Hardy-Weinberg Research Articles

Genetic and phenotypic frequency distribution of ACE, ADRB1, AGTR1, CYP2C9*3, CYP2D6*10, CYP3A5*3, NPPA and factors associated with hypertension in Chinese Han hypertensive patients.

We analyzed the polymorphisms of 7 antihypertensive drugs-related genes and the factors associated with hypertension in hypertensive patients of Han ethnicity in Qingyang, China. A total of 354 hypertensive patients of Han ethnicity were enrolled from Qingyang, China. The ACE (I/D), ADRB1 (1165G > C), AGTR1 (1166A > C), CYP2C9*3, CYP2D6*10, CYP3A5*3 and NPPA (T2238C) polymorphisms were assessed. Clinical data of patients was also obtained. The influencing factors of hypertension were evaluated. The genotype frequencies of ACE, ADRB1, AGTR1, CYP2C9, CYP3A5 and NPPA loci were in Hardy-Weinberg equilibrium, with mutation frequencies of 39.27%, 74.29%, 6.21%, 4.80%, 72.46% and 0.71%, respectively. CYP2D6 locus was not in Hardy-Weinberg equilibrium. There was no statistical difference in allele frequencies between different genders (P > .05). There was significant difference in the frequencies of ACE (I/D) and NPPA (T2238C) loci among different regions of China (P < .05). Gender, ACE (I/D) and ADRB1 (1165G > C) gene polymorphism, smoking, homocysteine and HDL levels were associated hypertension. The mutation frequencies of ADRB1 (1165G > C) and CYP3A5*3 were high in hypertensive patients of Han ethnicity in Qingyang, suggesting these patients may be more sensitive to beta-blockers and calcium ion antagonists. Meanwhile, hypertension was associated with gender, ACE (I/D) and ADRB1 (1165G > C) gene polymorphisms, smoking, homocysteine and HDL levels.

Patatin-like phospholipase domain-containing 3 gene (PNPLA3) polymorphic (rs738409) single nucleotide polymorphisms and susceptibility to nonalcoholic fatty liver disease: A meta-analysis of twenty studies.

To investigate the correlation between rs738409 polymorphism of patatin-like phospholipase domain-containing protein 3 (PNPLA3) gene (encoding I148m) and genetic susceptibility to nonalcoholic fatty liver disease (NAFLD). Web of Science, Embase, PubMed, Cochrane Library, China National Knowledge Infrastructure, Wanfang Data Knowledge Service Platform databases were subjected to study retrieving, from the earliest records to November 2022. International databases were searched using the key words (PNPLA3 gene or PNPLA3 polymorphism or patatin-like phospholipase domain-containing pro-tein3) and (nonalcoholic fatty liver disease or NAFLD or nonalcoholic steatohepatitis) and their possible combination. There was no limitation to language. Ethnicity and country restrictions were not applied. Hardy-Weinberg equilibrium about the genotype frequencies of rs738,409 polymorphism in group of controls was assessed using a chi-square goodness-of-fit test (P > .05). A chi-square-based Q test was applied to assess heterogeneity among studies. The random-effect model (DerSimonian-Laird method) was used when a probability value of P < .10, I2 > 50%. If not, the fixed-effect model (Mantel-Haenszel method) was adopted. The current meta-analysis was done by using STATA 16.0. Twenty studies are selected for this meta-analysis, which includes totally 3240 patients in the treatment group and 5210 patients in the control group. These studies demonstrated a significant increased association between rs738,409 and NAFLD under 5 models: allelic contrast (odds ratio [OR] = 1.98, 95% confidence interval [CI] = 1.65-2.37, Pheterogeneity = 0.000, Z = 7.346, P = .000), homozygote comparison (OR = 3.59, 95% CI = 2.56-5.04, Pheterogeneity = 0.000, Z = 7.416, P = .000), heterozygote comparison (OR = 1.93, 95% CI = 1.63-2.30, Pheterogeneity = 0.002, Z = 7.507, P = .000), the dominant allele model (OR = 2.33, 95% CI = 1.89-2.88, Pheterogeneity = 0.000, Z = 7.856, P = .000), and the recessive allele model (OR = 2.56, 95% CI = 1.96-3.35, Pheterogeneity = 0.000, Z = 6.850, P = .000). Subgroup analysis shows that the rs738,409 polymorphism of PNPLA3 gene in Caucasians and those with a sample size of < 300 is significantly associated with the susceptibility to nonalcoholic fatty liver. Sensitivity analysis shows that the results of meta-analysis are stable. PNPLA3 rs738,409 may play a significant role in increasing risk of NAFLD.

