Hardy-Weinberg Research Articles

A (GCC) repeat in SBF1 reveals a novel biological phenomenon in human and links to late onset neurocognitive disorder

The human SBF1 (SET binding factor 1) gene, alternatively known as MTMR5, is predominantly expressed in the brain, and its epigenetic dysregulation is linked to late-onset neurocognitive disorders (NCDs), such as Alzheimer’s disease. This gene contains a (GCC)-repeat at the interval between + 1 and + 60 of the transcription start site (SBF1-202 ENST00000380817.8). We sequenced the SBF1 (GCC)-repeat in a sample of 542 Iranian individuals, consisting of late-onset NCDs (N = 260) and controls (N = 282). While multiple alleles were detected at this locus, the 8 and 9 repeats were predominantly abundant, forming > 95% of the allele pool across the two groups. Among a number of anomalies, the allele distribution was significantly different in the NCD group versus controls (Fisher’s exact p = 0.006), primarily as a result of enrichment of the 8-repeat in the former. The genotype distribution departed from the Hardy–Weinberg principle in both groups (p < 0.001), and was significantly different between the two groups (Fisher’s exact p = 0.001). We detected significantly low frequency of the 8/9 genotype in both groups, higher frequency of this genotype in the NCD group, and reverse order of 8/8 versus 9/9 genotypes in the NCD group versus controls. Biased heterozygous/heterozygous ratios were also detected for the 6/8 versus 6/9 genotypes (in favor of 6/8) across the human samples studied (Fisher’s exact p = 0.0001). Bioinformatics studies revealed that the number of (GCC)-repeats may change the RNA secondary structure and interaction sites at least across human exon 1. This STR was specifically expanded beyond 2-repeats in primates. In conclusion, we report indication of a novel biological phenomenon, in which there is selection against certain heterozygous genotypes at a STR locus in human. We also report different allele and genotype distribution at this STR locus in late-onset NCD versus controls. In view of the location of this STR in the 5′ untranslated region, RNA/RNA or RNA/DNA heterodimer formation of the involved genotypes and alternative RNA processing and/or translation should be considered.

Variability in prion protein genotypes by spatial unit to inform susceptibility to chronic wasting disease

ABSTRACT Chronic wasting disease (CWD) is a fatal encephalopathy affecting North American cervids. Certain alleles in a host’s prion protein gene are responsible for reduced susceptibility to CWD. We assessed for the first time variability in the prion protein gene of elk (Cervus canadensis) present in Pennsylvania, United States of America, a reintroduced population for which CWD cases have never been reported. We sequenced the prion protein gene (PRNP) of 565 elk samples collected over 7 years (2014–2020) and found two polymorphic sites (codon 21 and codon 132). The allele associated with reduced susceptibility to CWD is present in the population, and there was no evidence of deviations from Hardy-Weinberg equilibrium in any of our sampling years (p-values between 0.14 and 1), consistent with the lack of selective pressure on the PRNP. The less susceptible genotypes were found in a frequency similar to the ones reported for elk populations in the states of Wyoming and South Dakota before CWD was detected. We calculated the proportion of less susceptible genotypes in each hunt zone in Pennsylvania as a proxy for their vulnerability to the establishment of CWD, and interpolated these results to obtain a surface representing expected proportion of the less susceptible genotypes across the area. Based on this analysis, hunt zones located in the southern part of our study area have a low proportion of less susceptible genotypes, which is discouraging for elk persistence in Pennsylvania given that these hunt zones are adjacent to the deer Disease Management Area 3, where CWD has been present since 2014.

MCPggaac haplotype is associated with poor graft survival in kidney transplant recipients with de novo thrombotic microangiopathy.

De novo thrombotic microangiopathy (TMA) is associated with poor kidney graft survival, and as we previously described, it is a recipient driven process with suspected genetic background. Direct Sanger sequencing was performed in 90 KTR with de novo TMA and 90 corresponding donors on selected regions in CFH, CD46, C3, and CFB genes that involve variations with a functional effect or confer a risk for aHUS. Additionally, 37 recipients of paired kidneys who did not develop TMA were analyzed for the MCPggaac haplotype. Three-years death-censored graft survival was assessed using Kaplan-Meier and Cox regression models. The distribution of haplotypes in all groups was in the Hardy-Weinberg equilibrium and there was no clustering of haplotypes in any group. In the TMA group, we found that MCPggaac haplotype carriers were at a significantly higher risk of graft loss compared to individuals with the wild-type genotype. Worse 3-year death-censored graft survival was associated with longer cold ischemia time (HR 1.20, 95% CI 1.06, 1.36) and recipients’ MCPggaac haplotype (HR 3.83, 95% CI 1.42, 10.4) in the multivariable Cox regression model. There was no association between donor haplotypes and kidney graft survival. Similarly, there was no effect of the MCPggaac haplotype on 3-year graft survival in recipients of paired kidneys without de novo TMA. Kidney transplant recipients carrying the MCPggaac haplotype with de novo TMA are at an increased risk of premature graft loss. These patients might benefit from therapeutic strategies based on complement inhibition.

