Allele Frequency Distribution Research Articles

Fingerprinting Chinese Sweetgum (Liquidambar formosana Hance) Accessions and Constructing a Core Collection Using Newly Developed SSR Markers

Liquidambar formosana, endemic to China, is a multifunctional tree species valued for its wood production, urban landscaping, and medicinal applications. Here, 111 superior L. formosana accessions were genotyped using 24 novel expressed sequence tag-simple sequence repeat (EST-SSR) markers to assess genetic diversity and structure, establish DNA fingerprints, and construct a core collection. A high degree of genetic diversity was detected in the tested accessions, with mean values for the number of observed alleles (Na), polymorphism information content (PIC), and Shannon’s information index (I) recorded at 8.458, 0.579, and 1.336 per locus, respectively. Cluster analysis, principal coordinate analysis (PCoA), and population structure analysis collectively categorized these accessions into two major groups. Specifically, those from the SangZ provenance formed a distinct group, whereas accessions from other provenances exhibiting extensive gene exchange were assigned to the second group. The combined values of the probability of identity (PI) and the probability of identity among siblings (PIsibs) across 24 SSR loci were 1.475 × 10−19 and 2.561 × 10−8, respectively, indicating a strong ability for fingerprint identification. Unique fingerprints for the 111 accessions were established using four selected core markers. A final core collection consisting of 34 accessions was constructed using the allele maximization (M) strategy, accounting for 30.63% of the analyzed accessions. No significant differences in genetic diversity indicators, allele frequency distributions, and accession dispersion patterns were observed between the core and original collections, suggesting that the core collection could effectively represent the entire collection. This work will promote the identification, management, and conservation of L. formosana germplasm resources while providing valuable materials for the subsequent selection and breeding of this tree species.

Genomic variation responding to artificial selection on different lines of Pekin duck.

Understanding the genomic variation in Pekin duck under artificial selection is important for improving the utilization of duck genetic resources. Here, the genomic changes in Pekin duck were analyzed by using the genome resequencing data from 96 individual samples, including 2 conservation populations and 4 breeding populations with different breeding backgrounds. The population structure, runs of homozygosity (ROH), effective population number (Ne), and other genetic parameters were analyzed. The breeding populations showed lower genetic diversity compared to the conservation populations. Maple Leaf duck and Cherry Valley duck retained low genetic diversity compared to other breeding populations, with Cherry Valley duck showing the lowest diversity and the highest inbreeding coefficient. This suggested that Cherry Valley and Maple Leaf ducks have undergone intensive selection compared to other breeding populations. By the analysis of runs of homozygosity (ROHs), some genes (e.g., IGF1R) associated with growth traits were identified. By the analysis of the selection signal, strong selection characteristics in certain genomic regions during the breeding of Peking duck across different selected lines were observed. In addition, copy number variations (CNVs) in Pekin duck populations were analyzed. Six regions of interest were identified, containing RPA1, DOT1L, SLC25A42, RALYL, TRPA1, and IGFBP2. Furthermore, the allele frequency distribution of these genes showed significant differences between breeding populations and conservation populations, indicating that these candidate genes could have undergone strong selection pressure during long-term selection for improved production. These findings contribute to a deeper understanding of the distinct evolutionary processes in Pekin ducks under artificial selection and provide valuable insights for future breeding strategies.

Ultra-deep sequencing of somatic mutations induced by a maize transposon.

Cells accumulate mutations throughout development, contributing to cancer, aging, and evolution. Quantitative data on the abundance of de novo mutations within plants or animals are limited, as new mutations are often rare within a tissue and fall below the limits of current sequencing depths and error rates. Here, we show that mutations induced by the maize Mutator (Mu) transposon can be reliably quantified down to a detection limit of 1 part in 12,000. We measured the abundance of millions of de novo Mu insertions across four tissue types. Within a tissue, the distribution of de novo Mu allele frequencies was highly reproducible between plants, showing that, despite the stochastic nature of mutation, repeated statistical patterns of mutation abundance emerge. In contrast, there were significant differences in the allele frequency distribution between tissues. At the extremes, root was dominated by a small number of highly abundant de novo insertions, while endosperm was characterized by thousands of insertions at low allele frequencies. Finally, we used the measured pollen allele frequencies to reinterpret a classic genetic experiment, showing that evidence for late Mu activity in pollen are better explained by cell division statistics. These results provide insight into the complexity of mutation accumulation in multicellular organisms and a system to interrogate the factors that shape mutation abundance.