Characterization of 25 new microsatellite markers for the green turtle (Chelonia mydas) and cross-species amplification in other marine turtle species

The green sea turtle, Chelonia mydas, is a migratory species with a strong natal homing behavior leading to a complex population structure worldwide. The species has suffered severe declines in local populations; it is therefore crucial to understand its population dynamics and genetic structure to adopt appropriate management policies. Here, we describe the development of 25 new microsatellite markers specific to C. mydas and suitable for these analyses. They were tested on 107 specimens from French Polynesia. An average allelic diversity of 8 alleles per locus was reported and observed heterozygosity ranged from 0.187 to 0.860. Ten loci were significantly deviant from the Hardy-Weinberg equilibrium, and 16 loci showed a moderate to high level of linkage disequilibrium (4-22%). The overall Fis was positive (0.034, p-value < 0.001), and sibship analysis revealed 12 half- or full-sibling dyads, suggesting possible inbreeding in this population. Cross-amplification tests were performed on two other marine turtle species, Caretta caretta and Eretmochelys imbricata. All loci successfully amplified on these two species, though 1 to 5 loci were monomorphic. These new markers will not only be relevant for further analyses on the population structure of the green turtle and the two other species, but they will also be invaluable for parentage studies, for which a high number of polymorphic loci are necessary. This can provide important insight into male reproductive behavior and migration, an aspect of sea turtle biology that is of critical importance for the conservation of the species.

Association of the rs2111234, rs3135499, rs8057341 polymorphisms in the NOD2 gene with leprosy: A case-control study in the Norte de Santander, Colombia population.

Leprosy is a chronic infectious disease caused by Mycobacterium leprae. The development of leprosy involves several factors, including the causative agent, the individual host's immune response, environmental factors, and the genetic background of the host. Specifically, the host's innate immune response, encoded by genes, determines their susceptibility to developing leprosy post-infection. Polymorphic variants in the nucleotide-binding oligomerization domain 2 (NOD2) gene are associated with leprosy among populations in a variety of endemic areas around the world. Colombia, a country located in the tropical zone, has several leprosy-endemic regions, including Norte de Santander. The aim of this study was to analyze the rs7194886, rs2111234, rs3135499, and rs8057341 single nucleotide polymorphisms (SNPs) in the NOD2 gene using a case-control study to determine whether they confer greater or lesser susceptibility to the development of leprosy. The TaqMan qPCR amplification system was used for SNPs detection. An association between the A-rs8057341 SNP (p = 0,006286) and resistance to leprosy was found. However, the rs3135499 (p = 0,9063) and rs2111234 (p = 0.1492) were not found to be associated with leprosy susceptibility. In addition, the rs7194886 SNP was not found to be in Hardy-Weinberg equilibrium (HWE) in the study population. The GAG haplotype, consisting of SNPs rs2111234-G, rs3135499-A, and rs8057341G, acts as a susceptibility factor for the development of leprosy in women. SNPs rs3135499 and rs8057341 are functionally related to decreased NOD2 expression according to an in-silico analysis. The SNPs rs8057341-A was related with resistance to leprosy and the haplotype rs2111234-G, rs3135499-A and rs8057341-G SNPs was related with susceptibility in the Norte de Santander Colombia, studied population.

A genetic Study of the Ghanaian Population Using 15 Autosomal STR Loci.

Autosomal short tandem repeat (STR) population data collected from a well characterized population are needed to correctly assigning the weight of DNA profiles in the courtroom and widely used for ancestral analyses. In this study, allele frequencies for the 15 autosomal short tandem repeat (STR) loci included in the AmpFlSTR® Identifiler® plus kit (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, FGA) were obtained by genotyping 332 unrelated individuals of Ghanaian origin. Statistical tests on STR genotype data showed no significant departure from Hardy-Weinberg equilibrium (HWE). The overall match probability, combined power of exclusion and combined power of discrimination for these loci were 1 in 3.85 × 1017, 0.99999893 and 0.99999998, respectively. Polymorphic information content (PIC) greater than 0.70 was observed for all loci except TH01 and D13S317. These statistical parameters confirm that this combination of loci is valuable for forensic identification and parentage analysis. Our results were also compared with those for 20 other human populations analyzed for the same set of markers. We observed that the Ghanaian population grouped with other African populations in two-dimensional principal coordinate (PCO) and a neighbor-joining (N-J) data mapping and placed closest to Nigerians. This observation reflects cultural similarities and geographical factors, coupled with the long history of migration and trading activities between Ghana and Nigeria. Our report provides what we believe to be the first published autosomal STR data for the general Ghanaian population using 15 loci genotyped using the AmpFlSTR® Identifiler® plus kit methodology. Our data show that the loci tested have sufficient power to be used reliably for DNA profiling in forensic casework and help to elucidate the genetic history of people living in the country.

