Experimental validation of the RATE tool for inferring HLA restrictions of T cell epitopes

BMC Immunology

Research

Cecilia S. Lindestam Arlehamn¹  Alessandro Sette¹  John Sidney¹  Bjoern Peters¹  Luise Westernberg¹  Sinu Paul¹  Veronique Schulten¹ 

[1]Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, 92037, San Diego, CA, USA

关键词: HLA restriction;    HLA association;    MHC;    Epitope;    T cell;    RATE;   

DOI  :  10.1186/s12865-017-0204-1

来源: Springer

【 摘 要 】

BackgroundThe RATE tool was recently developed to computationally infer the HLA restriction of given epitopes from immune response data of HLA typed subjects without additional cumbersome experimentation.ResultsHere, RATE was validated using experimentally defined restriction data from a set of 191 tuberculosis-derived epitopes and 63 healthy individuals with MTB infection from the Western Cape Region of South Africa. Using this experimental dataset, the parameters utilized by the RATE tool to infer restriction were optimized, which included relative frequency (RF) of the subjects responding to a given epitope and expressing a given allele as compared to the general test population and the associated p-value in a Fisher’s exact test. We also examined the potential for further optimization based on the predicted binding affinity of epitopes to potential restricting HLA alleles, and the absolute number of individuals expressing a given allele and responding to the specific epitope. Different statistical measures, including Matthew’s correlation coefficient, accuracy, sensitivity and specificity were used to evaluate performance of RATE as a function of these criteria. Based on our results we recommend selection of HLA restrictions with cutoffs of p-value < 0.01 and RF ≥ 1.3. The usefulness of the tool was demonstrated by inferring new HLA restrictions for epitope sets where restrictions could not be experimentally determined due to lack of necessary cell lines and for an additional data set related to recognition of pollen derived epitopes from allergic patients.ConclusionsExperimental data sets were used to validate RATE tool and the parameters used by the RATE tool to infer restriction were optimized. New HLA restrictions were identified using the optimized RATE tool.

【 授权许可】

CC BY   
© The Author(s). 2017