Cytokine gene polymorphisms in Iraqi Arabs

In this report, 224 unrelated healthy Iraqi Arabs (102 males and 122 females) were genotyped for 22 SNPs (single nucleotide polymorphisms) belong to 13 cytokine genes (IL1A, IL1B, IL1RA, IL1R, IL2, IL4, IL4R, IL6, IL10, IL12, IFNG, TNFA and TGFB1). The method of detection was PCR-SSP (polymerase chain reaction-sequence specific primer). The data were presented in terms of allele and genotype frequencies. Two-locus haplotype frequencies were also estimated for some SNPs. Genotype frequencies of detected cytokine gene polymorphisms are available in the Database of Allele Frequencies Net under the AFND number 3422 and the population name “Iraq Arab Cytokine”.     

Diversities of HLA-A, -B, -C, -DRB1 and -DQB1 loci in Chinese Kazak population and its genetic relatedness dissection with multiple populations: a comparative study

Studying the allele and haplotype distributions of human leukocyte antigen (HLA) loci at 2nd-field level in different populations was important. Allele and haplotype frequencies of HLA-A, -B, -C, -DRB1 and -DQB1 loci in 110 unrelated healthy Kazak individuals living in Xinjiang (China) were analyzed using polymerase chain reaction sequence based typing. Thirty HLA-A, 48 HLA-B, 24 HLA-C, 34 HLA-DRB1 and 18 HLA-DQB1 alleles were detected at the 2nd-field level in the Kazak population. Frequencies of HLA alleles, genotypes, and haplotypes were calculated, and some exhibited significantly different distributions among different populations. A neighbor-joining (NJ) tree, heatmap, multidimensional scaling (MDS) and principal component analysis (PCA) were used to explore the genetic relationships between the Kazak population and 32 reference populations distributed in Asia, Africa, America and Europe using frequency data of HLA-A, -B, -C and -DRB1 loci. The NJ tree, heatmap, and MDS of the 33 populations were constructed based on pairwise D_A values of populations obtained by the HLA-A, -B, -C and -DRB1 allele frequencies. Different PCA plots were constructed based on the allele frequencies of HLA-A, -B, -C and -DRB1 or estimated haplotypic frequencies of HLA-A, -B, -C loci. The data obtained in the present research can be used for research on HLA-related diseases or paternity relationships, and aid to finding the best matched donors in stem cell transplantation for Kazak individuals.     

HLA -A, -C, -B, -DRB1, -DQB1 and -DPB1 allele and haplotype frequencies in 4514 healthy Norwegians

We report HLA-A, -C, -B, -DRB1, -DQB1 and -DPB1 allele frequencies and estimated haplotype frequencies from 4514 healthy Norwegians who volunteered to participate in the Norwegian Bone Marrow Donor Registry. HLA genotyping was conducted on a Next Generation Sequencing platform. Data were analyzed using Arlequin and Pypop software. No significant deviations from Hardy-Weinberg Equilibrium were noted at any of the loci studied. We discuss the representability for the Norwegian population and argue that the presented HLA data could serve as a Norwegian reference panel.     

Study of HLA-A, -B, -C, -DRB1 and -DQB1 polymorphisms in COVID-19 patients

BackgroundHuman leukocyte antigen (HLA) plays an important role in immune responses to infections, especially in the development of acquired immunity. Given the high degree of polymorphisms that HLA molecules present, some will be more or less effective in controlling SARS-CoV-2 infection. We wanted to analyze whether certain polymorphisms may be involved in the protection or susceptibility to COVID-19.MethodsWe studied the polymorphisms in HLA class I (HLA-A, -B and -C) and II (HLA-DRB1 and HLA-DQB1) molecules in 450 patients who required hospitalization for COVID-19, creating one of the largest HLA-typed patient cohort to date.ResultsOur results show that there is no relationship between HLA polymorphisms or haplotypes and susceptibility or protection to COVID-19.ConclusionOur results may contribute to resolve the contradictory data on the role of HLA polymorphisms in COVID-19 infection.     

HLA-A, -B, -DRB1, -DQA1, and -DQB1 genotyping of 641 individuals from southern Brazil

Sixty hundred and forty-one Brazilian individuals from the north and northwestern state of Paraná, southern Brazil, were selected for the study. The HLA-A, -B, -DRB1, -DQA1, and -DQB1 genotyping were performed using rSSO and Micro SSP analysis. These genotype data are available in the Allele Frequencies Net Database under the population name “Brazil Paraná Caucasian” number “AFND3618”.     

