DRB Genes Research Articles

Anisakis Sensitization in the Croatian fish processing workers: Behavioral instead of occupational risk factors?

We undertook the first study systematically evaluating the risk of Anisakis-sensitization in Croatian fish-processing workers and potential genetic susceptibility to anisakiasis. Anti-Anisakis IgE seroprevalence and risk factors for 600 employees of Croatian fish processing facilities and 466 blood donor controls, were assessed by indirect ELISA targeted with: recombinant Ani s 1 and Ani s 7 allergens, an Anisakis crude extract, the commercial ImmunoCAP kit, and questionnaires. Genetic susceptibility to anisakiasis was evaluated by genotypisation of human leukocytes alleles (HLA). Anti-Anisakis seropositive and a fraction of negative subjects were also assessed by ELISA and Western Blot (WB) for IgG seroprevalence to Trichinella spp. Overall, the observed anti-Anisakis seroprevalence inferred by indirect ELISA was significantly higher in fish processing workers (1.8%, 95% CI 0.9–3.3%) compared to the controls (0%, 0–0.8%). Seven out of 11 Ani s 1 and Ani s 7-positives and none of selected 65 negative sera, tested positive on whole-Anisakis extract (ImmunoCAP), whereas Anisakis crude extract ELISA detected 3.9% (2.4–6.0%) seropositives in fish processing workers, three (14%) of which showed IgE reactivity to milk proteins. The highest risk associated with Anisakis-sensitization among workers was fishing in the free time, rather than any of attributes related to the occupational exposure. Although no association was observed between anti-Anisakis seropositivity and wearing gloves or protective goggles, the majority of workers (92%) wore protective gloves, minimizing the risk for Anisakis sensitization via skin contact. Six HLA alleles within DRB1 gene were significantly associated with seropositivity under dominant, allelic or recessive models. All sera confirmed negative for anti-Trichinella spp. IgG. The study exhaustively covered almost all marine fish processing workers in Croatia, reflecting real-time Anisakis sensitization status within the industry, already under the influence of wide array of allergens.

Early events following bovine leukaemia virus infection in calves with different alleles of the major histocompatibility complex \xa0DRB3 gene

Cattle maintaining a low proviral load (LPL) status after bovine leukaemia virus (BLV) infection have been recognized as BLV controllers and non-transmitters to uninfected cattle in experimental and natural conditions. LPL has been associated with host genetics, mainly with the BoLA class II DRB3 gene. The aim of this work was to study the kinetics of BLV and the host response in Holstein calves carrying different BoLA-DRB3 alleles. Twenty BLV-free calves were inoculated with infected lymphocytes. Two calves were maintained uninfected as controls. Proviral load, total leukocyte and lymphocyte counts, anti-BLVgp51 titres and BLVp24 expression levels were determined in blood samples at various times post-inoculation. The viral load peaked at 30 days post-inoculation (dpi) in all animals. The viral load decreased steadily from seroconversion (38 dpi) to the end of the study (178 dpi) in calves carrying a resistance-associated allele (*0902), while it was maintained at elevated levels in calves with *1501 or neutral alleles after seroconversion. Leukocyte and lymphocyte counts and BLVp24 expression did not significantly differ between genetic groups. Animals with < 20 proviral copies/30 ng of DNA at 178 dpi or < 200 proviral copies at 88 dpi were classified as LPL, while calves with levels above these limits were considered to have high proviral load (HPL) profiles. All six calves with the *1501 allele progressed to HPL, while LPL was attained by 6/7 (86%) and 2/6 (33%) of the calves with the *0902 and neutral alleles, respectively. One calf with both *0902 and *1501 developed LPL. This is the first report of experimental induction of the LPL profile in cattle.

HLA-DQB1/DRB1 Alleles Associate with Traditional Chinese Medicine Syndrome of Chronic Hepatitis B: A Potential Predictor of Progression.