Genetic polymorphisms and population genetic analyses of 57 autosomal InDel loci in Hubei Tujia group.

Introduction: The Tujia is the eighth most populous population in China, but its genetic structure has not been fully studied. Methods: In this study, we utilized 57 autosomal Insertion/deletion (InDel) loci to evaluate the genetic polymorphisms and efficiency of forensic applications in the Chinese Hubei Tujia group, and analyzed the genetic structure variances among the studied group and other 26 different reference populations from five continents in 1000 Genomes Project (1KG). Results: The results showed that 57 InDels have no significant deviations from Hardy-Weinberg equilibrium and linkage equilibrium. The combined power of discrimination (CPD) and the combined probability of exclusion (CPE) values for 57 InDels were 0.99999999999999999999999699822 and 0.999975177214539 in the Hubei Tujia group, respectively. In addition, the results of genetic structure analyses indicated that the Hubei Tujia group has close genetic relationships with the Chinese Han population and other East Asian populations. Discussion: These 57 autosomal InDels can be used as reliable tools for forensic individual identification and paternity testing, and are more suitable for East Asian populations. Furthermore, three InDels (rs72085595, rs145941537, and rs34529639) are promising for inferring ancestral information.

Single nucleotide variants in microRNA biosynthesis genes in Mexican individuals.

Background: MicroRNAs (miRNAs) are important regulators in a variety of biological processes, and their dysregulation is associated with multiple human diseases. Single nucleotide variants (SNVs) in genes involved in the processing of microRNAs may alter miRNA regulation and could present high allele heterogeneity in populations from different ethnic groups. Thus, the aim of this study was to genotype 15 SNVs in eight genes involved in the miRNA processing pathway in Mexican individuals and compare their frequencies across 21 populations from five continental groups. Methods: Genomic DNA was obtained from 399 healthy Mexican individuals. SNVs in AGO2 (rs2293939 and rs4961280), DGCR8 (rs720012), DICER (rs3742330 and rs13078), DROSHA (rs10719 and rs6877842), GEMIN3 (rs197388 and rs197414), GEMIN4 (rs7813, rs2740349, and rs4968104), TNRC6B (rs9611280), and XP05 (rs11077 and rs34324334) were genotyped using TaqMan probes. The minor allele frequency of each SNV was compared to those reported in the 1,000 Genomes database using chi-squared. Sankey plot was created in the SankeyMATIC package to visualize the frequency range of each variant in the different countries analyzed. Results: In Mexican individuals, all 15 SNVs were found in Hardy-Weinberg equilibrium, with frequencies ranging from 0.04 to 0.45. The SNVs rs4961280, rs2740349, rs34324334, and rs720012 in Mexican individuals had the highest minor allele frequencies worldwide, whereas the minor allele frequencies of rs197388, rs10719, rs197414, and rs1107 were among the lowest in Mexican individuals. The variants had high allele heterogeneity among the sub-continental populations, ranging from monomorphic, as was the case for rs9611280 and rs34324334 in African groups, to >0.50, which was the case for variants rs11077 and rs10719 in most of the populations. Importantly, the variants rs197388, rs720012, and rs197414 had FST values > 0.18, indicating a directional selective process. Finally, the SNVs rs13078 and rs10719 significantly correlated with both latitude and longitude. Conclusion: These data indicate the presence of high allelic heterogeneity in the worldwide distribution of the frequency of SNVs located in components of the miRNA processing pathway, which could modify the genetic susceptibility associated with human diseases in populations with different ancestry.

Genotyping for Scianna blood group system polymorphism in Pakistan.

