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Fig. 6 | Genome Medicine

Fig. 6

From: Exploring the pre-immune landscape of antigen-specific T cells

Fig. 6

Epitope-specific TCRα-TCRβ heterodimer frequencies can be estimated using TCRβ clonotype frequencies. a, b Matching paired TCRα-TCRβ sequencing data (PairSEQ assay, Howie et al.) against VDJdb. a Scatter plot of TCRα and TCRβ chain rearrangement frequencies matching a given epitope. b Product of marginal frequencies of TCRα and TCRβ chain rearrangements (i.e., TCR heterodimer frequencies assuming independent pairing) plotted against the frequencies of paired-chain records matching the same epitopes. Mean frequencies were computed as follows: (number of matching rearrangements)/(number of records in VDJdb for a given epitope)/(total number of rearrangements in the PairSEQ dataset). c As in a, but using TCRα and TCRβ frequencies estimated using the TCR rearrangement model. d As in b, but using TCRα and TCRβ frequencies estimated using the TCR rearrangement model. e Conditions required to estimate baseline T cell frequencies using TCRβ rearrangement frequencies alone. f Scatter plot of the mean theoretical rearrangement probabilities for TCRβ chain and paired TCRα-TCRβ chain rearrangements matching a given epitope. Epitopes lacking paired TCRα-TCRβ sequences, as well as epitopes represented by less than 30 TCRα or TCRβ sequences according to VDJdb, were excluded from the analysis. This figure uses 3-letter epitope abbreviations (see Additional file 1: Table S3 for full epitope names)

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