Frequency of occurrence of the PPAR family gene polymorphisms and their relationship with lipid levels in healthy young individuals

Objective . To determine the frequency of occurrence of the genotypes of the PPARG (Pro12Ala), PPARD (294T/C), and PPARA (G2528C) gene polymorphic variants, and to establish their relationship with blood lipid levels in healthy young individuals. Materials and methods . The study included healthy young individuals (n=90) aged 20.1 ± 0.6 years. The parameters of the lipidogram were evaluated: total cholesterol (TC), low-density lipoprotein cholesterol (LDL cholesterol), highdensity lipoprotein cholesterol (HDL cholesterol), triglycerides (TGs), atherogenicity coefficient (CA). The polymorphic variants of the PPAR genes were determined. The results of the study were processed using the STATISTICA 10.0 application package. Results . The genotype distribution of the Pro12Ala polymorphic variant of the PPARG gene (χ 2 =0.0079; p=0.73), 294T/C of the PPARD gene (χ 2 =0.26; p=0.65), and G2528C of the PPARA gene (χ 2 =4.72; p=0.8) in the healthy young individuals corresponded to the expected Hardy-Weinberg equilibrium. No significant differences between the lipid levels in carriers of different variants of the polymorphic PPARG gene (Pro12A1a) were obtained. Conclusion . Individuals with the C/C polymorphic variant had significantly higher TG levels, lower HDL cholesterol levels in the blood, and the highest CA compared with carriers of the T/T and T/C variants of the PPARD (294T/C) polymorphic gene. Carriers of the C/C polymorphic variant had significantly (p=0.049) higher LDL-C levels than carriers of the G/C variant of the PPARA (G2528C) polymorphic gene. The risk of hypertriglyceridemia is 9.6 times, of low HDL-C is 6.9 times, and of having an elevated CA rate is 5.2 times as high in individuals with the C/C polymorphic variant as in individuals with the T variants /T and T/C of the PPARD gene (294T/C).

Association of cluster determinant 36, scavenger receptor class B type 1, and major facilitator superfamily domain containing the 2a genetic polymorphism with serum lipid profile in aging population with type 2 diabetes mellitus.

BackgroundLipid metabolism disorder commonly happens in subjects with Type 2 diabetes mellitus (T2DM) which may be linked to genetic variants of lipid metabolism-related genes. However, few studies have explored the relationship between lipid metabolism-related gene polymorphism and serum lipid profile in aging subjects with T2DM. The present study was designed to explore the impact of genetic polymorphism of cluster determinant 36 (CD36) (rs1049673, rs1054516, rs2151916), scavenger receptor class B type 1 (SCARB1) (rs5888), and major facilitator superfamily domain containing the 2a (MFSD2A) (rs12083239, rs4233508, rs12072037) on the relationship between circulating lipids in aging subjects with T2DM.Methods205 T2DM patients and 205 age and gender matched control subjects were recruited. Information on demographic characteristics was collected by using a self-administered questionnaire. Fasting venous blood samples were taken for lipid-related gene genotyping and serum lipid profile measurement. The Chi-square test was used to compare percentage differences and to calculate P-value for Hardy-Weinberg equilibrium. Logistic regression and multiple linear regression were used to explore the risk or correlation between variables, and general linear model (GLM) was used to compare the means of serum lipids between the groups.ResultsIn T2DM group, CD36 rs1054516 and MFSD2A rs12072037 were correlated with serum TC level. In control group, CD36 rs1049673 was correlated with serum HDL-C level. Meanwhile, T2DM subjects with MFSD2A rs12083239 (CG), MFSD2A rs4233508 (TT), and MFSD2A rs12072037 (AA) had higher TG level than control subjects. T2DM subjects with CD36 rs1049673 (CG, GG), CD36 rs1054516 (CT), CD36 rs2151916 (TT, CT), SCARB1 rs5888 (GG), MFSD2A rs12083239 (GG, CG), MFSD2A rs4233508 (TT), and MFSD2A rs12072037 (CA, AA) had lower HDL-C level than control subjects. T2DM subjects with MFSD2A rs12072037 (AA) had lower LDL-C level than control subjects. In dominant model, major genotype (GG) of SCARB1 gene was associated with the risk of T2DM (OR = 0.636, P = 0.032).ConclusionThe genetic polymorphism of CD36 (rs1049673, rs1054516, rs2151916), SCARB1 (rs5888), and MFSD2A (rs12083239, rs4233508, rs12072037) were associated with serum lipids in T2DM subjects. The SCARB1 rs5888 major genotype (GG) was a protective factor for T2DM. Large scale cohort study is required to determine the relationship between lipid metabolism-related gene polymorphism, serum lipid profile and T2DM in aging subjects.

