Distribution Of Alleles Research Articles

Lack of association between the -2549 insertion/deletion variant of vascular endothelial growth factor and coronary artery disease in the Turkish population.

Coronary artery disease is the leading cause of death worldwide. Vascular endothelial growth factor is known to induce endothelial cell migration and proliferation, increase vascular permeability, and modulate thrombogenicity. The aim of this study is to investigate the relationship between the VEGF insertion/deletion (I/D) variant (rs35569394) and coronary artery disease susceptibility in the Turkish population. A total of 206 subjects, including 106 coronary artery disease patients and 100 controls, were included in this study. The VEGF I/D variant was genotyped using the polymerase chain reaction method. The frequency of the I/I, I/D, and D/D genotypes was 35.84 versus 37%, 33.97 versus 36%, and 30.19 versus 27% in patients and the control group, respectively. VEGF I/D genotype and allele distribution were not statistically significant between coronary artery disease patients and controls (p>0.05). There was no significant difference between VEGF I/D genotype distribution and patient characteristics including age, gender, disease duration, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, triglyceride, history of hypertension, history of diabetes mellitus, and smoking (p>0.05). This study suggests that the VEGF I/D variant is not a predisposing factor to coronary artery disease disease in a Turkish sample.

Distributions of MICA and MICB Alleles Typed by Amplicon-Based Next-Generation Sequencing in South Koreans.

Major histocompatibility complex class I chain-related genes A and B (MICA and MICB) play a role as ligands in activating the NKG2D receptor expressed in natural killer cells, γδ T-cells and αβ CD8 T-cells and have been defined in human diseases and haematopoietic stem cell transplantation (HSCT). MICA and MICB alleles were genotyped at the three-field level by amplicon-based next-generation sequencing (NGS) using a MiSeqDx system and compared with the results from previous studies in healthy South Korean donors. Exons 2-5 of MICA and exons 2-4 of MICB were amplified using a multiplex polymerase chain reaction (PCR). Sequence reads of ≥ 51 depth counts were consistently obtained for each sample exon, and target exons were determined to match reference sequences contained in the IPD-IMGT/HLA database. MICA and MICB alleles were tested using exon combinations. The program was designed to recognise specific sequences and discriminate between the MICA*008:01:01/*027 alleles. A total of 22 alleles were found in MICA and MICB. We observed 1 HLA-C ~ HLA-B ~ MICA ~ MICB ~ HLA-DRB1 haplotype with significant linkage disequilibrium between alleles at all neighbouring HLA loci. These results are consistent with previous microarray results. Genotyping of MICA and MICB was possible using 11-loci HLA genes. We updated the distribution of MICA and MICB based on three-field allele and haplotype frequencies containing linkage disequilibrium in South Koreans using amplicon-based NGS. These data suggest that high-resolution MICA and MICB typing data obtained using NGS may aid in performing HSCT and disease association studies.

The Possible Association of IL-6R Gene Polymorphisms in the Development of Diabetic Nephropathy.

Diabetic nephropathy (DN) is a common complication of type 2 diabetes (T2D). Chronic inflammation and a combination of environmental and genetic factors are involved in the pathogenesis and development of DN. This case-control study aimed to determine the relationship between rs7529229 and rs2228145 polymorphisms of the IL-6R gene with the incidence of nephropathy among T2D patients. Fifty-six diabetic patients with nephropathy and 57 T2D patients without nephropathy were included based on inclusion criteria, along with 150 healthy individuals. The frequencies of AC and CC genotype distributions of the rs2228145 polymorphism in DN patients were significantly higher than in healthy individuals (24.1 and 9.3% versus 10.7 and 6.7%, respectively, P= 0.02). Moreover, the frequency of allele C was higher in DN patients compared to healthy controls (21.30% versus 12%, P=0.025). However, genotype distribution and allele frequencies of the rs7529229 IL-6R polymorphism in DN patients were not statistically significant in comparison with diabetic patients and healthy individuals (P> 0.05). The results showed that the allele and genotype distribution frequencies of rs2228145 IL-6R gene polymorphism in patients with DN were significantly higher than in healthy individuals. Therefore, the presence of this polymorphism may be involved in the development of diabetic nephropathy in this population.

