allele distribution
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2022 ◽  
Author(s):  
Attila Zsolnai ◽  
Adrienn Csókás ◽  
László Szabó ◽  
László Patkó ◽  
Sándor Csányi ◽  
...  

AbstractStudies of wild boar, Sus scrofa Linnaeus 1758, in urban and suburban areas of Budapest, Hungary, have indicated that these populations do not have continuous contact. Based on the assumption that the city has a discrete population, we hypothesized that the urban wild boar would differ genetically from those in suburban areas. Analysis of single-nucleotide polymorphism (SNP) data using the GeneSeek Genomic Profiler (GGP) Porcine 50 K system (Neogen, Scotland, UK) differentiated three populations: Buda (B) from the Western bank of the Danube; Buda Surrounding (BS); and Valkó (V) from the Eastern bank of the Danube. The coefficient of genetic differentiation (FST) for the B and BS populations was low. The inbreeding coefficients of the populations BS and V were close to zero, while population B had a high positive value reflecting the influence of founders and the inbreeding of the continuous urban population. The genome regions that were most differentiated between the B and BS populations were analyzed based on the FST values of the SNP markers using a mixed linear multi-locus model and BayeScan software. The most differentiated marker, WU_10.2_18_56278226, was found on chromosome 18. The surrounding region contained several candidate genes that could play important roles in adaptations related to human-induced stress. Two of these, encoding the adenylate cyclase 1 (ADCY1) and inhibin beta A chain precursor (INHBA) genes, were sequenced. While IHBA gene did not display variation, the allele distribution of the ADCY1 gene in the B population was significantly different from that of the BS population supporting the parapatric differentiation of wild boar.


2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Wenwang Rao ◽  
Xiangfei Meng ◽  
Keqing Li ◽  
Yunshu Zhang ◽  
Xiang Yang Zhang

Abstract Background The apolipoprotein E (ApoE) gene polymorphisms are correlated with blood lipid levels and several neuropsychiatric symptoms. Therefore, this study aimed to examine whether the ApoE rs429358 affected the development and clinical symptoms of schizophrenia and to explore the relationship between apolipoproteins levels and clinical symptoms. Methods The ApoE rs429358 was genotyped using a case–control design. The Positive and Negative Syndrome Scale (PANSS) was employed to evaluate the psychopathology of all patients. Results A total of 637 patients with schizophrenia and 467 healthy controls were recruited. We found no significant differences in the genotype and allele distribution between the patient and control groups. A significant correlation between PANSS negative symptoms and ApoA1 levels (p = 0.048) or ApoB levels (p = 0.001) was found in patients with schizophrenia, which was also confirmed by linear regression analyses (p = 0.048 vs. p = 0.001). Interestingly, only in the T homozygote group, ApoA1 and ApoB levels were predictors of the PANSS negative symptom score (p = 0.008 vs. p = 0.012), while in the C allele carrier group, no correlation was observed. Conclusions This study found that the levels of ApoA1 and ApoB were negatively associated with negative symptoms of patients with schizophrenia. Furthermore, the association between ApoA1 or ApoB levels and psychopathology of schizophrenia was regulated by ApoE rs429358.


2021 ◽  
pp. 138-144
Author(s):  
Wei-De Lin ◽  
Fuu-Jen Tsai

<b><i>Introduction:</i></b> Multiple myeloma (MM) is an incurable, biologically heterogeneous disease of the plasma cells, associated with older age and is more common in men. Gaucher disease, caused by mutation in acid β-glucosidase (glucocerebrosidase, <i>GBA</i>) gene, has been linked to multiple cancers, especially MM. Pathological accumulation of glucosylceramide and complex glycosphingolipids coupled with chronic inflammation may be the cause of cancer in patients with Gaucher disease. In this study, we hypothesized patients with MM have mutations in the <i>GBA</i> gene and analyzed patients with MM to determine whether they have a higher frequency of <i>GBA</i> variants. <b><i>Methods:</i></b> Twenty-four MM samples were acquired from the Human Biobank, China Medical University Hospital, Taichung, Taiwan. <i>GBA</i> mutations were detected by polymerase chain reaction-directed DNA sequencing. <b><i>Results:</i></b> We found no mutations in the coding regions of <i>GBA</i> in any of the 24 study subjects. However, two single-nucleotide polymorphisms, rs2070679 and rs2361534, were identified. A significant difference was observed between the study and control groups (<i>p</i> = 0.0028) in rs2361534 allele distribution, with the C allele frequency being higher in patients (1/48, 2.1%) than in the control group (5/3030, 0.16%, Taiwan Biobank). <b><i>Conclusion:</i></b> In this study, the sample size was limited and GBA enzyme activity was not measured; therefore, we could not establish a direct correlation between MM and <i>GBA</i> mutations. However, the association of rs2361534 suggests that regions around this single-nucleotide polymorphism may be involved in MM. The relationship between MM and <i>GBA</i> mutations remains unclear. A large sample is required for a detailed analysis of this potential relationship.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dandan Li ◽  
Linna Peng ◽  
Shishi Xing ◽  
Chunjuan He ◽  
Tianbo Jin

