Association Between Two Single-nucleotide Polymorphism of TAAR1 Gene and Suicide Attempts

IntroductionTAAR1 is a G protein-coupled receptor expressed broadly throughout the brain. Recently, TAAR1 has been demonstrated to be an important modulator of the dopaminergic, serotonergic and glutamatergic activity.AimsAssessment of the relation between two single-nucleotide polymorphisms of TAAR1 gene, suicide attempts and alcohol abuse.MethodsA total of 150 Polish patients were included, 59 subjects after suicide attempt vs. 91 controls. The chosen SNPs (rs759733834 and rs9402439) were studied using RFLP-PCR methods. The Hardy-Weinberg equilibrium was tested in control group.Statistical testsChi2 or Yeates Chi2 Test were used.ResultsThe mean age of study subjects and controls was: 38 ± 12.3 and 42 ± 12.8 respectively; 49% study males vs. 54% male controls. We did not observe the association between the carriage of the genotypes GG, GA and AA of rs759733834 polymorphisms in either of the groups. The distribution of genotypes in respect to rs9402439 polymorphism (CC, CG, GG) was also insignificant. Among patients with alcohol dependence, the frequency G allele of rs9402439 polymorphism was lower compared to non-addicted ones (27 vs. 47%) P < 0.01.ConclusionsTAAR1 polymorphisms rs759733834 and rs9402439 are not related to suicide attempts. The carriage of allele G of rs9402439 polymorphism is related to lower risk of alcohol addiction OR 0.40 95%Cl 0.20–0.81. To our knowledge, this is the first study on the TAAR1 receptor and the risk of suicide and it might offer a new insight into genetic etiology of TAAR1 receptor.Disclosure of interestThe authors have not supplied their declaration of competing interest.

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Association between PNPLA8 gene polymorphism and schizophrenia in male patients

South African Journal of Psychiatry ◽

10.4102/sajpsychiatry.v19i3.455 ◽

2013 ◽

Vol 19 (3) ◽

pp. 2

Author(s):

Qiong Yu ◽

Yaqin Yu ◽

Jieping Shi ◽

Hong Sang

Keyword(s):

Phospholipase A2 ◽

Phospholipid Metabolism ◽

Genotypic Frequency ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Neuropsychiatric Diseases ◽

Hardy Weinberg Equilibrium ◽

Male Patients ◽

Calcium Independent Phospholipase A2 ◽

The Brain

Abnormal phospholipid metabolism in the brain plays an important role in neuropsychiatric diseases. Phospholipase A2 is crucial for maintaining normal neuro-physiological function. The aim of this study was to investigate the association between polymorphisms of the membrane-associated calcium-independent phospholipase A2 gamma (PNPLA8) gene and schizophrenia in Han Chinese in north China. The PCR-based ligase detection reaction was applied to detect 3 single nucleotide polymorphisms (SNPs) in the PNPLA8 gene among 201 Chinese pedigrees. The genotypic frequency of the PNPLA8 polymorphisms did not deviate from the Hardy-Weinberg equilibrium both in affected offspring and parental groups. Haploid relative risk (HRR) and transmission disequilibrium tests (TDT) showed that the 3 SNPs were not associated with schizophrenia (p>0.05), but further analysis with TDT showed that the rs40876 polymorphism was associated with schizophrenia in males (χ2=4.667, p=0.031). Our data suggest that rs40876 in PNPLA8 may be associated with schizophrenia in males.<div> </div>

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Association of the CD14 C159T and the Toll-like receptor 4 Asp299Gly polymorphisms with various phenotypes of asthma in adults from Crimea

Allergy and Asthma Proceedings ◽

10.2500/aap.2019.40.190007 ◽

2020 ◽

Vol 41 (2) ◽

pp. 134-140

Author(s):

Yuriy Bisyuk ◽

Andrew Dubovyi ◽

Ilona DuBuske ◽

Viktor Litus ◽

Lawrence M. DuBuske

Keyword(s):

