Single locus HLA sequencing with the nanopore technology for HLA disease association diagnosis

Associations between HLA genotype and disease susceptibility encompass almost all the classic HLA loci. The level of typing resolution enabling a correct identification of an HLA disease susceptibility gene depends on the disease itself and/or on the accumulated knowledge about the molecular involvement of the HLA allele(s) engaged. Therefore, the application of Next Generation Sequencing technologies to HLA disease association, which would improve typing resolution, could prove useful to better understand disease severity. In the present study, we tested a nanopore sequencing approach developed by Omixon Biocomputing Ltd, dedicated to on-demand locus typing for HLA and disease, as an alternative to the conventional widely used sequence specific oligoprobe (SSO) approach. A total of 145 DNA samples used in routine diagnosis by SSO were retrospectively analyzed with nanopore technology, for HLA-A*02 immunotherapy decision for A*29, B*27, B*51, B*57 identification in class I, and DRB1, DQA1, and DQB1 for bullous dermatosis, rheumatoid arthritis, diabetes, and celiac disease requests in class II. Each locus was typed in a separate experiment, except for DQB1 and DQA1, which were analyzed together. Concordance between typings reached 100% for all the loci tested. Ambiguities by nanopore were only found for missing exon coverage. This approach was found to be very well adapted to the routine flow imposed by the SSO technique. This study illustrates the use of the new NanoTYPE MONO kit for single locus HLA sequencing for HLA and disease association diagnosis.

Two-field resolution on-call HLA typing for deceased donors using nanopore sequencing

The current practice of HLA genotyping in deceased donors poses challenges due to limited resolution within time constraints. Nevertheless, the assessment of compatibility between anti-HLA sensitized recipients and mismatched donors remains a critical medical need, particularly when dealing with allele-specific (second field genotyping level) donor-specific antibodies. In this study, we present a customized protocol based on the NanoTYPE® HLA typing kit, employing the MinION® sequencer, which enables rapid HLA typing of deceased donors within a short timeframe of 3.75 h on average at a three-field resolution with almost no residual ambiguities. Through a prospective real-time analysis of HLA typing in 18 donors, we demonstrated the efficacy and precision of our nanopore-based method in comparison to the conventional approach and without delaying organ allocation. Indeed, this duration was consistent with the deceased donor organ donation procedure leading to organ allocation via the French Biomedicine Agency. The improved resolution achieved with our protocol enhances the security of organ allocation, particularly benefiting highly sensitized recipients who often present intricate HLA antibody profiles. By overcoming technical challenges and providing comprehensive genotyping data, this approach holds the potential to significantly impact deceased donor HLA genotyping, thereby facilitating optimal organ allocation strategies.

HLA sequencing identifies novel associations and suggests clinical relevance of DPB1*04:01 in ANCA-associated Granulomatosis with polyangiitis

Granulomatosis with polyangiitis (GPA) is a rare systemic autoimmune disease. Major contributions of HLA genes have been reported; however, HLA typing-based diagnosis or risk prediction in GPA has not been established. We have performed a sequencing-based HLA genotyping in a north Indian GPA cohort and controls to identify clinically relevant novel associations. PR3-ANCA-positive 40 GPA patients and 40 healthy controls from north India were recruited for the study. Targeted sequencing of HLA-A,-B,-C,-DRB1,-DQB1, and -DPB1 was performed. Allelic and haplotypic associations were tested. Molecular docking of susceptibility HLA alleles with reported super-antigen epitopes was performed. The association of substituted amino acids located at the antigen-binding domain of HLA was evaluated. Genetic association of five HLA-alleles was identified in GPA. The novel association was identified for C*15:02 (p = 0.04; OR = 0.27(0.09-0.88)). The strongest association was observed for DPB1*04:01 (p < 0.0001; OR = 6.2(3.08-11.71)), previously reported in European studies. 35 of 40 GPA subjects had at least one DPB1*04:01 allele, and its significant risk was previously not reported from the Indian population. Significantly associated haplotypes DRB1*03:01-DQB1*02:01-DPB1*04:01 (p = 0.02; OR = 3.46(1.11-12.75)) and DRB1*07:01-DQB1*02:02-DPB1*04:01 (p = 0.04; OR = 3.35(0.95-14.84)) were the most frequent in GPA patients. Ranging from 89 % to 100 % of GPA patients with organ involvement can be explained by at least one DPB1*04:01 allele. A strong interaction between the HLA and three epitopes of the reported super antigen TSST-1 of Staphylococcus aureus was confirmed. Our study highlighted the potential applicability of HLA typing for screening and diagnosis of GPA. A large multi-centric study and genotype-phenotype correlation analysis among GPA patients will enable the establishment of HLA-typing based GPA diagnosis.

Integrative HLA typing of tumor and adjacent normal tissue can reveal insights into the tumor immune response

BACKGROUND

The HLA complex is the most polymorphic region of the human genome, and its improved characterization can help us understand the genetics of human disease as well as the interplay between cancer and the immune system. The main function of HLA genes is to recognize "non-self" antigens and to present them on the cell surface to T cells, which instigate an immune response toward infected or transformed cells. While sequence variation in the antigen-binding groove of HLA may modulate the repertoire of immunogenic antigens presented to T cells, alterations in HLA expression can significantly influence the immune response to pathogens and cancer.

METHODS

RNA sequencing was used here to accurately genotype the HLA region and quantify and compare the level of allele-specific HLA expression in tumors and patient-matched adjacent normal tissue. The computational approach utilized in the study types classical and non-classical Class I and Class II HLA alleles from RNA-seq while simultaneously quantifying allele-specific or personalized HLA expression. The strategy also uses RNA-seq data to infer immune cell infiltration into tumors and the corresponding immune cell composition of matched normal tissue, to reveal potential insights related to T cell and NK cell interactions with tumor HLA alleles.

RESULTS

The genotyping method outperforms existing RNA-seq-based HLA typing tools for Class II HLA genotyping. Further, we demonstrate its potential for studying tumor-immune interactions by applying the method to tumor samples from two different subtypes of breast cancer and their matched normal breast tissue controls.

CONCLUSIONS

The integrative RNA-seq-based HLA typing approach described in the study, coupled with HLA expression analysis, neoantigen prediction and immune cell infiltration, may help increase our understanding of the interplay between a patient's tumor and immune system; and provide further insights into the immune mechanisms that determine a positive or negative outcome following treatment with immunotherapy such as checkpoint blockade.

Next-generation HLA sequencing reveals the novel HLA-A*33:244 allele

The novel HLA-A*33:244 allele contains a c.553G>A substitution in exon 3 compared with A*33:03:01:01.