Background and Aims Traditional Chinese medicine (TCM) has been widely applied in chronic hepatitis B (CHB) supplementary treatment in China. Kidney yang deficiency syndrome (KYDS), one of the most common TCM syndromes of CHB, is more likely to progress to liver cirrhosis or hepatocellular carcinoma than other syndromes. Polymorphisms in the human leucocyte antigen- (HLA-) DQB1 and -DRB1 genes were reported to be associated with hepatitis B virus infection outcomes. Here, we investigated whether HLA-DQB1 and HLA-DRB1 are associated with the classification of CHB TCM syndromes. Methods We genotyped HLA-DQB1 and HLA-DRB1 alleles in a total of 105 subjects, including 74 CHB patients (28 KYDS and 46 non-KYDS) and 31 healthy individuals from Sichuan Province of Southwest China, by polymerase chain reaction sequence-based typing (PCR-SBT). Moreover, a meta-analysis was carried out for further verification. Results The proportion of patients with high HBV DNA load (≥2000 IU/ml) in the KYDS group is higher than that in the non-KYDS group (60.70% [17/28] vs. 28.30% [13/46]); P=0.01). The frequencies of HLA-DQB1∗02:01 (P=0.04) and HLA-DRB1∗03:01 (P=0.04) in the KYDS group were significantly increased compared to the non-KYDS group. The gene test and meta-analysis showed that HLA-DRB1∗08:03 confers susceptibility to CHB (odds ratio = 1.57). Conclusion We found an association between HLA-DRB1/DQB1 polymorphisms and KYDS of CHB. Moreover, KYDS patients of CHB are characteristic with high HBV DNA loads. These findings help to reveal the biological mechanism of KYDS in high risk of CHB progression and suggest a potential prognostic value for disease outcome evaluation.

The Involvement of HLA Class II Alleles in Multiple Sclerosis: A Systematic Review with Meta-analysis.

Multiple Sclerosis (MS) displays a heterogeneous clinical onset and progression, which are mostly unpredictable, but demyelination of the central nervous system (CNS) leads to substantial deficits of sensory, motor, autonomic, and neurocognitive functions. Considering all genetic studies on MS, including the advanced genome-wide association studies, the risk linked to HLA alleles remains the highest among other susceptibility genetic variants. However, given the genetic variability of HLA alleles in different ethnic groups, we conducted a systematic review of reviews and meta-analyses aiming at summarizing all the results on the association between MS and HLA class II genes. We systematically searched meta-analyses and systematic reviews dealing with MS and HLA in all ethnicities. From 154 records, we included 5 articles collecting HLA data from 15,232 MS patients and 24,194 ethnically matched controls. DRB1∗15 (OR ranging from 1.39 in Chinese Han to 2.59 in Caucasians) and DQB1∗06:02 (OR ranging from 1.91 in Caucasians to 2.49 in Colombian) alleles confer an increased risk for MS transethnically (Caucasians, Chinese, South Americans, Carribeans, Middle Easterners, Japanese, and North Africans). DRB1∗01, DRB1∗09, DRB1∗11, DRB1∗12, and DRB1∗16 alleles were protective, in agreement with the type of amino-acidic (aa) residues (ranging from position 9 to 90) included in pockets 1, 4, 6, 7, and 9, which are most involved in peptide presentation. Changes in aa residues affect the capability of HLA molecules in binding myelin peptides. DQB1∗06:02 risk allele seems to be the most interesting target as humanized mice expressing only DQB1∗06:02 develop MS-like disease mediated by autoimmune reactions against myelin oligodendrocytic basic protein that stabilizes the myelin. Our summary of results from a high number of patients and controls suggests that allelic variants from both DQB1 and DRB1 genes are equally involved in MS susceptibility/protection transethnically.