Significance Of Gene Polymorphisms In Joint Destruction In Reactive Arthritis

in patients with reactive arthritis (ReA), cytokines produced by Th17 cells, one of them IL17, affect cell differentiation, recruitment, activation of immune cells, and release of antimicrobial peptides. Among the cytokines of the IL-17 family, it is IL-17A that is of decisive importance in the induction of pathological bone resorption through direct activation of osteoclast precursors during the formation of the articular syndrome The aim of our work was to study the distribution of allele and genotype frequencies of the polymorphic region G197A (rs2275913) of the IL-17A gene in patients with ReA. As a result of the study, there were no significant differences in the distribution of alleles of the G197A polymorphism of the IL-17A gene in patients with ReA and apparently healthy people. But when comparing genotypic variants, we revealed differences: healthy GG and mutant AA genotypes were more common in patients, while the heterozygous GA genotype was more common in healthy people

Investigating the Role of IL-17A gene rs2275913 Variant in Rosacea: In Silico Analysis Suggests Further Studies

Interleukine-17 (IL-17), a crucial component of the body's immune response against pathogens, is also implicated in various inflammatory processes. Notably, the skin of rosacea patients exhibits chronic inflammation, and IL-17 is known to induce the production of additional pro-inflammatory chemokines and cytokines. This inflammatory cascade can contribute to the hallmark features of rosacea, including dilated blood vessels, immune cell infiltration, and the development of papules and pustules. The study aimed to examine whether a specific genetic variation in the IL-17A gene (-197 G>A; rs2275913) is associated with rosacea susceptibility. We compared the IL-17A variant and rosacea risk in 31 healthy individuals and 25 with rosacea. Genotyping of the IL-17A variant was performed using the PCR-RFLP method. Genotype and allele frequency distributions were compared across groups using the chi-square test (χ2). Additionally, gene ontology (GO) analysis of the IL-17A gene using web-based tools is also demonstrated. No significant association between the rs2275913 polymorphism and rosacea susceptibility was observed in this study (p=0.124) but in silico analysis suggested that the IL-17A gene interaction network might play a role in the disease. Given its critical function in regulating IL-17A and related genes, particularly in immune defense and inflammatory processes, further investigation into its potential influence on rosacea development is required.

Characterizing selection on complex traits through conditional frequency spectra.

Natural selection on complex traits is difficult to study in part due to the ascertainment inherent to genome-wide association studies (GWAS). The power to detect a trait-associated variant in GWAS is a function of frequency and effect size - but for traits under selection, the effect size of a variant determines the strength of selection against it, constraining its frequency. Recognizing the biases inherent to GWAS ascertainment, we propose studying the joint distribution of allele frequencies across populations, conditional on the frequencies in the GWAS cohort. Before considering these conditional frequency spectra, we first characterized the impact of selection and non-equilibrium demography on allele frequency dynamics forwards and backwards in time. We then used these results to understand conditional frequency spectra under realistic human demography. Finally, we investigated empirical conditional frequency spectra for GWAS variants associated with 106 complex traits, finding compelling evidence for either stabilizing or purifying selection. Our results provide insight into polygenic score portability and other properties of variants ascertained with GWAS, highlighting the utility of conditional frequency spectra.