Uneven Influx of European-Specific Alleles of SLC45A2, SLC24A5, TYRP1, DRD2, EDAR, and OCA2 Genes into the Gene Pool of the Koryaks

The distribution of alleles highly specific to Europeans in the Koryak gene pool, which formed as a result of intensive interethnic admixture in the Northern Priokhotie, characterized by the prevailing genetic contribution from males of Eastern European origin, was analyzed. The loci rs16891982 (SLC45A2 gene), rs1426654 (SLC24A5 gene), rs1408799 (TYRP1 gene), rs1076563 (DRD2 gene), rs3827760 (EDAR gene), and rs1448485 (OCA2 gene), which are mainly associated with the pigmentation system, were selected for analysis. High heterogeneity was found in the frequency of European-specific alleles, ranging from 1.4% for the variant rs1076563-C of the DRD2 gene to 14.7% for the variant rs1426654-A of the SLC24A5 gene. The reasons for the uneven influx of European-specific alleles into the Koryak gene pool are discussed. It is possible that the formation of genetic structure of modern Koryaks under intensive interethnic admixture was accompanied by the influence of natural selection on some parts of the genome.

Associations between BCL11A and HBS1L-MYB polymorphisms and thalassemia risk

ObjectivesThis study investigated the associations of the rs4671393, rs1427407, and rs11886868 genetic variants of the BCL11A gene and the rs9399137 variant of the HBS1L-MYB gene with thalassemia in patients from the population of Punjab, Pakistan. MethodsA cohort of 600 participants, comprising 300 patients with thalassemia and 300 age- and sex-matched healthy controls, was recruited from various hospitals in Punjab, Pakistan. DNA was extracted from whole blood samples from all participants. Specific DNA regions containing four genetic variants of interest were amplified with polymerase chain reaction. ResultsThe genotypic frequencies of the rs4671393 SNP of BCL11A indicated that the heterozygous (AG) genotype of this SNP was significantly associated with a nearly two-fold increased thalassemia risk, with respect to the control group (OR = 1.77; 95% CI = 1.77–2.80; p = 0.01). Combining all genotypes into a joint model further confirmed their significant association with thalassemia risk. Similarly to the findings for rs4671393, the heterozygous (CT) genotype of rs11886868 exhibited a significant association with thalassemia risk (approximately two-fold increased risk. Analysis of both genotypes together revealed a marginally significant association (one-fold increased risk) with thalassemia in individuals carrying any variant allele of rs11886868. The allelic distribution of the rs1427407 SNP of BCL11A indicated that the heterozygous (GT) genotype of this SNP was significantly associated with thalassemia (approximately two-fold increased risk, with respect to the control group). Combining all genotypes into a joint model confirmed a significant association between the presence of any variant allele of rs1427407 and thalassemia (two-fold increased risk). The genotypic distribution frequencies of the heterozygous (CT) genotype for the rs9399137 SNP of HBS1L-MYB was similar to that of rs1427407, and exhibited a highly significant association with thalassemia risk (nearly two-fold increased risk). Analysis of both genotypes together revealed a significant association with thalassemia risk (one-fold increase) for individuals carrying any variant allele of rs9399137. ConclusionBCL11A and HBS1L-MYB polymorphisms were significantly associated with increased thalassemia risk.

Frequency of rs35803318 single nucleotide polymorphism of ACE2 gene among the Kazakhs

In the article the results of genotyping of DNA samples obtained from the study participants on the single nucleotidepolymorphism (SNP) rs35803318 (C/T) of the ACE2 gene were presented. Genotyping was carriedout by real-time polymerase chain reaction (PCR) using the technique Amplification of the Refractory MutationSystem (ARMS). The frequencies of rs35803318 (C/T) genotypes and alleles in 96 representatives of theKazakh ethnic group living in the Karaganda region were analyzed. The ACE2 gene (angiotensin-convertingenzyme 2) was extensively investigated due to its role in susceptibility to infection by the SARS-CoV-2 viruscausing COVID-19. The ACE2 gene encodes a protein that serves as a receptor for the virus, and its variationscan affect a person's susceptibility to infection. The ACE2 protein plays a role in the regulation of angiotensinand the effect on blood pressure. Therefore, there is a link between ACE2 gene polymorphisms, includingrs35803318, and the development of cardiovascular diseases. According to the results of our study,the CT genotype (63.5 %) is the most common among Kazakhs, the CC genotype was 20.8 % and theTT genotype was 15.6 %. The distribution of polymorphism alleles is as follows: allele C — 52.6 %, allele A— 47.4 %.

