# A Gene Feature Enumeration Approach for Describing HLA Allele Polymorphism

## TL;DR

This paper introduces a new system for describing HLA gene polymorphism by enumerating gene features, enabling more detailed analysis of sequence variation.

## Contribution

The paper proposes a novel system for describing HLA polymorphism through gene feature enumeration, allowing granular analysis even without antigen-recognition domain data.

## Key findings

- A gene feature enumeration system is proposed to describe HLA polymorphism in terms of gene features.
- The system allows for detailed dissection of HLA polymorphism at the gene feature level.
- The approach enables analysis of gene features even when antigen-recognition domain exons are absent.

## Abstract

HLA genotyping via next generation sequencing (NGS) poses challenges for the use of HLA allele names to analyze and discuss sequence polymorphism. NGS will identify many new synonymous and non-coding HLA sequence variants. Allele names identify the types of nucleotide polymorphism that define an allele (non-synonymous, synonymous and non-coding changes), but do not describe how polymorphism is distributed among the individual features (the flanking untranslated regions, exons and introns) of a gene. Further, HLA alleles cannot be named in the absence of antigen-recognition domain (ARD) encoding exons. Here, a system for describing HLA polymorphism in terms of HLA gene features (GFs) is proposed. This system enumerates the unique nucleotide sequences for each GF in an HLA gene, and records these in a GF enumeration notation that allows both more granular dissection of allele-level HLA polymorphism, and the discussion and analysis of GFs in the absence of ARD-encoding exon sequences.

Antigen Recognition Domain

European Molecular Biology Laboratory

Gene Feature

Gene Feature Enumeration

Human Leucocyte Antigen

International HLA and Immunogenetics Workshop

ImMunoGeneTics

Next Generation Sequencing

Untranslated Region