Polymorphism of genes involved in the regulation of blood pressure in elderly residents of the Arkhangelsk region

BACKGROUND: Living in the northern climate is associated with increased cardiovascular stress, which highlights the necessity for the study of candidate genes associated with the risk of cardiovascular diseases in both the native population and newcomers. Polymorphic loci of the renin-angiotensin system, NO-synthase, and endothelin-1 system genes have been identified as contributors to cardiovascular dysfunction and age-related blood pressure shifts. It is therefore crucial to assess the genetic polymorphism in the elderly population. AIM: To compare frequencies of gene alleles and genotypes involved in blood pressure regulation, including angiotensinogen AGT (rs699 and rs4762), angiotensin 2 type 1 receptor AGTR1 (rs5186), angiotensin converting enzyme ACE (rs4646994), endothelial NO synthase NOS3 and endothelin-1 EDN1 (rs5370) genes, in the native and non-native elderly population of the Arkhangelsk region. MATERIALS AND METHODS: A cross-sectional study was conducted in a random sample of Arkhangelsk residents between the ages of 60 and 74 years (N=604, with 36.4% of males). The molecular genetic analysis was conducted to determine the alleles and genotypes of six genes that are involved in blood pressure regulation. The Stata 18.0 software was used to assess the deviations of empirical genotype distributions from the predicted Hardy–Weinberg equilibrium and to compare the empirical distributions between the study groups. RESULTS: Alleles associated with the risk of cardiovascular diseases were minor in the study population. The genotype frequency distributions for the analyzed genetic variants were consistent with the Hardy–Weinberg principle, with the exception of the T704C variant of the AGT gene (rs699) in the native participants. The allele and genotype frequency distributions in the study sample were found to be similar to those reported worldwide and in European Russia. One exception was AGTR1 gene A1166C frequencies, with their 95% confidence intervals falling below the global level for both native and non-native elderly residents of the Arkhangelsk region. This may suggest that this allele is a selection variant associated with adaptation to the climate of the northern regions. CONCLUSION: The genetic polymorphism in blood pressure regulation was found to be similar between the native and non-native populations of the Arkhangelsk region. However, the AGTR1 gene A1166C frequency among the native population and newcomers was found to be lower than that observed globally.

Genetic profiling of Plasmodium falciparum antigenic biomarkers among asymptomatic pregnant women on intermittent preventive treatment with sulfadoxine-pyrimethamine from southwest Nigeria.

The genetic complexity of Plasmodium falciparum is contributory to the emergence of drug resistant-parasites. Intermittent preventive treatment of malaria in pregnancy with sulfadoxine-pyrimethamine (IPTp-SP) in malaria endemic settings is recommended by WHO. This study evaluated the prevalence of Plasmodium falciparum multidrug resistance-1 gene (Pfmdr-1), genetic diversity of merozoite surface proteins (msp-1, msp-2) and glutamate-rich protein (glurp) among pregnant women with sub-patent parasitaemia from southwest Nigeria. One hundred PCR-confirmed Plasmodium falciparum isolates, collected at first visit-V-1 (n=52), delivery (n=31) and cord blood (n=17), were selected for analysis. The Pfmdr-1 alleles was evaluated using restriction fragment length polymorphism (RLFP), while msp-1, msp-2 and glurp genes were genotyped. Allelic frequency distribution and multiplicity of infection were calculated at p-value ≤0.05. The Pfmdr-1 (N86/N86Y) combination was detected in 11.8%, 61.3% and 58.8% (p≤0.05) in V-1, Delivery and Cord isolates respectively. The N86Y haplotype was detected only in cord (5.9%). The allelic frequency distribution for msp-1 was 244 (K1=81, MAD20=84 and RO33=79), and msp-2; 110 alleles, representing 43.6% (FC27) and 56.4% (3D7). While glurp expressed 25 alleles, 84% (V-1), 12% (delivery) and 4% (cord), respectively (p≤0.05). The msp-1 and msp-2 recorded higher MOIs than glurp. Genetically diverse P. falciparum strains with Pfmdr-1 mutant alleles were detected in pregnant women with sub-patent parasitaemia in southwest Nigeria, which may reduce IPTp-SP effectiveness. Thus, continuous molecular surveillance of resistant-parasites to sulphadoxine-pyrimethamine and ACTs is essential.

