442","article-title":"Overlap and effective size of the human CD8+ T cell receptor repertoire","volume":"2","author":"Robins","year":"2010","journal-title":"Sci. Transl. Med."},{"issue":"5","key":"10.1016\/j.jaut.2017.04.002_bib72","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/nri3442","article-title":"The integration of T cell migration, differentiation and function","volume":"13","author":"Masopust","year":"2013","journal-title":"Nat. Rev. Immunol."},{"issue":"308","key":"10.1016\/j.jaut.2017.04.002_bib73","doi-asserted-by":"crossref","first-page":"308ra158","DOI":"10.1126\/scitranslmed.aaa9122","article-title":"TCR sequencing facilitates diagnosis and identifies mature T cells as the cell of origin in CTCL","volume":"7","author":"Kirsch","year":"2015","journal-title":"Sci. Transl. Med."},{"issue":"32","key":"10.1016\/j.jaut.2017.04.002_bib74","doi-asserted-by":"crossref","first-page":"3766","DOI":"10.1200\/JCO.2015.61.7142","article-title":"Cutaneous lymphoma international consortium Study of outcome in advanced stages of mycosis fungoides and sezary syndrome: effect of specific prognostic markers on survival and development of a prognostic model","volume":"33","author":"Scarisbrick","year":"2015","journal-title":"J.\u00a0Clin. Oncol."},{"issue":"2","key":"10.1016\/j.jaut.2017.04.002_bib75","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1136\/annrheumdis-2014-206226","article-title":"A\u00a0circulating reservoir of pathogenic-like CD4+ T cells shares a genetic and phenotypic signature with the inflamed synovial micro-environment","volume":"75","author":"Spreafico","year":"2016","journal-title":"Ann. Rheum. Dis."},{"issue":"6","key":"10.1016\/j.jaut.2017.04.002_bib76","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1097\/MIB.0000000000000752","article-title":"Characterization of T-cell receptor repertoire in inflamed tissues of patients with Crohn's disease through deep sequencing","volume":"22","author":"Chapman","year":"2016","journal-title":"Inflamm. Bowel Dis."},{"issue":"6","key":"10.1016\/j.jaut.2017.04.002_bib77","doi-asserted-by":"crossref","first-page":"3643","DOI":"10.3892\/ol.2016.4465","article-title":"Characterization of the T cell repertoire by deep T cell receptor sequencing in tissues and blood from patients with advanced colorectal cancer","volume":"11","author":"Tamura","year":"2016","journal-title":"Oncol. Lett."},{"issue":"4","key":"10.1016\/j.jaut.2017.04.002_bib78","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1038\/cmi.2014.134","article-title":"Alphabeta T cell receptors as predictors of health and disease","volume":"12","author":"Attaf","year":"2015","journal-title":"Cell Mol. Immunol."},{"issue":"3 Suppl","key":"10.1016\/j.jaut.2017.04.002_bib79","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1016\/j.jaci.2012.07.002","article-title":"Use and interpretation of diagnostic vaccination in primary immunodeficiency: a working group report of the basic and clinical immunology interest section of the american academy of allergy, asthma & immunology","volume":"130","author":"Orange","year":"2012","journal-title":"J.\u00a0Allergy Clin. Immunol."},{"issue":"9","key":"10.1016\/j.jaut.2017.04.002_bib80","doi-asserted-by":"crossref","first-page":"e1002889","DOI":"10.1371\/journal.ppat.1002889","article-title":"Deep sequencing of antiviral T-cell responses to HCMV and EBV in humans reveals a stable repertoire that is maintained for many years","volume":"8","author":"Klarenbeek","year":"2012","journal-title":"PLoS Pathog."},{"issue":"1","key":"10.1016\/j.jaut.2017.04.002_bib81","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1128\/JVI.02180-12","article-title":"High frequency of herpesvirus-specific clonotypes in the human T cell repertoire can remain stable over decades with minimal turnover","volume":"87","author":"Neller","year":"2013","journal-title":"J.\u00a0Virol."},{"issue":"2","key":"10.1016\/j.jaut.2017.04.002_bib82","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1158\/2326-6066.CIR-16-0210","article-title":"Tumor-infiltrating Merkel cell polyomavirus-specific T cells are diverse and associated with improved patient survival","volume":"5","author":"Miller","year":"2017","journal-title":"Cancer Immunol. Res."},{"key":"10.1016\/j.jaut.2017.04.002_bib83","article-title":"Rapid and continued T cell differentiation into long-term effector and memory stem cells in vaccinated melanoma patients","author":"Gannon","year":"2016","journal-title":"Clin. Cancer Res."