Genetic testing of Behçet's disease using next-generation sequencing to identify monogenic mimics and HLA-B*51

OBJECTIVE

Several monogenic autoinflammatory disorders and primary immunodeficiencies can present early in life with features that may be mistaken for Behçet's disease (BD). We aimed to develop a genetic analysis workflow to identify rare monogenic BD-like diseases and establish the contribution of HLA haplotype in a cohort of patients from the UK.

METHODS

Patients with clinically suspected BD were recruited from four BD specialist care centres in the UK. All participants underwent whole exome sequencing (WES), and genetic analysis thereafter by 1. examining genes known to cause monogenic immunodeficiency, autoinflammation or vasculitis by virtual panel application; 2. scrutiny of variants prioritised by Exomiser using Human Phenotype Ontology (HPO); 3. identification of copy number variants using ExomeDepth; and 4. HLA-typing using OptiType.

RESULTS

Thirty-one patients were recruited: median age 15 (4-52), and median disease onset age 5 (0-20). Nine/31 (29%) patients had monogenic disease mimicking BD: 5 cases of Haploinsufficiency of A20 with novel TNFAIP3 variants (p.T76I, p.M112Tfs*8, p.S548Dfs*128, p.C657Vfs*14, p.E661Nfs*36); 1 case of ISG15 deficiency with a novel nonsense variant (ISG15:p.Q16X) and 1p36.33 microdeletion; 1 case of Common variable immune deficiency (TNFRSF13B:p.A181E); and 2 cases of TNF receptor associated periodic syndrome (TNFRSF1A:p.R92Q). Of the remaining 22 patients, 8 (36%) were HLA-B*51 positive.

CONCLUSION

We describe a novel genetic workflow for BD, which can efficiently detect known and potentially novel monogenic forms of BD, whilst additionally providing HLA-typing. Our results highlight the importance of genetic testing before BD diagnosis, since this has impact on choice of therapy, prognosis, and genetic counselling.

5 years DKMS Chile: approach, results and impact of the first unrelated stem cell donor center in Chile

Introduction

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is performed worldwide to treat blood cancer and other life-threatening blood disorders. As successful transplantation requires an HLA-compatible donor, unrelated donor centers and registries have been established worldwide to identify donors for patients without a family match. Ethnic minorities are underrepresented in large donor registries. Matching probabilities are higher when donors and patients share the same ethnic background, making it desirable to increase the diversity of the global donor pool by recruiting donors in new regions. Here, we report the establishment and the first 5 years of operation of the first unrelated stem cell donor center in Chile, a high-income country in South America with a population of over 19 million.

Methods

We used online and in-person donor recruitment practices through patient appeals and donor drives in companies, universities, the armed forces, and public services. After confirmatory typing donors were subjected to medical work-up and cleared for donation.

Results

We recruited almost 170,000 donors in 5 years. There were 1,488 requests received for confirmatory typing and donor availability checks, of which 333 resulted in medical work-up, leading to 194 stem cell collections. Products were shipped to Chile (48.5%) and abroad. Even when the COVID-19 pandemic challenged our activities, the number of donors recruited and shipped stem cell products remained steady. In Chile there was an almost 8-fold increase in unrelated donor transplantation activity from 16 procedures in 2016-2018 to 124 procedures in 2019-2021, mainly for pediatric patients following the center's establishment. We estimate that 49.6% of Chilean patients would find at least one matched unrelated donor in the global DKMS donor pool.

Discussion

Establishing a DKMS donor center in Chile has significantly increased donor availability for Chilean patients and contributed to an increase of unrelated donor stem cell transplant activity.

SpecHLA enables full-resolution HLA typing from sequencing data

Reconstructing diploid sequences of human leukocyte antigen (HLA) genes, i.e., full-resolution HLA typing, from sequencing data is challenging. The high homogeneity across HLA genes and the high heterogeneity within HLA alleles complicate the identification of genomic source loci for sequencing reads. Here, we present SpecHLA, which utilizes fine-tuned reads binning and local assembly to achieve accurate full-resolution HLA typing. SpecHLA accepts sequencing data from paired-end, 10×-linked-reads, high-throughput chromosome conformation capture (Hi-C), Pacific Biosciences (PacBio), and Oxford Nanopore Technology (ONT). It can also incorporate pedigree data and genotype frequency to refine typing. In 32 Human Genome Structural Variation Consortium, Phase 2 (HGSVC2) samples, SpecHLA achieved 98.6% accuracy for G-group-resolution HLA typing, inferring entire HLA alleles with an average of three mismatches fewer, ten gaps fewer, and 590 bp less edit distance than HISAT-genotype per allele. Additionally, SpecHLA exhibited a 2-field typing accuracy of 98.6% in 875 real samples. Finally, SpecHLA detected HLA loss of heterozygosity with 99.7% specificity and 96.8% sensitivity in simulated samples of cancer cell lines.

Detection of Nonsynonymous Single Variants in Human HLA-DRB1 Exon 2 Associated with Renal Transplant Rejection

Background: HLA-DRB1 is the most polymorphic gene in the human leukocyte antigen (HLA) class II, and exon 2 is critical because it encodes antigen-binding sites. This study aimed to detect functional or marker genetic variants of HLA-DRB1 exon 2 in renal transplant recipients (acceptance and rejection) using Sanger sequencing. Methods: This hospital-based case-control study collected samples from two hospitals over seven months. The 60 participants were equally divided into three groups: rejection, acceptance, and control. The target regions were amplified and sequenced by PCR and Sanger sequencing. Several bioinformatics tools have been used to assess the impact of non-synonymous single-nucleotide variants (nsSNVs) on protein function and structure. The sequences data that support the findings of this study with accession numbers (OQ747803-OQ747862) are available in National Center for Biotechnology Information (GenBank database). Results: Seven SNVs were identified, two of which were novel (chr6(GRCh38.p12): 32584356C>A (K41N) and 32584113C>A (R122R)). Three of the seven SNVs were non-synonymous and found in the rejection group (chr6(GRCh38.p12): 32584356C>A (K41N), 32584304A>G (Y59H), and 32584152T>A (R109S)). The nsSNVs had varying effects on protein function, structure, and physicochemical parameters and could play a role in renal transplant rejection. The chr6(GRCh38.p12):32584152T>A variant showed the greatest impact. This is because of its conserved nature, main domain location, and pathogenic effects on protein structure, function, and stability. Finally, no significant markers were identified in the acceptance samples. Conclusion: Pathogenic variants can affect intramolecular/intermolecular interactions of amino acid residues, protein function/structure, and disease risk. HLA typing based on functional SNVs could be a comprehensive, accurate, and low-cost method for covering all HLA genes while shedding light on previously unknown causes in many graft rejection cases.

Characterisation of the first HLA-DQA1 allele with Aspartic Acid in the transmembrane domain, HLA-DQA1*05:71

HLA-DQA1*05:71, the first HLA-DQA1 allele with Aspartic Acid at residue 208 in the transmembrane domain.