Objective: To establish the occurrence of Scianna blood group alleles via genotyping in Pakistani blood donors. Study Design: Cross-sectional Analytical study. Setting: Department of Hematology, Army Medical College (AMC) in association with the Armed Forces Institute of Transfusion (AFIT) Rawalpindi. Period: January 2019 and January 2020. Material &amp; Methods: In this study 300 blood donors were incorporated after taking informed consent; DNA was extracted from their EDTA anticoagulated blood samples and tested for SC*01 and SC*02 alleles by Sequence-Specific Primer Polymerase Chain Reaction (PCR-SSP), which was ensued by gel electrophoresis. The allele frequencies were established and Hardy Weinberg equilibrium was determined. Chi-square test was applied to compare the observed and expected genotype frequencies as well as for comparison with published allele frequencies of other populations. We used SPSS version 22 for the analysis of study data. Results: All donors were homozygous for SC*01, demonstrating allele frequency for SC*01 nearly 1.00. Genotype frequencies were congruent with the Hardy Weinberg equilibrium. The difference between the allele frequencies of SC*01 and SC*02 alleles of population of Pakistan was not statistically significant when compared to those of other populations. Conclusion: This maiden research illustrates Scianna blood group distribution in Pakistani community by PCR-SSP. This method is cheap and proficient and can be applied in developing nations. The findings of this study can aid in the production of local red cell panels, detection of uncommon blood types, and setting up of a domestic rare blood donor platform.

Rs11479 in Thymidine Phosphorylase Associated with Prognosis of Patients with Colorectal Cancer Who Received Capecitabine-Based Adjuvant Chemotherapy.

Thymidine Phosphorylase (TYMP) gene was of potential significance in the process of colorectal cancer (CRC) development and played an important role in capecitabine metabolism. This study was to identify the association between TYMP polymorphism and prognosis of postoperative patients with CRC who received capecitabine-based adjuvant chemotherapy. A total of 218 patients with CRC who were treated with surgical resection and capecitabine-based adjuvant chemotherapy were included in this study retrospectively. Peripheral blood and peripheral blood mononuclear cell (PBMC) specimen of the patients were collected for the genotyping of TYMP polymorphism and TYMP mRNA expression, respectively. Univariate analysis of genotypes and prognosis was carried out by Kaplan-Meier survival analysis, Cox regression analysis was adopted in multivariate analysis. The mRNA expression of TYMP according to genotype status was analyzed using non-parameter test. Prevalence of rs11479 in TYMP among the 218 patients exhibited that minor allele frequency of rs11479 was 0.20 (GG 141 cases, GA 68 cases and AA 9 cases), which was in accordance with Hardy-Weinberg equilibrium (P=0.825). Association analysis suggested that the median disease-free survival (DFS) of patients with GG genotype and GA/AA genotype was 3.1 and 6.1 years, respectively (P=0.004). Furthermore, the median overall survival of patients with GG genotype and GA/AA genotype was 5.0 and 7.0 years, respectively (P=0.033). Multivariate Cox regression analysis exhibited that rs11479 polymorphism was an independent factor for DFS (HR = 1.64, P=0.009). Additionally, of the 65 PBMC specimens, mRNA expression results indicated that patients with GA/AA genotypes conferred significantly higher mRNA expression of TYMP than that of patients with GG genotype (P<0.001). Polymorphism rs11479 in TYMP gene might predict the prognosis of patients with CRC who received capecitabine-based adjuvant chemotherapy through mediation of the mRNA expression of TYMP. The conclusion of this study should be validated in prospective clinical trials subsequently.

Longitudinal Associations Between TPO Gene Variants and Thyroid Peroxidase Antibody Seroconversion in a Population-Based Study: Tehran Thyroid Study

