Journal: bioRxiv

Article Title: A generative reference grammar of healthy TCR repertoires reveals cancer-associated immune remodeling

doi: 10.64898/2026.04.29.721631

Figure Lengend Snippet: Overview of the CRAFT framework for learning a healthy-donor TCR embedding space and quantifying cancer-associated repertoire perturbation. (a) CRAFT model architecture. V, D, and J germline gene segments are tokenized using a hierarchical IMGT-based vocabulary (family, subfamily, allele) and encoded by a bidirectional encoder. An autoregressive decoder with two parallel output heads (V-D and D-J junctions) reconstructs CDR3-beta nucleotide sequences using character-level (A, C, G, T) tokenization, reflecting the known independence of V-D and D-J recombination events. (b) Model training on bulk TCR-beta repertoires from 666 healthy donors using multi-phase curriculum training with progressively increasing sequence complexity. (c) Model inference and embedding extraction via teacher-forced inference, with mean-pooled hidden states from both decoder heads concatenated to form the full CRAFT embedding. (d) Cancer repertoire profiling in the healthy-donor-derived reference space using geometric metrics.

Article Snippet: Bulk TCR-beta sequencing data from 666 healthy donors used for model training were obtained from Emerson et al. and are available through the Adaptive Biotechnologies immuneACCESS repository ( https://clients.adaptivebiotech.com/pub/emerson-2017-natgen ).

Techniques: CRAfT Assay, Sequencing, Extraction, Derivative Assay

Journal: JCI Insight

Article Title: Endothelial MHC expression is required to initiate T cell–mediated rejection of 3D-printed skin grafts

doi: 10.1172/jci.insight.201946

Figure Lengend Snippet: High-throughput sequencing of the β chain of T cell receptors. x and y axes show total amount of productive TCR β sequences in the skin or spleen samples with 1–2 immunodominant clones in 2 of 3 pairs of investigated samples.

Article Snippet: Comprehensive analysis of the TCR receptor β chain was performed by Adaptive Biotechnologies to assess the clonality of infiltrating lymphocytes in skin grafts and spleens of 3 different skin donors, all with the same HSC and PBMC donor (FFPE curls, 50 �m).

Techniques: Next-Generation Sequencing, Clone Assay