Abstract Background The variation of drug responses and target does among individuals is mostly determined by genes. With the development of pharmacogenetics and pharmacogenomics, the differences in drug response between different races seem to be mainly caused by the genetic diversity of pharmacodynamics and pharmacokinetics genes. Very important pharmacogenetic (VIP) variants mean that genes or variants play important and vital roles in drug response, which have been listed in pharmacogenomics databases, such as Pharmacogenomics Knowledge Base (PharmGKB). The information of Chinese ethnic minorities such as the Wa ethnic group is scarce. This study aimed to uncover the significantly different loci in the Wa population in Yunnan Province of China from the perspective of pharmacogenomics, to provide a theoretical basis for the future medication guidance, and to ultimately achieve the best treatment in the future. Results In this study, we recruited 200 unrelated healthy Wa adults from the Yunnan province of China, selected 52 VIP variants from the PharmGKB for genotyping. We also compared the genotype frequency and allele distribution of VIP variants between Wa population and the other 26 populations from the 1000 Genomes Project (http://www.1000Genomes.org/). Next, χ2 test was used to determine the significant points between these populations. The study results showed that compared with the other 26 population groups, five variants rs776746 (CYP3A5), rs4291 (ACE), rs3093105 (CYP4F2), rs1051298 (SLC19A1), and rs1065852 (CYP2D6) had higher frequencies in the Wa population. The genotype frequencies rs4291-TA, rs3093105-CA, rs1051298-AG and rs1065852-GA were higher than those of the other populations, and the allele distributions of rs4291-T and rs3093105-C were significantly different. Additionally, the difference between the Wa ethnic group and East Asian populations, such as CDX, CHB, and CHS, was the smallest. Conclusions Our research results show that there is a significant difference in the distribution of VIP variants between the Wa ethnic group and the other 26 populations. The study results will have an effect on supplementing the pharmacogenomics information for the Wa population and providing a theoretical basis for individualised medication for the Wa population.


2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Joanna Wielińska ◽  
Jerzy Świerkot ◽  
Katarzyna Kolossa ◽  
Bartosz Bugaj ◽  
Monika Chaszczewska-Markowska ◽  
...  

IL-17A and IL-17F together with their coreceptor (IL-17RA/RC) were reported to play a significant role in the pathogenesis of spondyloarthritis. The group of axial spondyloarthritis comprises ankylosing spondylitis (AS), a rheumatic disease characterized by chronic inflammation of the joints in the spine. This study is aimed at investigating IL-17A, IL-17F, IL-17RA, and IL-17RC polymorphisms as potential biomarkers of disease susceptibility, clinical parameters, and anti-TNF treatment outcome in a cohort of Polish ankylosing spondylitis patients. In total, 328 subjects, including 138 AS patients and 190 healthy volunteers, participated in the study. Genotyping of IL-17A rs2275913 (G/A), IL-17F rs763780 (A/G), IL-17RA rs4819554 (A/G), and IL-17RC rs708567 (G/A) was performed on real-time PCR instrument using LightSNiP assays. No significant differences were revealed in genotype and allele distribution between patients and controls despite the association of the IL-17RC rs708567 AA homozygosity with the earlier onset of the disease. Moreover, some relationships between IL-17F rs763780 and IL-17RA rs4819554 polymorphisms with clinical parameters related to the disease activity and anti-TNF treatment outcome were observed. IL-17F rs763780 G allele was found to be associated with high disease activity and BASDAI after 6 months and poor response to the treatment while higher VAS values were more common among IL-17RA rs4819554 G variant carriers. In conclusion, the IL-17F rs763780 polymorphism should be considered as a promising biomarker of disease activity and anti-TNF treatment outcome. The IL-17RA rs48419554 G allele may serve as a potential marker of disease severity in Polish AS patients.


2021 ◽  
Vol 18 (10) ◽  
pp. 943-948
Author(s):  
Yuan-yuan Li ◽  
Rui-jie Geng ◽  
Shun-ying Yu ◽  
Guan-jun Li ◽  
Zhou-ye Wang ◽  
...  