Introduction: Autoimmune thyroid diseases (AITD) are usually accompanied by anti-thyroid antibodies which can serve as early predictive markers. This study was designed to investigate the relationship between thyroid peroxidase (TPO) gene variants and the presence of TPOAb and to evaluate the effect of environmental factors associated with seroconversion from TPOAb-negative to TPOAb-positive. Methods: Participants from phases 1 and 2 of the Tehran Thyroid Study in (n = 5327, ≥20 years) were evaluated in terms of TPOAb positivity, and its relationship with 53 single nucleotide polymorphisms (SNPs) from within the TPO gene (cross-sectional approach). TPOAb-negative participants (n = 4815) were followed up for seroconversion for 5.5 years. The relationship between the TPO gene variants and the TPOAb seroconversion was evaluated (longitudinal approach). Results: There were 521 TPOAb-positive participants in the cross-sectional phase and 266 new TPOAb-positive cases observed during the follow-up period. After quality control (Hardy-Weinberg equilibrium (p < 1 × 10-5) and minor allele frequency < 0.05), 49 SNPs were qualified for association analyses. From this set fourteen SNPs were identified that were associated with TPOAb positivity. rs6605278, located in the 3'UTR TPO gene, was the most highly significantly associated of the variant and remained associated after adjustment for age, gender, body mass index (BMI), smoking, number of parity, and oral contraceptive consumption in both cross-sectional and longitudinal analyses (p < 0.05). Conclusions: TPOAb-positivity can be partially explained by variants in the TPO gene. New TPOAb-associated SNPs were observed in Iranians as an ethnically diverse population.

Single-nucleotide polymorphisms of matrix metalloproteinase genes are associated with graft fibrosis after kidney transplantation.

Further research needs to be conducted on the role of genetic variables in kidney transplantation fibrosis. In this study, we used next-generation sequencing (NGS) to examine the relationship between matrix metalloproteinase (MMP) genes and single-nucleotide polymorphisms (SNPs) in renal allograft fibrosis. This study comprised 200 patients, whose complete DNA samples were taken. The SNPs in MMP genes were identified using targeted NGS. Hardy-Weinberg equilibrium (HWE) and minor allele frequency (MAF) tests were conducted, followed by a linkage disequilibrium (LD) analysis. Finally, the SNPs and severity of kidney allograft fibrosis were evaluated using different inheritance models. In total, 41 MMP gene-related SNPs were identified using targeted sequencing, and 20 tagger SNPs were retained for further study. The general linear models (GLMs) revealed that sirolimus treatment had a substantial effect on kidney graft fibrosis. The multiple inheritance model analyses revealed that SNP rs9059 of the MMP9 gene was strongly associated with kidney graft fibrosis. The in-vitro experiments showed the MMP9 rs9509 mutation promotes the process of epithelial-mesenchymal transition (EMT) in the human kidney 2 (HK2) cells. The SNP rs9059 is associated with significant kidney allograft pathological changes by promoting EMT progression. Our findings provide insights into the etiology of renal allograft interstitial fibrosis and the MMP9 could be used as a potential treatment target in the future.

In silico analysis of single nucleotide polymorphism (rs34377097) of TBXA2R gene and pollen induced bronchial asthma susceptibility in West Bengal population, India.

Prevalence of asthma is increasing steadily among general population in developing countries over past two decades. One of the causative agents of broncho-constriction in asthma is thromboxane A2 receptor (TBXA2R). However few studies of TBXA2R polymorphism were performed so far. The present study aimed to assess potential association of TBXA2R rs34377097 polymorphism causing missense substitution of Arginine to Leucine (R60L) among 482 patients diagnosed with pollen-induced asthma and 122 control participants from West Bengal, India. Also we performed in-silico analysis of mutated TBXA2R protein (R60L) using homology modeling. Clinical parameters like Forced expiratory volume in 1 second (FEV1), FEV1/Forced vital capacity (FVC) and Peak expiratory flow rate (PEFR) were assessed using spirometry. Patients' sensitivity was measured by skin prick test (SPT) against 16 pollen allergens. Polymerase chain reaction-based Restriction fragment length polymorphism was done for genotyping. Structural model of wild type and homology model of polymorphic TBXA2R was generated using AlphaFold2 and MODELLER respectively. Electrostatic surface potential was calculated using APBS plugin in PyMol. Genotype frequencies differed significantly between the study groups (P=0.03). There was no significant deviation from Hardy-Weinberg equilibrium in control population (χ2=1.56). Asthmatic patients have significantly higher frequency of rs34377097TT genotype than control subjects (P=0.03). SPT of patients showed maximum sensitivity in A. indica (87.68%) followed by C. nusifera (83.29%) and C. pulcherima (74.94%). Significant difference existed for pollen sensitivity in adolescent and young adult (P=0.01) and between young and old adult (P=0.0003). Significant negative correlation was found between FEV1/FVC ratio and intensity of SPT reactions (P<0.0001). Significant association of FEV1, FEV1/FVC and PEFR was observed with pollen-induced asthma. Furthermore, risk allele T was found to be clinically correlated with lower FEV1/FVC ratio (P=0.015) in patients. Our data showed R60L polymorphism, which was conserved across mammals, significantly reduced positive electrostatic charge of polymorphic protein in cytoplasmic domain thus altered downstream pathway and induced asthma response. The present in-silico study is the first one to report association of TBXA2R rs34377097 polymorphism in an Indian population. It may be used as prognostic marker of clinical response to asthma in West Bengal and possible target of therapeutics in future.

