Association between Human Leukocyte Antigen and End-Stage Renal Disease in Patients from Transylvania, Romania

End-stage renal disease (ESRD) is the final stage of chronic kidney disease. This study explored the association between human leukocyte antigen (HLA) and ESRD. The interaction between genetic and environmental factors may also play a role in the development of ESRD. The study included 2392 ESRD patients who were awaiting renal transplantation. Blood samples were genotyped by SSOP and SSP-PCR methods. Multivariate logistic regression analysis showed that HLA-A*11 (p = 0.027), HLA-A*34 (p = 0.017), HLA-A*69 (p = 0.012), HLA-B*41 (p < 0.001), HLA-B*50 (p = 0.004), HLA-DRB1*10 (p = 0.027), and HLA-DRB1*14 (p = 0.004) were positively associated with ESRD (OR > 1); HLA-DRB1*07 (p < 0.001), HLA-DRB1*08 (p = 0.005), and HLA-DRB1*13 (p < 0.001) were protective against ESRD (OR < 1); and the three-locus haplotype HLA-A*02-B*41-DRB1*03, containing one susceptible allele, was strongly associated with ESRD (p < 0.001, OR = 3.15). In conclusion, this retrospective analysis of HLA typing in patients with ESRD of various etiologies suggests that molecular data on the HLA polymorphism should be collected in order to identify high-risk ESRD patients and to improve graft survival after kidney transplantation.

HLA allele and haplotype frequencies of registered stem cell donors in Chile

Patients in need of hematopoietic stem cell transplantation often rely on unrelated stem cell donors matched in certain human leukocyte antigen (HLA) genes. Donor search is complicated by the extensive allelic variability of the HLA system. Therefore, large registries of potential donors are maintained in many countries worldwide. Population-specific HLA characteristics determine the registry benefits for patients and also the need for further regional donor recruitment. In this work, we analyzed HLA allele and haplotype frequencies of donors of DKMS Chile, the first Chilean donor registry, with self-assessed "non-Indigenous" (n=92,788) and "Mapuche" (n=1,993) ancestry. We identified HLA alleles that were distinctly more abundant in the Chilean subpopulations than in worldwide reference populations, four of them particularly characteristic for the Mapuche subpopulation, namely B*39:09g, B*35:09, DRB1*04:07g, and DRB1*16:02g. Both population subsamples carried haplotypes of both Native American and European origin at high frequencies, reflecting Chile's complex history of admixture and immigration. Matching probability analysis revealed limited benefits for Chilean patients (both non-Indigenous and Mapuche) from donor registries of non-Chilean donors, thus indicating a need for ongoing significant donor recruitment efforts in Chile.

Haplotype-dependent HLA-DRB1-DQB1 susceptibility to occult HBV infection in Xi'an Han population

BACKGROUND

Occult hepatitis B virus (HBV) infection (OBI) is primarily characterized by the persistence of HBV-DNA in the liver tissues and/or in the serum without detectable HBsAg. Human leukocyte antigen (HLA) polymorphisms have been found to be strongly associated with HBV in different ethnic backgrounds. The association of HLA-DRB1-DQB1 haplotypes with OBI has not been previously reported in China. The aim of this study was to identify the potential association of HLA-DRB1-DQB1 haplotypes that may be involved in OBI genetic susceptibility.

METHODS

A case-control study was conducted between 107 OBI subjects and 280 healthy controls from the blood donors in the Shaanxi Province Blood Center. The HLA-DRB1, DQB1 loci were genotyped using polymerase chain reaction-sequence based typing (PCR-SBT). Based on the genotype data of the two loci, haplotype estimation was performed.

RESULTS

HLA-DRB1*07:01-DQB1*02:02 (pc = 0.344 × 10^-3 , OR = 3.489, 95%CI = 2.000-6.088) and HLA-DRB1*09:01-DQB1*03:03 (pc = 0.02, OR = 2.370, 95%CI = 1.450-3.873) serve as the possible risk and susceptibility haplotypes for OBI in Xi'an Han after Bonferroni correction.

CONCLUSIONS

This study demonstrated that HLA II haplotypes were significantly associated with OBI in the Xi'an Han population. To the best of our knowledge, this is the first study to associate HLA-DRB1-DQB1 haplotypes with OBI, which can provide valuable insights into the relationship between the various genetic factors and immune responses in the Xi'an population. The findings can also form the basis for future studies about the role of HLA in OBI.