Identification of Gene Diversity of Melanocortin-4 Receptor and its Relationship with the Birth and Body Size of Beef Cattle

Melanocortin-4 Receptor (MC4R) expressed in hypothalamus which is part of the brain that are involved in regulation of appetite, metabolism and bodyweight. This study aimed to identify the MC4R gene diversity in the second cross generation of Belgian Blue, Wagyu, and Brahman crossbred and its relationship with the body weight and size birth. Polymerase Chain Reaction (PCR) and DNA sequencing were used to identify Single Nucleotide Polymorphism (SNP). The result of this study showed that MC4R genes was polymorphic with one SNP at 1133 C&gt;G and included missense mutation. SNP 1133 C&gt;G has two of allels C and G with three genotypes. Test of Hardy Weinberg equilibrium showed that the population of cattle was in equilibrium. The heterozigosity values showed that the population of cattle had a low diversity of genetics. The result of association showed that SNP 1133 C&gt;G in MC4R Genes was not able to indicate the difference between the weight, body length, heart girth and wither’s height at birth. Based on this study, it can be concluded that the polymorphism of MC4R genes can only be used to distinguish cattle genotypes but cannot be used as the selection tools for body weight and size birth.&#x0D; Keywords: Crossbreed beef cattle, Diversity, Heterozigosity, MC4R gene, SNP.

Whey Protein Genetic Polymorphism and Dairy Traits in Goats of South India

Background: The present study investigated the polymorphism in β-lactoglobulin and α-lactalbumin genes in native Malabari and Attappady black breeds in comparison with Saanen Malabari crossbred goats. The polymorphisms in these proteins and their coding genes were reported to be associated with various dairy traits in ruminants. Methods: Polymorphism detection was carried out by polymerase chain reaction based restriction fragment length polymorphism method. Chi-square analysis was performed to analyse the status of each population. Association of β-lactoglobulin with dairy traits was performed with univariate analysis of variation. Sanger’s sequencing of 426 bp fragment of caprine β-LG gene was performed commercially and sequences were compared with those of other breeds of various geographical areas. Result: It was proved that all three populations under study observed Hardy-Weinberg equilibrium with respect to b-lactoglobulin locus. Statistical analysis revealed significant relationship of β-lactoglobulin with peak milk yield in Malabari population studied. Sequence analysis of exon 7 and 3' flanking region revealed a novel SNP at (C to A transversion) at 7062 position in the native breeds under study. Phylogenetic tree construction and analysis revealed the native Malabari and Attappady black to different clades. The caprine α-LA gene appeared to be monomorphic in all the three population under study. Genetic selection utilizing the association of β-lactoglobulin with peak yield could be used to improve the genetic makeup of goats for high production potential.

Association analysis of seven single nucleotide polymorphisms identified by genome-wide association study with age-related macular degeneration among ethnic Han Chinese population

