Adaptive Receptor Repertoire Profiling (ARRP) unit
The set of T cell and B cell antigen receptor proteins found in a blood or tissue sample, known as the repertoire, provide a window into underlying immune responses.
Consequently, repertoire analysis is becoming an essential component in the study of cancer, infectious diseases and autoimmunity, providing fundamental insights into disease pathogenesis and valuable biomarkers for diagnosis, prognosis and disease monitoring.
Anticipating the key role of repertoire analysis in immunology research, the Division of Infection and Immunity set up the Adaptive Receptor Sequencing Unit in 2021, initially funded by a grant from the Rosetrees Foundation, and now operating on a cost recovery model.
The Unit supports projects funded by multiple funders, including the Wellcome Trust, UK-RI and Cancer Research UK.
What does the unit do?
The unit is based on exploiting novel experimental and computational pipelines for the analysis of T cell receptor repertoires developed by Professor Benny Chain’s research group. It is involved with multiple collaborations within UCL and elsewhere.
The work of the unit involves three Distinct Components:
TCR Sequencing Unit.
The Sequencing Unit is located in UCL Cruciform Building. The Unit processes samples to prepare libraries for sequencing.
For example, the unit provides the T cell receptor repertoire sequencing for the TRACERx lung cancer study, identifying how tumor genetic heterogeneity impacts the host immune response.
Low Level Processing
Once the libraries are sequenced, the fastq files are processed to allow for:
Decombinator which is a fast and efficient tool for the analysis of T-cell receptor (TCR) repertoire sequences produced by deep sequencing.
The low level processing pipeline is broken into three stages from the fastq files:
1) Decombinator
2) Collapsinator
3) Translator
High Level Processing
The ARRP unit has also developed tools to allow for further and more in-depth analysis. Tools such as :
Pyrepseq: the immune repertoire analysis toolkit. This is toolkit can be used for studying adaptive immunity: modular implementations of algorithms for fast analyses, and bespoke plotting functions for compelling visualization
SCEPTR (Simple Contrastive Embedding of the Primary sequence of T cell Receptors) is a small, fast, and performant TCR representation model that can be used for alignment-free downstream TCR and TCR repertoire analysis such as TCR clustering or classification.