Human leukocyte antigen immunization in transfusion-dependent Moroccan patients with beta-thalassemia major: prevalence and risk factors

INTRODUCTION

Beta-thalassemia major patients need a regular blood transfusion to have an initial normal growth. However, these patients have an increased risk of developing alloantibodies. Our main goal was to study HLA alloimmunization in Moroccan Beta-thalassemia patients by confronting it with transfusion and demographic criteria, exploring the involvement of HLA typing profile in the development of HLA antibodies and in turn determining risk factors for their development.

METHODS

The study consisted of 53 Moroccan pediatric patients with Beta-thalassemia major. Screening for HLA alloantibodies was performed using Luminex technology Whereas HLA genotyping was done with sequence-specific primers (PCR-SSP).

RESULTS

In this study, 50.9% of patients have been identified as positive for HLA antibodies, with 59.3% having both HLA Class I and Class II antibodies. A significant increase frequency of DRB1*11 allele was revealed in non-immunized patients (34.6% vs. 0%, p = 0.001). Our results also revealed that the majority of our HLA immunized patients were women (72.4% vs. 27.6%, p = 0.001), and transfused with more than 300 units of RBC units (66.7% vs. 33.3%, p = 0.02). There were statistically significant differences when comparing these frequencies.

CONCLUSIONS

This paper revealed that the transfusion dependent Beta-thalassemia major patients are exposed to risk of developing HLA antibodies following transfusions with leukoreduced RBC units. The HLA DRB1*11 was a protective factor against HLA alloimmunization in our beta-thalassemia major patients.

The novel HLA-DQB1*03:02:01:14 allele was possibly generated by a recombination event

The novel HLA-DQB1*03:02:01:14 was likely generated by a recombination event between DQB1*03:02:01:01 and DQB1*03:03:02:01.

Genomic sequence of the HLA-A*02:01:209 allele identified in a solid organ recipient

The novel HLA-A allele HLA-A*02:01:209 sequence identified in a solid organ recipient.

The role of the HLA allelic repertoire on the clinical severity of COVID-19 in Canadians, living in the Saskatchewan province

AIMS

The HLA system has been implicated as an underlying determinant for modulating the immune response to SARS-CoV-2. In this study, we aimed to determine the association of patients' HLA genetic profiles with the disease severity of COVID-19 infection.

METHODS

Prospective study was conducted on COVID-19 patients (n = 40) admitted to hospitals in Saskatoon, Canada, between March and December 2020. Next-generation sequencing was performed on the patient samples to obtain high-resolution HLA typing profiles. The statistical association between HLA allelic frequency and disease severity was examined. The disease severity was categorized based on the length of hospital stay and intensive care needs or demise during the hospital stay.

RESULTS

HLA allelic frequencies of the high and low-severity cohorts were normalized against corresponding background allelic frequencies. In the high-severity cohort, A*02:06 (11.8-fold), B*51:01 (2.4-fold), B*15:01(3.1-fold), C*01:02 (3.3-fold), DRB1*08:02 (31.2-fold), DQ*06:09 (11-fold), and DPB1*04:02(4-fold) were significantly overrepresented (p < 0.05) making these deleterious alleles. In the low-severity cohort, A*24:02 (2.8-fold), B*35:01 (2.8-fold), DRB1*04:07 (5.3-fold), and DRB1*08:11 (22-fold) were found to be significantly overrepresented (p < 0.05) making these protective alleles. These above alleles interact with NK cell antiviral activity via the killer immunoglobulin-like receptors (KIR). The high-severity cohort had a higher predilection for HLA alleles associated with KIR subgroups; Bw4-80I (1.1-fold), and C1 (1.6-fold) which promotes NK cell inhibition, while the low-severity cohort had a higher predilection for Bw4-80T (1.6-fold), and C2 (1.6-fold) which promote NK cell activation.

CONCLUSION

In this study, the HLA allelic repository with the distribution of deleterious and protective alleles was found to correlate with the severity of the clinical course in COVID-19. Moreover, the interaction of specific HLA alleles with the KIR-associated subfamily modulates the NK cell-mediated surveillance of SARS-CoV-2. Both deleterious HLA alleles and inhibitory KIR appear prominently in the severe COVID-19 group focusing on the importance of NK cells in the convalescence of COVID-19.

Validation and application of new NGS-based HLA genotyping to clinical diagnostic practice

Next-generation sequencing (NGS) has revolutionized clinical genotyping, providing high-resolution HLA genotyping with a low ambiguity rate. This study aimed to develop new NGS-based HLA genotyping (HLAaccuTest, NGeneBio, Seoul, KOREA) on the Illumina MiSeq platform and validate the clinical performance. The analytical performance of HLAaccuTest was validated for 11 loci comprising HLA-A, -B, -C, -DRB1/3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 using 157 reference samples. Among the 345 clinical samples, 180 were tested for performance evaluation and protocol optimization, and 165 were used in clinical trials in the validation phase for five loci, including HLA-A, -B, -C, -DRB1, and -DQB1. In addition, the improvement in the resolution of ambiguous alleles was also evaluated and compared with other NGS-based HLA genotyping for 18 reference samples, including five overlapping samples in analytical performance validation. All reference materials produced 100% concordant results for 11 HLA loci, 96.9% (2092 of 2160 HLA alleles) of the clinical samples were matched with the SBT results in the pre-validation phase. After the optimization phase, the clinical trials in the validation phase showed 99.7% (1645/1650 alleles) concordance with the complete resolution for 34 ambiguity results. The retesting of five discordant cases resolved all issues and yielded 100% concordant results with the SBT method. Additionally, for ambiguity using 18 reference materials with ambiguous alleles, about 30% of ambiguous alleles were more resolved than Trusight HLA v2. HLAaccuTest was successfully validated using a large volume of clinical samples and is fully applicable to the clinical laboratory.

Development of a high-resolution mass-spectrometry-based method and software for human leukocyte antigen typing

Introduction

The human leukocyte antigen (HLA) system plays a critical role in the human immune system and is strongly associated with immune recognition and rejection in organ transplantation. HLA typing method has been extensively studied to increase the success rates of clinical organ transplantation. However, while polymerase chain reaction sequence-based typing (PCR-SBT) remains the gold standard, cis/trans ambiguity and nucleotide sequencing signal overlay during heterozygous typing present a problem. The high cost and low processing speed of Next Generation Sequencing (NGS) also render this approach inadequate for HLA typing.

Methods and materials

To address these limitations of the current HLA typing methods, we developed a novel typing technology based on nucleic acid mass spectrometry (MS) of HLA. Our method takes advantage of the high-resolution mass analysis function of MS and HLAMSTTs (HLA MS Typing Tags, some short fragment PCR amplification target products) with precise primer combinations.

