Immunogenetr: A comprehensive toolkit for clinical HLA informatics.

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.