To assess the association of 7 single nucleotide polymorphisms (SNPs) including rs13278062 (TNFRSF10A), rs3750846 (ARMS2-HTRA1), rs429358 (APOE), rs5817082 (CEPT), rs2043085 (LIPC), rs1626340 (TGFBR1), and rs8135665 (SLC16A8) identified through genome-wide association study (GWAS) with age-related macular degeneration (AMD) among ethnic Han Chinese from Sichuan, China. A cohort of 576 AMD patients and 572 healthy controls were enrolled in a case-control study. The SNPs were genotyped by a Mass array MALDI-TOF System. On the premise that the genotype distribution of each SNP locus in both groups satisfied Hardy-Weinberg equilibrium, the genetic pattern was analyzed and the scores of allele and genotype frequencies ware compared. There was a significant association between TNFRSF10A rs13278062 and AMD under the heterozygous model (P = 0.000, OR = 1.529, 95%CI = 1.196-1.954) and the dominant model (P = 0.002, OR = 1.459, 95%CI = 1.154-1.865), suggesting that subjects carrying rs13278062GT and rs13278062TT + GT are more likely to develop the AMD, whereas no significant difference was observed for rs13278062 under other models. No association was detected with the other six SNPs and AMD under various genetic models. This case-control association study has indicated that TNFRSF10A rs13278062 is associated with AMD under the heterozygous and dominant models, suggesting that the TNFRSF10A variant may be involved in the development of AMD among ethnic Han Chinese population.

Candidate K232A mutation of DGAT1 gene associated with production and reproduction traits in Indian Dairy cattle

The present study was conducted on Hardhenu and Sahiwal cows to evaluate the genetic diversity and the effect of candidate K232A mutation of diacylglycerol O-acyltransferase (DGAT1) gene on performance traits. PCR product of 413 bp size targeting K232A mutation of DGAT 1 gene was genotyped by Eae1 restriction enzyme and further confirmed by sequencing. The PCR-RFLP analysis for K232A showed that the frequencies of alleles K and A were 0.80 and 0.20 in Hardhenu and 0.98 and 0.02 in Sahiwal cattle, respectively. The frequencies of genotypes for KK and KA genotype were estimated as 0.60 and 0.40 in Hardhenu and 0.96 and 0.04 in Sahiwal cattle, respectively. Chi-square test showed that K232A SNP did not meet with the Hardy–Weinberg equilibrium (p < .01) in Hardhenu cattle. Association analysis revealed that KA genotype was significantly associated with total milk yield (p < .01) and 305 days milk yield (p < .01)in Hardhenu cattle. Hardhenu cows having KA genotype comparatively revealed favorable mean values for AFS (880.31 ± 26.65), AFC (1166.36 ± 19.94), SP (157.46 ± 22.80), CI (441.41 ± 44.28) and AI/Conception (1.80 ± 0.17), indicating that KA genotype can be used as a candidate marker for simultaneous improvement of both production and reproduction traits.

The rs12532734 Polymorphism Near the Solute Carrier 26A3 Gene Locus Is Associated With Gallstone Disease in Children.

Gallstones are increasingly frequent in children. In this candidate gene study, we genotyped 5 gene variants ( ANO1 , SPTLC3 , TMEM147 , TNRC6B , rs12532734) from a recent gallstone genome-wide association study (GWAS) in a cohort of 214 children with gallstones and 172 gallstone-free adult controls. In total, 138 genotyped children presented with symptomatic gallstone disease, 47 underwent cholecystectomy, and 126 received ursodeoxycholic acid (UDCA) as therapy for stones. Among 5 tested variants, the rs12532734 polymorphism modulated the gallstone risk in the studied cohort. Its genotype distribution significantly ( P = 0.025) departed from the Hardy-Weinberg equilibrium among cases, and the common allele was associated with increased odds of developing gallstones at young age (OR = 1.69, P = 0.014). SLC26A3 is the nearest gene to rs12532734 and is involved in the transepithelial bicarbonate and chloride transport. The association of rs12532734 with pediatric gallstones is a novel finding warranting further investigations also with regard to biliary bicarbonate flux and bile composition.