Гено-фенотипические особенности муковисцидоза у российских детей из Чеченской и Карачаево-Черкесской Республик

Background: Cystic fibrosis (CF) is an autosomal recessive disease that occurs with a frequency of 1:1,500 to 1:5,000 newborns, according to the World Health Organization. In the Russian Federation, the average incidence of the disease is 1:10,000 newborns. The medical and social significance of this disease is associated with the early disability of patients, the need for long-term treatment and constant follow-up, as well as the heterogeneity of phenotypic manifestations, which in turn requires early diagnosis using molecular genetic methods. The aim of the study: To study the clinical and molecular genetic characteristics of children with CF from the Chechen and Karachay-Cherkess Republics. Materials and methods: The study included 237 patients with a confirmed diagnosis of CF. Molecular genetic diagnostics was performed using the method of mass parallel sequencing using a hybridization target panel that includes the entire CFTR gene. Sequencing was performed on the MiSeq platform. All causal nucleotide variants were validated using Sanger sequencing. Results: The most common amino acid variants of the CFTR gene in patients with CF from the Chechen Republic are: p.Y515* (94 alleles/78.3%), p.E92K (18 alleles/15%). The presence of variants p.Y515* and p.E92K in the heterozygous state in the genotype is more often a favorable prognostic factor for the absence of pancreatic lesion. The main distinctive clinical feature of these patients is the onset of the disease with manifestations of pseudo-Bartter syndrome. The major amino acid variant of the CFTR gene in patients with CF from the Karachay-Cherkess Republic is: p.W1282* (28 alleles/70%). The number of patients with pseudo-Bartter syndrome was 54.5%. In 90% of cases, in patients who are homo- and heterozygous according to p.W1282*, a severe degree of pancreatic insufficiency was noted. Conclusion: Patients with cystic fibrosis from the Chechen and Karachay-Cherkess Republics are a difficult category of patients, despite neonatal screening, and cystic fibrosis therapy developed and implemented. This is partly due to the peculiarities of the phenotype and the unique distribution of alleles and genotypes of the CFTR gene. The high number of homozygous variants of the CFTR gene in patients from the Chechen and Karachay-Cherkess Republics is probably due to monoethnic marital assortativity.

Clonality in black locust (Robinia pseudoacacia L.) and implications for seed production

Key messageThe strong clonal growth of black locust (Robinia pseudoacacia L.) not only influences the stand structure of natural or artificially established stands, but also the genetic composition of seed harvested from such clonal stands. For the commercial production of genetically diverse seeds, the stand structure should be taken into account or, at best, seeds harvested from seed orchards should be used.ContextBlack locust is characterised by intensive asexual reproduction through the formation of root suckers. By this means clonal structures can develop within black locust stands, in which ramets of a single clone can dominate extensive areas.AimsWe want to analyse to what extent clonal structures within black locust stands negatively influence the genetic composition and diversity in seed harvested in such stands. We discuss how a potential reduction in genetic diversity can be reduced by measures taken during harvesting and whether the harvesting of seed orchards may be a better alternative.MethodsWe compare the genetic composition and diversity of parent trees and seed harvested from a clonal black locust stand with a seed orchard in which multiple ramets of selected clones were arranged in a randomised design.ResultsWithin the clonal stand, parent contributions to the seed lot analysed proved to be strongly uneven. Selfing rates were high and large full-sib families dominated within the seed lot. Although the relatively strong pollination from unknown pollen donors, probably located outside of the stand, prevented a massive loss of alleles, high selfing rates and the formation of large full-sib families led to an unequal distribution of alleles within the progeny. Within the seed orchard—even though it had a lower number of clones than expected—the randomised design promoted a more diverse pollination pattern.ConclusionWe conclude that for black locust, seed orchards have the greater potential to ensure a balanced genetic composition of harvested seed lots. If economic considerations make it necessary to harvest seed stands, this should only be done in a considered manner and, if possible, with knowledge of the clonal structures of the stand.