Assessment of IL- 35 Gene Polymorphism in Periodontitis Patients with and without Diabetes - A Cross-Sectional Study

ABSTRACT Aim: To evaluate the IL-35 Gene Polymorphism in Periodontitis subjects with and without type 2 diabetes mellitus. Methodology: 96 participants were categorized into three groups, Group 1: Systemically and Periodontally healthy individuals, Group 2: Systemically healthy patients with Generalized chronic periodontitis, Group 3: Generalized chronic periodontitis with type 2 diabetes Mellitus. Genomic DNA was extracted from the whole venous blood samples collected from the participants using The PureLink Genomic Kit. The region spanning rs1580809257 and rs1580801731 were amplified using appropriate primer and reaction conditions. Determination of genotypes for each of the polymorphisms assessed using Amplification Refractory Mutation System (ARMS) - based PCR and Restriction Fragment Length Polymorphism (RFLP). The distribution of genotype and allele frequencies for Case and control groups were compared using the Chi-square test. Hardy Weinberg equilibrium is calculated. Results: The gene and allele frequency were found to be similar in all three groups. Conclusion: The study reveals that polymorphism of rs1580809257 and rs1580801731 in the IL-35 gene is neither associated with Periodontitis patients nor Periodontitis with Diabetes patients.

Genetic Analysis of Autosomal Short Tandom Repeats Loci in The Libyan Western Mountain Population

There is a little investigation of the genetic diversity of the Libyan population. This study aimed to explore STR loci in the Libyan western mountain population to analyse its genetic landscape. Allele frequency for 15 autosomal STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, THO1, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, FGA) included in the Identifiler®Plus kit were investigate in 120 random unrelated individuals from the Westerner Mountain area of Libya. No deviations from Hardy-Weinberg equilibrium were seen, with the exception of D8S1179, D21S11, D3S1358, TH01 and FGA loci. A total of 129 alleles were observed with the corresponding allelic frequencies ranging between 0.00417 and 0.47917 of the studied sites were observed, and that alleles 8 and 12 are the highest frequency for all studied areas for the TPOX and D5S818 sites respectively had a value of (0.47917). D18S51 was also observed to be the most diverse site (Expected heterozygosity: 0.88312 and probability of matching: 0.0354). The results indicate that the 15 STR loci have a significant genetic diversity among studied individuals and are suitable for personal identification in the criminal field, and the importance of this work lies in the creation of a database of frequency distribution of allelic frequencies to be used for criminal identification, identification of missing persons and paternity tests.

Using mathematical constraints to explain narrow ranges for allele-sharing dissimilarities.

Allele-sharing dissimilarity (ASD) statistics are measures of genetic differentiation for pairs of individuals or populations. Given the allele-frequency distributions of two populations-possibly the same population-the expected value of an ASD statistic is computed by evaluating the expectation of the pairwise dissimilarity between two individuals drawn at random, each from its associated allele-frequency distribution. For each of two ASD statistics, which we term and , we investigate the extent to which the expected ASD is constrained by allele frequencies in the two populations; in other words, how is the magnitude of the measure bounded as a function of the frequency of the most frequent allelic type? We first consider dissimilarity of a population with itself, obtaining bounds on expected ASD in terms of the frequency of the most frequent allelic type in the population. We then examine pairs of populations that might or might not possess the same most frequent allelic type. Across the unit interval for the frequency of the most frequent allelic type, the expected allele-sharing dissimilarity has a range that is more restricted than the [0, 1] interval. The mathematical constraints on expected ASD assist in explaining a pattern observed empirically in human populations, namely that when averaging across loci, allele-sharing dissimilarities between pairs of individuals often tend to vary only within a relatively narrow range.

Determination of HLA Tissue Type According to the Etiology of Patients with Chronic Renal Failure.