Late Onset ◽

Adult Population ◽

Additive Models ◽

Atopic Asthma ◽

Control Group ◽

Nucleotide Polymorphisms ◽

Toll Like Receptor ◽

Toll Like Receptor 4 ◽

Single Nucleotide ◽

Gender And Age

Background: This study assessed gene polymorphisms of the CD14 receptor (C-159T) and Toll-like receptor 4 (Asp299Gly) in a patient population in Crimea, Ukraine, stratified by clinical (early versus late onset; frequent versus occasional relapses; fixed versus reversible obstruction) and immunologic (atopic versus nonatopic; eosinophilic; neutrophilic or paucigranulocytic inflammation) subtype. Methods: Two polymorphisms, CD14 C-159T and TLR4 Asp299Gly, were assessed in 331 patients with asthma. The control group included 285 volunteers who were nonatopic. The single nucleotide polymorphisms were studied by using polymerase chain reaction with electrophoretic detection. Results: There were increased odds of asthma development in patients with the Asp299Gly TLR4 mutation compared with the general population underdominant odds ratio (OR) 1.52 [95% confidence interval (CI), 1.00‐2.32] and overdominant (OR 1.55 [95% CI, 1.01‐2.38]) models after adjustment for gender and age. In addition, mutations in this gene decreased the odds of nonatopic asthma in underdominant (OR 0.26 [95% CI, 0.07‐0.93]; p = 0.027), overdominant (OR 0.27 [95% CI, 0.07‐0.96]; p = 0.033), and log-additive models (OR 0.26 [95% CI, 0.07‐0.93]; p = 0.026) compared with the atopic subgroup after adjustment for gender, age, number of exacerbations, and type of airway inflammation. Allele frequencies for CD14 and TLR4 polymorphisms did not show statistical differences between the patients with asthma and the control subjects. Conclusion: CD14 C-159T polymorphisms were not associated with asthma in the adult population in Crimea. TLR4 Asp299Gly polymorphisms were associated with asthma and with decreased odds of nonatopic asthma compared with atopic asthma in the adult population in Crimea.

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Assessing single nucleotide polymorphism selection methods for the development of a low-density panel optimized for imputation in South African Drakensberger beef cattle

Journal of Animal Science ◽

10.1093/jas/skab118 ◽

2021 ◽

Author(s):

Simon F Lashmar ◽

Donagh P Berry ◽

Rian Pierneef ◽

Farai C Muchadeyi ◽

Carina Visser

Keyword(s):

South African ◽

Clustering Algorithm ◽

Imputation Accuracy ◽

Developed Countries ◽

Genotype Imputation ◽

Selection Strategy ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Single Nucleotide Polymorphism Selection ◽

The Mean

Abstract A major obstacle in applying genomic selection (GS) to uniquely adapted local breeds in less-developed countries has been the cost of genotyping at high densities of single nucleotide polymorphisms (SNP). Cost reduction can be achieved by imputing genotypes from lower to higher densities. Locally adapted breeds tend to be admixed and exhibit a high degree of genomic heterogeneity thus necessitating the optimization of SNP selection for downstream imputation. The aim of this study was to quantify the achievable imputation accuracy for a sample of 1,135 South African (SA) Drakensberger using several custom-derived lower-density panels varying in both SNP density and how the SNP were selected. From a pool of 120,608 genotyped SNP, subsets of SNP were chosen 1) at random, 2) with even genomic dispersion, 3) by maximizing the mean minor allele frequency (MAF), 4) using a combined score of MAF and linkage disequilibrium (LD), 5) using a partitioning-around-medoids (PAM) algorithm, and finally 6) using a hierarchical LD-based clustering algorithm. Imputation accuracy to higher density improved as SNP density increased; animal-wise imputation accuracy defined as the within-animal correlation between the imputed and actual alleles ranged from 0.625 to 0.990 when 2,500 randomly selected SNP were chosen versus a range of 0.918 to 0.999 when 50,000 randomly selected SNP were used. At a panel density of 10,000 SNP, the mean (standard deviation) animal-wise allele concordance rate was 0.976 (0.018) versus 0.982 (0.014) when the worst (i.e., random) as opposed to the best (i.e., combination of MAF and LD) SNP selection strategy was employed. A difference of 0.071 units was observed between the mean correlation-based accuracy of imputed SNP categorized as low (0.01<MAF≤0.1) versus high MAF (0.4<MAF≤0.5). Greater mean imputation accuracy was achieved for SNP located on autosomal extremes when these regions were populated with more SNP. The presented results suggested that genotype imputation can be a practical cost-saving strategy for indigenous breeds such as the South African Drakensberger. Based on the results, a genotyping panel consisting of approximately 10,000 SNP selected based on a combination of MAF and LD would suffice in achieving a less than 3% imputation error rate for a breed characterized by genomic admixture on the condition that these SNP are selected based on breed-specific selection criteria.