Abstract 28 Comparative Analysis of the Cord Blood Bank in Quebec

IntroductionIn the context of the regional diversity observed in the population of Quebec, the Héma-Québec Cord Blood Bank (HQ CBB) representation differs from that of the Héma-Québec Stem Cell Registry (HQ Registry). The Bank encourages registrants of non-European descent to promote diversity, and only collects from health centers around Montreal and Quebec cities because of proximity concerns.ObjectiveIn this study, we aimed to analyze allele frequencies in the HQ CBB to assess similarities and differences in reference to the HQ Registry.MethodsThe HQ Registry was previously typed using high-resolution genotyping. For the HQ CBB, ambiguous two-field HLA-A, -B, -C, and -DRB1 typing data were obtained from cord blood units. Statistical analyses were performed using the GENE[RATE] population analysis tools to estimate allele and haplotype frequencies by administrative region determined by registered postal codes. Hardy-Weinberg equilibrium was verified by the nested likelihood procedure. Finally, genetic distance was compared between the HQ Registry and the HQ CBB by region using Non-metric Multi-dimensional Scaling (NMDS).ResultsBecause of the small sample size in certain regions, HLA frequency was analyzed for 7 of the 17 regions within the HQ CBB with typings from 11,472 cord blood units. The HLA allele frequencies were previously assessed for the Registry, with 3,806 donors originating from 14 administrative regions. The Hardy-Weinberg equilibrium was rejected at least in relation to one locus in 3 regions (Capitale-Nationale, Montreal, and Laval), which differs from the results obtained from the Registry, in which the equilibrium was rejected only for Montreal. As in the Registry, allele frequencies in the HQ CBB varied by region but had limited overlap with the HQ Registry. Two regions (Chaudière-Appalaches and Laval) demonstrated significant differences in allele frequencies as represented in the HQ Registry versus the HQ CBB.DiscussionWe observed differences in the Quebec population representation between the HQ CBB and the HQ Registry. This probably represents selection bias related to recruitment strategies and inclusion criteria. Importantly, the complementarity of these two stem cell sources could allow for a more diverse donor pool, and this understanding could also guide the recruitment strategies.

Association of gallstone and polymorphisms of UGT1A1*27 and UGT1A1*28 in patients with hepatitis B virus-related liver failure.

Genetic variation in UDP-glucuronosyltransferase 1A1 gene (UGT1A1) is a lithogenic risk factor for gallstone formation. This study aimed to assess genotype and allele frequencies of common UGT1A1 variants in patients with gallstone and hepatitis B virus (HBV)-related hepatic failure. This study enrolled 113 healthy individuals (CTRL), 54 patients with HBV infection (HBV), 134 patients with gallstone-free hepatic failure and HBV infection, and 34 patients with gallstone-related hepatic failure and HBV infection (GRHF). Peripheral venous blood samples were collected for genomic DNA isolation. Polymerase chain reaction amplification was carried out for UGT1A1, followed by direct sequencing. Analysis for genotype and allele frequencies of UGT1A1 variants (UGT1A1*6, UGT1A1*27, UGT1A1*28, and UGT1A1*60) was performed. The allele distributions of the four groups did not deviate from Hardy–Weinberg equilibrium. Allele (A) and genotype (CA) frequency distributions of UGT1A1*27 were significantly different between GRHF and CTRL, or between GRHF and HBV. GRHF and CTRL exhibited significant differences in allele (A) and genotype (CA) frequency distributions of UGT1A1*28. Linkage disequilibrium analysis suggested that haplotype G-G-[TA]7-T may be associated with gallstone in HBV-related hepatic failure. Our data reveal that UGT1A1*27 and UGT1A1*28 variants are significantly observed in patients with GRHF compared to healthy individuals.

Efficacy and safety of warfarin therapy in patients with atrial fibrillation using genotype-guided dosing method

The aim. To evaluate the efficacy and safety of warfarin (WF) therapy in patients with atrial fibrillation (AF) using pharmacogenetic dosing method at an anticoagulant monitoring office according to the results of a one-year prospective follow-up. Materials and methods. The study involved 110 patients with AF (mean age 68.72 ± 0.79; men – 57, women – 53). By the method of stratified randomization, the patients with AF were divided into two groups: the main group – 50 patients with AF and genotype-guided dosing method, the control group – 60 patients with AF and clinical dosing method. The outcomes were examined after the one-year follow-up: excessive hypocoagulation episodes (INR &gt; 4) and bleeding. CYP2C9, CYP4F2, VKORC1 gene polymorphisms were determined using multiplex real time polymerase chain reaction; INR was controlled monthly; CHA2DS2-VASC, HAS-BLED, SAMe-TT2R2 scale scores were evaluated; TTR was calculated using the Rosendaal method. Results. The distribution of CYP2C9, CYP4F2, VKORC1 genotypes in the main and control groups were in accordance with the Hardy–Weinberg equilibrium. In patients with AF and genotype-guided dosing, the frequency and risk of excessive hypocoagulation episodes (χ2 = 5.11; P &lt; 0.05; RR = 0.50 (CI 0.27; 0.94)) and bleeding (χ2 = 9.57; P &lt; 0.05; RR = 0.41 (CI 0.22; 0.77)) were significantly lower. However, the groups did not differ in TTR. The validity of genetic-guided dosing was confirmed by the comparability of the medians and the direct correlation between the calculated and therapeutic WF doses (r = +0.57; P &lt; 0.05). There were no relationships between TTR, excessive hypocoagulation episodes, hemorrhagic complications and clinical and genetic factors in the main group. Conclusions. In patients with AF, the use of genotype-guided dosing method in the anticoagulant monitoring office helped to reduce the frequency and risk of excessive hypocoagulation episodes and bleeding as well as eliminate the influence of endogenous and exogenous factors in the personalized management of patients.

