Nomenclature for factors of the HLA system, 2010

Recognition of the HLA-DQB1*03:96 allele in a Taiwanese individual

One nucleotide substitution in codon 130 of HLA-DQB1*03:03:02:01 results in a novel allele HLA-DQB1*03:96.

Genomic full-length sequence of the novel HLA-C*06:364 allele

HLA-C*06:364 differs from HLA-C*06:02:01:01 by a non-synonymous nucleotide substitution in exon 3.

The novel HLA-B*15:02:15 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual

HLA-B*15:02:15 differs from HLA-B*15:02:01:01 by one nucleotide in exon 2.

Identification of the novel HLA-DPA1*02:07:04 allele by next-generation sequencing

The novel HLA-DPA1*02:07:04 allele was detected during the HLA typing for kidney transplantation.

Characterisation of two new HLA-A alleles: HLA-A*01:454 and HLA-A*31:229

HLA-A*01:454 and HLA-A*31:229, two novel HLA-A alleles detected during routine typing by next-generation sequencing.

Identification of the novel HLA-DPB1*1591:01 allele by next-generation sequencing

The novel HLA-DPB1*1591:01 allele was detected during the HLA typing for kidney transplantation.

The novel HLA-DPB1*05:01:20 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual

HLA-DPB1*05:01:20 differs from HLA-DPB1*05:01:01:01 by one nucleotide in exon 3.

Identification of the novel HLA-DRB1*11:298 allele in a Chinese cord blood donor

HLA-DRB1*11:298 shows one single nucleotide substitution at position 397 T>G compared with HLA-DRB1*11:01:01:01.

Characterisation of the novel HLA-C*15:274 allele using short and long-read sequencing technologies

The novel HLA-C*15:274 allele, first described in a potential bone marrow donor from Brazil.

Characterisation of the novel HLA-C*08:275 allele, first identified in a Brazilian individual

The novel HLA-C*08:275 allele, first described in a potential bone marrow donor from Brazil.

Characterisation of two novel HLA-DRB1 alleles, HLA-DRB1*04:01:24 and HLA-DRB1*13:353

Two novel HLA-DRB1 alleles were detected using next generation sequencing.

Genomic sequence of five new variants of HLA-DQA1 in non-coding regions

Characterisation of HLA-DQA1*01:02:01:30, HLA-DQA1*01:03:01:14, HLA-DQA1*03:03:01:20, HLA-DQA1*04:01:01:13, HLA-DQA1*05:05:01:40 alleles in Spanish individuals.

Characterisation of the novel HLA-B*35:593 allele using short and long-read sequencing technologies

The novel HLA-B*35:593 allele, first described in a potential bone marrow donor from Brazil.

The novel HLA-C*14:155 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual

HLA-C*14:155 differs from HLA-C*14:02:01:01 by one nucleotide in exon 1.

The novel HLA-B*15:659 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual

HLA-B*15:659 differs from HLA-B*15:02:01:01 by one nucleotide in exon 2.

The novel HLA-C*03:652 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual

HLA-C*03:652 differs from the HLA-C*03:04:01:01 by one nucleotide in exon 3.

A novel HLA-C*03 variant, HLA-C*03:620, identified in a Chinese individual

HLA-C*03:620 differs from the HLA-C*03:04:01:02 allele by one nucleotide substitution in the exon 3.

The HLA-DRB1*12:92 and HLA-DRB1*12:101 alleles were identified by next-generation sequencing

Compared with HLA-DRB1*12:02, the alleles HLA-DRB1*12:92 and HLA-DRB1*12:101 each show one nucleotide substitution respectively.

Two new HLA-DQB1*03:02:01 variants with substitutions in intron 2: HLA-DQB1*03:02:01:19 and -DQB1*03:02:01:21

Two different single nucleotide substitutions in intron 2 give rise to novel HLA-DQB1*03:02:01 alleles.

Identification of the novel HLA-DQA1*02:32 allele by next-generation sequencing

HLA-DQA1*02:32 differs from DQA1*02:01:01 by one nucleotide substitution in codon 210 in exon 4.

Two novel HLA class II alleles, HLA-DRB1*09:57 and HLA-DRB1*09:58 in Chinese individuals

Compared with HLA-DRB1*09:01:02:05, the alleles HLA-DRB1*09:57 and HLA-DRB1*09:58 each show one nucleotide change, respectively.

Characterisation of the novel HLA-A*30:218 allele using two different sequencing technologies

The novel HLA-A*30:218 allele, first described in a potential bone marrow donor from Brazil.

The novel HLA-A*24:627 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual

The HLA-A*24:627 allele differs from HLA-A*24:02:01:01 by one nucleotide substitution in codon 172 in exon 2.

The novel HLA-DPA1*02:86 allele was identified by next-generation sequencing

HLA-DPA1*02:86 differs from HLA-DPA1*02:01:01 by a single nucleotide substitution at position 680 C > A in exon 4.