HLA Diversity in Transylvanian Ethnic Groups: Consequences for Hematopoietic Cell Transplantation

The HLA profile is essential in cell and tissue transplantation, particularly in patients with autoimmune conditions and infections. Due to the extreme polymorphism in certain HLA loci, it also serves as a key tool for population genetic analysis. This study aimed to identify the allele and haplotype distributions of HLA class I (A, B, and C) and class II (DRB1) genotypes in unrelated hematopoietic stem cell donors. A retrospective analysis was conducted between 2016 and 2020 on 9832 Transylvanian volunteers, divided into Romanian and Hungarian groups based on self-reported ethnicity. Using PCR-SSO for HLA typing, significant differences were found in allele frequencies between ethnic groups. A total of 19 HLA-A, 31 HLA-B, 14 HLA-C, and 13 HLA-DRB1 distinct allele groups were identified between ethnic groups. Notably, B*18, B*51, and C*12 were more frequent in Romanians, while B*44, B*40, and C*07 were more common in Hungarians. Differences in haplotype distributions were also observed, with HLA-A*02~B*18~C*07~DRB1*11 being significantly more frequent in Romanians. Understanding these population-specific HLA profiles can improve donor matching for hematologic diseases, enhancing patient outcomes and access to life-saving hematopoietic stem cell transplantation.

Interleukin-6 Receptor Gene rs1800795 Polymorphism and Expression of Interleukin-6 in Gingival Tissue in Patients with Periodontitis.

Periodontitis is a multifactorial inflammatory disease. This chronic periodontal disease is caused by a bacterial infection in the gums, which triggers a host inflammatory response. To eliminate the bacterial infection, immune response mechanisms are activated, leading to inflammation and damage to the periodontal tissues. This process involves many cytokines, including IL-6, a cytokine with antibacterial properties. An ongoing bacterial infection in the periodontal tissues leads to its excessive production, which increases inflammation. In this study, we examined IL-6 receptor gene rs1800795 polymorphism in patients with periodontitis in comparison with healthy subjects, as well as the correlation between rs1800795 genotypes and clinical parameters. Additionally we examined the expression of IL-6 in gingival tissue in patients with periodontitis and control subjects, as well as the correlation between gingival expression of IL-6 and clinical parameters. This study included 200 patients with periodontitis and 158 healthy subjects as the control group. Biopsy specimens of gingival tissue in which IL-6 expression was detected were taken from 14 patients with periodontitis and 8 controls who had undergone minor surgery. There were no statistically significant differences in the distribution of IL-6 rs1800795 genotypes and alleles between patients with periodontitis and control subjects. There were also no statistically significant correlations between IL-6 rs1800795 genotypes and clinical parameters in patients with periodontitis. There were no differences in IL-6 expression in the gingival tissue between patients with periodontitis and controls. There was also no correlation between IL-6 expression in the gingival tissue of patients with periodontitis and clinical parameters. In the control group, IL-6 expression in gingival tissue correlated negatively with the approximal plaque index, which reflects the size of bacterial plaques. The results of our study suggest a protective role for IL-6 against bacterial growth in the periodontal tissue. However, it should be noted that several parameters directly or indirectly affect the accumulation of bacterial plaque.

Genome-Wide Search for Gene Mutations Likely Conferring Insecticide Resistance in the Common Bed Bug, Cimex lectularius.

Insecticide resistance in the bed bug Cimex lectularius is poorly understood due to the lack of genome sequences for resistant strains. In Japan, we identified a resistant strain of C. lectularius that exhibits a higher pyrethroid resistance ratio compared to many previously discovered strains. We sequenced the genomes of the pyrethroid-resistant and susceptible strains using long-read sequencing, resulting in the construction of highly contiguous genomes (N50 of the resistant strain: 2.1 Mb and N50 of the susceptible strain: 1.5 Mb). Gene prediction was performed by BRAKER3, and the functional annotation was performed by the Fanflow4insects workflow. Next, we compared their amino acid sequences to identify gene mutations, identifying 729 mutated transcripts that were specific to the resistant strain. Among them, those defined previously as resistance genes were included. Additionally, enrichment analysis implicated DNA damage response, cell cycle regulation, insulin metabolism, and lysosomes in the development of pyrethroid resistance. Genome editing of these genes can provide insights into the evolution and mechanisms of insecticide resistance. This study expanded the target genes to monitor allele distribution and frequency changes, which will likely contribute to the assessment of resistance levels. These findings highlight the potential of genome-wide approaches to understand insecticide resistance in bed bugs.

