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Antigens Involved in Adaptive Immunity01:26

Antigens Involved in Adaptive Immunity

An antigen is any substance the immune system identifies as foreign and potentially harmful to the body, prompting an immune response. Antigens have two functional properties: immunogenicity and reactivity. Immunogenicity is the ability of an antigen to stimulate a specific immune response. At the same time, reactivity describes the antigen's ability to react with the cells and antibodies produced in response to it.
Complete Antigens
Complete antigens possess both immunogenicity and reactivity.

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Immunogenetr: A comprehensive toolkit for clinical HLA informatics.

Busra Coskun1, Nicholas K Brown2

  • 1School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States.

Human Immunology
|December 4, 2025
PubMed
Summary

A new R package, immunogenetr, standardizes clinical human leukocyte antigen (HLA) data analysis. It facilitates informatics best practices and data alignment for HLA laboratories, improving data interpretation and workflows.

Keywords:
Genotype List stringHLA genotypingHLA matchingInformaticsLaboratory information systemR package

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Area of Science:

  • Bioinformatics
  • Immunogenetics
  • Computational Biology

Background:

  • Clinical human leukocyte antigen (HLA) data analysis lacks standardized informatics resources.
  • There is a need for tools that align clinical HLA data with established informatics best practices and data standards.

Purpose of the Study:

  • To develop an R package, immunogenetr, to facilitate the use of modern informatics processes for clinical HLA data.
  • To provide a resource for clinical HLA laboratories to adopt best practices in informatics and data standards.

Main Methods:

  • Developed the immunogenetr R package utilizing tidyverse principles.
  • Implemented the Genotype List (GL) string as the primary data structure for encoding complete HLA genotypes.
  • Included functions for data conversion, parsing, validation, searching, and matching/mismatching of HLA alleles.

Main Results:

  • The immunogenetr package offers functions for converting data to/from GL strings, validating allele names, and performing customizable matching/mismatching analyses.
  • Functions support host-versus-graft, graft-versus-host, and bidirectional comparisons with configurable mismatch counting.
  • The package is open-source and available on CRAN and GitHub, enabling broad accessibility.

Conclusions:

  • immunogenetr enables standardized HLA informatics analyses across clinical and research workflows.
  • The package promotes the adoption of best practices and data standards in clinical HLA data management.
  • This tool enhances the utility of modern informatics for clinical HLA laboratories.