Concepts of Prakriti (Human Constitution) and its Association with Hematological Parameters, Body Mass Index (BMI), Blood Groups and Genotypes

Background: Ayurveda is an ancient system of personalized medicine, documented and practiced in India since 1500 B.C. According to this system an individual’s basic constitution to a large extent determines predisposition and prognosis to diseases as well as the therapy and life-style regime. Ayurveda describes seven broad Prakriti (Physical constitution) Prakriti is defined as the sum of physical, physiological, psychological traits of an individual which represents genotypes. Objective: In this article we have attempted to narrate concepts of Prakriti and its relation with hematological parameter, body mass index, blood groups and genotypes. Material and Method: Present article is based on critical review of Ayurvedic textual information, published research works, modern literature and research works conducted at various institutes. The possible correlation has been made between collected information and has been presented in systematic way. Result: In Pitta Prakriti individual’s hematological parameters like Hemoglobin (Hb%), Packed cell volume (PCV), and Red blood corpuscles (RBC) count are significantly on the higher side of normal range in comparison to Vata and Kapha Prakriti . Higher level of cluster of differentiation (CD) 14 markers in Pitta Prakriti , CD25 and CD56 in Kapha Prakriti individuals. Vata Prakriti individuals have “A” blood group, maximum Pitta Prakriti individuals have “O” blood group while maximum Kapha Prakriti individuals have “B” blood group and genotype correlation shows that HLA DRB1 ((human leukocyte antigen, dimer beta chain) gene polymorphism, CYP2C19 (Cytochrome P450 2C19) gene polymorphism and PGM1 (Phosphoglucomutase 1) polymorphism have scientific variations with the human Prakriti concept. Conclusion: Prakriti of individual has strong relation with Hematological parameters (CBC, lipid profile, Liver function test (LFT)), Body mass index (BMI), anthropometry, blood groups and genotypes.

Association of biomarkers of inflammation and HLA-DRB1 gene locus with risk of developing rheumatoid arthritis in females.

Rheumatoid arthritis (RA) is an autoimmune disease causing chronic inflammation of the joints. Multiple factors, including HLA-DRB1 gene variants, influence the susceptibility to RA. The HLA-DRB1 gene is part of a family of genes called the human leukocyte antigen (HLA) complex. In this study, we compared the inflammatory biomarkers values, including erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP), between patients with RA and healthy control group of females of the Public Institution Health Centre of Sarajevo Canton. In addition, we estimated the frequencies of the HLA-DRB1 gene variants and their association with the risk for RA development in females. The haematological and biochemical tests were completed on automated analyzers. To assess the association between the HLA-DRB genes and the risk of RA in females, low-resolution genotyping of the HLA-DRB1, DRB3, DRB4, and DRB5 gene loci was performed by the sequence-specific polymerase chain reaction method (PCR-SSP). ESR and CRP were the most sensitive acute-phase reactants in females with RA and there was a correlation between ESR and CRP values in RA patients. There was significantly positive association between of the HLA-DRB1*03, *04, *08, *10, *11, and *14 variants and elevated values of ESR in RA patients, but negative between HLA-DRB1*03, *13 and *15 alleles and elevated CRP values. Furthermore, our results confirm genetic susceptibility to RA in a female population to the members of the HLA-DRB1*04 and *03 allelic groups, the DRB1*04/DRB1*04 and DRB1*03/DRB1*04 genotypes, and the DRB1*04-DRB4* or DRB1*03-DRB3* haplotypes, which, therefore, represent risk factors for the development of this disease. According to our results, the DRB1*01/DRB1*15 and DRB1*07/DRB1*16 genotypes and the HLA-DRB5 gene locus represent a protective factor for RA. The presence of specific HLA-DRB1 gene variants increases the risk of developing RA, while other variants provide protection against disease. Therefore, HLA typing could be helpful in the prediction of RA development and establishing and confirming a definitive diagnosis of autoimmune diseases in some subjects. A strong association with the higher levels of ESR and CRP could be used to establish definitive diagnosis and introduce of early treatment of RA to prevent the occurrence of RA symptoms.

