{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T14:31:27Z","timestamp":1790778687091,"version":"4.1.0"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,5,1]],"date-time":"2023-05-01T00:00:00Z","timestamp":1682899200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/100019527","name":"APRC","doi-asserted-by":"publisher","award":["9610471"],"award-info":[{"award-number":["9610471"]}],"id":[{"id":"10.13039\/100019527","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The specificity of a T-cell receptor (TCR) repertoire determines personalized immune capacity. Existing methods have modeled the qualitative aspects of TCR specificity, while the quantitative aspects remained unaddressed. We developed a package, TCRanno, to quantify the specificity of TCR repertoires. We created deep-learning-based, epitope-aware vector embeddings to infer individual TCR specificity. Then we aggregated clonotype frequencies of TCRs to obtain a quantitative profile of repertoire specificity at epitope, antigen and organism levels. Applying TCRanno to 4195 TCR repertoires revealed quantitative changes in repertoire specificity upon infections, autoimmunity and cancers. Specifically, TCRanno found cytomegalovirus-specific TCRs in seronegative healthy individuals, supporting the possibility of abortive infections. TCRanno discovered age-accumulated fraction of severe acute respiratory syndrome coronavirus 2 specific TCRs in pre-pandemic samples, which may explain the aggressive symptoms and age-related severity of coronavirus disease 2019. TCRanno also identified the encounter of Hepatitis B antigens as a potential trigger of systemic lupus erythematosus. TCRanno annotations showed capability in distinguishing TCR repertoires of healthy and cancers including melanoma, lung and breast cancers. TCRanno also demonstrated usefulness to single-cell TCRseq+gene expression data analyses by isolating T-cells with the specificity of interest.<\/jats:p>","DOI":"10.1093\/bib\/bbad175","type":"journal-article","created":{"date-parts":[[2023,5,7]],"date-time":"2023-05-07T23:02:06Z","timestamp":1683500526000},"source":"Crossref","is-referenced-by-count":7,"title":["Quantitative annotations of T-Cell repertoire specificity"],"prefix":"10.1093","volume":"24","author":[{"given":"Jiaqi","family":"Luo","sequence":"first","affiliation":[{"name":"Department of Computer Science, City University of Hong Kong , 83 Tat Tree Ave, Kowloon Tong, Hong Kong , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueying","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Computer Science, City University of Hong Kong , 83 Tat Tree Ave, Kowloon Tong, Hong Kong , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiping","family":"Zou","sequence":"additional","affiliation":[{"name":"Department of Computer Science, City University of Hong Kong , 83 Tat Tree Ave, Kowloon Tong, Hong Kong , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lingxi","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Computer Science, City University of Hong Kong , 83 Tat Tree Ave, Kowloon Tong, Hong Kong , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, City University of Hong Kong , 83 Tat Tree Ave, Kowloon Tong, Hong Kong , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Computer Science, City University of Hong Kong , 83 Tat Tree Ave, Kowloon Tong, Hong Kong , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuai Cheng","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Computer Science, City University of Hong Kong , 83 Tat Tree Ave, Kowloon Tong, Hong Kong , China"},{"name":"Department of Biomedical Engineering, City University of Hong Kong , 83 Tat Tree Ave, Kowloon Tong, Hong Kong , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,5]]},"reference":[{"key":"2023052022431157800_ref1","article-title":"Allelic variation in class I HLA determines CD8 + T cell repertoire shape and cross-reactive memory responses to SARS-CoV-2 MGH COVID-19 collection and processing team","author":"Francis","year":"2022","journal-title":"Sci Immunol"},{"key":"2023052022431157800_ref2","article-title":"A new way of exploring immunity\u2013linking highly multiplexed antigen recognition to immune repertoire and phenotype","author":"10x 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