Results

We correctly typed HLA by measuring the molecular weights of HLAMSTTs with single nucleotide polymorphisms (SNPs). In addition, we developed a supporting HLA MS typing software to design PCR primers, construct the MS database, and select the best-matching HLA typing results. With this new method, we typed 16 HLA-DQA1 samples, including 6 homozygotes and 10 heterozygotes. The MS typing results were validated by PCR-SBT.

Discussion

The MS HLA typing method is rapid, efficient, accurate, and readily applicable to typing of homozygous and heterozygous samples.

Extended genomic sequence of the HLA-DRB1*13:129 allele identified in a donor from the Gujarati population

The full-length genomic sequence of the HLA-DRB1*13:129 allele was identified in a donor of Gujarati population.

Extended genomic HLA typing identifies previously unrecognized mismatches in living kidney transplantation

Introduction

Antibody mediated rejection (ABMR) is the most common cause of long-term allograft loss in kidney transplantation (KT). Therefore, a low human leukocyte antigen (HLA) mismatch (MM) load is favorable for KT outcomes. Hitherto, serological or low-resolution molecular HLA typing have been adapted in parallel. Here, we aimed to identify previously missed HLA mismatches and corresponding antibodies by high resolution HLA genotyping in a living-donor KT cohort.

Methods

103 donor/recipient pairs transplanted at the University of Leipzig Medical Center between 1998 and 2018 were re-typed using next generation sequencing (NGS) of the HLA loci -A, -B, -C, -DRB1, -DRB345, -DQA1, -DQB1, -DPA1, and -DPB1. Based on these data, we compiled HLA MM counts for each pair and comparatively evaluated genomic HLA-typing with pre-transplant obtained serological/low-resolution HLA (=one-field) typing results. NGS HLA typing (=two-field) data was further used for reclassification of de novo HLA antibodies as "donor-specific".

Results

By two-field HLA re-typing, we were able to identify additional MM in 64.1% (n=66) of cases for HLA loci -A, -B, -C, -DRB1 and -DQB1 that were not observed by one-field HLA typing. In patients with biopsy proven ABMR, two-field calculated MM count was significantly higher than by one-field HLA typing. For additional typed HLA loci -DRB345, -DQA1, -DPA1, and -DPB1 we observed 2, 26, 3, and 23 MM, respectively. In total, 37.3% (69/185) of de novo donor specific antibodies (DSA) formation was directed against these loci (DRB345 ➔ n=33, DQA1 ➔ n=33, DPA1 ➔ n=1, DPB1 ➔ n=10).

Conclusion

Our results indicate that two-field HLA typing is feasible and provides significantly more sensitive HLA MM recognition in living-donor KT. Furthermore, accurate HLA typing plays an important role in graft management as it can improve discrimination between donor and non-donor HLA directed cellular and humoral alloreactivity in the long range. The inclusion of additional HLA loci against which antibodies can be readily detected, HLA-DRB345, -DQA1, -DQB1, -DPA1, and -DPB1, will allow a more precise virtual crossmatch and better prediction of potential DSA. Furthermore, in living KT, two-field HLA typing could contribute to the selection of the immunologically most suitable donors.

A simple approach for detecting HLA-A*02 alleles in archival formalin-fixed paraffin-embedded tissue samples and an application example for studying cancer immunoediting

The HLA system represents a central component of the antigen presentation machinery. As every patient possesses a defined set of HLA molecules, only certain antigens can be presented on the cell surface. Thus, studying HLA type-dependent antigen presentation can improve the understanding of variation in susceptibility to various diseases, including infectious diseases and cancer. In archival formalin-fixed paraffin-embedded (FFPE) tissue, the HLA type is difficult to analyze because of fragmentation of DNA, hindering the application of commonly used assays that rely on long DNA stretches. Addressing these difficulties, we present a refined approach for characterizing presence or absence of HLA-A*02, the most common HLA-A allele in the Caucasian population, in archival samples. We validated our genotyping strategy in a cohort of 90 samples with HLA status obtained by an NGS-based method. 90% (n = 81) of the samples could be analyzed with the approach. For all of them, the presence or absence of HLA-A*02 alleles was correctly determined with the method, demonstrating 100% sensitivity and specificity (95% CI: 91.40%-100% and 91.19%-100%). Furthermore, we provide an example of application in an independent cohort of 73 FFPE microsatellite-unstable (MSI) colorectal cancer samples. As MSI cancer cells encompass a high number of mutations in coding microsatellites, leading to the generation of highly immunogenic frameshift peptide antigens, they are ideally suited for studying relations between the mutational landscape of tumor cells and interindividual differences in the immune system, including the HLA genotype. Overall, our method can help to promote studying HLA type-dependency during the pathogenesis of a wide range of diseases, making archival and historic tissue samples accessible for identifying HLA-A*02 alleles.

Genomic sequence of the HLA-A*01:109 allele identified in a solid organ donor

The full-length genomic sequence of the HLA-A*01:109 allele identified in a solid organ donor.

Identification of the novel HLA-DQA1*02:01:09:01 allele by two different next-generation sequencing platforms

A synonymous nucleotide substitution in exon 3 results in the novel HLA-DQA1*02:01:09:01 allele.

The novel HLA-C*12:365 allele identified in a Gujarati individual from India

The novel HLA-C allele HLA-C*12:365 identified in an individual from the Gujarati population.

Recommendations for living donor kidney transplantation

This Guide for Living Donor Kidney Transplantation (LDKT) has been prepared with the sponsorship of the Spanish Society of Nephrology (SEN), the Spanish Transplant Society (SET), and the Spanish National Transplant Organization (ONT). It updates evidence to offer the best chronic renal failure treatment when a potential living donor is available. The core aim of this Guide is to supply clinicians who evaluate living donors and transplant recipients with the best decision-making tools, to optimise their outcomes. Moreover, the role of living donors in the current KT context should recover the level of importance it had until recently. To this end the new forms of incompatible HLA and/or ABO donation, as well as the paired donation which is possible in several hospitals with experience in LDKT, offer additional ways to treat renal patients with an incompatible donor. Good results in terms of patient and graft survival have expanded the range of circumstances under which living renal donors are accepted. Older donors are now accepted, as are others with factors that affect the decision, such as a borderline clinical history or alterations, which when evaluated may lead to an additional number of transplantations. This Guide does not forget that LDKT may lead to risk for the donor. Pre-donation evaluation has to centre on the problems which may arise over the short or long-term, and these have to be described to the potential donor so that they are able take them into account. Experience over recent years has led to progress in risk analysis, to protect donors' health. This aspect always has to be taken into account by LDKT programmes when evaluating potential donors. Finally, this Guide has been designed to aid decision-making, with recommendations and suggestions when uncertainties arise in pre-donation studies. Its overarching aim is to ensure that informed consent is based on high quality studies and information supplied to donors and recipients, offering the strongest possible guarantees.