Chronic kidney disease (CKD) is a prominent public health concern, is defined as functional and structural damage to the kidneys. This study aims to investigate the association between human leukocyte antigen (HLA) alleles individuals with CKD and the different etiological subgroups of diesease. Genomic DNA was obtained from peripheral blood samples of 1,079 patients with retrospective CKD and 1,111 healthy control individuals. HLA genotyping was conducted using the Luminex based low-resolution method. Allele frequency distributions were calculated with the help of Arlequin v3.11 population genetics statistics program and SPSS v23.0 program, and p<0.05 values were accepted as significant by chi-square tests. HLA A*02 (21.83%), B*35 (18.30%), DRB1*11 (21.41%) alleles were observed most frequently in individuals with CKD, respectively. In our study, B*08, B*49, B*50 alleles in the HLA B locus (p=0.002, p=0.012 p=0.009) and DRB1*03, *04 alleles in the HLA DRB1 locus (p<0.001, p<0.001) were found positively associated with CKD. A*02, A*11, A*74 alleles at the HLA A locus (p=0.003, p<0.001, p=0.009) and B*27, B*39, B* alleles at the HLA B locus 40, B*59 (p<0.001, p<0.001, p<0.001, p=0.009), DRB1*07, *08, *09, *13, *16 (p<0.001, p=0.012, p=0.007, p<0.001, p<0.001) alleles were determined as negatively associated with the disease. Among the etiological groups of CKD, cystic kidney disease (36.8%), hypertension (16.8%) and urological anomalies (16.6%) were negatively associated with the HLA-DR*13 allele. Since CKD shows serious morbidity and mortality, this comprehensive study of HLA subgroups gave an explanatory idea about which alleles associated with the disease in terms of susceptibility and protection.

Field-evolved resistance to neonicotinoids in the mosquito, Anopheles gambiae, is associated with mutations of nicotinic acetylcholine receptor subunits combined with cytochrome P450-mediated detoxification

New insecticides prequalified for malaria control interventions include modulators of nicotinic acetylcholine receptors that act selectively on different subunits leading to variable sensitivity among arthropods. This study aimed to investigate the molecular mechanisms underlying contrasting susceptibility to neonicotinoids observed in wild populations of two mosquito sibling species. Bioassays and a synergist test with piperonyl butoxide revealed that the sister taxa, Anopheles gambiae and An. coluzzii, from Yaounde, Cameroon, both have the potential to develop resistance to acetamiprid through cytochrome P450-mediated detoxification. However, contrary to An. coluzzii, An. gambiae populations are evolving cross-resistance to several active ingredients facilitated by mutations of nicotinic acetylcholine receptors (nAChRs). We sequenced coding regions on the β1 and α6 nAChR subunits where variants associated with resistance to neonicotinoids or to spinosyns have been found in agricultural pests and detected no mutation in An. coluzzii. By contrast, six nucleotide substitutions including an amino acid change in one of the loops that modulate ligand binding and affect sensitivity were present in the resistant species, An. gambiae. Allele frequency distributions were consistent with the spread of beneficial mutations that likely reduce the affinity of An. gambiae nAChRs for synthetic modulators. Our findings provide critical information for the application and resistance management of nAChR modulators in malaria prevention.

Numerical solution of the forward Kolmogorov equations in population genetics using Eta functions

This paper introduces a new numerical method for solving forward Kolmogorov equations in population genetics. Since there's no simple analytical expression for the distribution of allele frequencies (DAF), we use these equations to derive it. The accuracy of solving these equations depends on the choice of base functions, so we use Eta-based functions for better approximations. By employing the operational matrix of integral, we simplify the partial differential equation to an algebraic one. The method's error bounds, stability, and validity are demonstrated through numerical examples. Finally, we apply this method to analyze the behavior of forward Kolmogorov equations under various evolutionary forces.

