Mono-allelic amplification of exons 2-4 using allele group-specific primers for sequence-based typing (SBT) of the HLA-A, -B and -C genes: preparation and validation of ready-to-use pre-SBT mini-kits

Identification of a novel HLA-C*08 allele, HLA-C*08:242 in a Chinese individual

The novel HLA-C*08:242 allele was identified in an individual from the Sichuan province of China. This article is protected by copyright. All rights reserved.

Associations between HLA-A, -B, and -C alleles and iodinated contrast media-induced hypersensitivity in Koreans

A common cause of drug hypersensitivity reactions is iodinated contrast media (ICM). ICM-induced hypersensitivity had been considered to be a non-immunological reaction, but evidence for an immunological mechanism has increased recently. Thus, we evaluated whether HLA-A, -B, and -C alleles were associated with ICM-induced hypersensitivity. In total, 126 patients who underwent contrast-enhanced computed tomography studies through outpatient clinics at a tertiary referral hospital between 2008 and 2012 were assessed. Sixty-one patients experienced ICM-induced hypersensitivity and the remainder, 65, were ICM-tolerant patients (control). ICM-induced hypersensitivity patients showed 51 with immediate, 7 with non-immediate, 3 with both or mixed type. HLA-A, -B, and -C genotyping was performed using a PCR sequence-based typing method. Four kinds of ICM were used: iopromide, iohexol, iobitridol, and iodixanol. The most used ICM among the hypersensitivity patients was iopromide. Significant difference in the frequency of HLA-B*58:01 (odds ratios [OR], 3.90; p = 0.0200, 95% confidence interval [CI], 1.16-13.07) was observed between ICM-induced immediate hypersensitivity and control. There were statistically significant differences in the frequencies of the HLA-B*38:02 (OR, 10.24; p = 0.0145; 95% CI, 1.09-96.14) and HLA-B*58:01 (OR, 3.98; p = 0.0348; 95% CI, 1.03-15.39) between iopromide-induced immediate hypersensitivity and control. The mechanism of ICM-induced hypersensitivity remains unknown, but this study showed associations, although weak, with HLA-B*58:01 alleles for ICM-induced immediate hypersensitivity and HLA-B*38:02 and HLA-B*58:01 for iopromide-induced immediate hypersensitivity as risk predictors. Further studies are needed to validate the associations in larger samples and to identify the functional mechanism behind these results.

Identification of the novel HLA-A*68:100 allele by PCR-SBT in a Chinese bone marrow donor

The novel HLA-A*68:100 allele differs from HLA-A*68:01:02:01 by one nucleotide substitution in exon 3 at position 371.

HLA Correlations with Clinical Phenotypes and Risk of Metabolic Comorbidities in Singapore Chinese Psoriasis Patients

INTRODUCTION

Psoriasis is a systemic, chronic inflammatory disease that not only afflicts the skin but is also associated with cardiovascular disease and metabolic syndrome. The strongest susceptibility loci for the disease is within the human leukocyte antigen (HLA) complex, though specific HLA allelic associations vary between populations.

OBJECTIVE

Our objective was to investigate HLA associations with clinical phenotypes of psoriasis and metabolic syndrome in Chinese psoriasis cases.

METHODS

We conducted an observational case-control study in Singapore with a cohort of psoriasis cases consecutively recruited from an outpatient specialist dermatological center (n = 120) compared with 130 healthy controls.

RESULTS

Significant HLA associations with psoriasis were observed with HLA-A*02:07, B*46:01, C*01:02, and C*06:02. The three-locus haplotype of A*02:07-C*01:02-B*46:01 was also significant (odds ratio [OR] 3.07; p = 9.47 × 10^-5). We also observed an association between nail psoriasis and HLA-A*02:07 carriers (OR 4.50; p = 0.002), whereas C*06:02 carriers were less prone to have nail involvement (OR 0.16; p = 0.004). HLA-A*02:07 was also identified as a possible risk allele for hypertension (OR 2.90; p < 0.05), and C*01:02 was a possible risk allele for dyslipidemia (OR 3.36; p < 0.05), both known to be common comorbidities in patients with psoriasis.

CONCLUSION

Our results demonstrate the growing importance of discerning population-specific clinical phenotypes and their association with certain HLA alleles in psoriasis.

