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. 2023 Jan 5;29(1):258–269. doi: 10.1038/s41591-022-02110-9

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 10 — Box and whisker plot showing frequencies of (a) mucosal associated invariant T (MAIT) cells, (b) γδ T cells, (c), germline-encoded mycolyl lipid-reactive (GEM) T cells, and (d) invariant natural killer T (iNKT) cells, estimated from canonical TCR CDR3α sequences in PBMC samples collected from controllers (n = 77) and progressors (n = 61). Mucosal associated invariant T cells (MAIT), gammadelta, iNKT, and germline-encoded, mycolyl lipid reactive (GEM) T cells were defined as MAIT match score >=0.95, TCRDJ gene, TCRAV10;TCRAJ18 CVVSDRGSTLGRLYF, and TCRAV01-02;TCRAJ09 CAV[RL].TGGFKTIF, respectively, with ‘[]’ containing the permitted amino acid and ‘.’ denoting any amino acid. The horizontal lines represent medians, the bounds of the boxes indicate the 25% and 75% percentile and the whiskers represent the minima and maxima. Each dot represents an individual sample (controllers, n = 77; progressors, n = 61). The Mann-Whitney U test (two-sided) was used to compare frequencies between groups. P-values have not been corrected for multiple comparisons.