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Association between CTSS gene polymorphism and the risk of acute atherosclerotic cerebral infarction in Chinese population: a case–control study

Bioscience Reports ◽

10.1042/bsr20180586 ◽

2018 ◽

Vol 38 (6) ◽

Cited By ~ 2

Author(s):

Lian Luo ◽

Mingli Zhu ◽

Jiajun Zhou

Keyword(s):

Cerebral Infarction ◽

Case Control Study ◽

Case Control ◽

Cathepsin S ◽

Control Group ◽

Study Group ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Independent Risk Factors ◽

Control Study

Objective: To investigate the association between the gene polymorphisms of rs774320676, rs768437857, rs928508030, and rs2275235 loci of Cathepsin S (CTSS) and risk of acute atherosclerotic cerebral infarction. Methods: A total of 315 patients with acute atherosclerotic cerebral infarction (study group) and 220 healthy subjects (control group) were enrolled in the present study. The genetic polymorphism of rs774320676, rs768437857, rs928508030, and rs2275235 loci of CTSS of subjects was analyzed by PCR-Sanger sequencing. Results: The proportion of carriers with mutant T allele at rs774320676 locus and mutant G allele at rs928508030 locus of CTSS in study group was significantly higher than the proportion in control group (P=0.000, adjusted odds ratio (OR) = 1.332, 95% confidence interval (CI) = 1.200–1.460; P<0.001, adjusted OR = 1.185, 95% CI = 1.055–1.314; P=0.002). The T allele at rs774320676 locus and the G allele at rs928508030 locus of CTSS were independent risk factors for acute atherosclerotic cerebral infarction (OR = 2.534, 95% CI = 1.020–4.652, P=0.006; OR = 2.016, 95% CI = 1.031–4.385, P=0.031). Conclusion: The single nucleotide polymorphisms (SNPs) of rs774320676 and rs928508030 of CTSS gene were related with risk for acute atherosclerotic cerebral infarction. The T allele at rs774320676 locus and G allele at rs928508030 locus of CTSS were genetic susceptibility genes of acute atherosclerotic cerebral infarction.

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Genotyping of Essential Hypertension Single-Nucleotide Polymorphisms by a Homogeneous PCR Method with Universal Energy Transfer Primers

Clinical Chemistry ◽

10.1093/clinchem/48.12.2131 ◽

2002 ◽

Vol 48 (12) ◽

pp. 2131-2140 ◽

Cited By ~ 66

Author(s):

Chikh Bengra ◽

Theodore E Mifflin ◽

Yuri Khripin ◽

Paolo Manunta ◽

Scott M Williams ◽

...

Keyword(s):

Essential Hypertension ◽

Single Nucleotide Polymorphisms ◽

Restriction Endonucleases ◽

Control Group ◽

Italian Population ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Hypertensive Patients ◽