Crystal structure of suboptimal viral fragments of Epstein Barr Virus Rta peptide-HLA complex that stimulate CD8 T cell response

Peptides presented by Human leukocyte antigen (HLA) class-I molecules are generally 8-10 amino acids in length. However, the predominant pool of peptide fragments generated by proteasomes is less than 8 amino acids in length. Using the Epstein - Barr virus (EBV) Rta-epitope (ATIGTAMYK, residues 134-142) restricted by HLA-A*11:01 which generates a strong immunodominant response, we investigated the minimum length of a viral peptide that can constitute a viral epitope recognition by CD8 T cells. The results showed that Peripheral blood mononuclear cells (PBMCs) from healthy donors can be stimulated by a viral peptide fragment as short as 4-mer (AMYK), together with a 5-mer (ATIGT) to recapitulate the full length EBV Rta epitope. This was confirmed by generating crystals of the tetra-complex (2 peptides, HLA and β2-microglobulin). The solved crystal structure of HLA-A*11:01 in complex with these two short peptides revealed that they can bind in the same orientation similar to parental peptide (9-mer) and the free ends of two short peptides acquires a bulged conformation that is directed towards the T cell receptor. Our data shows that suboptimal length of 4-mer and 5-mer peptides can complement each other to form a stable peptide-MHC (pMHC) complex.

A novel HLA-A*24 allele, A*24:231, was identified by sequence-based typing

HLA-A*24:231 has one nucleotide change from HLA-A*24:02:01:01 at position 784 G>C.

Identification of the novel HLA-B*27:103 allele in a Chinese bone marrow donor

HLA-B*27:103 has one nucleotide change from HLA-B*27:04:01 at position 121C > T.

HLA genotyping by next-generation sequencing of complementary DNA

Background

Genotyping of the human leucocyte antigen (HLA) is indispensable for various medical treatments. However, unambiguous genotyping is technically challenging due to high polymorphism of the corresponding genomic region. Next-generation sequencing is changing the landscape of genotyping. In addition to high throughput of data, its additional advantage is that DNA templates are derived from single molecules, which is a strong merit for the phasing problem. Although most currently developed technologies use genomic DNA, use of cDNA could enable genotyping with reduced costs in data production and analysis. We thus developed an HLA genotyping system based on next-generation sequencing of cDNA.

Methods

Each HLA gene was divided into 3 or 4 target regions subjected to PCR amplification and subsequent sequencing with Ion Torrent PGM. The sequence data were then subjected to an automated analysis. The principle of the analysis was to construct candidate sequences generated from all possible combinations of variable bases and arrange them in decreasing order of the number of reads. Upon collecting candidate sequences from all target regions, 2 haplotypes were usually assigned. Cases not assigned 2 haplotypes were forwarded to 4 additional processes: selection of candidate sequences applying more stringent criteria, removal of artificial haplotypes, selection of candidate sequences with a relaxed threshold for sequence matching, and countermeasure for incomplete sequences in the HLA database.

Results

The genotyping system was evaluated using 30 samples; the overall accuracy was 97.0% at the field 3 level and 98.3% at the G group level. With one sample, genotyping of DPB1 was not completed due to short read size. We then developed a method for complete sequencing of individual molecules of the DPB1 gene, using the molecular barcode technology.

Conclusion

The performance of the automatic genotyping system was comparable to that of systems developed in previous studies. Thus, next-generation sequencing of cDNA is a viable option for HLA genotyping.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4300-7) contains supplementary material, which is available to authorized users.

Dual non-contiguous peptide occupancy of HLA class I evoke antiviral human CD8 T cell response and form neo-epitopes with self-antigens

Host CD8 T cell response to viral infections involves recognition of 8-10-mer peptides presented by MHC-I molecules. However, proteasomes generate predominantly 2-7-mer peptides, but the role of these peptides is largely unknown. Here, we show that single short peptides of <8-mer from Latent Membrane Protein 2 (LMP2) of Epstein Barr Virus (EBV) can bind HLA-A*11:01 and stimulate CD8+ cells. Surprisingly, two peptide fragments between 4-7-mer derived from LMP2(340-349) were able to complement each other, forming combination epitopes that can stimulate specific CD8+ T cell responses. Moreover, peptides from self-antigens can complement non-self peptides within the HLA binding cleft, forming neoepitopes. Solved structures of a tetra-complex comprising two peptides, HLA and β2-microglobulin revealed the free terminals of the two peptides to adopt an upward conformation directed towards the T cell receptor. Our results demonstrate a previously unknown mix-and-match combination of dual peptide occupancy in HLA that can generate vast combinatorial complexity.

Identification of the novel HLA-A*11:141 allele in a Chinese bone marrow donor

HLA-A*11:141 has 1 nucleotide change from HLA-A*11:01:01 at position 470G>C.

