Immuneaccess platform

Genomic data that support the findings of this study have been deposited in the immuneACCESS platform (Adaptive Biotechnologies, https://clients.adaptivebiotech.com/pub/pagliuca-2021-jcii). All other remaining data (including rearrangement details of the downsampled TCR data sets) are available within the article and supplement.

For sequencing of T-cell receptors (TCRs) to determine the clonality of TCPs, DNA was isolated using an All-Prep DNA/RNA Kit (Qiagen) following the manufacturer's instructions. TCRβ sequencing was performed using a hsTCRb Kit (Adaptive Biotechnologies) following the manufacturer's instructions and analyzed with the corresponding ImmunoSEQ-Analyzer 3.0 software. Briefly, the most variable complementary-determining region 3 (CDR3), spanning the recombination site of V-D-J recombinations of TCR β-chains was sequenced. Productive rearrangements were regarded as unique in-frame nucleotide sequences without stop codon, leading to a functional TCR. Productive frequency means the individual frequency of a specific productive rearrangement (clone) among all productive rearrangements. Clonality was calculated based on productive entropy normalized to the total number of productive rearrangements. Sample overlap was investigated using the Morisita index considering unique clones, individual frequencies of clones and the probability of a common origin of two samples. TCR sequencing data is accessible at the ImmuneACCESS platform http://adaptivebiotech.com/pub/amini-2019-frontimmunol (Adaptive Biotechnologies).