Recovery of tumour-infiltrating lymphocyte TCR pairs using alphabetr and data from ref. [22].

The data were processed by associating chains with their tumour sources through exact matching of the CDR3 nucleotide sequences from the mixed tumour samples to CDR3 libraries obtained from blood samples from each patient. The data were then simplified by selecting only those chains associated with one tumour. We then used alphabetr to identify TCRαβ pairs. The numbers of pairs unambiguously identified in ref. [22] were determined by directly matching nucleotide sequences to the CDR3 libraries, and only those pairs for which both chains could be directly associated with the corresponding tumour sample were included in the analysis.