HLA-DQ genotype distribution and risk evaluation of celiac disease in Northwest China

BACKGROUND

Celiac disease (CD) is an autoimmune small bowel disease. Genetic susceptibility for CD is mainly determined by the human leukocyte antigen (HLA)-DQ haplotypes. The risk of CD conferred by HLA genotypes varies geographically and across populations, however, this has not yet been documented in Chinese patients with CD.

AIMS

To investigate the distribution of HLA-DQ and the related risks of CD development in Northwest China.

METHODS

A total of 75 CD patients and 300 healthy individuals were genotyped for HLA-DQ using the Illumina NextSeq, and the relative risks of the different genotypes were evaluated.

RESULTS

In total, 68.00% of CD patients and 21.00% of controls carried HLA-DQ2.5 heterodimers (p < 0.001). We identified four CD risk gradients. Individuals carrying a double dose of DQB1*02 had the highest risk of developing CD (1:16); however, with heterozygosis (DQB1*02:02/DQB1*02:01) having the highest risk (1:9). HLA-DQ2.5 individuals with a single copy of HLA-DQB1*02, in either the cis or trans configuration, were at a medium risk (1:38). Non-DQ2.5 carriers of DQ8 or DQ2.2 were at low risk, while only carriers of DQ7.5 or DQX.5 were at very low risk. Patients with the HLA-DQ2.5 genotype had more severe mucosal damage compared with the HLA-DQ2.5 genotype negative CD patients (70.59% vs. 41.67%, p = 0.016).

CONCLUSION

Genetic susceptibility to CD is highly prevalent in the Northwest Chinese population and the highest risk of developing CD was associated with the DQ2.5/DQ2.2 genotype. The DQ2.5 allele is involved in the severity of mucosal injury.

A fast, cheap, and easy protocol for celiac disease HLA haplotype typing using buccal swabs

Celiac disease (CeD) is a complex autoimmune disorder characterized by intestinal immune-derived injury that develops in response to dietary gluten consumption. Human Leucocyte Antigen (HLA) complex haplotype typing is one of the main tests for CeD diagnosis, together with anti-endomysium and anti-transglutaminase autoantibody detection in blood and inflammation observation in the intestine, being the former mainly used for the initial discarding of the pathogenesis. Among the many types of HLA proteins, HLA-DQ2.5 and HLA-DQ8 are considered essential for CeD development. These receptors are only expressed when specific alleles are present, which can be accurately predicted by the presence of the tagging SNPs rs2187668 and rs7454108, respectively. Taking advantage of this premise, we present here an easy workflow to assess HLA genotyping in saliva by a quick and cheap isopropanol-ethanol precipitation-based DNA extraction method followed by the genotyping of two tagging SNPs for the most frequent CeD risk-associated HLA haplotypes. All the actual diagnostic methods for CeD are performed after acquisition of intestine biopsies or blood samples by invasive techniques. Therefore, the development of non-invasive methods would be of a great improvement and advantage for patients, especially children, as an alternative method for initial CeD screening.

Conception of Saviour Siblings: Religious Views in Malaysia

The advancement of human reproductive technology has made it possible for parents with a child affected by a haematological disorder to select and bring into being, a prospective child who can act as a matched stem cell donor. This can be done through the use of preimplantation genetic diagnosis (PGD) coupled with human leukocyte antigen (HLA) typing (PGD-HLA typing), or HLA tying as a standalone procedure, where a healthy embryo, which is an HLA match to the existing sick sibling, is chosen for implantation. The creation of such a sibling (saviour sibling) is normally taken as a last resort when there is no related or unrelated matched donor. While the conception of a saviour sibling may serve as a reliable and realistic treatment option for the ailing child, it also poses new moral questions that challenge a religiously pluralistic society such as Malaysia. The use of PGD-HLA typing may be controversial as it involves creating a life to save a life, selection of compatible human embryos and destruction of the unselected embryos. At present, there is no legal framework regulating the conception of saviour siblings. The development of ethically sound and appropriate local laws and policies should consider the views of religious communities, especially when it involves a controversial subject such as the conception of saviour siblings. This article seeks to explore the perceptions of religious scholars and representatives of the major religions professed and practised in Malaysia, namely Islam, Buddhism, Christianity and Hinduism, through qualitative interviews.

High Throughput Genetic Characterisation of Caucasian Patients Affected by Multi-Drug Resistant Rheumatoid or Psoriatic Arthritis

Rheumatoid and psoriatic arthritis (RA and PsA) are inflammatory rheumatic disorders characterised by a multifactorial etiology. To date, the genetic contributions to the disease onset, severity and drug response are not clearly defined, and despite the development of novel targeted therapies, ~10% of patients still display poor treatment responses. We characterised a selected cohort of eleven non-responder patients aiming to define the genetic contribution to drug resistance. An accurate clinical examination of the patients was coupled with several high-throughput genetic testing, including HLA typing, SNPs-array and Whole Exome Sequencing (WES). The analyses revealed that all the subjects carry very rare HLA phenotypes which contain HLA alleles associated with RA development (e.g., HLA-DRB1*04, DRB1*10:01 and DRB1*01). Additionally, six patients also carry PsA risk alleles (e.g., HLA-B*27:02 and B*38:01). WES analysis and SNPs-array revealed 23 damaging variants with 18 novel “drug-resistance” RA/PsA candidate genes. Eight patients carry likely pathogenic variants within common genes (CYP21A2, DVL1, PRKDC, ORAI1, UGT2B17, MSR1). Furthermore, “private” damaging variants were identified within 12 additional genes (WNT10A, ABCB7, SERPING1, GNRHR, NCAPD3, CLCF1, HACE1, NCAPD2, ESR1, SAMHD1, CYP27A1, CCDC88C). This multistep approach highlighted novel RA/PsA candidate genes and genotype-phenotype correlations potentially useful for clinicians in selecting the best therapeutic strategy.

Extended genomic sequence of the HLA-DRB1*15:68 and HLA-DRB1*16:10:01 alleles in solid organ donors

The full-length sequence of HLA-DRB1*15:68 and HLA-DRB1*16:10:01 identified in solid organ donors.

Extended genomic sequence of the HLA-DRB1*14:04:07 and -DRB1*15:53 alleles from Gujarati individuals

The extended genomic sequences of HLA-DRB1*14:04:07 and -DRB1*15:53 alleles were identified in the Gujarati individuals.

