Immunogenetr: a comprehensive toolkit for clinical HLA informatics

IF 2.1 4区医学 Q3 IMMUNOLOGY

Human Immunology Pub Date : 2026-01-01 Epub Date: 2025-12-03 DOI:10.1016/j.humimm.2025.111619

Busra Coskun , Nicholas K. Brown

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引用次数: 0

Abstract

There is significant interest in using modern informatics processes for clinical HLA data, but there are few resources developed for clinical use. To help clinical HLA laboratories make use of best practices in informatics and align with published data standards, we developed immunogenetr for the R programming language. immunogenetr was built with tidyverse functions and principles, and uses Genotype List (GL) string, which encodes complete HLA genotypes, including ambiguities, in a single human- and machine-readable object, as the primary data structure. The package includes functions to easily convert HLA genotyping data to and from GL strings, parse and rebuild GL strings, validate and truncate allele names, search for specific alleles within a GL string, and perform matching and mismatching. The functions are highly customizable, with matching and mismatching functions including options for host-versus-graft, graft-versus-host, and bidirectional comparisons, along with configurable homozygous mismatch counting, aligned with published guidelines. The package is open-source and available on CRAN and GitHub. This manuscript gives an overview of immunogenetr, with examples of how the functions can be used in informatics pipelines. Together, this package enables standardized HLA informatics analyses across clinical and research workflows.

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免疫遗传学：临床HLA信息学的综合工具包。

人们对使用现代信息学方法获取临床HLA数据非常感兴趣，但用于临床使用的资源很少。为了帮助临床HLA实验室利用信息学的最佳实践并与已发布的数据标准保持一致，我们开发了针对R编程语言的免疫基因。immunogenetr采用了tidyverse的功能和原理，并使用基因型列表（GL）字符串作为主要数据结构，该字符串在单个人类和机器可读对象中编码完整的HLA基因型（包括歧义）。该软件包包括一些功能，可以轻松地将HLA基因分型数据与GL字符串进行转换，解析和重建GL字符串，验证和截断等位基因名称，在GL字符串中搜索特定的等位基因，以及执行匹配和不匹配。这些功能是高度可定制的，具有匹配和不匹配功能，包括宿主对移植物、移植物对宿主和双向比较选项，以及可配置的纯合不匹配计数，与已发布的指南保持一致。该软件包是开源的，可以在CRAN和GitHub上获得。这篇手稿给出了免疫遗传学的概述，并举例说明如何在信息学管道中使用这些功能。总之，该软件包能够在临床和研究工作流程中进行标准化的HLA信息学分析。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Human Immunology 医学-免疫学

CiteScore

5.40

自引率

7.40%

发文量

107

审稿时长

12 days

期刊介绍： The journal''s scope includes understanding the genetic and functional mechanisms that distinguish human individuals in their immune responses to allografts, pregnancy, infections or vaccines as well as the immune responses that lead to autoimmunity, allergy or drug hypersensitivity. It also includes examining the distribution of the genes controlling these responses in populations. Research areas include: Studies of the genetics, genomics, polymorphism, evolution, and population distribution of immune-related genes Studies of the expression, structure and function of the products of immune-related genes Immunogenetics of susceptibility to infectious and autoimmune disease, and allergy The role of the immune-related genes in hematopoietic stem cell, solid organ, and vascularized composite allograft transplant Histocompatibility studies including alloantibodies, epitope definition, and T cell alloreactivity Studies of immunologic tolerance and pregnancy T cell, B cell, NK and regulatory cell functions, particularly related to subjects within the journal''s scope Pharmacogenomics and vaccine development in the context of immune-related genes Human Immunology considers immune-related genes to include those encoding classical and non-classical HLA, KIR, MIC, minor histocompatibility antigens (mHAg), immunoglobulins, TCR, BCR, proteins involved in antigen processing and presentation, complement, Fc receptors, chemokines and cytokines. Other immune-related genes may be considered. Human Immunology is also interested in bioinformatics of immune-related genes and organizational topics impacting laboratory processes, organ allocation, clinical strategies, and registries related to autoimmunity and transplantation.