Human leukocyte antigen associations with renal function among ethnic minorities in the United Kingdom.

Human leukocyte antigens (HLA) have been associated with renal function, but previous studies report contradictory findings. There has been a lack of research into how HLA affects renal function in Black, Asian and Minority Ethnic (BAME) people in the UK, despite BAME people being disproportionately affected by renal dysfunction. This study included >27 000 UK Biobank subjects of six ethnicities (>12 100 Irish, >5400 Indian, >4000 Black Caribbean, >3000 Black African, >1600 Pakistani, and >1400 Chinese) aged 39 to 73. Subjects' high-resolution HLA genotypes were imputed using HLA*IMP:02 software. Regression analysis was used to compare 108 imputed HLA alleles with two measures of estimated glomerular filtration rate (eGFR): one based on serum creatinine; one based on serum cystatin. Secondary analysis compared CKD stage 2 subjects to healthy controls. Nine imputed HLA alleles were associated with eGFR (adjusted P < .05). Six associations were based on creatinine in Black African subjects: HLA-B*53:01 (beta = -2.628, adjusted P = 4.69 × 10-4 ); C*04:01 (beta = -1.667, adjusted P = .0269); DPA1*02:01 (beta = -1.569, adjusted P = .0182); and DPA1*02:02 (beta = -1.716, adjusted P = .0251) were linked to decreased renal function, while DRB1*03:01 (beta = 3.200, adjusted P = 3.99 × 10-3 ) and DPA1*01:03 (beta = 2.276, adjusted P = 2.31 × 10-5 ) were linked to increased renal function. Two of these (HLA-B*53:01 and C*04:01) are commonly inherited together. In Irish subjects, HLA-DRB1*04:01 (beta = 1.075, adjusted P = .0138) was linked to increased eGFR (based on cystatin); in Indian subjects, HLA-DRB1*03:01 (beta = -1.72, adjusted P = 4.78 × 10-3 ) and DQB1*02:01 (beta = -1.755, adjusted P = 2.26 × 10-3 )were associated with decreased eGFR (based on cystatin). No associations were found in the other three ethnic groups. Nine HLA alleles appear to be associated with kidney function in BAME people in the UK. This could have applications for the diagnosis and treatment of renal disease and could help reduce health inequalities in the UK.

Cost-effectiveness of HLA-DQB1/HLA-B pharmacogenetic-guided treatment and blood monitoring in US patients taking clozapine.

Less than 1% of adult patients with schizophrenia taking clozapine develop agranulocytosis, and most of these cases occur within the first weeks of treatment. The human leukocyte antigen (HLA) region has been associated with genetic susceptibility to clozapine-induced agranulocytosis (single amino acid changes in HLA-DQB1 (126Q) and HLA-B (158T)). The current study aimed to evaluate the cost-effectiveness, from a healthcare provider's perspective, of an HLA genotype-guided approach in patients with treatment-resistant schizophrenia who were taking clozapine and to compare the results with the current absolute neutrophil count monitoring (ANCM) schemes used in the USA. A semi-Markovian model was developed to simulate the progress of a cohort of adult men and women who received clozapine as a third-line antipsychotic medication. We compared current practices using two genotype-guided strategies: (1) HLA genotyping followed by clozapine, with ANCM only for patients who tested positive for one or both alleles (genotype-guided blood sampling); (2) HLA genotyping followed by clozapine for low-risk patients and alternative antipsychotics for patients who tested positive (clozapine substitution scheme). Up to a decision threshold of $3.9 million per quality-adjusted life-year (90-fold the US gross domestic product per capita), the base-case results indicate that compared with current ANCM, genotype-guided blood sampling prior to clozapine initiation appeared cost-effective for targeted blood monitoring only in patients with HLA susceptibility alleles. Sensitivity analysis demonstrated that at a cost of genotype testing of up to USD700, HLA genotype-guided blood monitoring remained a cost-effective strategy compared with either current ANCM or clozapine substitution.

Identification of the novel HLA-DQB1*06:209 allele in a Chinese individual.

HLA-DQB1*06:209 has one nucleotide change from HLA-DQB1*06:01:01 at position 260 G>C in exon 2.

A novel HLA-DQB1*03 variant, HLA-DQB1*03:23:03, identified in a Chinese individual.

HLA-DQB1*03:23:03 has two nucleotide change from HLA-DQB1*03:03:02:01 at position 254 and 260.