Human Leucocyte Antigens as Prognostic Markers in Head and Neck Squamous Cell Carcinoma

BACKGROUND

The induction and regulation of immune responses depend on human leucocyte antigen (HLA) molecules that present peptides derived from mutated neoantigens or tumor-associated antigens to cytotoxic T cells. The natural variation of HLA molecules might differ between tumor patients and the normal population. Thus, there might be associations between the frequencies of HLA alleles and the survival of tumor patients.

METHODS

This issue was studied in a cohort of 84 patients with head and neck squamous cell carcinomas (HNSCCs) of different localizations. The cohort was followed up for more than 10 years. HLA-A/B/C CTS-PCR-SSP typing at 1 field level from blood samples was performed, and the results were correlated with survival.

RESULTS

HLA-A*02 was the most prevalent allele in our cohort and was present in 51.1% of patients. The HLA-A*25 and HLA-C*06 alleles exhibited a significantly higher frequency in cancer patients than in the normal population of 174 blood and kidney donors (p = 0.02 and p = 0.01, respectively, Fisher's exact test). For HLA-C*04, a negative impact on overall survival in univariate analysis (p = 0.045) and a negative, but statistically insignificant effect on survival toward poorer survival in multivariate analysis (HR: 1.82; 95% CI: 0.99-3.34, p = 0.053) were observed. In addition, HLA-A*02 was also beneficial for overall survival and progression-free survival in multivariate analysis (HR 0.54; 95% CI: 0.31-0.92; p = 0.023).

CONCLUSION

HLA-A*02 allele expression might not only predict better survival but might also indicate superior tumor antigen presentation and, thus, help to select patients who could benefit from T-cell-dependent immunotherapies.

Detection of a novel HLA-B allele, HLA-B*48:54 in a Chinese individual

The novel HLA-B*48:54 allele was identified in an individual from the Sichuan province of China. This article is protected by copyright. All rights reserved.

HLA-DRB1∗16 and -DQB1∗05 alleles are strongly associated with autoimmune pancreatitis in a cohort of hundred patients

BACKGROUND/OBJECTIVES

Autoimmune diseases are often associated with human leukocyte antigen (HLA) haplotypes, indicating that changes in major histocompatibility complex (MHC)-dependent self-peptide or antigen presentation contribute to autoimmunity. In our study, we aimed to investigate HLA alleles in a large European cohort of autoimmune pancreatitis (AIP) patients.

METHODS

Hundred patients with AIP, diagnosed and classified according to the International Consensus Diagnostic Criteria (ICDC), were prospectively enrolled in the study. Forty-four patients with chronic pancreatitis (CP) and 254 healthy subjects served as control groups. DNA was isolated from blood samples and two-digit HLA typing was performed with sequence-specific primer (SSP-) PCR. HLA allele association strength to AIP was calculated as odds ratio.

RESULTS

We uncovered a strong enrichment of HLA-DQB1 homozygosity in type 1 and type 2 AIP patients. Moreover, a significantly increased incidence of the HLA-DRB1∗16 and HLA-DQB1∗05 alleles and a concomitant lack of the HLA-DRB1∗13 allele was detected in AIP type 1 and type 2 patients. In contrast, the HLA-DQB1∗02 allele was underrepresented in the 'not otherwise specified' (NOS) AIP subtype. We detected no significant difference in the HLA-DRB3, HLA-DRB4 and HLA-DRB5 allele frequency in our cohort.

CONCLUSIONS

Although AIP type 1 and type 2 are characterized by distinct histopathological characteristics, both subtypes are associated with the same HLA alleles, indicating that the disease might rely on similar immunogenic mechanisms. However, AIP NOS represented another subclass of AIP.

Human Leukocyte Antigen (HLA) Testing in Pharmacogenomics

The genetic region on the short arm of chromosome 6 where the human leukocyte antigen (HLA) genes are located is the major histocompatibility complex. The genes in this region are highly polymorphic, and some loci have a high degree of homology with other genes and pseudogenes. Histocompatibility testing has traditionally been performed in the setting of transplantation and involves determining which specific alleles are present. Several HLA alleles have been associated with disease risk or increased risk of adverse drug reaction (ADR) when treated with certain medications. Testing for these applications differs from traditional histocompatibility in that the desired result is simply presence or absence of the allele of interest, rather than determining which allele is present. At present, the majority of HLA typing is done by molecular methods using commercially available kits. A subset of pharmacogenomics laboratories has developed their own methods, and in some cases, query single nucleotide variants associated with certain HLA alleles rather than directly testing for the allele. In this chapter, a brief introduction to the HLA system is provided, followed by an overview of a variety of testing technologies including those specifically used in pharmacogenomics, and the chapter concludes with details regarding specific HLA alleles associated with ADR.

Self-reported Wheat Sensitivity in Irritable Bowel Syndrome and Healthy Subjects: Prevalence of Celiac Markers and Response to Wheat-free Diet

Background/Aims

Most patients with irritable bowel syndrome (IBS) report food-related aggravation of symptoms. Wheat/gluten is one of the most commonly incriminated. We studied the prevalence of self-reported wheat sensitivity in patients with IBS and in a healthy population from a region in India consuming mixed-cereal diets, correlated it with serological and human leukocyte antigen (HLA) markers of celiac disease, and evaluated the response to a wheat-free diet.

Methods

We surveyed 204 patients with IBS and 400 healthy persons for self-reported wheat sensitivity. Testing for IgA anti-tissue transglutaminase and HLA DQ2 or DQ8 was done in individuals who reported wheat sensitivity. Consenting persons with wheat sensitivity were put on wheat-free diet and monitored for symptom change.

Results

Twenty-three of 204 patients with IBS (11.3%) and none of the healthy subjects self-reported wheat sensitivity. Of 23 patients, 14 (60.9%) were positive for HLA DQ2 or DQ8 and none for anti-tissue transglutaminase antibody. After 6 weeks on wheat-free diet, all 19 participating patients reported clinical improvement; fewer patients had bloating, diarrhea, constipation, and easy fatigue.

Conclusions

Eleven percent of patients with IBS self-reported wheat sensitivity. None of them had positive celiac serology; 60.9% were positive for HLA DQ2 and DQ8, suggesting a possible genetic basis. All of them improved symptomatically on a wheat-free diet.

A novel HLA-C*15 allele, HLA-C*15:192, identified by next generation sequencing in a Chinese individual

Identification of the novel HLA-C*15:192 allele that differs from HLA-C*15:02:01:01 at one position in exon 2.