Characterization of the novel HLA-A*31:01:53 allele by next generation sequencing in a Chinese individual

HLA-A*31:01:53 differs from HLA-A*31:01:02:01 by one nucleotide change at nucleotide 900 in exon 5 from G to A.

Characterisation of the novel HLA-A*02:1140 allele, first identified in a Brazilian individual

The novel HLA-A*02:1140 allele, first described in a potential bone marrow donor from Brazil.

The HLA region in ANCA-associated vasculitis: characterisation of genetic associations in a Scandinavian patient population

OBJECTIVE

The antineutrophil cytoplasmic antibody (ANCA)-associated vasculitides (AAV) are inflammatory disorders with ANCA autoantibodies recognising either proteinase 3 (PR3-AAV) or myeloperoxidase (MPO-AAV). PR3-AAV and MPO-AAV have been associated with distinct loci in the human leucocyte antigen (HLA) region. While the association between MPO-AAV and HLA has been well characterised in East Asian populations where MPO-AAV is more common, studies in populations of European descent are limited. The aim of this study was to thoroughly characterise associations to the HLA region in Scandinavian patients with PR3-AAV as well as MPO-AAV.

METHODS

Genotypes of single-nucleotide polymorphisms (SNPs) located in the HLA region were extracted from a targeted exome-sequencing dataset comprising Scandinavian AAV cases and controls. Classical HLA alleles were called using xHLA. After quality control, association analyses were performed of a joint SNP/classical HLA allele dataset for cases with PR3-AAV (n=411) and MPO-AAV (n=162) versus controls (n=1595). Disease-associated genetic variants were analysed for association with organ involvement, age at diagnosis and relapse, respectively.

RESULTS

PR3-AAV was significantly associated with both HLA-DPB1*04:01 and rs1042335 at the HLA-DPB1 locus, also after stepwise conditional analysis. MPO-AAV was significantly associated with HLA-DRB1*04:04. Neither carriage of HLA-DPB1*04:01 alleles in PR3-AAV nor of HLA-DRB1*04:04 alleles in MPO-AAV were associated with organ involvement, age at diagnosis or relapse.

CONCLUSIONS

The association to the HLA region was distinct in Scandinavian cases with MPO-AAV compared with cases of East Asian descent. In PR3-AAV, the two separate signals of association to the HLD-DPB1 region mediate potentially different functional effects.

PyPop: a mature open-source software pipeline for population genomics

Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well. Here, we present PyPop 1.0.0, a new major release of the package, which implements new features using the more robust infrastructure of GitHub, and is distributed via the industry-standard Python Package Index. New features include implementation of the asymmetric linkage disequilibrium measures and, of particular interest to the immunogenetics research communities, support for modern nomenclature, including colon-delimited allele names, and improvements to meta-analysis features for aggregating outputs for multiple populations. Code available at: https://zenodo.org/records/10080668 and https://github.com/alexlancaster/pypop.

Identification of the novel allele, HLA-A*30:01:22, in a Saudi individual

A single nucleotide substitution in exon 5 of HLA-A*30:01:01:01 results in the novel HLA-A*30:01:22 allele.

Detection of the HLA-C*07:04:29 allele in a Chinese individual

HLA-C*07:04:29 differs from HLA-C*07:04:01:01 by a single substitution in exon 4.

The novel HLA-DPB1*1500:01N allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual

HLA-DPB1*1500:01N differs from HLA-DPB1*05:01:01:01 by one nucleotide in exon 3.

Identification of the novel HLA-C allele, HLA-C*07:02:150

A novel HLA-C*07 allele, now officially designated HLA-C*07:02:150, was identified by next-generation sequencing.

Identification of two novel HLA-DRB1 alleles, HLA-DRB1*08:03:13 and HLA-DRB1*08:119

Compared with HLA-DRB1*08:03:02:01, the alleles HLA-DRB1*08:03:13 and HLA-DRB1*08:119 each show one nucleotide substitution, respectively.

Identification of the novel HLA-C allele, HLA-C*12:351Q, using next-generation sequencing

The novel allele HLA-C*12:351Q differs from HLA-C*12:02:02:01 by a single nucleotide deletion in exon 5.

Detection of the novel HLA-B*55:01:31, HLA-C*07:1113 alleles and confirmation of HLA-C*12:392

Novel HLA-B*55:01:31, HLA-C*07:1113 alleles and confirmatory HLA-C*12:392 allele were detected during the HLA typing process.