Genetic variations of tumor necrosis factor-α and prostaglandin-endoperoxide synthase 2 genes among Egyptian patients with type 2 diabetes mellitus and diabetic nephropathy

ObjectivesThe current study aimed to determine whether genetic differences in the tumor necrosis factor-α (TNF-α) and prostaglandin-endoperoxide synthase 2 (PTG2) genes are linked to type 2 diabetes mellitus (T2DM) and diabetic nephropathy (DN). BackgroundDN is a major cause of chronic kidney disease (CKD). Unfortunately, the precise pathogenic mechanisms of DN are not completely understood. Recent data suggest a link between inflammatory cytokines and the chronic complications of T2DM. TNF-α and PTG2 are key mediators of inflammation. Subjects and methodsThis is a case-control study that includes 100 patients (group 1: 50 diabetic patients with diabetic nephropathy and group 2: 50 patients without diabetic nephropathy) and 50 age- and sex-matched healthy controls (group 3). Genotyping of TNF-α (rs3651525) and PTGS2 (rs689466) by real-time PCR was applied. ResultsTNF-α (rs3651525) and PTGS2 (rs689466) genotype frequency and allelic distribution are in Hardy-Weinberg equilibrium (HWE). When T2DM patients with nephropathy were compared to those without DN, regression analysis for the PTGS2 rs689466 and TNF-rs361525 single nucleotide polymorphisms (SNPs) demonstrated that none of the SNP genotypes showed a major risk factor for DN susceptibility. As regards TNF-α rs361525, GA and AA genotypes were significantly associated with a higher risk of T2DM when compared to GG, and A allele showed a 3.721-fold increased risk.TNF-α rs361525 AA genotype (OR, 10.980; 95% CI 1.385–87.066) and TNF-rs361525 GA genotype (OR, 3.050; 95% CI 1.315–7.0758) are the most substantially linked parameters with the risk of diabetes mellitus in univariate analysis.According to the multivariate analysis, the AA and GA genotypes of the SNP rs361525 significantly affect the development of diabetes mellitus. No remarkable association was found between the PTGS2 (rs689466) polymorphism and diabetes mellitus and diabetic nephropathy. ConclusionIn contrast to the lack of a significant correlation between PTGS2 (rs689466) and DM or DN, TNF-α rs361525 was connected to the possibility of developing diabetes mellitus in our study.

Genome-wide characterization of three IGFs in hybrid yellow catfish (Pseudobagrus fulvidraco ♀× Pseudobagrus vachellii ♂) and the association of IGF2 allelic variants with growth traits

“Huangyou No. 1”, a new hybrid yellow catfish (Pseudobagrus fulvidraco ♀× Pseudobagrus vachellii ♂) with heterosis in growth traits, is an economically important freshwater fish in China. Among genes related to growth traits, Insulin-like growth factors (IGFs) are recognized as key factors during embryonic development and growth period. Thus, we identified and characterized IGF1, IGF2 and IGF3 gene from hybrid yellow catfish. Phylogenetic analysis showed that the IGF genes were evolutionarily-constrained and their function was conserved. Transcriptional studies indicated that three IGF mRNA expression were most abundant in liver, despite the ubiquitous expression in nine tested tissues. Further, two opposite temporal expression patterns were observed in these three IGF genes during 16 embryogenesis and larval development stages of hybrid yellow catfish, of which IGF2 and IGF3 shared the similar profile highly expressed after gastrula. Finally, single nucleotide polymorphisms (SNPs) of IGF2 were screened and genotyped in 264 hybrid yellow catfish by Sanger sequencing. Only a non-synonymous mutation (SNP 97 T > C) obeyed Hardy-Weinberg equilibrium. Association analysis indicated SNP 97 T > C significantly associated with nine growth traits (body length, full length, head length, body height, caudal peduncle height, caudal peduncle length, body width, body weight and fatness; P < 0.05). This association was also validated in a second population with 183 individuals. Overall, results from our studies highlight the importance of IGF system in mediating growth development of hybrid yellow catfish, and provide a potential marker for “Huangyou No. 1” breeding.