Association of HLA class II (-DRB1,-DQB1,-DPB1) alleles and haplotypes on susceptibility to aplastic anemia in northern Chinese Han

The Human Leukocyte Antigen (HLA) genes, playing key roles in mediating the immune response, especially HLA class II alleles were suggested to play a role in the activation of autoreactive T-cells in aplastic anemia (AA). Previous studies in different ethnic groups have indicated that some of HLA-A,-B,-DRB1 alleles had a protective or susceptive association with the prevalence, pathogenesis and development of AA. HLA class II genes, especially HLA-DQB1 and -DPB1 alleles or haplotypes at high-resolution level associated with AA have not been fully identified in northern Chinese Han populations. The aim of this study was to identify association of the variations in HLA class II region with AA in northern Chinese Han population. A recent case-control study, including 96 AA patients and 824 healthy controls was performed. The high-resolution HLA genotyping was conducted by PCR-SBT, -SSO and NGS-ION S5^TM platform. Based on genotypic data of the three loci, haplotype estimation was carried out. HLA-DRB1*15:01 (Pc = 2.87 × 10^-3; OR = 2.11, 95% CI = 1.45–3.07) and HLA-DQB1*06:02 (Pc = 1.86 × 10^-2; OR = 2.01, 95% CI = 1.32–3.06) were the risk and predisposition alleles to AA in northern Chinese Han after considering multiple testing. Moreover, the HLA-DRB1*15:01-DQB1*06:02 (Pc = 4.90 × 10^-3; OR = 2.09, 95% CI = 1.37–3.19) and HLA-DRB1*14:05-DQB1*05:03 (Pc = 2.65 × 10^-2; OR = 2.82, 95%CI = 1.45–5.50) haplotypes had direct strong relevance to AA and were the susceptible haplotypes. HLA-DPB1 alleles and 23 polymorphic amino acid residues spanning exon 2 ~ 4 of DPβ1 molecules have showed no statistically significant associations between AA and controls. The present findings establish a novel link between inherited HLA-DRB1,-DQB1,-DPB1 risk alleles and haplotypes in northern Chinese Han with AA, and open new avenues for development of targeted therapies to prevent or redirect immunopathology in AA.     

HLA-A, -B, -C, -DPB1, -DQB1 and -DRB1 allele frequencies of North Tanzanian Maasai

Locus-specific amplicon sequencing was used to HLA type 336 participants of Maasai ethnicity at the HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1 loci. Participants were recruited from three study villages in North Tanzania, for the purpose of investigating risk factors for trachomatous scarring in children. Other than HLA-A, all loci significantly deviated from Hardy-Weinberg equilibrium, possibly due to high relatedness between individuals: 238 individuals shared a house with at least one another participant. The most frequent allele for each locus were A*68:02 (14.3 %), B*53:01 (8.4 %), C*06:02 (19.2 %), DRB1*13:02 (17.7 %), DQB1*02:01 (16.9 %) and DPB1*01:01 (15.7 %), while the most common inferred haplotype was A*68:02 ～ B*18:01 ～ C*07:04 ～ DRB1*08:04 ～ DQB1*04:02 ～ DPB1*04:01 (1.3 %).     

HLA-A, -B, -DRB1, -DQA1, and -DQB1 polymorphism in thais

In this study we examined HLA-A, -B, -DRB1, -DQA1, and -DQB1 gene, allele, and haplotype frequencies in two ethnic Thai populations. We compared these frequencies to the known HLA class I and II allele profiles of non-Thai mainland and insular Southeast (SE) Asians. HLA-A locus gene and allele frequencies, are comparatively homogeneous in both Thai and non-Thai SE Asians. In contrast, HLA-B, -DRB1, -DQA1, and -DQB1 gene and allele frequencies, show more ethnic and geographic variation in SE Asians. Conserved haplotypes, or combinations of linked HLA class I and II alleles were detected in Thais, but at relatively low frequencies. It would appear that ethnic Thais, reflect an admixture of peoples from both the northern mainland and southern island groups of SE Asia.     