Missense variant rs75603675 within TMPRSS2 gene is associated with the increased risk of severe form of COVID-19

Host genetics among other factors play an important role in COVID-19 disease severity. TMPRSS2, a serine protease, facilitates the priming of the SARS-CoV-2 spike protein, which is essential for the virus to enter the host cell. Several studies had targeted the TMPRSS2 polymorphisms with respect to SARS-CoV-2 infection and COVID-19 disease severity. Initially, the Whole Exome Sequencing (WES) of 7 healthy individuals and 22 COVID-19 patients with different degrees of disease severity was conducted to find the mutational landscape in different genes. A total of 26 single nucleotide polymorphisms (SNPs) were identified of which six were within the exons of TMPRSS2 (four synonymous and two nonsynonymous variants) while the rest of the 20 SNPs were recognized within the flanking intronic regions of TMPRSS2 gene. The nonsynonymous SNPs, rs75603675 and rs12329760, were further evaluated for association with disease severity in a larger sample size of 120 individuals by PCR followed by Sanger sequencing. Neither allelic nor genotypic distributions of rs12329760 were significantly associated with COVID-19 disease severity. However, individuals harboring the A allele of rs75603675 was found to have higher risk of severe COVID-19 compared to the C allele [OR (95%CI): 1.95 (1.11–3.39), p = 0.019]. Also, the genotype A/A [OR (95%CI): 5.13 (1.00–26.38), p = 0.033] of rs75603675 was associated with increased risk of severe COVID-19 under the recessive genetic inheritance model. Although the impact of COVID-19 pandemic has waned due to vaccination and public health measures, continued research on the association of COVID-19 disease severity and infection susceptibility with host genetics is required to shed valuable insights on the future long-term health effects of COVID-19 and impact of new variants on different populations and enable implication of proper informed healthcare strategies during future public health crises.

Frequency of HLA-B27 Haplotype Among Patients with Acute Anterior Uveitis and Controls in Ethiopia

ABSTRACT Purpose We compared the distribution of the HLA-B27 allele among Ethiopian patients with acute anterior uveitis (AAU) and controls without that disease. Methods The clinical features of patients were collected from their medical records. HLA-B27 genotyping was performed for 64 patients, with AAU using the real-time polymerase chain reaction (RT-PCR), and the results were compared to those from a panel of 192 healthy, unrelated volunteer control participants (refraction patients and volunteers) free of signs of anterior uveitis. Other outcomes were assessed comparing HLA-B27 positive vs. negative patients. Results The histocompatibility antigen HLA-B27 was identified in 6 out of 64 (9.4%) AAU patients, compared with 1.0% in controls (Odds Ratio = 9.8, 95% CI (1.93, 50.01)). Sub-group analysis of the cases revealed that patients with HLA-B27 positivity had a higher incidence of ocular hypertension (Odds Ratio = 5.93, 95% CI (1.29, 27.2)). Conclusion The antigen HLA-B27 was represented ~10-fold more frequently in the patient group than in the control group. HLA-B27 allele distribution in both cases and controls is lower than in reports from Caucasian and Asian populations, but similar to South Africa.

HLA-A, -B, -C and -DRB1 Association with Autism Spectrum Disorder Risk: A Sex-Related Analysis in Italian ASD Children and Their Siblings.

Autism Spectrum disorders (ASD) are diagnosed more often in males than in females, by a ratio of about 3:1; this is likely to be due to a difference in risk burden between the sexes and/or to "compensatory skills" in females, that may delay the diagnosis of ASD. Identifying specific risk factors for ASD in females may be important in facilitating early diagnosis. We investigated whether HLA- class I: -A, -B, -C and class II -DRB1 alleles, which have been suggested to play a role in the development of ASD, can be considered as sex-related risk/protective markers towards the ASD. We performed HLA allele genotyping in 178 Italian children with ASD, 94 healthy siblings, and their parents. HLA allele distribution was compared between children with ASD, sex-matched healthy siblings, and a cohort of healthy controls (HC) enrolled in the Italian bone marrow donor registry. Allele transmission from parents to children with ASD and their siblings was also assessed. Our findings suggest that HLA-A*02, B*38, and C*12 alleles are more frequently carried by females with ASD compared to both HC and healthy female siblings, indicating these alleles as potential risk factors for ASD in females. Conversely, the HLA-A*03 allele was more commonly transmitted to healthy female siblings, suggesting it might have a protective effect. Additionally, the HLA-B*44 allele was found to be more prevalent in boys with ASD, indicating it is a potential risk factor for male patients. This is the first Italian study of sex-related HLA association with ASD. If confirmed, these results could facilitate early ASD diagnosis in female patients, allowing earlier interventions, which are crucial in the management of neurodevelopmental disorders.

