Identification of the novel HLA-A*24:585:02 allele using next-generation sequencing

Abstract

We identified a novel HLA-A*24 allele, now named HLA-A*24:585:02, identified using next-generation sequencing (NGS). This new allele carries three nucleotide substitutions in exon 1 when compared with the HLA-A*24:02:01:01 allele.

The HLA-A*24:585:02 allele was identified in a Korean donor of hematopoietic stem cell transplantation. The HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1 and -DQB1 loci were typed using commercial reagents provided in the AllType NGS Assay kit (One Lambda, Inc., Canoga Park, CA). The library was sequenced on an Illumina NextSeq system platform (Illumina, San Diego, CA). Sequences were analyzed using the TypeStream Visual NGS analysis software (version 3.0.0; One Lambda, Inc.) and the IPD-IMGT/HLA database (version 3.49.0.0; http://www.ebi.ac.uk/ipd/imgt/hla/).1

The sequence of the HLA-A*24:585:02 allele showed three nucleotide changes when compared to the HLA-A*24:02:01:01 allele. These altered nucleotides were identified to be guanine (G) instead of cytosine (C) in codon −16.3 at position 27, cytosine (C) instead of guanine (G) in codon −15.1 at position 28 and thymine (T) instead of cytosine (C) in codon −15.3 at position 30 of exon 1 (Figure 1). The nucleotide substitution in codon −16 did not result in a coding change. The nucleotides substitutions in codon −15 resulted in change from Valine (GTC) to Leucine (CTT). The sequence of the HLA-A*24:585:02 allele also showed differences from the HLA-A*24:585:01 allele, with guanine (G) instead of cytosine (C) in codon −16.3 at position 27 and thymine (T) instead of cytosine (C) in codon −15.3 at position 30 of exon 1. The nucleotide substitutions did not result in a coding change. The extended HLA typing result for the donor with the new allele was as follows: HLA-A*02:06:01:01, 24:585:02; -B*15:01:01:01, 46:01:01:01; -C*01:02:01:01, 04:01:01:11; -DRB1*08:03:02:02, 14:02:01:01; -DRB3*01:01:02:01; -DQA1*01:03:01:07, 05:03:01:02; -DQB1*03:14:01, 06:01:01:01.