Methylenetetrahydrofolate reductase (MTHFR) C677T and A1298C polymorphisms in Turkish postmenopausal women with osteoporosis

Osteoporosis is a common age-related skeletal disease, characterized by changes in the microarchitectural structure of bone tissue and decreased bone mass, especially affecting postmenopausal women. Genetic and environmental factors affecting bone metabolism play a role in the development of osteoporosis. Methylenetetrahydrofolate reductase (MTHFR) is an important enzyme involved in the conversion of homocysteine to methionine. Genetic variations in the MTHFR gene lead to impaired function or inactivation of this enzyme. A decrease in MTHFR enzyme activity and an increase in homocysteine levels affect bone metabolism. In this study, we aimed to investigate the relationship between C677T and A1298C polymorphisms and osteoporosis in Turkish postmenopausal women. DNA samples were extracted from 200 volunteers. The PCR-RFLP technique was used to identify the MTHFR gene polymorphisms C677T and A1298C. The statistical significance of the analysis’s results was assessed. C677T genotype and allele frequency distributions were not statistically different between postmenopausal osteoporosis and healthy control groups (p = 0.249, p = 0.754), while A1298C genotype and allele frequency distributions were found to be statistically significant (p = 0.002, p = 0.013). The results of our study showed that the A1298C polymorphism may be a genetic factor associated with osteoporosis in this specific population. However, the C677T polymorphism did not show a significant connection. To gain a more comprehensive understanding of the genetic basis of osteoporosis, future research with larger sample sizes and the consideration of additional genetic and environmental factors is essential. Additionally, it is crucial to account for ethnic disparities, gene-gene interactions, and gene-environment interplays. These insights can inform the development of personalized preventive and therapeutic strategies for individuals at risk of osteoporosis in diverse populations.

Accumulating waves of random mutations before fixation.

Mutations provide variation for evolution to emerge. A quantitative analysis of how mutations arising in single individuals expand and possibly fixate in a population is essential for studying evolutionary processes. While it is intuitive to expect that a continuous influx of mutations will lead to a continuous flow of mutations fixating in a stable constant population, joint fixation of multiple mutations occur frequently in stochastic simulations even under neutral selection. We quantitatively measure and analyze the distribution of joint fixation events of neutral mutations in constant populations and discussed the connection with previous results. We propose a new concept, the mutation "waves," where multiple mutations reach given frequencies simultaneously. We show that all but the lowest frequencies of the variant allele frequency distribution are dominated by single mutation "waves," which approximately follow an exponential distribution in terms of size. Consequently, large swaths of empty frequencies are observed in the variant allele frequency distributions, with a few frequencies having numbers of mutations far in excess of the expected average values over multiple realizations. We quantify the amount of time each frequency is empty of mutations and further show that the discrete mutation waves average out to a continuous distribution named as the wave frequency distribution, the shape of which is predictable based on few model parameters.

Frequency Distributions of Alleles and Genotypes and Lung Cancer Risk of Polymorphisms DCK, SLC29A1, and SLC29A3 in South Indian Healthy Population.