Distinct immunological signatures discriminate severe COVID-19 from non-SARS-CoV-2-driven critical pneumonia

Immune profiling of COVID-19 patients has identified numerous alterations in both innate and adaptive immunity. However, whether those changes are specific to SARS-CoV-2 or driven by a general inflammatory response shared across severely ill pneumonia patients remains unknown. Here, we compared the immune profile of severe COVID-19 with non-SARS-CoV-2 pneumonia ICU patients using longitudinal, high-dimensional single-cell spectral cytometry and algorithm-guided analysis. COVID-19 and non-SARS-CoV-2 pneumonia both showed increased emergency myelopoiesis and displayed features of adaptive immune paralysis. However, pathological immune signatures suggestive of T cell exhaustion were exclusive to COVID-19. The integration of single-cell profiling with a predicted binding capacity of SARS-CoV-2 peptides to the patients' HLA profile further linked the COVID-19 immunopathology to impaired virus recognition. Toward clinical translation, circulating NKT cell frequency was identified as a predictive biomarker for patient outcome. Our comparative immune map serves to delineate treatment strategies to interfere with the immunopathologic cascade exclusive to severe COVID-19.

Identification of a novel HLA-A*11 allele, HLA-A*11:399, in a Chinese Individual

One nucleotide substitution in codon 90 of HLA-A*11:01:01:01 results in a novel allele, HLA-A*11:399.

Discovery of the novel HLA-C*01:179 allele in a southern Chinese patient

One nucleotide substitution in codon 189 of HLA-C*01:02:01:01 results in a novel allele, HLA-C*01:179.

A noninvasive diagnostic approach to retrospective donor HLA typing in kidney transplant patients using urine

Antibody-mediated rejection (AMR) is a major obstacle to long-term kidney transplantation. AMR is mostly caused by donor specific HLA antibodies, which can arise before or any time after transplantation. Incomplete donor HLA typing and unavailability of donor DNA regularly preclude the assessment of donor-specificity of circulating anti-HLA antibodies. In our centre, this problem arises in approximately 20% of all post-transplant HLA-antibody assessments. We demonstrate that this diagnostic challenge can be resolved by establishing donor renal tubular cell cultures from recipient´s urine as a source of high-quality donor DNA. DNA was then verified for genetic origin and purity by fluorescence in situ hybridization and short tandem repeat analysis. Two representative cases highlight the diagnostic value of this approach which is corroborated by analysis of ten additional patients. The latter were randomly sampled from routine clinical care patients with available donor DNA as controls. In all 12 cases, we were able to perform full HLA typing of the respective donors confirmed by cross-comparison to results from the stored 10 donor DNAs. We propose that this noninvasive diagnostic approach for HLA typing in kidney transplant patients is valuable to determine donor specificity of HLA antibodies, which is important in clinical assessment of suspected AMR.

Discovery of the novel HLA-A*11:396 allele in a Chinese Han individual

One nucleotide substitution in codon 73 of HLA-A*11:01:01:01 results in a novel allele, HLA-A*11:396.

Conception of Saviour Siblings: Ethical Perceptions of Selected Stakeholders in Malaysia

The conception of saviour siblings using preimplantation genetic diagnosis coupled with human leukocyte antigen (HLA) typing or HLA typing alone is controversial and receives a wide divergence of legal responses among countries around the world. The resulting child conceived through this procedure is dubbed a 'saviour sibling' as the child can potentially act as a compatible donor for an elder ailing sibling who needs a haematopoietic stem cell transplantation. At present, the acceptability of this procedure in Malaysia is ambiguous as there is no specific statute governing assisted reproductive technology, and the guideline issued by the Malaysian Medical Council does not expressly address this issue. The ethical arguments relating to the conception of saviour siblings in the current literature are mainly thought to reflect a liberal viewpoint which is predominantly Western in nature. This paper seeks to explore the perception of selected key stakeholders on the acceptability of and ethical concerns related to this procedure in the Malaysian context. The findings indicate that stakeholders generally support the conception of saviour siblings and some of their concerns echo the Western viewpoint. Interestingly, many were highly anxious about its economic implication, which is rarely discussed in the current literature on saviour siblings.

[Definition and standardization of histocompatibility requests depending on patient course and donor type: Guidelines from the Francophone Society of Bone Marrow Transplantation and Cellular Therapy (SFGM-TC) and the Francophone Society of Histocompatibility and Immunogenetics (SFHI)]

Standardization of histocompatibility tests for allogeneic hematopoietic cell transplants, harmonization of information transmitted to clinicians are part of quality improvement and optimization of human and economic resources. New HLA typing technologies provide high-resolution information within a reasonable time frame. Knowledge of high-resolution HLA typing for the patient and their relatives is essential for a better interpretation of compatibilities. HLA-DPB1 typing must be considered in transplant field regardless of the donor type. The benefits of using search and match programs are considerable. It saves time and reduces additional typing costs by providing rapid information about the likelihood to identify a matched unrelated donor. A backup therapy considering alternative cell sources or treatment can therefore be quickly implemented. The importance of knowledge and consideration of patient immunization for donor choice was explored in previous workshops of the SFGM-TC (2018 and 2019). The published recommendations remain applicable. The routine follow-up protocol and in case of desensitization will be detailed here. This harmonization must be accompanied by the standardization of information to be returned to the clinician regarding the donor finding possibilities for the patient. This will guarantee a similar quality level in every center.

Characterization of the novel HLA-DQB1*03:362 allele in a Chinese family

A novel variant of HLA-DQB1*03 differs from DQB1*03:02:01:01 by one nucleotide substitution in Exon 2.

The HLA groups and their relationship with clinical features in Turkish children and adolescents with celiac disease

BACKGROUND

We aimed to investigate the relationship between human leukocyte antigens (HLA)-groups and clinical features, and degree of intestinal injury in children with celiac disease (CD).

METHODS

Study group included 73 (50 females, 68.5%) children with CD. Demographic and clinical features, accompanying autoimmune diseases, family history for CD and degree of damage in small intestinal mucosa (according to Marsh classification) at the time of diagnosis were determined. Twenty-two siblings of celiac patients without CD (15 females, 65.2%) consisted control group 1, and 66 (40 females, 60.6%) people from the normal population consisted control group 2.

RESULTS

The allele frequencies of HLA B8, B50, C6, C7, DR3, DR7, DQ2, and DR3 homozygosity were higher in the patient group. HLA DQ2 positivity was 89% in the patient group, 73.9 and 45.5% in control groups 1 and 2, respectively (p < 0.0001). HLA A30, C14, DR11, DQ3 frequency were lower in patients compared to both control groups. HLA-DR15 alleles in patient and control group 1 was significantly lower compared to the general population (p < 0.05). Thirty (41.1%) patients had typical, 43 (58.9%) patients had atypical presentation. Thirteen (17.8%) patients had other autoimmune diseases. There was no association between coexisting autoimmune diseases and the HLA antigens. Fifteen patients (20.5%) had a positive family history for CD; patients with HLA A69, B41 and C12 alleles had a higher positive family history (p < 0.05). Intestinal mucosal damage was as follows: 5 patients (6.8%) had Marsh 2, 25 (34.3%) Marsh 3a, 28 (38.4%) Marsh 3b, 15 (20.5%) Marsh 3c. Patients with HLA-DR15 alleles had more frequent Marsh 3a lesions (p < 0.05).