Search for DQ2 5 and DQ8 alleles using a lower cost technique in patients with type 1 diabetes and celiac disease in a population of southern Brazil

ABSTRACT Objective To evaluate the frequency of DQ2.5 and DQ8 alleles using the Tag-single-nucleotide polymorphism (Tag-SNP) technique in individuals with type 1 diabetes mellitus (T1DM) and celiac disease (CD) in southern Brazil. Materials and methods In a prospective design, we performed the search for DQA1*0501 and DQB1*0201 alleles for DQ2.5 and DQB1*0302 for DQ8 through Real-Time Polymerase Chain Reaction (RT-PCR) technique, using TaqMan Genotyping Assays (Applied Biosystems, USA). The diagnosis of CD was established by duodenal biopsy and genotypic determination performed by StepOne Software v2.3. Allelic and genotypic frequencies were compared between groups using Chi-square and Fisher's exact tests and the multiple comparisons using Finner's adjustment. Results Three hundred and sixty two patients with a median age of 14 years were divided into 3 groups: T1DM without CD (264); T1DM with CD (32) and CD without T1DM (66). In 97% of individuals with T1DM and CD and 76% of individuals with CD without T1DM, respectively, the alleles DQ2.5 and/or DQ8 were identified (p < 0.001). DQ2.5 was more common in individuals with CD (p = 0.004) and DQ8 was more common in individuals with type 1 diabetes (p = 0.008). Conclusions The evaluation of the alleles for DQ2.5 and DQ8 by Tag-SNP technique showed a high negative predictive value among those with T1DM, similar to that described by the conventional technique. The high frequency of DQ8 alleles in individuals with T1DM did not allow differentiating those at higher risk of developing T1DM.

[POPULATION AND CLUSTER APPROACH TO ASSESSMENT OF REPRODUCTIVE HEALTH OF WOMEN].

The purpose of this study was to explore the possibility of using a population approach to assessing the risk of reproductive health disorders in women of childbearing age. We observed 240 clinically healthy women aged 20 to 43 years, half of them lived in the Middle Black Earth region of Russia, and 120 women lived in Tajikistan. The study identified population differences in women with different ethnic backgrounds and regions of residence according to a set of genetic, hormonal, and immune signs. All women underwent venous blood sampling for the purpose of HLA typing by molecular genetic analysis and determining the range of normative values ​​of hormonal and immune status parameters. DNA samples were obtained from peripheral blood lymphocytes using reagent kits and a protocol for isolating DNA from various biological materials from DLAtomTM DNAPrep 100 (Russia). Hormonal status was studied in terms of follicle-stimulating hormone, luteinizing hormone, prolactin, estradiol, progesterone, 17-OH-progesterone; Thyroid hormones - thyroid-stimulating hormone, total triiodothyronine, total thyroxine; Androgens - testosterone, dihydroepiandrosterone; Steroid hormone-cortisol. In order to exclude the variability of the data, the examination was carried out on the 3-5th days of the menstrual cycle: luteinizing hormone, follicle-stimulating hormone, estradiol, prolactin, testosterone and on the 20-22nd Day of the progesterone cycle. Statistical data processing was carried out on the basis of SPSS programs and included descriptive and comparative nonparametric statistics, discriminant, regression analysis, one - factorial analysis of variance, calculation of 95% confidence intervals, construction of ROC curves. The study included the determination of allelic variants at the three loci of the HLA-D genes (HLA-DRB1, HLA-DQA1, HLA-DQB1) controlling the immune response. Population differences in the locus of the HLA-DRB1 gene were determined. The HLA-DRB1 * 08 and HLA-DRB1 * 12 alleles are found in the Russian women's population, and the HLA-DRB1 * 04 and HLA-DRB1 * 17 alleles are more reliably detected in the Tajik women's population, while the HLA-DRB1 * 04 allele Is associated with a higher incidence of miscarriage. The population characteristics of the HLA-DQA1 gene locus were also established. In the group of women of the Russian population, the incidence of HLA-DQA1 * 0101 and HLA-DQA1 * 0103 alleles is significantly higher, of which the former is associated with protective properties for reproductive pathology, and the latter, on the contrary, with miscarriage. At the same time, the alleles HLA-DQA1 * 0201 and HLA-DQA1 * 0301 were significantly more often detected in the compared with the population of Tajik women. As in the previous case, for the HLA-DQA1 * 0201 allele reproductive health disorders are not characteristic, and in the case of the HLA-DQA1 * 0301 allele they accompany it. Our studies have revealed that there are differences between the populations of Russian and Tajik women in a number of parameters of the hormonal and immune status, as well as at the level of allelic variants of genes that control the immune response. The population approach, based on the use of discriminant analysis, is a highly effective way of grouping women according to their reproductive health status and the risk factors that caused reproductive damage. The risk factors that caused the reproductive failure are different in combination and manifestation in the populations of Russian and Tajik women, except for the adverse allelic variants of the HLA-DRB1 * 04 and HLA-DQA1 * 0103 genes, which are the same in both populations. The obtained data also show that in different populations in the evaluation of reproductive health a differentiated approach is needed both to establish physiological norms in these categories of parameters and to assess the reproductive health of women.