Identification of a novel HLA allele, HLA-B*15:416, in a bone marrow hematopoietic stem cell donor

The novel HLA-B*15:416 allele differs from HLA-B*15:01:01:01 by a single nucleotide substitution at codon 114.

A novel allele, HLA-A*33:97 was identified in a Chinese bone marrow donor

HLA-A*33:97 has one base substitution at position 287 A>T in exon 2 compared to HLA-A*33:03:01.

Identification of a novel HLA allele, HLA-B*08:163, in a platelet donor

The novel HLA-B*08:163 allele differs from HLA-B*08:01:01:01 by a single nucleotide substitution at codon 105.

Identification of a novel HLA-C allele, HLA-C*07:477 in a Drung Chinese individual

HLA-C*07:477 has one nonsynonymous nucleotide change from HLA-C*07:02:01:01 in codon 176, exon 3 (AAG>GAG).

A novel HLA-DRB1 allele, HLA-DRB1*12:48

HLA-DRB1*12:48 differs from DRB1*12:09, by a single synonymous nucleotide at position 266.

A novel HLA-B allele, HLA-B*35:269

HLA-B*35:269 differs from HLA-B*35:01:01:01, by a single synonymous nucleotide at position 103.

A novel HLA-A allele, HLA-A*02:544

The novel allele HLA-A*02:544 has two nucleotide changes from its most closely related allele, HLA-A*02:148. Firstly at nucleotide 255 where C → T (codon 60 GAC → GAT), resulting in a non-coding change as GAC and GAT both code for the same amino acid aspartic acid. Secondly at nucleotide 368 where T → G (codon 98 TTT → TGT) resulting in a coding change, 98 phenylalanine is changed to cysteine.

Identification of a novel HLA allele, HLA-B*53:39, in a Guadaloupean individual

The novel HLA-B*53:39 allele differs from HLA-B*53:01 by a single nucleotide substitution at codon 45 (ACG>AAG).

A novel HLA-C allele, C*08:01:10 was identified in a Chinese leukemia patient

HLA-C*08:01:10 differs from HLA-C*08:01:01 by a single non-coding change at nucleotide 339 G>A.

A novel allele, HLA-B*54:29, identified by sequence-based typing in a Chinese bone marrow donor

HLA-B*54:29 allele differs from B*54:01:01 at nucleotide position 442 A>C in exon 3.

Identification of the novel HLA-B*15:257 allele by polymerase chain reaction sequence-based typing in a Chinese individual

HLA-B*15:257 has one nucleotide change in exon 2 at position 232C>G from B*15:01:01:01.

A novel HLA-C allele, HLA-C*06:45, identified by sequence-based typing in a Chinese individual

HLA-C*06:45 differs from HLA-C*06:02 by a single G to A substitution at position 187.

Identification of a novel HLA-C*07:02:25 allele by polymerase chain reaction sequence-based typing in a Chinese leukemia patient

Nucleotide sequence of HLA-C*07:02:25 allele was different from that of HLA-C*07:02:01:01 by a single nucleotide substitution at position 78C>G.

Identification of a new HLA-A*02 allele, HLA-A*02:305 N, which differs from the HLA-A*02:01:01 allele by a single nucleotide deletion in exon 4

The HLA-A*02:305N new allele lacks a nucleotide in exon 4 compared to HLA-A*02:01:01 allele.

HLA-B*51:79 is a novel allele associated with a conserved haplotype

The B*51:79 allele displays a conserved haplotype association with HLA-A*68:01, C*01:02, DRB1*14:01 and DQB1*05:03.

Characterization of a novel HLA allele HLA-B*15:25:03 in a Chinese individual

Nucleotide sequence of HLA-B*15:25:03 allele was different from that of HLA-B*15:25:01 at position 819 G to A.

Identification of a novel HLA-B*13:41 allele in a Chinese bone marrow donor

Nucleotide sequence of HLA-B*13:41 allele was different from that of B*13:02:01 at position 538 C>T and 539 T>G, resulting in an amino acid from Leu to Trp at codon 156.

Identification of a novel HLA-B*52 allele in a Brazilian individual: B*52:21

HLA-B*52:21 differs from the closest, HLA-B*52:01:02, by two nucleotides (CTG → TGG), leading to an amino acid substitution from Leu to Trp at codon 156.

Identification of a new HLA-A*11:78N allele by polymerase chain reaction sequence-based typing

Nucleotide sequence of HLA-A*11:78N allele was different from that of HLA-A*11:01:01 by two nucleotides deletion at positions 286 and 287, resulting in reading frameshift and has premature stop codon at position 73 in exon 2.