Introduction Gemcitabine, a cytotoxic drug, is used to treat a variety of solid tumors, such as pancreatic, lung, and breast malignancies. The efficiency rates for gemcitabine have decreased due to an increase in genetic instability. The association between gene polymorphisms and the efficacy of gemcitabine therapy may be better known by understanding the intricacies of genetics that target a few or more genes in drug-targeting metabolic pathways. Moreover, several studies have documented differences in the therapeutic response among various ethnicities to gemcitabine chemotherapy. Therefore, the purpose of this study was to determine the normative frequencies of gene polymorphisms linked to the metabolic pathway of gemcitabine (DCK -360C>G (80143932), SLC29A1 -201A>G (760370), SLC29A1 +913C>T (9394992), SLC29A3 +4967C>A (10999776)) in Southern part of Indian healthy population and compared it with the 1000 genome population. In addition, the association of the above single nucleotide polymorphisms (SNPs) with lung cancer susceptibility was also evaluated. Methods The present study used real-time polymerase chain reaction (RT-PCR) for performing genotyping in 184 healthy participants as well as 123 South Indian patients with lung cancer. The frequencies of alleles and genotypes of the aforementioned genetic variants were in Hardy-Weinberg equilibrium (p > 0.05). Results The minor allele frequencies (MAF) of the SNPs DCK -360C>G (80143932), SLC29A1 -201A>G (760370), SLC29A1+913C>T (9394992), SLC29A3 +4967C>A (10999776) were 3.8%, 17.7%, 27.7%, 29.3% respectively in healthy population. The MAF of the SNPs, DCK -360C>G (80143932), SLC29A1 -201A>G (760370), SLC29A1 +913C>T (9394992), SLC29A3 +4967C>A (10999776) in lung cancer patients was 2%, 15%, 23.2%, and 24.4% respectively. A trend toward a protective effect against lung cancer was observed with SLC29A1 +913C>T (9394992). Conclusion The observed frequencies of alleles and genotypes in the South Indian population were significantly different as compared to the 1000 genome population. In the present study, an association of SLC29A1 rs9394992 C>T between lung cancer patients and healthy subjects showed a trend toward protective effect against lung cancer risk.There was no association found between the other studied SNPs and lung cancer risk.

Investigation of the effect of catechol-o-methyltransferase gene rs4680 polymorphism on trigeminal neuralgia susceptibility

Research has been conducted to explore the genetic basis of trigeminal neuralgia, a persistent pain condition that impacts the trigeminal nerve. COMT is an enzyme responsible for inactivating substances and hormones containing catechol and catecholamines. Previous research has linked COMT gene polymorphism with various pain conditions, including migraine. Our research aimed to investigate the correlation between trigeminal neuralgia and the rs4680 polymorphism of the COMT gene. We conducted a research project which included 10 individuals diagnosed with trigeminal neuralgia and 30 healthy individuals as controls. Following collection of blood samples, we isolated DNA from the samples and then genotyping of COMT rs4680 polymorphism was performed with Real-Time PCR, using TaqMan SNP Genotyping Assay. Among the trigeminal neuralgia patients, 2 of them exhibited the AA genotype, 6 had the AG genotype, and 2 had the GG genotype for COMT rs4680. The AG genotype was notably prevalent. No statistically significant differences in the distributions of COMT genotypes and allele frequencies were found between the experimental (patients) and the control group. However, the AG genotype appeared to be more frequent in the patient group. Moving forward, we plan to expand our study by increasing the number of patients and control subjects. This will enable us to further elucidate the potential relationship between COMT gene polymorphism and trigeminal neuralgia.

Association between ATG16L1 rs2241880(T300A) and rs4663421 and ANCA‑associated vasculitis in the Guangxi population of China: Propensity score matching analysis.

Antineutrophil cytoplasmic antibody-associated vasculitis (AAV) is a rare autoimmune disease with an unclear pathogenesis. The present study investigated the associations between autophagy-related protein 16-like 1 (ATG16L1) rs2241880(T300A) and rs4663421 and AAV. A total of 177 patients with AAV and 216 healthy controls were included. Propensity score matching was used to match the two groups of subjects in terms of sex, age and ethnicity. Analyses of the relationships between these genetic polymorphisms and AAV susceptibility, including comparisons of allele and genotype frequency distribution, linkage disequilibrium analysis and analysis of single nucleotide polymorphism (SNP) interactions between two loci were performed. The association between the loci and laboratory test results and renal pathology were also analysed. A total of 154 pairs of patients with AAV and healthy controls was successfully matched. Neither polymorphism was associated with AAV susceptibility. However, SNP interaction in the model constructed with the two loci was statistically significant (P=0.018), and the combination of the AA genotype of rs2241880(T300A) and GG genotype of rs4663421 was associated the highest disease risk. The differences in the Birmingham Vasculitis Activity Score (BVAS), C-reactive protein (CRP) levels and 24-h urine protein level between patients with the rs2241880(T300A) AA + AG genotypes and the GG genotype were statistically significant (P<0.05). Furthermore, significant differences in the severity of glomerulosclerosis and global sclerosis were detected between individuals with the AA + AG genotype and those with the GG genotype at the rs2241880(T300A) locus (P<0.05). Similarly, there were statistically significant differences in degree of segmental sclerosis between individuals with CC + CG genotypes and those with GG genotypes at the rs2243421 locus (P<0.05). In summary, the single gene polymorphisms of these loci were not associated with genetic susceptibility to AAV. However, SNP interactions may serve a role in the risk of AAV. The rs2241880(T300A) polymorphism may be associated with BVAS, CRP levels and 24-h urine protein level in AAV. These SNPs may be associated with glomerulosclerosis and segmental sclerosis.