Search for DQ2.5 and DQ8 alleles using a lower cost technique in patients with type 1 diabetes and celiac disease in a population of southern Brazil.

OBJECTIVE: To evaluate the frequency of DQ2.5 and DQ8 alleles using the Tag-single-nucleotide polymorphism (Tag-SNP) technique in individuals with type 1 diabetes mellitus (T1DM) and celiac disease (CD) in southern Brazil. MATERIALS AND METHODS: In a prospective design, we performed the search for DQA1*0501 and DQB1*0201 alleles for DQ2.5 and DQB1*0302 for DQ8 through Real-Time Polymerase Chain Reaction (RT-PCR) technique, using TaqMan Genotyping Assays (Applied Biosystems, USA). The diagnosis of CD was established by duodenal biopsy and genotypic determination performed by StepOne Software v2.3. Allelic and genotypic frequencies were compared between groups using Chi-square and Fisher's exact tests and the multiple comparisons using Finner's adjustment. RESULTS: Three hundred and sixty two patients with a median age of 14 years were divided into 3 groups: T1DM without CD (264); T1DM with CD (32) and CD without T1DM (66). In 97% of individuals with T1DM and CD and 76% of individuals with CD without T1DM, respectively, the alleles DQ2.5 and/or DQ8 were identified (p < 0.001). DQ2.5 was more common in individuals with CD (p = 0.004) and DQ8 was more common in individuals with type 1 diabetes (p = 0.008). CONCLUSIONS: The evaluation of the alleles for DQ2.5 and DQ8 by Tag-SNP technique showed a high negative predictive value among those with T1DM, similar to that described by the conventional technique. The high frequency of DQ8 alleles in individuals with T1DM did not allow differentiating those at higher risk of developing T1DM.

A Cross-Validation Design Using Age and HLA Alleles for the Assessment of Clinical Schizophrenia Risk.

BACKGROUND: Schizophrenia (SCH) is a highly heritable disease that occurs mostly in young adults. Genetic factors usually play important roles in the onset of SCH. Human leukocyte antigen complex (HLA) genes are considered to be the important genetic predisposition factor and the genetic markers in SCH and other diseases. METHODS: To screen SCH-associated HLA alleles, alleles for HLA-DRB1 and HLA-DQB1 loci were determined using the PCR-SSP typing kit. Statistically significant differences between observed and expected frequencies of allele combinations were identified. To further determine allele combinations related to SCH, an analysis of the age of onset of SCH in the patient who carried an allele or specific allele combination was conducted. Finally, a crossvalidation of the two sets of analytical results was carried out. Statistical differences in frequency values between the SCH group and the control population were observed for five HLA alleles. RESULTS: The results of cross-validation showed that there was a significant difference for a combination of DRB1*07 and DQB1*02, whereas no significant differences were observed for the other four alleles. CONCLUSIONS: We suggested that the combination of DRB1*07-DQB1*02 may be related to SCH susceptibility. The cross-validation design using age and HLA alleles could enable additional discoveries pertaining to the relationship between specific HLA allele combinations at different loci and the onset of complex diseases.

Genome-wide assessment of Parkinson's disease in a Southern Spanish population.

Here, we set out to study the genetic architecture of Parkinson's disease (PD) through a Genome-Wide Association Study in a Southern Spanish population. About 240 PD cases and 192 controls were genotyped on the NeuroX array. We estimated genetic variation associated with PD risk and age at onset (AAO). Risk profile analyses for PD and AAO were performed using a weighted genetic risk score. Total heritability was estimated by genome-wide complex trait analysis. Rare variants were screened with single-variant and burden tests. We also screened for variation in known PD genes. Finally, we explored runs of homozygosity and structural genomic variations. We replicate PD association (uncorrected p-value < 0.05) at the following loci: ACMSD/TMEM163, MAPT, STK39, MIR4697, and SREBF/RAI1. Subjects in the highest genetic risk score quintile showed significantly increased risk of PD versus the lowest quintile (odds ratio = 3.6, p-value < 4e(-7)), but no significant difference in AAO. We found evidence of runs of homozygosity in 2 PD-associated regions: one intersecting the HLA-DQB1 gene in 6 patients and 1 control; and another intersecting the GBA-SYT11 gene in PD case. The GBA N370S and the LRRK2 G2019S variants were found in 8 and 7 cases, respectively, replicating previous work. A structural variant was found in 1 case in the PARK2 gene locus. This current work represents a comprehensive assessment at a genome-wide level characterizing a novel population in PD genetics.

Assessment of the genetic basis of rosacea by genome-wide association study.