},{"issue":"6220","key":"10.1016\/j.jaut.2017.04.002_bib84","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1126\/science.1260668","article-title":"T\u00a0cell immunity. Functional heterogeneity of human memory CD4(+) T cell clones primed by pathogens or vaccines","volume":"347","author":"Becattini","year":"2015","journal-title":"Science"},{"issue":"301","key":"10.1016\/j.jaut.2017.04.002_bib85","doi-asserted-by":"crossref","first-page":"301ra131","DOI":"10.1126\/scitranslmed.aac5624","article-title":"High-throughput pairing of T cell receptor alpha and beta sequences","volume":"7","author":"Howie","year":"2015","journal-title":"Sci. Transl. Med."},{"issue":"1","key":"10.1016\/j.jaut.2017.04.002_bib86","doi-asserted-by":"crossref","first-page":"e1005313","DOI":"10.1371\/journal.pcbi.1005313","article-title":"Identifying T cell receptors from high-throughput sequencing: dealing with promiscuity in TCRalpha and TCRbeta pairing","volume":"13","author":"Lee","year":"2017","journal-title":"PLoS Comput. Biol."},{"issue":"2","key":"10.1016\/j.jaut.2017.04.002_bib87","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1038\/nbt.2492","article-title":"High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire","volume":"31","author":"DeKosky","year":"2013","journal-title":"Nat. Biotechnol."},{"issue":"35","key":"10.1016\/j.jaut.2017.04.002_bib88","doi-asserted-by":"crossref","first-page":"11073","DOI":"10.1021\/jacs.6b04465","article-title":"Reversible oligonucleotide chain blocking enables bead capture and amplification of T-cell receptor alpha and beta chain mRNAs","volume":"138","author":"Hanson","year":"2016","journal-title":"J.\u00a0Am. Chem. Soc."},{"issue":"3","key":"10.1016\/j.jaut.2017.04.002_bib89","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1038\/nprot.2016.024","article-title":"Ultra-high-throughput sequencing of the immune receptor repertoire from millions of lymphocytes","volume":"11","author":"McDaniel","year":"2016","journal-title":"Nat. Protoc."},{"issue":"9","key":"10.1016\/j.jaut.2017.04.002_bib90","doi-asserted-by":"crossref","first-page":"2507","DOI":"10.1002\/eji.201343453","article-title":"Pairing of T-cell receptor chains via emulsion PCR","volume":"43","author":"Turchaninova","year":"2013","journal-title":"Eur. J. Immunol."},{"issue":"6","key":"10.1016\/j.jaut.2017.04.002_bib91","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1038\/icb.2016.16","article-title":"Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells","volume":"94","author":"Eltahla","year":"2016","journal-title":"Immunol. Cell Biol."},{"issue":"1","key":"10.1016\/j.jaut.2017.04.002_bib92","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1186\/s13073-016-0335-7","article-title":"Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq","volume":"8","author":"Redmond","year":"2016","journal-title":"Genome Med."},{"issue":"17","key":"10.1016\/j.jaut.2017.04.002_bib93","doi-asserted-by":"crossref","first-page":"8292","DOI":"10.1093\/nar\/gkw700","article-title":"Selective single cell isolation for genomics using microraft arrays","volume":"44","author":"Welch","year":"2016","journal-title":"Nucleic Acids Res."},{"issue":"5","key":"10.1016\/j.jaut.2017.04.002_bib94","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","article-title":"Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets","volume":"161","author":"Macosko","year":"2015","journal-title":"Cell"},{"issue":"7","key":"10.1016\/j.jaut.2017.04.002_bib95","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1038\/nbt.2938","article-title":"Linking T-cell receptor sequence to functional phenotype at the single-cell level","volume":"32","author":"Han","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.jaut.2017.04.002_bib96","article-title":"TCR repertoire sequencing identifies synovial Treg cell clonotypes in the bloodstream during active inflammation in human arthritis","author":"Rossetti","year":"2016","journal-title":"Ann. Rheum. Dis."}],"container-title":["Journal of Autoimmunity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0896841117300963?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0896841117300963?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T08:16:20Z","timestamp":1760256980000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0896841117300963"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,6]]},"references-count":96,"alternative-id":["S0896841117300963"],"URL":"https:\/\/doi.org\/10.1016\/j.jaut.2017.04.002","relation":{},"ISSN":["0896-8411"],"issn-type":[{"value":"0896-8411","type":"print"}],"subject":[],"published":{"date-parts":[[2017,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Immune dysregulation in immunodeficiency disorders: The role of T-cell receptor sequencing","name":"articletitle","label":"Article Title"},{"value":"Journal of Autoimmunity","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jaut.2017.04.002","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2017 Elsevier Ltd. All rights reserved.","name":"copyright","label":"Copyright"}]}}