Objective To investigate the relation between nicotinic acetylcholine receptor subunit (nAChR) genes and schizophrenia, and the relation between tag single nucleotide polymorphism (rs1317286, rs1044396, rs6494212, rs16969968, and rs684513) and schizophrenia in Han Chinese people.Methods The protein-protein interaction (PPI) network among nAChR protein and 350 proteins encoded by schizophrenia-related susceptibility genes was constructed through the String database to explore whether nAChR genes were associated with schizophrenia in these known databases. Then, five single nucleotide polymorphisms (SNPs) of CHRNA3 (rs1317286), CHRNA4 (rs1044396), CHRNA7 (rs6494212), and CHRNA5 (rs16969968, rs684513) were analyzed in a sample of 1,035 schizophrenic patients and 816 healthy controls. The interaction between the markers was analyzed using multifactor dimensionality reduction (MDR) software. Power analysis was performed using the Quanto program.Results There are no significant differences in genotype or allele distribution were identified between the patients and controls (p>0.05). The haplotypes constructed by four markers rs1317286, rs6494212, rs16969968, and rs684513 were not associated with schizophrenia either. However, a significant association between models made of rs1317286, rs1044396, rs6494212, and rs684513 and schizophrenia was revealed in interaction analysis (p<0.05).Conclusion The nAChR protein may have effects on the development of schizophrenia through the interaction with proteins encoded by schizophrenia-related susceptibility genes, but no relation was found between selected polymorphisms and schizophrenia in the collected Han Chinese people. However, interaction analysis suggested four-SNP model has an important effect on schizophrenia.


2021 ◽  
Author(s):  
Techale Birhan Mekonnen ◽  
Hongxu Dong ◽  
Mihrete Getinet ◽  
Aregash Gabizew ◽  
Andrew Paterson ◽  
...  

Abstract The genetic architectures of agronomic and yield-related traits are expected to involve multiple loci that are unlikely all to segregate for alternative alleles in a single bi-parental population. Therefore, the identification of quantitative trait loci (QTL) that are expressed in diverse genetic backgrounds of multiple bi-parental populations provides evidence about both background-specific and common genetic variants. The purpose of this study was to map QTLs for agronomic and yield related traits using three connected mapping populations of different genetic backgrounds, to gain insight into the genomic landscape of these important traits in elite Ethiopian sorghum germplasm. The three bi-parental populations, each with 207 F 2:3 lines were evaluated using an alpha lattice design with two replications under two moisture stress environments. Data analysis was done separately for each population using composite interval mapping, finding a total of 105 QTLs. All the QTLs identified from individual populations were projected on a combined consensus map, comprising a total of 25 meta QTLs for seven traits. The consensus map allowed us to deduce locations of a larger number of markers than possible in any individual map, providing a reference for genetic studies in different genetic backgrounds. The meta QTLs identified in this study could be used for marker-assisted breeding programs in sorghum after validation. Only one trait reduced leaf senescence, showed a striking bias of allele distribution, indicating substantial standing variation among the lines that might be employed in improving drought tolerance of sorghum.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Monika Buraczynska ◽  
Jerry Jacob ◽  
Karolina Gwiazda-Tyndel ◽  
Andrzej Ksiazek

Abstract Background The low-density lipoprotein receptor (LDLR) plays a significant role in maintaining the cellular cholesterol homeostasis. Mutations in the LDLR gene can lead to a significant rise in plasma LDL levels that may result in an increased risk of atherosclerosis and coronary heart disease. The purpose of this study was to assess the potential association of the LDLR rs688 polymorphism with cardiovascular disease (CVD) in patients with end-stage kidney disease (ESKD) undergoing hemodialysis. Methods In this case-control study the polymorphism was genotyped by the allele specific PCR method in 800 patients with ESKD and 500 healthy controls. The genotype and allele distribution was compared in subgroups of patients with CVD (552) versus those without CVD (248). Results A significant difference was observed in genotype distribution among ESKD patients and healthy controls. The frequencies of the T allele and TT genotype in ESKD group were significantly higher, with OR (95% CI) 2.2 (1.87–2.6), p <  0.0001 and 5.84 (3.94–8.65), p <  0.0001, respectively. In the he ESKD cohort the distribution of the rs688 was compared between CVD+ and CVD- subgroups. A strong association of the polymorphism with the CVD risk was observed in this analysis. The frequencies of the T allele and TT genotype were significantly higher in CVD+ subgroup, with OR (95% CI) 3.4 (2.71–4.26), p <  0.0001 and 13.2 (7.87–22.09), p <  0.0001, respectively. A multivariate logistic regression analysis was performed to estimate the association between rs688 T variant and risk of CVD. After adjustment for age, sex, BMI, hypertension and diabetes, both CT and TT genotypes were associated with an increased risk of developing CVD in the dominant, recessive and codominant models of inheritance. No significant differences in serum LDL cholesterol levels were found when compared between genotypes. Conclusions The present study is the first to demonstrate the association of the LDLR gene polymorphism with increased susceptibility to cardiovascular disease in ESKD patients. This finding needs further investigation to confirm that LDLR rs688 might be a novel genetic risk factor with some prognostic capacity for CVD in ESKD patients.