A Two-Level, Intramutant Spectrum Haplotype Profile of Hepatitis C Virus Revealed by Self-Organized Maps

RNA viruses replicate as complex mutant spectra termed viral quasispecies. The frequency of each individual genome in a mutant spectrum depends on its rate of generation and its relative fitness in the replicating population ensemble. The advent of deep sequencing methodologies allows for the first-time quantification of haplotype abundances within mutant spectra. There is no information on the haplotype profile of the resident genomes and how the landscape evolves when a virus replicates in a controlled cell culture environment. Here, we report the construction of intramutant spectrum haplotype landscapes of three amplicons of the NS5A-NS5B coding region of hepatitis C virus (HCV). Two-dimensional (2D) neural networks were constructed for 44 related HCV populations derived from a common clonal ancestor that was passaged up to 210 times in human hepatoma Huh-7.5 cells in the absence of external selective pressures. The haplotype profiles consisted of an extended dense basal platform, from which a lower number of protruding higher peaks emerged. As HCV increased its adaptation to the cells, the number of haplotype peaks within each mutant spectrum expanded, and their distribution shifted in the 2D network. The results show that extensive HCV replication in a monotonous cell culture environment does not limit HCV exploration of sequence space through haplotype peak movements. The landscapes reflect dynamic variation in the intramutant spectrum haplotype profile and may serve as a reference to interpret the modifications produced by external selective pressures or to compare with the landscapes of mutant spectra in complex in vivo environments. IMPORTANCE The study provides for the first time the haplotype profile and its variation in the course of virus adaptation to a cell culture environment in the absence of external selective constraints. The deep sequencing-based self-organized maps document a two-layer haplotype distribution with an ample basal platform and a lower number of protruding peaks. The results suggest an inferred intramutant spectrum fitness landscape structure that offers potential benefits for virus resilience to mutational inputs.

Human leukocyte antigen class I association with occult hepatitis B virus infection in the Shaanxi Han group: Analysis at the haplotype level

BACKGROUND

Human leucocyte antigen (HLA) class I genes and haplotypes correlate with hepatitis B virus (HBV) infection. Occult HBV infection (OBI), a special type of chronic HBV infection, is defined as HBV surface antigen negative patients with or those without serologic markers by the means of HBV DNA detection in human plasma or in liver tissue by a diagnostic test. So far, the associations of HLA I haplotypes with OBI have not been reported previously in China.

METHODS

A case-control study between 107 OBI subjects and 280 healthy controls from blood donors in the Blood Center of the Shaanxi Province was conducted in the present association analysis. The HLA-A, -B and -C loci of case-control subjects were detected and genotyped by polymerase chain reaction-sequence based typing. The HLA-A, -B and -C haplotypic frequencies were calculated by the maximum likelihood method.

RESULTS

The HLA-A*33:03-C*07:01G (p_c  = 0.039, odds ratio [OR] = 8.996, 95% confidence interval [CI] = 1.825-44.338), B*44:03-C*07:01G (p_c  = 0.0069, OR = 12.000, 95% CI = 2.507-57.436) and A*33:03-B*44:03-C*07:01G (p_c  = 0.04, OR = 7.094, 95% CI = 1.387-36.288) haplotypes showed a a significant positive association with OBI. Independent effects demonstrated that HLA-B*44:03 and HLA-C*07:01G gave the main contribution to risk, whereas HLA-A*33:03 was associated only by linkage disequilibrium.

CONCLUSIONS

This present study is the first to demonstrate that HLA I haplotypes are associated with OBI in the Shaanxi Han population. The present results suggest that HLA-B*44:03-C*07:01G might be a potential risk factor for OBI. Comparisons of the frequencies of HLA I haplotypes at high resolution were made between OBI from northern Chinese Han and controls. Frequencies of HLA-A-B, A-C, B-C, A-B-C between the OBI group (gray column) and the control group (blank column) were compared. Haplotypes with p < 0.05 in either group were shown. p values for multiple comparisons (p_c ) were corrected by Bonferroni correction (*p_c  < 0.05).

Estimating HLA haplotype frequencies from homozygous individuals - A Technical Report

We estimated HLA haplotype frequencies based on individuals homozygous for 4, 5 or 6 loci. Validation of our approach using a sample of over 3.4 million German individuals was successful. Compared to an expectation‐maximization algorithm, the errors were larger. However, our approach allows the unequivocal detection of rare haplotypes.

