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dc.contributor.authorLi, Boen_US
dc.contributor.authorLi, Taiwenen_US
dc.contributor.authorPignon, Jean-Christopheen_US
dc.contributor.authorWang, Binbinen_US
dc.contributor.authorWang, Jinzengen_US
dc.contributor.authorShukla, Sacheten_US
dc.contributor.authorDou, Ruoxuen_US
dc.contributor.authorChen, Qianmingen_US
dc.contributor.authorHodi, F. Stephenen_US
dc.contributor.authorChoueiri, Toni K.en_US
dc.contributor.authorWu, Catherineen_US
dc.contributor.authorHacohen, Niren_US
dc.contributor.authorSignoretti, Sabinaen_US
dc.contributor.authorLiu, Jun S.en_US
dc.contributor.authorLiu, X. Shirleyen_US
dc.date.accessioned2017-03-28T23:51:36Z
dc.date.issued2016en_US
dc.identifier.citationLi, B., T. Li, J. Pignon, B. Wang, J. Wang, S. Shukla, R. Dou, et al. 2016. “Landscape of tumor-infiltrating T cell repertoire of human cancers.” Nature genetics 48 (7): 725-732. doi:10.1038/ng.3581. http://dx.doi.org/10.1038/ng.3581.en
dc.identifier.issnen
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:31731849
dc.description.abstractWe developed a computational method to infer the complementarity determining region 3 (CDR3) sequences of tumor infiltrating T-cells in 9,142 RNA-seq samples across 29 cancer types. We identified over 600 thousand CDR3 sequences, including 15% with full-length. CDR3 sequence length distribution and amino acid conservation, as well as variable gene usage of infiltrating T-cells in many tumors, except brain and kidney cancers, resembled those in the peripheral blood of healthy donors. We observed a strong association between T-cell diversity and tumor mutation load, and predicted SPAG5 and TSSK6 as putative immunogenic cancer/testis antigens in multiple cancers. Finally, we identified 3 potential immunogenic somatic mutations based on their co-occurrence with CDR3 sequences. One of them, PRAMEF4 F300V, was predicted to bind strongly to both MHC-I and MHC-II, with matched HLA types in its carriers. Our analyses have the potential to simultaneously identify immunogenic neoantigens and the tumor-reactive T-cell clonotypes.en
dc.language.isoen_USen
dc.relation.isversionofdoi:10.1038/ng.3581en
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC5298896/pdf/en
dash.licenseLAAen_US
dc.titleLandscape of tumor-infiltrating T cell repertoire of human cancersen
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden
dc.relation.journalNature geneticsen
dash.depositing.authorLi, Boen_US
dc.date.available2017-03-28T23:51:36Z
dc.identifier.doi10.1038/ng.3581*
dash.authorsorderedfalse
dash.contributor.affiliatedLiu, Jun
dash.contributor.affiliatedLi, Bo
dash.contributor.affiliatedPignon, Jean-Christophe
dash.contributor.affiliatedSignoretti, Sabina
dash.contributor.affiliatedHacohen, Nir


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