Genotyping of MHC class II DRB3 gene using PCR-RFLP and DNA sequencing in small ruminant breeds of Western Himalayan state of Himachal Pradesh, India

Sheep and goat farming especially under migratory system is an important activity in state of Himachal Pradesh. DRB locus of major histocompatibility complex is widely studied for its association with disease resistance. Present study was planned to analyse genetic diversity of DRB3 locus in small ruminant breeds of Himachal Pradesh using PCR-RFLP and DNA sequencing. 63, 68, 80 and 73 true to the breed animals belonging to Gaddi sheep, Rampur-Bushair sheep, Gaddi goats and Chegu goats, respectively were utilized. Amplification of exon 2 of DRB3 gene yielded 285bp amplified product in different breeds. Three different digestion patterns corresponding to 2 alleles and seven digestion patterns corresponding to 4 alleles were observed with PstI and HaeIII restriction digestion. For Pst 1 digestion frequency of AA, AB and BB genotypes ranged from 0.09 to 0.22, 0.40 to 0.53 and 0.28 to 0.46 in different breeds studied. For HaeIII digestion frequency of five genotypes (AA, BB, CC, AB and AC) which were detected in all breeds varied from 0.18 to 0.32, 0.11 to 0.13, 0.07 to 0.17, 0.18 to 0.30 and 0.09 to 0.3 in different breeds, while frequency of CD and AD genotype unique to Rampur-Bushair sheep population was 0.09 and 0.06, respectively. The observed allele number (No) ranged from 5 to 6 in different breeds while effective allele number (Ne) ranged from 4.46 to 5.15 in different populations. Hobs and Hexp values ranged 0.42 to 0.49 and 0.55 to 0.59, respectively in different breeds. The nucleotide variability was detected using sequences from different breeds which was found at 36 places. In the present study the specific amplification of the exon 2 of DRB3 gene of native sheep and goat populations demonstrated marked polymorphism. Further association studies need to be carried out to investigate the association of these SNPs of DRB region with parasitic diseases.

Polymorphisms in major histocompatibility complex genes and its associations with milk quality in Murrah buffaloes

Animal breeding programs have used molecular genetic tools as an auxiliary method to identify and select animals with superior genetic merit for milk production and milk quality traits as well as disease resistance. Genes of the major histocompatibility complex (MHC) are important molecular markers for disease resistance that could be applied for genetic selection. The aim of this study was to identify single nucleotide polymorphisms (SNPs) and haplotypes in DRB2, DRB3, DMA, and DMB genes in Murrah breed and to analyze the association between molecular markers and milk, fat, protein and mozzarella production, fat and protein percentage, and somatic cell count. Two hundred DNA samples from Murrah buffaloes were used. The target regions of candidate genes were amplified by polymerase chain reaction (PCR) followed by sequencing and identification of polymorphisms. Allele and genotype frequencies, as well as linkage disequilibrium between SNPs, were calculated. Genotypes were used in association analyses with milk production and quality traits. Except for the DMA gene, identified as monomorphic, the other genes presented several polymorphisms. The DMB, DRB2, and DRB3 genes presented two, six, and seven SNPs, respectively. Fifty-seven haplotype blocks were constructed from 15 SNPs identified, which was used in association analyses. All the studied traits had at least one associated haplotype. In conclusion, it is suggested that the haplotypes found herein can be associated with important traits related to milk production and quality.

Sex-specific DLA Class II haplotypes are associated with primary hypoadrenocorticism in Standard Poodle dogs

Abstract Autoimmune Addison’s Disease (AAD) is a life-threatening endocrine disorder that occurs spontaneously in humans and dogs and whose clinical features are highly similar between the species. Associations between MHC class II genes and AAD have been shown in several human studies. Our goal was to identify MHC class II associations with AAD in a large population of Standard Poodles, a breed highly predisposed to AAD. We sequenced exon 2 of the class II genes DRB1, DQA1, and DQB1 in 110 affected and 101 unaffected Standard Poodles and tested for association with AAD. Two haplotypes were found to confer risk of developing AAD in a gender-specific manner: 015:01-006:01-023:01 in males (□2 p = 0.03, OR 2.1) and 009:01-001:01-008:011 in females (□2 p = 0.02, OR 8.43). Sex-specific associations have been previously described in human populations, but this is the first report of this kind in dogs. Consistent with findings in other studies, we also found the DQA1*006:01 allele (□2 p = 0.04) to be associated with AAD in males independent of haplotype. In females, the haplotype 009:01-001:01-008:011 appears to confer a very high risk for developing AAD, though its frequency was rare (9 of 124 females) in our study population. Further studies are warranted to assess the usefulness of this haplotype as a genetic risk marker for AAD in female Standard Poodles. Our findings highlight the importance of evaluating MHC class II-disease associations in large populations, and accounting for both gender and population structure in order to uncover clinically relevant associations.