Identification of 8-Digit HLA-A, -B, -C, and -DRB1 Allele and Haplotype Frequencies in Koreans Using the One Lambda AllType Next-Generation Sequencing Kit

Background

Recent studies have successfully implemented next-generation sequencing (NGS) in HLA typing. We performed HLA NGS in a Korean population to estimate HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies up to an 8-digit resolution, which might be useful for an extended application of HLA results.

Methods

A total of 128 samples collected from healthy unrelated Korean adults, previously subjected to Sanger sequencing for 6-digit HLA analysis, were used. NGS was performed for HLA-A, -B, -C, and -DRB1 using the AllType NGS kit (One Lambda, West Hills, CA, USA), Ion Torrent S5 platform (Thermo Fisher Scientific, Waltham, MA, USA), and Type Steam Visual NGS analysis software (One Lambda).

Results

Eight HLA alleles showed frequencies of ≥10% in the Korean population, namely, A*24:02:01:01 (19.5%), A*33:03:01 (15.6%), A*02:01:01:01 (14.5%), A*11:01:01:01 (13.3%), B*15:01:01:01 (10.2%), C*01:02:01 (19.9%), C*03:04:01:02 (11.3%), and DRB1*09:01:02 (10.2%). Nine previous 6-digit HLA alleles were further identified as two or more 8-digit HLA alleles. Of these, eight alleles (A*24:02:01, B*35:01:01, B*40:01:02, B*55:02:01, B*58:01:01, C*03:02:02, C*07:02:01, and DRB1*07:01:01) were identified as two 8-digit HLA alleles, and one allele (B*51:01:01) was identified as three 8-digit HLA alleles. The most frequent four-loci haplotype was HLA-A*33:03:01-B*44:03:01:01-C*14:03-DRB1*13:02:01.

Conclusions

We identified 8-digit HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies in a healthy Korean population using NGS. These new data can be used as a representative Korean data for further disease-related HLA type analysis.

Study on the polymorphisms of HLA-ABCDQB1DRB1 alleles and haplotypes in Hubei Han population of China

The present study aimed to analyse the frequencies of human leukocyte antigen HLA-ABCDQB1 and HLA-DRB1 alleles and haplotypes in a subset of 3,732 Han population from Hubei of China. All samples were typed in the HLA-ABCDQB1 and HLA-DRB1 loci using the sequence-based typing method; subsequently, the HLA polymorphisms were analysed. A total of 47 HLA-A, 89 HLA-B, 43 HLA-C, 49 HLA-DRB1 and 24 HLA-DQB1 alleles were identified in the Hubei Han population. The top three most frequent alleles in the HLA-ABCDQB1 and HLA-DRB1 were A*11:01 (0.2617), A*24:02 (0.1590), A*02:07 (0.1281); B*46:01 (0.1502), B*40:01 (0.1409) and B*58:01 (0.0616); C*01:02 (0.2023), C*07:02 (0.1691) and C*03:04 (0.1175); and DQB1*03:01 (0.2000), DQB1*03:03 (0.1900), DQB1*06:01 (0.1187); DRB1*09:01 (0.1790), DRB1*15:01 (0.1062) and DRB1*12:02 (0.0841), respectively. Meanwhile, the three most frequent two-loci haplotypes were A*02:07-C*01:02 (0.0929), B*46:01-C*01:02 (0.1366) and DQB1*03:03-DRB1*09:01 (0.1766). The three most frequent three-loci haplotypes were A*02:07-B*46:01-C*01:02 (0.0883), B*46:01-DQB1*03:03-DRB1*09:01 (0.0808) and C*01:02-DQB1*03:03-DRB1*09:01 (0.0837). The three most frequent four-loci haplotypes were A*02:07-B*46:01-C*01:02-DQB1*03:03 (0.0494), B*46:01-DRB1*09:01-C*01:02-DQB1*03:03 (0.0729) and A*02:07-B*46:01-DQB1*03:03-DRB1*09:01 (0.0501). The most frequent five-loci haplotype was A*02:07-B*46:01-C*01:02-DQB1*03:03-DRB1*09:01 (0.0487). Heat maps and multiple correspondence analysis based on the frequencies of HLA specificity indicated that the Hubei Han population might be described into Southern Chinese populations. Our results lay a certain foundation for future population studies, disease association studies and donor recruitment strategies.