Rosacea is a common, chronic skin disease that is currently incurable. Although environmental factors influence rosacea, the genetic basis of rosacea is not established. In this genome-wide association study, a discovery group of 22,952 individuals (2,618 rosacea cases and 20,334 controls) was analyzed, leading to identification of two significant single-nucleotide polymorphisms (SNPs) associated with rosacea, one of which replicated in a new group of 29,481 individuals (3,205 rosacea cases and 26,262 controls). The confirmed SNP, rs763035 (P=8.0 × 10(-11) discovery group; P=0.00031 replication group), is intergenic between HLA-DRA and BTNL2. Exploratory immunohistochemical analysis of HLA-DRA and BTNL2 expression in papulopustular rosacea lesions from six individuals, including one with the rs763035 variant, revealed staining in the perifollicular inflammatory infiltrate of rosacea for both proteins. In addition, three HLA alleles, all MHC class II proteins, were significantly associated with rosacea in the discovery group and confirmed in the replication group: HLA-DRB1*03:01 (P=1.0 × 10(-8) discovery group; P=4.4 × 10(-6) replication group), HLA-DQB1*02:01 (P=1.3 × 10(-8) discovery group; P=7.2 × 10(-6) replication group), and HLA-DQA1*05:01 (P=1.4 × 10(-8) discovery group; P=7.6 × 10(-6) replication group). Collectively, the gene variants identified in this study support the concept of a genetic component for rosacea, and provide candidate targets for future studies to better understand and treat rosacea.

HLA-DQ2/DQ8 and HLA-DQB1*02 homozygosity typing by real-time polymerase chain reaction for the assessment of celiac disease genetic risk: evaluation of a Spanish celiac population.

Celiac disease (CD) is a complex autoimmune disorder caused by ingestion of gluten in genetically susceptible individuals. Different genetic risk factors have been identified, but virtually all patients are human leukocyte antigen (HLA)-DQ2 and/or HLA-DQ8 positive. We describe a new, fast, accurate and simple real-time polymerase chain reaction (PCR)-based assay for the genotyping and homozygosity analysis of the CD-related HLA alleles. The assay overcomes the major limitations of protocols currently in use, allowing HLA-DQ2/DQ8 genotyping by using only three real-time PCR reactions. For the appraisal of DQ2 homozygosity, only one more reaction is needed. These reactions are easily automated and suitable for large screening studies in diagnostic procedures, as it is demonstrated by their successful application in our HLA diagnostic laboratory. Finally, we assessed the clinical relevance of this real-time PCR-based assay by studying a cohort of fully characterized patients. As expected, all CD patients had at least one of the CD-associated alleles, and the highest CD risk was indicated by the presence of the HLA-DQ2.5 heterodimer (HLA-DQA1*05-DQB1*02) with HLA-DQB1*02 in homozygosity.

Assessment of the influence of HLA class I and class II loci on the prevalence of keloid disease in Jamaican Afro-Caribbeans.

Keloid disease (KD) is a common abnormal cutaneous fibrotic disorder of unknown aetiopathogenesis. KD is reported to have a strong genetic component as it is often familial and has a high incidence in certain ethnicities, in particular those of Afro-Caribbean origin. Genetic risk factors combined with aberrant lesional inflammatory responses point to the human leukocyte antigen (HLA) system as a viable target for investigating disease aetiology. Sequence specific primer polymerase chain reaction with allele sequencing was used to determine HLA-DQA1 and DQB1 allele frequencies (AF) for 165 KD patients and 119 healthy controls of black Jamaican Afro-Caribbean origin. HLA class I alleles A*01, A*03, A*25, B*07 and Cw*08:02, previously identified as KD associated in a different ethnicity, were also analysed. Allele sequencing confirmed typing accuracy but no statistically significant differences in AF were identified between KD patients and controls. Furthermore, KD subgroups including patient gender, family history and multiple- or single-site scarring did not show significant allele-disease associations.

Multiplexed, ligation-dependent probe amplification for rapid and inexpensive HLA-DQB1 allelotyping.

Many effective options exist to accurately type DNA for human leukocyte antigen (HLA) alleles. However, most of the existing methods are excessively costly in terms of overall monetary costs, DNA requirements, and proprietary software. We present a novel assay capable of resolving heterozygous HLA-DQB1 allelotypes at two digits, with even greater specificity for the HLA-DQB1*06 allele family, by using the multiplexed ligation-dependent probe amplification technology. This assay provides more specific allele data than genome-wide analysis and is more affordable than sequencing, making it a useful intermediate for researchers seeking to accurately allelotype human DNA samples.

A new HLA-DQB1 sequence, DQB1*02:01:04, discovered during an external quality assessment exercise.

HLA-DQB1*02:01:04 differs from DQB1*02:01:01 by one nucleotide (G>A) at position 303 in exon 2 resulting in a silent substitution (codon 69 - GAG >GAA), conserved glutamate.