HLA-A, -B and -DRB1 genotyping and haplotype frequencies of 3892 cord blood units in the Hong Kong Chinese Cord Blood Registry

HLA-A, -B and -DRB1 gene and haplotype frequencies have been calculated from 3892 southern Chinese unrelated cord blood units in a Hong Kong Cord Blood Registry. This is the first large-scale paper to report the distribution of A-B-DRB1 alleles in Hong Kong Chinese Cord Blood Units. This information is important for estimating the optimal and economically cost-effective donor size and likelihood of obtaining appropriately matched cord blood units for Chinese patients awaiting haematopoietic stem cell transplantation. The data are available in the Allele Frequencies Net Database under the population name ‘‘Hong Kong Chinese Cord Blood Registry’’ and the identifier (AFND003358).     

HLA-A, -B, -C, -DRB1 and -DQB1 allele and haplotype frequencies in a population of 432 healthy unrelated individuals from Albania

This paper reports the HLA-A, -B, -C, -DRB1 and -DQB1 allele and haplotype polymorphism in a population of 432 healthy individuals from Albania. First-field HLA genotyping was performed by polymerase chain reaction sequence-specific priming and/or oligonucleotide methods. The data were analyzed statistically using gene counting and Arlequin software packages. No deviation from Hardy Weinberg Equilibrium was detected at any of the loci studied. The HLA genotypic data of the population sample reported here are available publicly in the Allele Frequencies Net Database and they can serve as a reference database for further HLA-based population genetics studies including the Albanian population.     

HLA-A, -B, -C, -DRB1 and -DQB1 alleles and haplotypes in 951 Southeast Asia Malays from Peninsular Malaysia

A total of 951 Southeast Asia Malays from Peninsular Malaysia were genotyped for HLA-A, -B, -C -DRB1, and -DQB1 loci using polymerase chain reaction sequence-specific oligonucleotide probe hybridization methods. In this report, there were significant deviation from Hardy-Weinberg proportions for the HLA-A (p < 0.0001), -B (p < 0.0001), -DRB1 (p < 0.0001) and -DQB1 (p < 0.01) loci. Minor deviations from HWEP were detected for HLA-C (p = 0.01). This genotype data was available in Allele Frequencies Network Database (AFND) Gonzalez-Galarza et al. (2015).     

HLA-A, -B, -C, -DRB1 and -DQB1 alleles and haplotypes in 271 Southeast Asia Indians from Peninsular Malaysia

A total of 271 Southeast Asia Indians from Peninsular Malaysia were genotyped for HLA-A, -B, -C, -DRB1, and -DQB1 loci using polymerase chain reaction sequence-specific oligonucleotide probe hybridization methods. In this report, HLA-B and HLA-DQB1 was in Hardy-Weinberg proportions (HWEP) (p > 0.05). We observed significant deviation from the HWEP for HLA-A (p < 0.05), HLA-C (p < 0.01) and HLA-DRB1 (p < 0.01) loci. This genotype data is available in Allele Frequencies Network Database (AFND) Dos Santos et al. (2016).     

Estimation of high-resolution HLA-A, -B, -C, -DRB1 allele and haplotype frequencies based on 8862 German stem cell donors and implications for strategic donor registry planning

Human leukocyte antigen (HLA) haplotype frequency distributions in specific populations can be applied to optimize both individual stem cell donor searches and donor registry planning. We present allele and haplotype frequencies derived from a data set of 8862 German stem cell donors who were typed at high resolution for the HLA-A, HLA-B, HLA-C, and HLA-DRB1 genes upon registration. Calculated haplotype frequencies were used to estimate the probability p to find matching donors subject to donor registry size n. The impact of various matching standards on p(n) was analyzed. When high-resolution matching for HLA-A, HLA-B, HLA-C, and HLA-DRB1 is required, p(1,000,000) is 0.678. The corresponding value for n = 7,000,000 is 0.859. In a scenario with low-resolution matching and no consideration of HLA-C, p(1,000,000) is 0.863 and thus larger than p(7,000,000) in the scenario with stricter matching requirements. As recent findings support the importance of high-resolution matching of HLA-A, HLA-B, HLA-C, and HLA-DRB1 for outcomes of hematopoietic stem cell transplantation, our results are highly relevant for strategic planning and resource allocation of donor centers and registries.     

Distribution of HLA-A, -B and -DRB1 antigenic groups and haplotypes from the Brazilian bone marrow donor registry (REDOME)

To improve assistance for patients awaiting a bone marrow transplant from an unrelated donor, it is important to genetically characterize the Brazilian volunteer bone marrow donors registry (REDOME). Our objective was to describe the antigenic groups and haplotype frequencies of HLA-A, HLA-B and HLA-DRB1 in the five regions of Brazil and by self-reported ethnicity groups using the REDOME data. Our study included 3,038,286 individuals. HLA antigenic groups and haplotype frequencies were estimated using an Expectation-Maximization (EM) algorithm. All described HLA-A*, HLA-B* and HLA-DRB1* groups were identified in this study. A*02 (25.9%), B*35 (11.8%) and DRB1*13 (13.4%) are the most frequent antigenic groups in REDOME, and the A*01-B*08-DRB1*03 haplotype is the most frequent in the registry. The antigenic group and haplotype frequency data obtained in this study could be helpful for national donor recruitment strategies across the country.     