Implications of HLA diversity among regions for bone marrow donor searches in Japan

Japan is an island country, and the Japanese people have had minimal genetic exchange with other ethnolinguistic groups. Consequently, the population is highly uniform and has limited HLA diversity relative to people from other countries. However, Japan has three ethnolinguistic groups, and HLA distributions differ depending on geographic region. To collect an HLA-rich variety of bone marrow bank donor registrants, it is essential to know the precise distribution of HLA in Japan. We analyzed HLA alleles and haplotypes based on HLA information of 177 041 bone marrow donor registrants. Registrants were grouped depending on the prefecture and region (a group of prefectures) as commonly used in Japan. The prefectures did not show the same distributions, but the tendency was similar for each region. We found that Okinawa Prefecture and the mainland can be clearly divided as haplotypes: [A*24:02-C*01:02-B*54:01-DRB1*04:05] and [A*24:02-C*01:02-B*59:01-DRB1*04:05] were typically found in Okinawa (P = .02, P < .001). Moreover, these types were found almost exclusively in Japan and Korea. Donor registration centers of the Japan Marrow Donor Program are currently located in all prefectures. It is essential to deploy registration centers to collect registrants with a large variety of HLA types covering all of Japan.

High-Resolution HLA Typing of HLA-A, -B, -C, -DRB1, and -DQB1 in Kinh Vietnamese by Using Next-Generation Sequencing

Human leukocyte antigen (HLA) genotyping displays the particular characteristics of HLA alleles and haplotype frequencies in each population. Although it is considered the current gold standard for HLA typing, high-resolution sequence-based HLA typing is currently unavailable in Kinh Vietnamese populations. In this study, high-resolution sequence-based HLA typing (3-field) was performed using an amplicon-based next-generation sequencing platform to identify the HLA-A, -B, -C, -DRB1, and -DQB1 alleles of 101 unrelated healthy Kinh Vietnamese individuals from southern Vietnam. A total of 28 HLA-A, 41 HLA-B, 21 HLA-C, 26 HLA-DRB1, and 25 HLA-DQB1 alleles were identified. The most frequently occurring HLA alleles were A^∗11:01:01, B^∗15:02:01, C^∗07:02:01, DRB1^∗12:02:01, and DQB1^∗03:01:01. Haplotype calculation showed that A^∗29:01:01∼B^∗07:05:01, DRB1^∗12:02:01∼DQB1^∗3:01:01, A^∗29:01:01∼C^∗15:05:02∼B^∗07:05:01, A^∗33:03:01∼B^∗58:01:01∼DRB1^∗03:01:01, and A^∗29:01:01∼C^∗15:05:02∼B^∗07:05:01∼DRB1^∗10:01:01∼DQB1^∗05:01:01 were the most common haplotypes in the southern Kinh Vietnamese population. Allele distribution and haplotype analyses demonstrated that the Vietnamese population shares HLA features with South-East Asians but retains unique characteristics. Data from this study will be potentially applicable in medicine and anthropology.

Estimation of German KIR Allele Group Haplotype Frequencies

The impact of the highly polymorphic Killer-cell immunoglobulin-like receptor (KIR) gene cluster on the outcome of hematopoietic stem cell transplantation (HCST) is subject of current research. To further understand the involvement of this gene family into Natural Killer (NK) cell-mediated graft-versus-leukemia reactions, knowledge of haplotype structures, and allelic linkage is of importance. In this analysis, we estimate population-specific KIR haplotype frequencies at allele group resolution in a cohort of n = 458 German families. We addressed the polymorphism of the KIR gene complex and phasing ambiguities by a combined approach. Haplotype inference within first-degree family relations allowed us to limit the number of possible diplotypes. Structural restriction to a pattern set of 92 previously described KIR copy number haplotypes further reduced ambiguities. KIR haplotype frequency estimation was finally accomplished by means of an expectation-maximization algorithm. Applying a resolution threshold of ½ n, we were able to identify a set of 551 KIR allele group haplotypes, representing 21 KIR copy number haplotypes. The haplotype frequencies allow studying linkage disequilibrium in two-locus as well as in multi-locus analyses. Our study reveals associations between KIR haplotype structures and allele group frequencies, thereby broadening our understanding of the KIR gene complex.

High-resolution HLA-A, -B and -DRB1 allele and haplotype frequencies in 7823 Han marrow donors of Liaoning province, China

BACKGROUND

The human leukocyte antigen (HLA) system is the most polymorphic gene cluster in humans. High-resolution donor-recipient matching for HLA genes improves patient survival after unrelated hematopoietic stem cell transplantation.

MATERIALS AND METHODS

In this study, we analyzed the high-resolution allele and haplotype frequencies at the HLA-A, -B and -DRB1 loci in the Liaoning Han population and analyzed its relationships with other populations.