Cholesterol 7α-Hydroxylase Gene-204A/C Polymorphism in Normal and Gestational Diabetic Pregnancies

To investigate the cholesterol 7α-hydroxylase gene ( CYP7A1)-204A/C single nucleotide polymorphism and its relationship with the blood lipid levels of pregnant women with gestational diabetes mellitus (GDM) and normal pregnant women. The genotype and allele frequencies of CYP7A1-204A/C gene polymorphism of 1037 normal pregnant women, the normal controls, and 627 pregnant women with GDM were examined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. Total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) and blood glucose (Glu) were measured by enzymatic assay. Chemiluminescence determination of plasma insulin (Ins) was conducted. Apolipoproteins A1 (apoA1) and B (apoB) were measured by the turbidimetric immunoassay. Allele frequencies of A and C at the CYP7A1-204A/C polymorphic locus were 0.586 and 0.414, respectively, in the GDM group and 0.557 and 0.443, respectively in the control group. The distribution of genotype frequencies in both groups showed conformity with the Hardy-Weinberg principle. There was no significant difference in allele and genotype frequencies between the GDM group and the control group. In the control group, carriers of the genotype AA were associated with significantly higher concentrations of apoA1 and lower levels of Ins and homeostatic model assessment of insulin resistance (HOMA-IR) compared with those with genotype CC (all P<0.05). In the non-obese subgroup of the control subjects, carriers of the genotype CC were associated with significantly higher plasma TG or apoA1 levels compared with those with genotype AA ( P<0.05). In the GDM group, carriers with genotype AA of CYP7A1-204A/C polymorphism had elevated levels of gestational weight gain (GWG) compared with those with genotype CC ( P<0.05). These results suggest that 204A/C polymorphism in the CYP7A1 gene is not associated with GDM, but may be closely associated with gestational weight gain in pregnant women with GDM. Variants in this locus are strongly associated with plasma apoA1, Ins, and HOMA-IR levels in the controls and elevated plasma TG levels in non-obese controls.

Novel SNPs of TNF-a and IL-6 that Regulate Serum Level in Obese Patients

Background Obesity is an abnormal amount of fats in the body that can result from several factors majorly including environmental and genetic fac- tors. The worldwide prevalence of obesity has increased tremendously in the last three decades and is now considered a global epidemic. Despite the negative impacts of obesity on human health and its majorly associated risk factors such as heart disease, diabetes, and certain types of cancers, no effective strategies have been employed to bring down its rate which can reach an alarming level in the next few years.Objective Previously, various studies have reported the high serum concentrations of two cytokines tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6) in obese patients. These genes (TNF-α and IL-6) are released from the adipose tissues stimulated by obesity. Considering their pivotal association with obesity, this study has been designed to investigate the relationship between SNPs of TNF-α and IL-6 and their high serum lev- els in obesity.Results Here, we utilized R language to perform statistical analyses such as correlation, normality testing, ROC, and regression analysis on serum levels of TNF-α and IL-6 between obese and control groups. Furthermore, the frequencies of clinical data and Hardy-Weinberg Equilibrium tests for allele and the genotypes analysis of the cytokines were performed. Conclusion The results of this study indicate that serum levels of TNF-α and IL-6 were significantly correlated with obesity SNPs.

Solute Carrier Family 45 Member 2 Germline Variants in the Colombian Population with Melanoma

