Feb 15, 2015

A Gene Feature Enumeration Approach for Describing HLA Allele Polymorphism

BioRxiv : the Preprint Server for Biology
Steven J Mack

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. ARD : Antigen Recognition Domain EMLB : European Molecular Biology Laboratory GF : Gene Feature GFE : Gene Feature Enumeration HLA : Human Leucocyte Antigen IHIW : International HLA and Immunogenetics Workshop IMGT : ImMunoGeneTics NGS...Continue Reading

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Mentioned in this Paper

Gene Polymorphism
GATA1 protein, human
Untranslated Regions
Exons
Genes
ADI1
HLA Antigens
Molecular Biology Shared Resource
TAPBP protein, human
Massively-Parallel Sequencing

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