Polymorphism Of Orosomucoid-Like 3 ORMDL3 Rs4795405 C&gt;T In Iraqi Patients with Asthma

The aim of this study was to investigate the association of polymorphism of Orosomucoid-like 3 ORMDL3 rs4795405 C/T gene to the susceptibility of asthma among Iraqi asthmatic patients. Forty-five asthmatic patients (23 males and 22 females), their age 19-70 years and 35 healthy controls( 18 males and 17 females) ,their age 18-71years were selected from Wasit Province using a convenient sampling method. Genetic polymorphism of Orosomucoid-like 3 ORMDL3 rs4795405 C&gt;T was carried out using TaqMan -PCR. both patients and control groups, the distribution frequencies of genotypes and alleles of the rs4795405 C/T gene were in Hardy-Weinberg equilibrium (P&lt;0.05) .The most common genotype in both control and asthma patients was the heterozygous genotype CT with a percentage of 67% and 66% respectively. The genotype CC was higher in the asthmatic group (20%) compared to the control group (14%). In contrast, genotype TT, the less predominant genotype, was less in the asthmatic group were less in asthmatic group (13%) compared control group (20%).The C allele was more frequent in asthma patients than in healthy controls (53.33%vs47.14%), whereas the T allele was frequent in healthy controls than in asthma patients (52.86% vs 46.67%) with no significant differences. The association analysis displayed that the individuals carrying the homozygous CC genotype were more likely to have a increased risk of asthma with OR=1.5(CI95% 0.4537to4.9593) ,P=0.5063.The heterozygous genotypes CT was not associated with asthma with OR=1.0 (CI95%0.4103 to2.6538 ),P=0.9288 . The TT genotype decreases the association with asthma OR=0.6 (CI950.1865 to2.0302), P =0.4253. These results suggested that the T allele might play a protective role against asthma whereas the C allele might consider a risk factor in asthma. The subgroup analysis revealed that the asthma risk of females with ORMDL3 CC genotype was 2.4 fold increases the risk of asthma OR=2.4889 (CI95% 0.5478to11.3081), P= 0.2377 The TC and TT genotype decreases the association with the disease with with OR = 0.8485 (CI 95% 0.2312to3.1142), P = 0.8044 and OR= 0.2121(CI95% 0.02 to2.2473)P =0.1979 respectively. Among males, ORMDL3 CT genotype ncreased asthmatic risk among patients’ males 1.3 fold, OR= 1.3333 (CI95%0.3433 to 5.1781), P=0.6777. The genotype CC decreases the association with the disease OR=0.3810 (CI95%0.0317to 4.5813), P=0.4469. While, the homozygous TT genotype was not associated with the disease OR=1.0294 (CI95% 0,2313 to4.5814), P=0.9696. The analysis of genetic model for Orosomucoid-lik 3 ORMDL3 rs4795405 showed the recessive model (CC+CT/ TT ) increased the association with the asthma OR=1.6250 P=0.4253.The Over-dominant model(CT+TT/ CC) and the dominant model(CT+TT/ CC) decreased the association with asthma OR=0.9583,P=0.9288and OR= 0.6667 ,P=0.5063 respectively.