Concurrent detection of the mitochondrial DNA copy number and the +35G/C polymorphism in the mitochondrial transcription factor A gene in endometriosis

Background and aimEndometriosis is a chronic gynecological inflammatory disease. The mitochondrial DNA copy number (mtDNA CN) and mitochondrial transcription factor A (TFAM) are known to contribute to human pathologies and cancer. Therefore, this study aims to reveal the association of mtDNA CN and TFAM+35G/C (rs1937) polymorphism with the risk of endometriosis in Egyptian females. Materials and methodsThis case-control study involved 160 Egyptian females divided into two groups: 80 endometriosis cases and 80 controls. The mtDNA CN was quantified using a real-time quantitative PCR (qPCR), and the TFAM +35G/C SNP (rs1937) was genotyped using the TaqMan allelic discrimination assay technique. ResultsThe mtDNA CN was markedly decreased in endometriosis cases compared to controls (P < 0. 001). TFAM rs1937 genotypes and allele distributions were all in Hardy-Weinberg equilibrium. The GC genotype and the ‘C’ allele frequency (P = 0.015 and P = 0.017, respectively) were substantially greater in endometriosis cases. ConclusionDecreased mtDNA CN and the GC genotype of TFAM +35G/C polymorphism were significantly associated with the risk of endometriosis in Egyptian females.

The prognostic difference study on the individualized clopidogrel administration in Hmong and Dong patients based on the CYP2C19 gene polymorphism after percutaneous coronary intervention.

This study explored the distribution characteristics of CYP2C19 gene polymorphism among Hmong and Dong patients in the Qiandongnan region of Guizhou province after percutaneous coronary intervention (PCI). The aim was to assess the clinical impact of individualized clopidogrel administration based on CYP2C19 genotypes. A total of 208 patients were classified into ultra-fast, fast, intermediate, and slow metabolic groups. They were randomly assigned to clopidogrel individualized administration (IA) or conventional treatment (CA) groups. Patients were followed for 6 months to evaluate major adverse cardiovascular events (MACE) and adverse reactions. The CYP2C19 genotype distribution was in Hardy-Weinberg equilibrium, showing consistency in the population. While no significant ethnic differences were found in genotype and metabolic distribution, allele distribution varied, with Hmong patients exhibiting a higher proportion of CYP2C19*1 alleles than Dong patients. Following individualized administration, the IA group demonstrated lower incidences of non-fatal myocardial infarction and emergency revascularization compared to the CA group. Bleeding events were higher in the IA group, but the total MACE incidence was lower. No statistical difference in MACE and adverse drug reactions (ADR) was observed in the CA group across metabolic types, but MACE incidence was higher in intermediate and slow metabolic groups. In the IA group, no significant difference in MACE was noted among metabolic types, but ADR incidence varied significantly, particularly in dyspnea. The study highlighted significant CYP2C19 allele distribution differences between Hmong and Dong patients post-PCI in Qiandongnan. Patients with slow metabolic profiles demonstrated higher MACE incidence with conventional clopidogrel dosage, whereas CYP2C19-guided therapy reduced MACE without increasing bleeding risk. These findings supported clinical individualized clopidogrel administration in post-PCI patients in the Qiandongnan region, contributing to rational clopidogrel use.

High Resolution Class I HLA -A, -B, and -C Diversity in Eastern and Southern African Populations.

Africa remains significantly underrepresented in high-resolution Human Leukocyte Antigen (HLA) data, despite being one of the most genetically diverse regions in the world. This critical gap in genetic information poses a substantial barrier to HLA-based research on the continent. In this study, Class I HLA data from Eastern and Southern African populations were analysed to assess genetic diversity across the region. We examined allele and haplotype frequency distributions, deviations from Hardy-Weinberg Equilibrium (HWE), linkage disequilibrium (LD), and conducted neutrality tests of homozygosity across various populations. Additionally, the African HLA data were compared to those of Caucasian and African American populations using the Jaccard index and multidimensional scaling (MDS) methods. The study revealed that South African populations exhibited 50.4% more genetic diversity within the Class I HLA region compared to other African populations. Zambia showed an estimated 36.5% genetic diversity, with Kenya, Rwanda and Uganda showing 35.7%, 34.2%, and 31.1%, respectively. Furthermore, an analysis of in-country diversity among different tribes indicated an average Class I HLA diversity of 25.7% in Kenya, 17% in Rwanda, 2.8% in South Africa, 13.6% in Uganda, and 6.5% in Zambia. The study also highlighted the genetic distinctness of Caucasian and African American populations compared to African populations. Notably, the differential frequencies of disease-promoting and disease-preventing HLA alleles across these populations emphasize the urgent need to generate high-quality HLA data for all regions of Africa and its major ethnic groups. Such efforts will be crucial in enhancing healthcare outcomes across the continent.