Complete nucleotide sequence characterization of DRB5 alleles reveals a homogeneous allele group that is distinct from other DRB genes

Next Generation Sequencing allows for testing and typing of entire genes of the HLA region. A better and comprehensive sequence assessment can be achieved by the inclusion of full gene sequences of all the common alleles at a given locus. The common alleles of DRB5 are under-characterized with the full exon-intron sequence of two alleles available. In the present study the DRB5 genes from 18 subjects alleles were cloned and sequenced; haplotype analysis showed that 17 of them had a single copy of DRB5 and one consanguineous subject was homozygous at all HLA loci. Methodological approaches including robust and efficient long-range PCR amplification, molecular cloning, nucleotide sequencing and de novo sequence assembly were combined to characterize DRB5 alleles. DRB5 sequences covering from 5′UTR to the end of intron 5 were obtained for DRB5*01:01, 01:02 and 02:02; partial coverage including a segment spanning exon 2 to exon 6 was obtained for DRB5*01:03, 01:08N and 02:03. Phylogenetic analysis of the generated sequences showed that the DRB5 alleles group together and have distinctive differences with other DRB loci. Novel intron variants of DRB5*01:01:01, 01:02 and 02:02 were identified. The newly characterized DRB5 intron variants of each DRB5 allele were found in subjects harboring distinct associations with alleles of DRB1, B and/or ethnicity. The new information provided by this study provides reference sequences for HLA typing methodologies. Extending sequence coverage may lead to identify the disease susceptibility factors of DRB5 containing haplotypes while the unexpected intron variations may shed light on understanding of the evolution of the DRB region.

Genetic polymorphism of MHC DRB3 (Major Histocompatibility Complex) of Bali cattle at Maiwa Breeding Center, South Sulawesi Indonesia

One of the obstacles in the development of Bali cattle is a common disease such as Jembrana, Brucellosis or Anthrax. Breeding programs for disease resistance are an effort to produce superior livestock resistant to disease. The Major Histocompatibility Complex (MHC) is a group of loci that consists of a collection of important (major) genes that control the immune response. It is known that alleles variations of the MHC genes have a relationship with natural immunity to several diseases in cattle. The aim of this study was to identify the diversity of MHC genes in the Bali cattle population at the Maiwa Breeding Center (MBC). A total of 629 heads of Bali cattle were used as samples in this study. The MHC DRB3 gene was amplified with primers flanking the region of exon 2 using a PCR machine. The product of amplification is 284 bp in lenght. Genotyping and identification of the MHC alleles were carried out by the PCR-RFLP method using PstI restriction enzymes. The results showed that the alleles variation of the MHC gene showed that P allele frequency were 0.856 and 0.938, while the p allele were 0.145 and 0.062 in Barru and Enrekang population, respectively. Observed heterozygosity values obtained in 0.144 showed that the genetic diversity of the MHC genes in the Bali cattle population at MBC was low. The chi-square values (p<0.05) showed that the MHC gene of the Bali cattle at MBC was not in the Hardy Weinberg equilibrium and indicated the possibility of a strong selection of the MHC gene. MHC gene diversity data can be used as one of the references to develope Bali cattle at the MBC.

Molecular characterization of MHC II DRB3 gene of swamp- and riverine-type water buffaloes.