Correlation between platelet-derived growth factor-B gene polymorphism and coronary heart disease.

ObjectThe aim of the present work was to investigate the correlation of plasma platelet‐derived growth factor (PDGF)‐BB level and single nucleotide polymorphism (SNP, rs1800817 and rs2285094) of PDGF‐B gene with the onset and stability condition of coronary heart disease (CHD).MethodsTotally, 335 subjects were included in and divided into CHD (n = 247) and control group (n = 88) according to coronary angiography. Besides, the patients in the CHD group were divided into acute coronary syndrome (ACS) group (n = 165) and stable angina pectoria (SAP) group (n = 82), based on CHD stability condition. The plasma PDGF‐BB level was measured by ELISA, and the genotype of PDGF‐B was examined through qPCR assay.ResultsThe PDGF‐BB level was positively correlated with hsCRP level (r = 0.149, p < 0.05). The genotype frequencies of SNP rs1800817 and rs2285094 match Hardy–Weinberg equilibrium. There was weak linkage disequilibrium between SNP rs1800817 and rs2285094: D′ = 0.419, r 2 = 0.04, which has no correlation with CHD. There was no statistical difference in plasma PDGF‐BB level among different genotypes in rs1800817 and rs2285094. There were no differences in the plasma PDGF‐BB level among patients with any genotype of SNP rs1800817 and rs2285094, no matter how it was grouped. Logistic regression results indicated that the plasma PDGF‐BB level was the independent risk factor of CHD onset (OR = 1.003, 95% CI 1.001–1.006, p = 0.014).ConclusionsHigh plasma PDGF‐BB level is the risk factor of CHD and has correlation with instability of CHD. The plasma PDGF‐BB level change may be related to inflammatory response. PDGF‐B gene rs1800817 and rs2285094 polymorphisms are not correlated with CHD.

Relationship of -31G/C (rs9904341) polymorphism in the survivin gene &lt;i&gt;BIRC5&lt;/i&gt; and the risk of bladder cancer

Purpose: To study the relationship between the -31G/C (rs9904341) polymorphism in the promoter region of the survivin protein gene and the predisposition to bladder cancer (BC) in patients of the Krasnoyarsk region. Material and methods. The allelic composition of the studied gene was determined in a group of 158 BC patients, consisting of 30 women and 128 men (mean age 65.6 ± 10.7, median: 66.5; C25–C75: 59–72). The control group included 117 healthy donors and consisted of 27 women and 90 men with an average age of 60.2 ± 5.1 (median: 60; C25–C75: 57–63.25). The allelic composition was determined using the bioluminescent method. A sample with the GC genotype confirmed by sanger sequencing (center for collective use “genomika”, Novosibirsk, Russia) was used as a control. The Mann–Whitney U test was used to compare quantitative data. the studied sample was in Hardy–Weinberg equilibrium (p&gt;0.5). The pearson χ2 test was used to compare the frequencies of gene variants among BC cases and control samples. The association between variants rs9904341 and BC was assessed in terms of odds ratio (OR) with a 95 % confidence interval (CI); p values&lt;0.05 were considered significant. Results. The allelic composition was determined for the genes of patients and control group participants: GG – 62 (39.2%) vs 43 (36.8%); GC – 82 (51.9%) vs 54 (46.2%); CC – 14 (8.9%) vs 20 (17.15%). The relationship between the presence of the C allele and BC was assessed using the recessive inheritance model, combining all carriers – heterozygotes and homozygotes. The frequency of occurrence of genotypes for patients and the control group was established: GG + GC – 144 (91.1%) vs 97 (82.9%); CC – 14 (8.9%) vs 20 (17.1%). Thus, carriers of the CС genotype were significantly less in patients: OR (95% CI) 0.47 (0.23–0.98), p=0.04. The relationship with tumor invasion was not significant (p=0.08). Conclusion. Based on the results of detecting the rs9904341 (G/C) polymorphism among BC patients of the Krasnoyarsk region, a protective effect of the carriage of the CC genotype was found. In order to study the allelic composition with the threat of recurrence of the disease, additional research is needed.

Distribution of 22 Single Nucleotide Polymorphisms in 13 Cytokine Genes in Malays, Chinese, and Indians in Peninsular Malaysia.