2021 ◽  
Author(s):  
Patryk Rodek ◽  
Małgorzata Kowalczyk ◽  
Jan Kowalski ◽  
Aleksander Owczarek ◽  
Piotr Choręza ◽  
...  

Abstract Background: In recent years, a growing body of evidence highlights a causal link between glutamate and depression. The membrane excitatory amino acid transporter 2 (EAAT2), encoded by SLC1A2 is responsible for the uptake and redistribution of most of the synaptic glutamate. Glycine, an inhibitory neurotransmitter, acts as an obligatory co-agonist of N-methyl-D-aspartate (NMDA) receptors and modulates excitatory neurotransmission. The clearance of synaptic glycine is performed by glycine transporters encoded by SLC6A9 and SLC6A5. Higher synaptic glycine and glutamate levels could enhance the activation of NMDA receptors, therefore counteract the hypofunction of glutamate neurotransmission described in major depressive disorder (MDD). The aim of the study was to assess whether polymorphisms of SCL1A2, SCL6A5 and SCL6A9 play a role in the development of MDD and its clinical picture in the Polish population. Methods: The study group consisted of 161 unrelated Caucasian patients with MDD, and 462 healthy controls. Polymorphisms of SLC1A2, SLC6A5 and SLC6A9 were genotyped with PCR-RLFP and TaqMan assays. The relationship between the studied single nucleotide polymorphisms (SNPs) was assessed based on the comparison of genotype and allele distribution in the study and the control group. The research also evaluated the relationships between the studied polymorphisms and clinical variables such as age of disease onset, number of episodes, duration of depression or severity of symptoms.Results: We found a statistically significant association between SLC1A2 rs4354668 polymorphism and MDD development (the frequency of rs4354668 CC genotype and allele C was 2-fold higher in patients than in the control). Such associations were not detected for SLC6A5 and SLC6A9 polymorphisms. No statistically significant impact of the studied SNPs on clinical variables of MDD was also observed. Conclusions: The results of the current study indicate an association of rs4354668 polymorphism in SCL1A2 with depression development in Polish population. Further studies with larger samples should be performed in the future to clarify the current findings.


2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Hongchao Cai ◽  
Yaning Feng ◽  
Peiwen Fan ◽  
Yuping Guo ◽  
Gulina Kuerban ◽  
...  

Abstract Background T cell epitopes are polypeptide fragments presented to T cell receptors by MHC molecules encoded by human leukocyte antigen (HLA) genes after antigen-presenting cell processing, which is the basis for the study of antigen immune mechanism and multi-epitope vaccine. This study investigated T cell response to HPV16 E6 and E7 in patients with cervical squamous cell carcinoma (CSCC). Also, the HLA-A allele distribution was compared among patients and evaluated as a factor to predict prognosis in these patients. Materials and methods This study recruited a total of 76 patients with International Federation of Gynaecology and Obstetrics (FIGO) stage IIB–IIIB CSCC. Mononuclear cells were isolated from the peripheral blood before any treatment and then enzyme-linked immunosorbent spot (ELISpot) assay was employed to measure the E6 and E7-specific T cell response. HLA‐A alleles were typed using Sanger sequencing‐based typing techniques with DNA extracted from the peripheral blood. The correlation between the T cell responses, HLA‐A allele distribution and patient prognosis were analysed using the Kaplan–Meier method, univariate and multivariate Cox proportional hazard models. Results The frequency of HPV E6-specific T cell responses in patients with pelvic lymph node metastasis was lower than that in patients without metastasis (P = 0.022). The 5-year overall survival (OS) rates of patients were 87.5% for those responding to multiple overlapping peptides, 72.7% for those responding to 1–2 overlapping peptides and 47.7% for non-responders (P = 0.032). Cox regression analysis indicated that the presence of HLA*A02:07 was independently associated with worse OS (hazard ratio [HR] 3.042; 95% confidence interval [CI] 1.348–6.862; P = 0.007), while concurrent chemoradiation therapy (CCRT) was independently associated with better OS (HR 0.475; 95% CI 0.232–0.975; P = 0.042). Conclusion The results of our study demonstrated that the level of HPV16 E6-specific T cell response and HLA*A02:07 were correlated with prognosis in patients with advanced CSCC.


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