This is a project which is currently making use of HPC facilities at Newcastle University. It is active.
For further information about this project, please contact:
Resident memory T cells are implicated in numerous interstitial lung diseases. Current strategies for treatment are of varying benefit, with some of these diseases having no proven pharmacological treatment. Interrogating the specificity of the T cells driving disease may yield new treatment strategies. This project aims to use immune receptor sequencing and clustering to identify disease-associated T cells, and will take advantage of T cell receptor publicity to identify groups of patients with shared disease aetiologies.
Python (inc. scikit-learn and Tensorflow), bash command line tools for NGS data processing and TRUST4/T1K will be used to sequence immune receptors and infer HLA genotypes from samples. Clustering of immune receptors will be undertaken using tcrdist3, to define neighbourhoods of receptors that are plausibly related to the same antigen. OLGA will be used to determine the probability of generation of T cell receptor sequences in order to aid identification of antigen-associated expansions.