Fig. 5

Frequency of δ1 clonotypes present at >1 % in RE brain tissue. PCR fragments amplified with a Vδ1-specific forward primer were sequenced on a MiSeq DNA sequencing platform. Sequences were assigned to individual T cell clonotypes based on three criteria: (1) nucleotides coding for the last four amino acids of the variable (V) region, which contribute to the third complementarity determining region (the IMGT algorithm lists amino acid changes with respect to a reference Vδ1 sequence, which is shown in the figure, (2) the number and identity of diversity (D) gene segments, and (3) the identity of the joining (J) gene sequences. There are three possible D gene segments and four possible J gene segments. Clonotypes were selected from each sample that comprised >1 % of the total repertoire in each sample. Collectively, these 49 clonotypes made up more than 70 % of the repertoire of γδ T cells expressing Vδ1 in each of the RE brain tissue samples. Of these, several dominant clones were evident (bold-faced type). A heat map was generated from the quantitative data; the vertical columns show the relative abundance of each clonotype in each sample. The data are clustered to show which cases have the most similar repertoires. Additional file 3: Table S3 shows the quantitative data