Characterization of the novel HLA‐DQA1*05:05:14 allele by sequencing‐based typing

Abstract

HLA‐DQA1*05:05:14 differs from HLA‐DQA1*05:05:01:04 by one nucleotide substitution in codon −8 in exon 1.

We report here a novel HLA‐DQA1*05:05 allele, now named DQA1*05:05:14 that carries one nucleotide substitution in exon 1 when compared to the DQA1*05:05:01:04 allele, identified in a volunteer bone marrow donor. The HLA typing was performed using Next Generation Sequencing (AllType NGS, One Lambda, Canoga Park, CA) on the Ion S5 system platform (ThermoFisher Scientific, Waltham, MA), ¹ from exons 1 to 4. The reads were analyzed using the TypeStream Visual Software version 2.1 (One Lambda). This donor was found to have a new DQA1*05:05 allele and was consequently typed A*02:01, 32:01; B*14:02, 44:02; C*02:02, 07:04; DRB1*11:01, 11:01; DRB3*02:02, 02:02; DQA1*05:05:01, 05:05:14; DQB1*03:01P, 03:01P; DPA1*01:03, 01:03; DPB1*02:01, 04:02. Using the IPD‐IMGT/HLA Database, ² nucleotide sequence alignment with HLA‐DQA1 alleles shows that this new allele has one nucleotide change from DQA1*05:05:01:04 in codon −8 in exon 1, where C → T, (ACC → ACT, Figure 1), not resulting in a coding change. This nucleotide change was confirmed by performing the typing twice in two different laboratories. We were confident in the phasing as the sample displayed a mean read length of 332 base pairs over all the loci, the mismatched A base was attributed 76 times to the new HLA‐DQA1*05:05. The nucleotide sequence of the exons 1–4 of the new allele has been submitted to the GenBank database (Accession No. OP393478) and to the IPD‐IMGT/HLA Database (Submission No. HWS10062886). The name DQA1*05:05:14 has been officially assigned by the WHO Nomenclature Committee for Factors of the HLA System in September 2022. This follows the agreed policy that, subject to the conditions stated in the most recent Nomenclature Report, ³ 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 1 of HLA‐DQA1*05:05:14 with the sequence of HLA‐DQA1*05:05:01:04. Dashes indicate nucleotide identity with the HLA‐DQA1*05:05:01:04 allele. Numbers above the sequence indicate codon position.

AUTHOR CONTRIBUTIONS

Marine Cargou and Jonathan Visentin contributed to the design of the study. Marine Cargou and Jonathan Visentin participated in the writing of the paper. Marine Cargou, Marco Andreani, Mariarosa Battarra, Mamy Ralazamahaleo and Jonathan Visentin participated in the performance of the research. Marine Cargou, Marco Andreani, Mariarosa Battarra, Mamy Ralazamahaleo and Jonathan Visentin participated in data analysis. Marco Andreani, Mariarosa Battarra and Mamy Ralazamahaleo were involved in critical revision of the manuscript.

CONFLICT OF INTEREST

The authors confirm that there are no conflicts of interest.

Cargou M, Andreani M, Battarra M, Ralazamahaleo M, Visentin J. Characterization of the novel HLA‐DQA1*05:05:14 allele by sequencing‐based typing. HLA. 2023;101(3):299‐300. doi: 10.1111/tan.14902

DATA AVAILABILITY STATEMENT

The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions. The sequence is freely available in the IPD‐IMGT/HLA Database.