Characterisation of the Novel HLA‐A*02:1295N Allele by Sequencing‐Based Typing

ABSTRACT

HLA‐A*02:1295N differs from HLA‐A*02:02:01:01 by one nucleotide substitution in codon 157 in exon 3.

We report here a novel HLA‐A*02 allele, now named A*02:1295N that carries one nucleotide substitution in exon 3 when compared to the A*02:02:01:01 allele, identified in a potential bone marrow donor. The HLA typing was performed using Next Generation Sequencing reagents provided by GenDX NGSgo‐MX6‐1 (Utrecht, Netherlands) run on the Illumina MiSeq system (San Diego, CA). The reads were analysed using NGSEngine software (GenDX, version 3.3). The subject was found to have a new A*02 allele and was consequently typed as HLA‐A*02:1295N, 36:01; ‐C*04:01, 16:01; ‐B*15:16, 53:01; ‐DRB1*01:02, 09:01; ‐DQB1*02:02, 05:01; ‐DPB1*13:01, 835:01. Using the IPD‐IMGT/HLA Database [1], nucleotide sequence alignment with HLA‐A alleles shows that this new allele has one nucleotide change from A*02:02:01:01 in codon 157 of exon 3, where A → T, resulting in a coding change (codon 157: AGA → TGA, Arginine → STOP, Figure 1). This is the first time this polymorphism has been described in an HLA‐A allele. This nucleotide change was confirmed using Next Generation Sequencing reagents provided by One Lambda (AllType NGS, Canoga Park, CA) run on the Miseq system platform (Illumina, San Diego, CA). The reads were analysed using the TypeStream Visual Software version 3.1 (One Lambda, Canoga Park, CA). The nucleotide sequence of the new allele has been submitted to the GenBank database (accession number PX965950) and to the IPD‐IMGT/HLA Database (Submission No. HWS10103030). The name A*02:1295N has been officially assigned by the WHO Nomenclature Committee for Factors of the HLA System in April 2026. This follows the agreed policy that, subject to the conditions stated in the most recent Nomenclature Report [2], names will be assigned to new sequences as they are identified. Lists of such new names will be published in the following WHO Nomenclature Report.

FIGURE 1.

Alignment of the sequence of exon 3 of A*02:1295N with the sequence of A*02:02:01:01. Dashes indicate nucleotide identity with the HLA‐A*02:02:01:01 allele. Numbers above the sequence indicate codon position.

Conflicts of Interest

The authors declare no conflicts of interest.

Data Availability Statement

The data that support the findings of this study are available from the corresponding author upon reasonable request. The sequence is freely available in the IPD‐IMGT/HLA Database.