Objective:Major histocompatibility complex (MHC) is a set of molecular proteins on the surface of antigen presenting cells encoded by a large gene family which are important parts of the immune system. This study was conducted to convey information on the genetic characteristics of the MHC II DRB3 gene in riverine and swamp buffaloes.Materials and Methods:Characterization of MHC II DRB3 gene was carried out using polymerase chain reaction (PCR)-based assay. Thirty-milliliter milk samples were collected from 10 swamp-type and 10 riverine-type buffaloes. RNA from milk samples were extracted using Trizol and then followed by reverse transcription-PCR (RT-PCR).Results:The phylogenetic analysis with 1,000 bootstrap replications clearly showed complex parsimony in MHC II DRB3 gene between 10 riverine- and 10 swamp-type but also confirmed that the samples are similar to Bubalus bubalis. Aligned sequences of the 20 water buffaloes were compared with three other ruminants (Bos taurus, Ovis aries, and Capra hircus) and non-ruminant (Sus scrofa) that serve as an outgroup. MHC sequences from GenBank show that there was an average of 705 identical pairs, with 22 transitional pairs and 30 transversional pairs with a ratio of 0.7.Conclusion:Based on the molecular data, the current study conforms to other works of literature that this gene is highly polymorphic which can be due to its function in the immune responsiveness and disease resistance. Further study on the immunological response of MHC II DRB3 to infection may elucidate its underlying function and role in the protection against specific disease of animals.

Construction and benchmarking of a multi-ethnic reference panel for the imputation of HLA class I and II alleles.

Genotype imputation of the human leukocyte antigen (HLA) region is a cost-effective means to infer classical HLA alleles from inexpensive and dense SNP array data. In the research setting, imputation helps avoid costs for wet lab-based HLA typing and thus renders association analyses of the HLA in large cohorts feasible. Yet, most HLA imputation reference panels target Caucasian ethnicities and multi-ethnic panels are scarce. We compiled a high-quality multi-ethnic reference panel based on genotypes measured with Illumina’s Immunochip genotyping array and HLA types established using a high-resolution next generation sequencing approach. Our reference panel includes more than 1,300 samples from Germany, Malta, China, India, Iran, Japan and Korea and samples of African American ancestry for all classical HLA class I and II alleles including HLA-DRB3/4/5. Applying extensive cross-validation, we benchmarked the imputation using the HLA imputation tool HIBAG, our multi-ethnic reference and an independent, previously published data set compiled of subpopulations of the 1000 Genomes project. We achieved average imputation accuracies higher than 0.924 for the commonly studied HLA-A, -B, -C, -DQB1 and -DRB1 genes across all ethnicities. We investigated allele-specific imputation challenges in regard to geographic origin of the samples using sensitivity and specificity measurements as well as allele frequencies and identified HLA alleles that are challenging to impute for each of the populations separately. In conclusion, our new multi-ethnic reference data set allows for high resolution HLA imputation of genotypes at all classical HLA class I and II genes including the HLA-DRB3/4/5 loci based on diverse ancestry populations.

HLA-DR Class II expression on myeloid and lymphoid cells in relation to HLA-DRB1 as a genetic risk factor for visceral leishmaniasis.

Genetic variation at HLA-DRB1 is a risk factor for visceral leishmaniasis (VL) caused by Leishmania donovani. The single nucleotide polymorphism rs9271252 upstream of the DRB1 gene provides a perfect tag for protective versus risk HLA-DRB1 four-digit alleles. In addition to the traditional role of the membrane-distal region of HLA class II molecules in antigen presentation and CD4 T-cell activation, the membrane-proximal region mediates 'non-traditional' multi-functional activation, differentiation, or death signals, including in DR-expressing T cells. To understand how HLA-DR contributes to disease pathogenesis, we examined expression at the protein level in circulating myeloid (CD14+ , CD16+ ) and lymphoid (CD4+ , CD8+ , CD19+ ) cells of VL patients (pre- and post-treatment) compared with endemic healthy controls (EHC). Although DR expression is reduced in circulating myeloid cells in active disease relative to EHC and post-treatment groups, expression is enhanced on CD4+ DR+ and CD8+ DR+ T cells consistent with T-cell activation. Cells of all myeloid and lymphoid populations from active cases were refractory to stimulation of DR expression with interferon-γ (IFN-γ). In contrast, all populations except CD19+ B cells from healthy blood bank controls showed enhanced DR expression following IFN-γ stimulation. The rs9271252 genotype did not impact significantly on IFN-γ-activated DR expression in myeloid, B or CD8+ T cells, but CD4+ T cells from healthy individuals homozygous for the risk allele were particularly refractory to activated DR expression. Further analysis of DR expression on subsets of CD4+ T cells regulating VL disease could uncover additional ways in which pleiotropy at HLA DRB1 contributes to disease pathogenesis.