Emerging potential of immunopeptidomics by mass spectrometry in cancer immunotherapy

With significant advances in analytical technologies, research in the field of cancer immunotherapy, such as adoptive T cell therapy, cancer vaccine, and immune checkpoint blockade (ICB), is currently gaining tremendous momentum. Since the efficacy of cancer immunotherapy is recognized only by a minority of patients, more potent tumor-specific antigens (TSAs, also known as neoantigens) and predictive markers for treatment response are of great interest. In cancer immunity, immunopeptides, presented by human leukocyte antigen (HLA) class I, play a role as initiating mediators of immunogenicity. The latest advancement in the interdisciplinary multiomics approach has rapidly enlightened us about the identity of the "dark matter" of cancer and the associated immunopeptides. In this field, mass spectrometry (MS) is a viable option to select because of the naturally processed and actually presented TSA candidates in order to grasp the whole picture of the immunopeptidome. In the past few years the search space has been enlarged by the multiomics approach, the sensitivity of mass spectrometers has been improved, and deep/machine-learning-supported peptide search algorithms have taken immunopeptidomics to the next level. In this review, along with the introduction of key technical advancements in immunopeptidomics, the potential and further directions of immunopeptidomics will be reviewed from the perspective of cancer immunotherapy.

The novel HLA-C*03:94:02 allele identified by next-generation sequencing in a Chinese individual

HLA-C*03:94:02 differs from HLA-C*03:94:01 by a single nucleotide substitution in exon 2 (codon 17 GGA->GGG).

Characterisation of the novel HLA-DPB1*1437:01 and HLA-DPB1*1438:01 alleles by next-generation sequencing

The novel HLA-DPB1*1437:01 and HLA-DPB1*1438:01 alleles first identified in the Chinese individuals.

Characterization of the novel HLA-B*40:538 allele by next-generation sequencing

The HLA-B*40:538 allele differs from HLA-B*40:01:02:01 at position 905 C→T in exon 5.

Two novel HLA class I alleles: HLA-A*02:1148 and HLA-B*44:386

Identification of the novel HLA-A*02:1148 and HLA-B*44:386 alleles by next-generation sequencing.

Identification of a new HLA-B allele, HLA-B*35:594

A novel HLA-B*35 allele, officially designated HLA-B*35:594, was identified by next-generation sequencing.

Identification of the novel HLA-DQA1*05:107 allele

Full length sequence characterisation of the novel HLA-DQA1*05:107 allele from whole genome sequencing data.

Frequencies of HLA-B alleles in Indonesian Malay Ethnic

Background

The HLA-B alleles have been used as a marker to predict drug-induced adverse reactions and as a major contributor to hypersensitivity reactions. We examined the feasibility of HLA-B alleles as pharmacogenomic markers of drug-induced hypersensitivity in an Indonesian Malay Ethnic.

Methods

Fifty-eight Indonesian individuals of Malay ethnicity were enrolled in this study. HLA-B alleles were determined using reverse sequence-specific oligonucleotide probe coupled with xMAP technology.

Results

HLA-B*15:02 (15.52%), HLA-B*35:05 (9.48%), and HLA-B*07:05 (7.76%) were frequent alleles in the Indonesian Malay ethnic populations. We discovered at least eight pharmacogenomics markers of drug-induced hypersensitivity: HLA-B*15:02, HLA-B*15:21, HLA-B*13:01, HLA-B*35:05, HLA-B*38:02, HLA-B*51:01, HLA-B*57:01, and HLA-B*58:01. HLA-B*15:02 was in the same serotype group with HLA-B*15:21, which is a B-75 serotype associated with genetic predisposition for carbamazepine-induced Stevens-Johnson syndrome and toxic epidermal necrolysis. The Indonesian population, represented by Malay, Javanese, and Sundanese ethnicities, was similar to South East Asian, Han Chinese, and Taiwanese populations based on HLA-B*15:02 frequency as the most common allele found in Malay ethnics.

Conclusion

We provided valuable information on the frequency of drug hypersensitivity-associated HLA-B alleles in Indonesian Malay ethnic population, which can improve treatment safety.

The novel HLA-B*44:387 allele shows a -21 methionine residue in the signal peptide

Characterization of the novel HLA‐B*44:387 allele.

Detection of the HLA-B*40:01:35 allele in a Taiwanese individual

Nucleotide substitutions in codons -1 and 84 of HLA-B*40:01:01 result in a novel allele, HLA-B*40:01:35.

Full-length sequence of the novel allele, HLA-B*58:01:40, identified in a Chinese individual

HLA-B*58:01:40 differs from HLA-B*58:01:01 by a single nucleotide change in exon 3, 507 C- > T (codon 145.3 CGC- > CGT).

The novel HLA-B*38:103N allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual

HLA-B*38:103N differs from HLA-B*38:02:01:01 by one nucleotide in exon 3.

Identification of the novel HLA-DQA1*05:101 allele by next-generation sequencing in a family

HLA-DQA1*05:101 differs from HLA-DQA1*05:01:01:02 by one nucleotide substitution at codon 221 (CGT>TGT) in exon 4.

Identification of four novel HLA alleles: HLA-B*27:265, -B*35:569, -DRB1*08:117 and -DPB1*1435:01

Identification of four new HLA alleles (B*27:265, B*35:569, DRB1*08:117, and DPB1*1435:01) in Brazilian bone marrow donors.