RESULTS

The 3 most frequent alleles at the HLA-A, -B and -DRB1 loci were A*24:02, A*02:01:01G, A*11:01; B*13:02, B*46:01, B*40:01:01G; DRB1*09:01, DRB1*15:01 and DRB1*07:01, respectively. The most frequent 2-locus haplotypes were A*30:01-B*13:02 and B*13:02-DRB1*07:01. A*30:01-B*13:02-DRB1*07:01 was determined to be the predominant 3-locus haplotype. Hot maps and multiple correspondence analyses based on the frequencies of HLA specificities, which allow statistical visualization of dependent and independent relationships among variables, indicate that the Liaoning Han population is closely related to Northern populations of China and shows relative close relationships with Asian populations.

CONCLUSION

These data will provide an outline of the HLA characteristics of healthy individuals in our region and help bone marrow transplantation patients find suitable HLA-matched donors.

HLA alleles and haplotypes in Burmese (Myanmarese) and Karen in Thailand

This is the first report on human leukocyte antigen (HLA) allele and haplotype frequencies at three class I loci and two class II loci in unrelated healthy individuals from two ethnic groups, 170 Burmese and 200 Karen, originally from Burma (Myanmar), but sampled while residing in Thailand. Overall, the HLA allele and haplotype frequencies detected by polymerase chain reaction sequence-specific primer (PCR-SSP) at five loci (A, B, C, DRB1 and DRQB1) at low resolution showed distinct differences between the Burmese and Karen. In Burmese, five HLA-B*15 haplotypes with different HLA-A and HLA-DR/DQ combinations were detected with three of these not previously reported in other Asian populations. The data are important in the fields of anthropology, transplantation and disease-association studies.

Variation in the prion protein sequence in Dutch goat breeds

Scrapie is a neurodegenerative disease occurring in goats and sheep. Several haplotypes of the prion protein increase resistance to scrapie infection and may be used in selective breeding to help eradicate scrapie. In this study, frequencies of the allelic variants of the PrP gene are determined for six goat breeds in the Netherlands. Overall frequencies in Dutch goats were determined from 768 brain tissue samples in 2005, 766 in 2008 and 300 in 2012, derived from random sampling for the national scrapie surveillance without knowledge of the breed. Breed specific frequencies were determined in the winter 2013/2014 by sampling 300 breeding animals from the main breeders of the different breeds. Detailed analysis of the scrapie-resistant K222 haplotype was carried out in 2014 for 220 Dutch Toggenburger goats and in 2015 for 942 goats from the Saanen derived White Goat breed. Nine haplotypes were identified in the Dutch breeds. Frequencies for non-wild type haplotypes were generally low. Exception was the K222 haplotype in the Dutch Toggenburger (29%) and the S146 haplotype in the Nubian and Boer breeds (respectively 7 and 31%). The frequency of the K222 haplotype in the Toggenburger was higher than for any other breed reported in literature, while for the White Goat breed it was with 3.1% similar to frequencies of other Saanen or Saanen derived breeds. Further evidence was found for the existence of two M142 haplotypes, M142 /S240 and M142 /P240 . Breeds vary in haplotype frequencies but frequencies of resistant genotypes are generally low and consequently selective breeding for scrapie resistance can only be slow but will benefit from animals identified in this study. The unexpectedly high frequency of the K222 haplotype in the Dutch Toggenburger underlines the need for conservation of rare breeds in order to conserve genetic diversity rare or absent in other breeds.

Determination of HLA-A, -C, -B, -DRB1 allele and haplotype frequency in Japanese population based on family study

The present study investigates the human leucocyte antigen (HLA) allele and haplotype frequencies in Japanese population. We carried out the frequency analysis in 5824 families living across Japanese archipelago. The studied population has mainly been typed for the purpose of transplant, especially the hematopoietic stem cell transplantation (HSCT). We determined HLA class I (A, B, and C) and HLA class II (DRB1) using Luminex technology. The haplotypes were directly counted by segregation. A total of 44 HLA‐A, 29 HLA‐C, 75 HLA‐B, and 42 HLA‐DRB1 alleles were identified. In the HLA haplotypes of A‐C‐B‐DRB1 and C‐B, the pattern of linkage disequilibrium peculiar to Japanese population has been confirmed. Moreover, the haplotype frequencies based on family study was compared with the frequencies estimated by maximum likelihood estimation (MLE), and the equivalent results were obtained. The allele and haplotype frequencies obtained in this study could be useful for anthropology, transplantation therapy, and disease association studies.