Introduction: Cytokines are cell signaling glycoproteins that are particularly important in immunity and inflammatory responses. Therefore, variations, such as single nucleotide polymorphisms (SNPs), in genes encoding for cytokines may have important consequences for their roles in health. Materials and Methods: A total of 222 unrelated, healthy, and un-admixed Malays (n = 97), Chinese (n = 77), and Indians (n = 48) with a median age of 30 years old (range 21-50) were typed for 22 cytokine gene SNPs: IL-1α -889 T/C, IL-1β (-511 T/C, +3962 T/C), IL-1R pst1 1970 T/C, IL-1RA mspa1 11100 T/C, IL-4Rα +1902 G/A, IL-12 - 1188 C/A, IFN-γ +874 A/T, TGF-β (cdn 10 C/T, cdn 25 G/C), TNF-α (-308 A/G, -238 A/G) IL-2 (+166 G/T, -330 T/G), IL-4 (-1098 T/G, -590 T/C, -33 T/C), IL-6 (-174 C/G, nt565 G/A), and IL-10 (-1082 G/A, -819 C/T, -592 A/C). This involved using well-established polymerase chain reaction procedures with sequence-specific primers and restriction fragment length polymorphism methods. Results: The majority of the screened cytokine gene SNPs are polymorphic in all three ethnicities. Exceptions include TGF-β cdn 25 (G/C), IL-1β +3962 (T/C), and TNF-α -238 (A/G), which were all observed to be monomorphic in Malays, Chinese and Indians. Many of the analyzed cytokine gene SNP genotypes deviated from Hardy-Weinberg equilibrium and the three ethnic study groups were all well-separated from reference Asian, African and European populations in a principal component analysis plot. Conclusion: We successfully typed 22 SNPs in 13 cytokine genes from genetic material collected from unrelated and un-admixed Malay, Chinese and Indian individuals in Peninsular Malaysia. These new cytokine gene population datasets reveal interesting contrasts with other populations.

Analysis of the difference in SLCO1B1 and APOE gene polymorphisms between Mongolian and Han populations.

Objective: To analyze SLCO1B1 and APOE polymorphisms and their clinical significance in the Mongolian and Han populations in Ordos, Inner Mongolia. Methods: Mongolian patients (n = 200)with cardiovascular disease admitted to our hospital from January 2018 to December 2020 were selected as the Mongolian population group. Han patients (n = 200) with cardiovascular diseases admitted during the same period were selected as the Han population group. Mutations in SLCO1B1 and APOE were detected by real-time fluorescence qPCR, and the differences between the two groups were analyzed. Results: The nucleotide polymorphisms of SLCO1B1 and APOE in the Mongolian and Han populations were consistent with the Hardy-Weinberg law. There were significant differences in gender, age, BMI, hypertension, alcohol consumption, dyslipidemia and low-density lipoprotein cholesterol levels between the two groups. APOE genotypes were classified according to those related to the efficacy of statins and the risk of atherosclerosis, and there was a significant difference between the two groups. Conclusion: There were differences in SLCO1B1 and APOE polymorphisms between the Mongolian and Han populations in Ordos. These may explain the differences in the incidence of cardiovascular diseases and the lipid-lowering efficacy of statins between the two populations.

Relationship between vitamin D receptor gene polymorphisms and second acid-fast bacilli smear-positive during treatment for tuberculosis patients.

Tuberculosis (TB) treatment is associated with Vitamin D. This study aimed to explore the relationship between Vitamin D receptor (VDR) gene polymorphisms and second acid-fast bacilli (AFB) smear-positive during treatment for TB patients. This was a cross-sectional study. Seven hundred and thirty-one TB patients whose single nucleotide polymorphism site (SNPs) of VDR gene were detected from December 2019 to December 2020 in XinJiang of China. The genotypic distributions in each group were tested separately for Hardy-Weinberg equilibrium. The tetragram test was used to construct haplotypes to evaluate the association between each haplotype and second AFB smear-positive occurrence. No significant deviations were observed with all the four polymorphism sites in the genotypic distributions (P>0.05). Linkage disequilibrium (LD) analysis showed that there was LD between SNPs of VDR gene (r2=0.74, D`>0.9). Each haplotype was not considered to be the influencing factor of second AFB smear-positive. There is no association between VDR gene polymorphism (ApaI, BsmI, FokI and TaqI) and second AFB smear-positive.