CONCLUSIONS

B8, B50, C6, C7, DR3, DR7, DR3/DR3, DQ2 alleles were risk factors for CD in the Turkish population. HLA C14, DR11, DR15, and DQ3 alleles were found to have a protective role in the same population.

Reduced PCR-generated errors from a hybrid capture-based NGS assay for HLA typing

Next generation sequencing (NGS) assays are state of the art for HLA genotyping. To sequence on an Illumina sequencer, the DNA of interest must be enriched, fragmented, and bookended with known oligonucleotide sequences, a process known as library construction. Many HLA genotyping assays enrich the target loci by long-range PCR (LR-PCR), prior to fragmentation. This PCR step has been reported to introduce errors in the DNA to be sequenced, including inaccurate replication of repeated sequences, and the in vitro recombination of alleles encoded on separate chromosomes. An alternative library construction method involves fragmentation of genomic DNA, followed by hybrid-capture (HC) enrichment of target HLA loci. This HC-based method involves PCR, but with far fewer cycles. Consequently, the HC method had significantly fewer PCR-induced errors, including more faithful replication of repeated sequences, and the near elimination of recombinant sequences. These improvements likely produce more accurate NGS sequencing data of HLA loci.

HLApers: HLA Typing and Quantification of Expression with Personalized Index

The plethora of RNA-seq data which have been generated in the recent years constitutes an attractive resource to investigate HLA variation and its relationship with normal and disease phenotypes, such as cancer. However, next generation sequencing (NGS) brings new challenges to HLA analysis because of the mapping bias introduced by aligning short reads originated from polymorphic genes to a single reference genome. Here we describe HLApers, a pipeline which adapts widely used tools for analysis of standard RNA-seq data to infer HLA genotypes and estimate expression. By generating reliable expression estimates for each HLA allele that an individual carries, HLApers allows a better understanding of the relationship between HLA alleles and phenotypes manifested by an individual.

New challenges, new opportunities: Next generation sequencing and its place in the advancement of HLA typing

The Human Leukocyte Antigen (HLA) system has a critical role in immunorecognition, transplantation, and disease association. Early typing techniques provided the foundation for genotyping methods that revealed HLA as one of the most complex, polymorphic regions of the human genome. Next Generation Sequencing (NGS), the latest molecular technology introduced in clinical tissue typing laboratories, has demonstrated advantages over other established methods. NGS offers high-resolution sequencing of entire genes in time frames and price points considered unthinkable just a few years ago, contributing a wealth of data informing histocompatibility assessment and standards of clinical care. Although the NGS platforms share a high-throughput massively parallel processing model, differing chemistries provide specific strengths and weaknesses. Research-oriented Third Generation Sequencing and related advances in bioengineering continue to broaden the future of NGS in clinical settings. These diverse applications have demanded equally innovative strategies for data management and computational bioinformatics to support and analyze the unprecedented volume and complexity of data generated by NGS. We discuss some of the challenges and opportunities associated with NGS technologies, providing a comprehensive picture of the historical developments that paved the way for the NGS revolution, its current state and future possibilities for HLA typing.

The frequency of HLA-DQ2/DQ8 haplotypes and celiac disease among the first-degree relatives of patients with celiac disease

AIM

We evaluated the frequency of human leukocyte antigen (HLA) DQ2/DQ8 haplotypes as well as celiac disease (CD) among the first-degree relatives (FDRs) of CD patients, compared with healthy controls, and compared the HLA typing with serologic tests in this population.

BACKGROUND

Until now, no study has examined the frequency of HLA-DQ2/DQ8 haplotypes among the FDRs of Iranian patients with CD.

METHODS

In the current case-control study, 100 FDRs of CD patients and 151 healthy controls were included. Demographic characteristics were assessed using a research-made questionnaire. A blood sample was collected from each participant for HLA-DQ typing and measuring serum levels of anti-gliadin and anti-transglutaminase (anti-tTG) antibodies.

RESULTS

The mean age of the FDRs of CD patients and controls was 30 and 35 years, respectively. Also, 51% (n=51) of the FDRs and 51.7% (n=78) of controls were female. CD was diagnosed among 3% (n=3) of the FDRs of CD patients. No significant difference was found in terms of the frequency of HLA-DQ alleles between the FDRs of CD patients and controls. Out of 100 FDRs of CD patients, 40% had HLA-DQ2 allele, 16% carried HLA-DQ8 allele, and 4% had both alleles. Surprisingly, the CD was diagnosed in three subjects among 60 FDRs of CD patients with HLA-DQ2 allele (3% of the whole population). This diagnosis was based on the results of serological tests as well as endoscopy and intestinal biopsy.

CONCLUSION

CD was confirmed among 3% (n=3) of the FDRs of CD patients. We found that HLA typing is not effective in predicting CD among FDRs of CD patients. Other methods such as serological tests have a higher priority compared with HLA-DQ typing.

Adult-onset type 1 diabetic patients with less severe clinical manifestation have less risk DR-DQ genotypes than childhood-onset patients

BACKGROUND

The aim of this study was to investigate differences in clinical features and HLA genotypes between adult-onset and childhood-onset patients with type 1 diabetes in a Chinese population.

MATERIALS AND METHODS

This study enrolled 716 Han Chinese patients with type 1 diabetes from Guangdong (258 childhood-onset and 458 adult-onset) to compare their clinical features. Of them 214 patients with classical type 1 diabetes (100 childhood-onset and 114 adult-onset) were selected for HLA DR and DQ genotyping by next-generation sequencing.

RESULTS

Adult-onset patients were characterized by longer duration of symptoms before diagnosis, lower frequency of DKA at disease onset, less frequent autoantibody positivity, higher serum C-peptide concentrations, and better glycemic control. These findings were replicated in the restricted cohort of 214 patients with classical type 1 diabetes. Compared with childhood-onset patients, adult-onset patients had a lower frequency of the DR9 haplotype, as well as lower frequency of high-risk DR3/DR4 and DR3/DR9 genotypes, but higher frequency of DR3/DR3 genotype and DR3/X, DR4/X or DR9/X (X, non-risk) genotypes.

CONCLUSIONS

Adult-onset type 1 diabetic patients with susceptible haplotypes (DR3, DR4 or DR9) were more likely to carry protective DR-DQ haplotypes than childhood-onset patients, which suggested the association between less risk DR-DQ genotypes and the less severe clinical manifestation in adult-onset patients.

Characterization of the novel HLA-A*30:154 allele by next-generation sequencing

A*30:154 differs from A*30:01:01:01 by one nucleotide substitution at codon 39 in exon 2 from C to A.