Background: The solute carrier family 45-member 2 (SLC45A2) gene, located on chromosome 5p13.2, is involved in melanin biosynthesis. Single-nucleotide variants (SNVs) in this gene are associated with skin, eye, and hair color variations in the population. SNVs p.L374F (C/T) and p.E272K (C/G) are additionally associated with protection against melanoma. Objectives: This study aimed to evaluate the association of SNVs p.L374F and p.E272K with the development of melanoma in a sample of individuals from Bogotá, Colombia. Methods: In this case-control study, DNA samples were obtained from individuals after signing an informed consent form. Genotyping was performed by real-time polymerase chain reaction high-resolution melting (PCR-HRM). Results: Phototype II was found in 19% of the subjects, phototype III in 70%, and phototype IV in 11%. Eighty percent of the subjects had brown eyes and dark brown hair color. Both SNVs were in Hardy-Weinberg equilibrium. The p.Glu272Lys variant was found to be a protective factor for melanoma, while the p.Phe374Leu variant was found to be a risk factor. The study also found that a CG haplotype was a risk factor for melanoma [odds ratio (OR), 2.75; 95% CI, 1.22 - 6.22; P = 0.021]. The study also found a strong correlation between variants and phototypes, as well as the sex of the patients. The study also analyzed the impact of these variants on the protein structure and found that the p.Phe374Leu variant has a probable pathogenic effect on the function of the protein. Conclusions: The frequencies found for the SLC45A2 gene variants are consistent with other studies conducted in the Latin American population, where the predominant phototypes are II and III. The CG haplotype is associated with a higher risk of melanoma.

Low genetic diversity among introduced axis deer: comments on the genetic paradox and invasive species

Abstract Human-mediated introductions and subsequent establishment and spread of nonnative species have the potential to create a founder effect in such populations, which typically results in low genetic diversity and potential for inbreeding. However, several exotic invasive species exhibit a “genetic paradox” in which they thrive and adapt to novel environments while also avoiding complications from low genetic diversity. Axis deer (Axis axis) were introduced into Texas, Hawaii, South America, Australia, and Croatia during the 19th and 20th centuries and successfully established large populations from a few founding individuals. Mitochondrial (Cytochrome-b, Cytb; displacement loop, D-loop) and nuclear (10 microsatellites) markers were used to assess genetic diversity within and between axis deer populations in Texas and Hawaii and then compared to other introduced (Australia and Croatia) and native (India) populations. Overall, mtDNA divergence was 0.54% (Cytb) and 1.55% (D-loop) indicating high mitochondrial similarity within the species. Further, each invasive population was composed of only one or two mtDNA haplotypes. Microsatellite allele diversity also was low within and between populations in Texas and Hawaii resulting in monomorphic loci and Hardy–Weinberg equilibrium violations in both populations. The low genetic diversity in native Indian axis deer and within and between invasive populations suggests that the introduced populations experienced founder effects following introduction, and yet overcame this potential handicap by undergoing successful establishment and expansion. Axis deer appear to be another successful invasive species characterized by the genetic paradox where they exhibit genetic profiles that suggest inbreeding effects should be imminent, yet display no signs of inbreeding and are highly successful adapting to novel environments.

Determination of declined genetic diversity of Holstein stud bulls based on microsatellite markers

Semen importing countries are trying to select the most suitable studs according to their breeding goals, while the globally widespread use of common genetic material has been turning the loss of genetic diversity into a possible danger. The aim of this study was to evaluate the genetic diversity of 304 high-yielding Holstein stud bulls whose semen were produced in Turkiye, Europe and the Americas. The values of allele frequencies, expected heterozygosity (He), observed heterozygosity (Ho), Hardy-Weinberg (HW) Equilibrium, the number of alleles per locus (Na), allelic richness (Rs), polymorphic information content (PIC) and F-statistics were calculated and compared the results with similar studies. It was observed that some indicator values of the genetic diversity were decreased compared to the values of the other studies in Holstein breed. Especially the decrease in some values of SPS115 locus was statistically significant. It is thought that this could be as a result of SPS115 to be close to possible QTL regions associated with traits which indicates overall potential of selection in stud bulls. Therefore, while applying a selection program to populations, national genetic resource management strategies that maintain genetic diversity should not be forgotten besides gaining high yield.

Assessment of NLRP3 Gene Polymorphisms with Periodontitis as Compared with Healthy Periodontium in Iraqi Arabs Patients.