Detection of Polymorphisms in the exon 2 region of the DRB3 gene in Naqu yaks

In the present study, the second exon of the DRB3 gene of the major histocompatibility complex (MHC) from 94 Naqu yaks was amplified and sequenced, and its variation and phylogeny of nucleotides and haplotypes were analyzed. The results showed that 71 single-nucleotide polymorphism (SNPs) were identified, and 147 haplotypes were reconstructed. The average number of nucleotide differences was 16.80965, the nucleotide diversity was 0.05982, and the haplotype diversity was 0.9964. In addition, fewer haplotypes of exon 2 of DRB3 were shared among different ecotype strains, and a large number of privatized haplotypes (93.2%) were observed. Based on the results of the present study, the high genetic diversity of Naqu yaks could reflect their epidemic history and geographical distribution. In addition, the abundant diversity in the MHC region was estimated not only to enhance the current understanding of the status of genetic diversity for the conservation of Naqu yaks but also to improve the relative environmental suitability and disease-resistant breeding of these animals.

Challenges of next-generation sequencing in conservation management: Insights from long-term monitoring of corridor effects on the genetic diversity of mouse lemurs in a fragmented landscape.

Long‐term genetic monitoring of populations is essential for efforts aimed at preserving genetic diversity of endangered species. Here, we employ a framework of long‐term genetic monitoring to evaluate the effects of fragmentation and the effectiveness of the establishment of corridors in restoring population connectivity and genetic diversity of mouse lemurs Microcebus ganzhorni. To this end, we supplement estimates of neutral genetic diversity with the assessment of adaptive genetic variability of the major histocompatibility complex (MHC). In addition, we address the challenges of long‐term genetic monitoring of functional diversity by comparing the genotyping performance and estimates of MHC variability generated by single‐stranded conformation polymorphism (SSCP)/Sanger sequencing with those obtained by high‐throughput sequencing (next‐generation sequencing [NGS], Illumina), an issue that is particularly relevant when previous work serves as a baseline for planning management strategies that aim to ensure the viability of a population. We report that SSCP greatly underestimates individual diversity and that discrepancies in estimates of MHC diversity attributable to the comparisons of traditional and NGS genotyping techniques can influence the conclusions drawn from conservation management scenarios. Evidence of migration among fragments in Mandena suggests that mouse lemurs are robust to the process of fragmentation and that the effect of corridors is masked by ongoing gene flow. Nonetheless, results based on a larger number of shared private alleles at neutral loci between fragment pairs found after the establishment of corridors in Mandena suggest that gene flow is augmented as a result of enhanced connectivity. Our data point out that despite low effective population size, M. ganzhorni maintains high individual heterozygosity at neutral loci and at MHC II DRB gene and that selection plays a predominant role in maintaining MHC diversity. These findings highlight the importance of long‐term genetic monitoring in order to disentangle between the processes of drift and selection maintaining adaptive genetic diversity in small populations.

Genetic predictors of the development and recurrence of Graves' disease.