Genomic insight into COVID-19 severity in MAFLD patients: a single-center prospective cohort study.

This study investigated the influence of single nucleotide polymorphisms (SNPs) in genes associated with the interferon pathway (IFNAR2 rs2236757), antiviral response (OAS1 rs10774671, OAS3 rs10735079), and viral entry (ACE2 rs2074192) on COVID-19 severity and their association with nonalcoholic fatty liver disease (MAFLD). We did not observe a significant association between the investigated SNPs and COVID-19 severity. While the IFNAR2 rs2236757 A allele was correlated with higher creatinine levels upon admission and the G allele was correlated with lower band neutrophils upon discharge, these findings require further investigation. The distribution of OAS gene polymorphisms (rs10774671 and rs10735079) did not differ between MAFLD patients and non-MAFLD patients. Our study population's distribution of ACE2 rs2074192 genotypes and alleles differed from that of the European reference population. Overall, our findings suggest that these specific SNPs may not be major contributors to COVID-19 severity in our patient population, highlighting the potential role of other genetic factors and environmental influences.

Renin and CYP P450 gene variations significantly associated with essential hypertension: A prospective pharmacogenomics study

ObjectiveThis study aims to investigate the association between Renin-angiotensin aldosterone system (RAAS) and Cytochrome P450 gene polymorphisms in hypertension patients of the South Indian population using pharmacogenomics profile. MethodsHypertension cases (N = 147) and control subjects (n = 150) were collected from Tamil Nadu, India. A case-control association study was conducted to assess the involvement of RAAS gene polymorphisms (REN rs397514691, REN rs544315427, REN rs567667202) and CYP gene polymorphisms (CYP2D6 rs754164689, CYP2D6 rs1058172, CYP3A4 rs765598920) in essential hypertensive patients. Genotyping was performed using the PCR-RFLP method, and significant results were validated through RT-PCR analysis. ResultsThe genotype and allele distribution of REN rs397514691 and rs544315427 variants significantly associated with hypertensive patients (Variant Allele Frequency (VAF) = 0.11; VAF = 0.27, respectively). CYP2D6 polymorphisms rs754164689 and rs1058172 variant alleles were significantly associated with female hypertensive patients, suggesting a potential risk allele for essential hypertension in the South Indian population. REN and CYP3A4 variants, highly connected in pharmacology action, were validated through RT-PCR amplification studies, providing new insights into their role in the development of hypertension. Association confirmation was achieved through multifactor dimensionality reduction analysis. ConclusionThe genes associated with specific variants, particularly REN and CYP2D6, may serve as potential markers for the early diagnosis of hypertension and as new drug targets, particularly in the female population.

Distribution of polymorphic variants of the mannose-binding lectin gene (MBL2) in children with mild and severe asthma

Asthma is one of the most common inflammatory diseases in the world. One of the factors in the development of this disease is a low concentration of mannose-binding lectin (MBL), encoded by the MBL2 gene. Purpose. To study the distribution of genotypes and alleles of polymorphic variants of the MBL2 gene in children with asthma. Material and methods. The study included children with diagnosed bronchial asthma (n=400) (Krasnoyarsk). The control group consisted of children comparable in gender and age to the patients (n=229) and newborns (n=302). GINA-202 guidelines were used to determine the severity of the disease. Results. Statistically significant differences were identified for polymorphisms localized in the first exon of the gene – rs1800450 and rs1800451. A low occurrence of the BB rs1800450 genotype in sick and healthy children was revealed, which may be associated with early mortality or disability due to severe infections with severe MBL deficiency. Homozygotes for the mutant allele C of the rs1800451 MBL2 polymorphism were not found in any of the comparison groups, which indicates a rare distribution of this allele in Caucasian populations. Conclusion. The present study showed that polymorphisms in the MBL2 gene play a predisposing role in the development of diseases of the bronchopulmonary system using the example of asthma.