The nod-like receptor pyrin domain-containing protein 3 (NLRP3) inflammasome regulates the maturation and release of the cytokines as well as the activation of caspase in response to danger signals derived from pathogenic infection, tissue damage, andmetabolic changes that have a role in the pathogenesis of different diseases as periodontitis. Yet, the susceptibility to this illness could be determined by population-based genetic differences. The aim of this study was to determine whether periodontitis in Arab populations from Iraq is correlated with NLRP3 gene polymorphisms and measure clinical periodontal parameters and investigate their association with genetic polymorphisms of the NLRP3. The study sample consisted of 94 participants ranging from 30 to 55 years old, both males and females who fulfilled the study's criteria. The selected participants were divided into two groups: the periodontitis group (62 subjects) and the healthy control group (32 subjects). The examination of clinical periodontal parameters of all participants was carried out, followed by a collection of venous blood for NLRP3 genetic analysis using the polymerase chain reaction-sequencing technique. The genetic analysis of NLRP3 genotypes at four single nucleotide polymorphisms (SNPs) (rs10925024, rs4612666, rs34777555, and rs10754557), by Hardy-Weinberg equilibrium, identified nonsignificant differences in studied groups. The C-T genotype among periodontitis was significantly different from controls, while the C-C genotype among control was significantly different from periodontitis at NLRP3 rs10925024. Overall, there were 35 SNPs in the periodontitis group and 10 SNPs in the control group for rs10925024 with significant differences versus nonsignificant differences of the other SNPs between the studied groups. Clinical attachment loss and NLRP3 rs10925024 additionally demonstrated a significant positive correlation in the periodontitis subjects. The findings suggested that polymorphisms of the NLRP3 gene may have a role and increasing the genetic susceptibility to periodontal disease in Arabs Iraqi patients.

VARIATIONS AND EXPRESSION OF VERY LOW-DENSITY LIPOPROTEIN RECEPTOR (VLDLR) mRNA IN THE LIVER AND OVARY OF A LOW EGG PRODUCTION STRAIN OF LOCAL IRAQI HENS

This work was conducted to study the association of variations in the VLDLR gene and mRNA expression in the liver and the ovary of local Iraqi hens with some productive and blood traits. The VLDLR gene variations were studied using blood samples of 173 pedigreed hens, 47 weeks old while the expression was studied using tissue samples of the ovary and liver in 30 pedigreed hens, 60 weeks old. Genotypic and allelic frequencies, production traits, and biochemical serum blood were investigated. The results showed that the genotypic and allelic frequencies of the VLDLR in 173 chickens did not agree with Hardy-Weinberg equilibrium (P&lt;0.0307). The genotypic frequencies were 94.7 and 5.3% for both GG and GT genotypes respectively, while the allele frequency of genes G and T were 97.4 and 2.6%, respectively. The results showed an increase (P&lt;0.0001) in egg production and egg weight for the groups of birds that follow the GG genotypes compared to those that follow the genotypes GT. High levels of VLDLR mRNA were present in the liver and the ovary of high-egg-yield layers but were absent or rare in hens with low-egg production rates. The high expression of VLDLR mRNA caused a reduction in serum triglyceride; LDL and VLDL compared with a low expression where showed increases in these traits while other traits were not affected between different levels of expression. This study suggests that the expression level of VLDLR may be a new molecular marker to screen for high egg production in low-egg production local chickens.

Prevalence of Genetic Diamine Oxidase (DAO) Deficiency in Female Patients with Fibromyalgia in Spain

Diamine oxidase (DAO) is an enzyme that metabolizes intestinal histamine. Single nucleotide polymorphisms (SNPs) of the Amine Oxidase Copper Containing 1 (AOC1) gene can lead to low enzymatic activity or functionality in histamine metabolism. This study aimed to determine the prevalence of DAO deficiency for four variants of the AOC1 gene, p.Thr16Met (rs10156191), p.Ser332Phe (rs1049742), p.His664Asp (rs1049793), and c.691G > T (rs2052129), in 98 Spanish women with fibromyalgia between the ages of 33 and 60 years, and compare the distribution of allelic and genotypic frequencies with those of European population samples in Hardy-Weinberg equilibrium extracted from the Allele Frequency Aggregator (ALFA) database. The patients' DNA was extracted, and analyzed using SNPE Multiplex (Single Nucleotide Primer Extension). The prevalence of genetic DAO deficiency was 74.5% based on the four variants of the AOC1 gene. SNP deficits were found at frequencies of 53.1% for p.Thr16Met, 49% for c.691G > T, 48% for p.His664Asp, and 19.4% for p.Ser332Phe. The allele and genotypic frequencies of the women with fibromyalgia did not differ from the European population. Variants of the AOC1 gene that are associated with genetic DAO deficiency could serve as a disruptive biomarker in patients with fibromyalgia. This study was registered in ClinicalTrials.gov Identifier: NCT05389761.