HLA-A, -B, -C,and -DRB1 genotyping and haplotype frequencies for a Hong Kong Chinese population of 7595 individuals

HLA-A, -B, -C and -DRB1 gene and haplotype frequencies have been calculated from 7595 southern Chinese unrelated donors in a Hong Kong Bone Marrow Donor Registry. This is the first large-scale paper to report the distribution of A-C-B-DRB1 alleles in Hong Kong Chinese. This information is important for phylogenetic, comparative studies and estimating the optimal and cost-effective donor size and likelihood of obtaining appropriately matched donors for Chinese patients awaiting haematopoietic stem cell transplantation. The allele and haplotype data are available in the Allele Frequencies Net Database under the population name ‘‘Hong Kong Chinese BMDR’’ and the identifier (AFND003357).     

西北地区汉族人群HLA-A、-B、-DRB1基因座单倍型分析

目的 分析西北地区汉族群体HLA-A、-B和-DRB1基因座等位基因频率和HIA-A-B、B-DRB1和A-B-DRB1单倍型，获得单倍型频率数据。方法 采用序列特异性寡核苷酸探针反向斑点杂交技术对西北地区62个家系和101个无关个体HLA-A、-B和-DRB1基因座进行基因分型，分析HLA单倍型。结果 在西北地区汉族人群中检出15个HLA-A等位基因，28个HLA-B等位基因，13个HLA-DRB1等位基因，A02、A11、A24、B13、B15、1340、DRB1＊04、DRB1＊07、DRB1＊09和DRB1＊15基因频率较高（〉10％），A02（0．3244）、B13（0．1200）和DRB1＊15（0．1400）等位基因频率最高。分析得出HLA-A-B、B-DRB1、A-B-DRB1单倍型分别有122、147和278种，83种A-B-DRB1单倍型有至少两条以上相同的单倍型，占总单倍型数的18．44％（83／450）。A30-B13-DRB1＊07、A02-B46-DRB1＊09、A01-B37-DRB1＊10、A24-B15-DRB＊15、A02-B46-DRB1＊08、A33-B58-DRB1＊03是最常见的单倍型。结论 西北地区汉族群体HLA单倍型多态性较为丰富，等位基因频率和单倍型频率数据可用于骨髓移植供者的选择、法医学亲权鉴定以及人类学研究。     

HLA-A, -B,and -DRB1 allele and haplotype diversity in a cohort of Brazilian renal transplant candidates

The distribution of organs for renal transplant depends on HLA matching between donor and recipient. This study aimed to characterize the allele and haplotype frequencies of HLA-A, -B, and -DRB1 in a cohort of renal transplant candidates populations in the region of Sao José do Rio Preto (State of São Paulo), to compare the allele frequencies between Caucasian and Black in that region, as well as to compare these frequencies with different Brazilian populations reported. The HLA-A, -B, and -DRB1 allele and haplotypes frequencies were analyzed in a sample of 2.624 individuals and classified according to the ethnic group (2.347 Caucasians and 277 Blacks). The HLA class I (A, B) and class II (DRB1) specificities were determined by complement-dependent microlymphocytotoxic (CDC) and Polymerase Chain Reaction/Sequence Specific Priming (PCR-SSP) methods, respectively. Twenty-one HLA-A, 34 HLA-B and 13 HLA-DRB1 allelic groups were identified. The most frequent alleles for each locus were HLA-A¹02, HLA-B¹35, and HLA-DRB1¹11. The most frequent haplotypes found were A¹01 B¹08 DRB1¹03 among Caucasians and A¹29 B¹15 DRB1¹04 among Blacks. The most common alleles for each locus among RTx were HLA-A¹02, HLA-B¹35 and HLA-DRB1¹11. The haplotypes A¹01 B¹08 DRB1¹03 and A¹29 B¹44 DRB1¹07 prevailed among Caucasians and Blacks, respectively. This study provides the first data on the HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies of renal transplant candidates populations in the region of Sao José do Rio Preto.