Graves' disease affects approximately 3 % of women and 0.5 % of men. The first-choice therapy is based on the administration of thyrostatic drugs. However, approximately half of patients relapse within two years of discontinuation. These patients must then decide whether to re-initiate thyrostatics, which may have serious side effects, or to undergo surgery or radioiodine treatment. Familial forms of Graves' disease indicate a significant genetic component, with twin studies demonstrating a contribution of genetic factors up to 70-80 %. The autoimmune nature of the disease involves the human leukocyte antigen (HLA) complex, which has a decisive impact on each individual's immune response. Within HLA, some variants of the DRB1, DQA1 and DQB1 genes appear to be possible predictors of the development and recurrence of Graves' disease. Outside the HLA region, many variants of immunocompetent genes have also been identified as potential Graves' disease predictors. Apart from the immune system, some thyroid-specific genes have been described in relation to the disease. Here, we present current knowledge regarding the genetic components involved in the development and recurrence of Graves' disease. Further, we present original pilot results from a cohort of Czech Graves' disease patients regarding the HLA variants.

P122 - Association of HLA-A, -B and -DRB1 genes with endemic nephropathy and urothelial carcinoma of upper urinary tract in Croatia

P122 - Association of HLA-A, -B and -DRB1 genes with endemic nephropathy and urothelial carcinoma of upper urinary tract in Croatia

ALPHLARD: a Bayesian method for analyzing HLA genes from whole genome sequence data

BackgroundAlthough human leukocyte antigen (HLA) genotyping based on amplicon, whole exome sequence (WES), and RNA sequence data has been achieved in recent years, accurate genotyping from whole genome sequence (WGS) data remains a challenge due to the low depth. Furthermore, there is no method to identify the sequences of unknown HLA types not registered in HLA databases.ResultsWe developed a Bayesian model, called ALPHLARD, that collects reads potentially generated from HLA genes and accurately determines a pair of HLA types for each of HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes at 3rd field resolution. Furthermore, ALPHLARD can detect rare germline variants not stored in HLA databases and call somatic mutations from paired normal and tumor sequence data. We illustrate the capability of ALPHLARD using 253 WES data and 25 WGS data from Illumina platforms. By comparing the results of HLA genotyping from SBT and amplicon sequencing methods, ALPHLARD achieved 98.8% for WES data and 98.5% for WGS data at 2nd field resolution. We also detected three somatic point mutations and one case of loss of heterozygosity in the HLA genes from the WGS data.ConclusionsALPHLARD showed good performance for HLA genotyping even from low-coverage data. It also has a potential to detect rare germline variants and somatic mutations in HLA genes. It would help to fill in the current gaps in HLA reference databases and unveil the immunological significance of somatic mutations identified in HLA genes.

Determining Mhc-DRB profiles in wild populations of three congeneric true lemur species by noninvasive methods

The major histocompatibility complex (MHC) is a highly polymorphic and polygenic genomic region that plays a crucial role in immune-related diseases. Given the need for comparative studies on the variability of immunologically important genes among wild populations and species, we investigated the allelic variation of MHC class II DRB among three congeneric true lemur species: the red-fronted lemur (Eulemur rufifrons), red-bellied lemur (Eulemur rubriventer), and black lemur (Eulemur macaco). We noninvasively collected hair and faecal samples from these species across different regions in Madagascar. We assessed DRB exon 2 polymorphism with a newly developed primer set, amplifying nearly all non-synonymous codons of the antigen-binding sites. We defined 26 DRB alleles from 45 individuals (17 alleles from E. rufifrons (N = 18); 5 from E. rubriventer (N = 7); and 4 from E. macaco (N = 20). All detected alleles are novel and show high levels of nucleotide (26.8%) and non-synonymous codon polymorphism (39.4%). In these lemur species, we found neither evidence of a duplication of DRB genes nor a sharing of alleles among sympatric groups or allopatric populations of the same species. The non-sharing of alleles may be the result of a geographical separation over a long time span and/or different pathogen selection pressures. We found dN/dS rates > 1 in the functionally important antigen recognition sites, providing evidence for balancing selection. Especially for small and isolated populations, quantifying and monitoring DRB variation are recommended to establish successful conservation plans that mitigate the possible loss of immunogenetic diversity in lemurs.