Unique Restriction ◽

Set Up

Abstract Background: Human hypertension is a complex, multifactorial disease with a heritability of more than 30–50%. A genetic screening test based on analysis of multiple single-nucleotide polymorphisms (SNPs) to assess the likelihood of developing hypertension would be helpful for disease management. Methods: Tailed allele-specific primers were designed to amplify by PCR six biallelic SNP loci [three in G protein-coupled receptor kinase type 4 (GRK4): R65L, A142V, and A486V; two in angiotensinogen: −6G→A and M235T; and one in aldosterone synthase: −344C→T] associated with essential hypertension. PCRs of SNP loci were coupled (via a common sequence of 21 nucleotide tails) to incorporate Universal Amplifluor™ primers labeled with fluorescein or sulforhodamine in a homogeneous format. Use of Amplifluors in SNP PCRs produced labeled amplicons, the fluorescence of which was quantified by a microplate reader and then analyzed via an Excel macro to provide genotypes for all six SNP loci. Unique restriction endonucleases were identified for five SNP loci that could independently confirm homogeneous PCR results when needed. Results: We developed six homogeneous PCR assays that were set up, performed, and fluorometrically analyzed in 96-well microplates. Allele frequencies were determined for six SNPs in 60 Italian hypertensive patients and a control group of 60 normotensive persons. A significant correlation (P = 0.034) between one SNP [GRK4 (A486V)] and the hypertensive patients was observed. Genotyping results for five of six SNPs were confirmed by digesting corresponding amplicons with locus-specific restriction endonucleases. Conclusions: We developed a simple and homogeneous fluorescent protocol that has been used to determine the SNP genotype for six loci in a population of hypertensive and normotensive persons. We also observed a significant association (P = 0.034) between one SNP (A486V) and an Italian population of mildly hypertensive patients.

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Association of single-nucleotide polymorphisms in the ESR2 and FSHR genes with poor ovarian response in infertile Jordanian women

Clinical and Experimental Reproductive Medicine ◽

10.5653/cerm.2020.03706 ◽

2021 ◽

Vol 48 (1) ◽

pp. 69-79

Author(s):

Amer Mahmoud Sindiani ◽

Osamah Batiha ◽

Esra’a Al-zoubi ◽

Sara Khadrawi ◽

Ghadeer Alsoukhni ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Statistical Significance ◽

Ovarian Response ◽

Control Group ◽

P Value ◽

Case Group ◽

Nucleotide Polymorphisms ◽

Poor Ovarian Response ◽

Single Nucleotide ◽

Number Of Patients

Objective: Poor ovarian response (POR) refers to a subnormal follicular response that leads to a decrease in the quality and quantity of the eggs retrieved after ovarian stimulation during assisted reproductive treatment (ART). The present study investigated the associations of multiple variants of the estrogen receptor 2 (ESR2) and follicle-stimulating hormone receptor (FSHR) genes with POR in infertile Jordanian women undergoing ART.Methods: Four polymorphisms, namely ESR2 rs1256049, ESR2 rs4986938, FSHR rs6165, and FSHR rs6166, were investigated in 60 infertile Jordanian women undergoing ART (the case group) and 60 age-matched fertile women (the control group), with a mean age of 33.60±6.34 years. Single-nucleotide polymorphisms (SNPs) were detected by restriction fragment length polymorphism and then validated using Sanger sequencing.Results: The p-value of the difference between the case and control groups regarding FSHR rs6166 was very close to 0.05 (p=0.054). However, no significant differences were observed between the two groups in terms of the other three SNPs, namely ESR2 rs1256049, ESR2 rs4986938, and FSHR rs6165 (p=0.561, p=0.433, and p=0.696, respectively).Conclusion: The association between FSHR rs6166 and POR was not statistically meaningful in the present study, but the near-significant result of this experiment suggests that statistical significance might be found in a future study with a larger number of patients.

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The G allele in IL-10-1082 G/A may have a role in lowering the susceptibility to panic disorder in female patients

Acta Neuropsychiatrica ◽

10.1017/neu.2016.25 ◽

2016 ◽

Vol 28 (6) ◽

pp. 357-361 ◽

Cited By ~ 2

Author(s):

Han-Joon Kim ◽

Yong-Ku Kim

Keyword(s):

Panic Disorder ◽

Patient Group ◽

Control Group ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Female Patients ◽

Immune System Activation ◽

Tnf Α ◽

System Activation ◽

And Control

BackgroundImmune system activation is involved in the pathophysiology of panic disorder (PD). We investigated INF-γ+874 A/T, TNF-α-308 G/A, and IL-10-1082 G/A single nucleotide polymorphisms (SNPs) to determine their association with PD.MethodThis study enroled 135 PD patients and 135 healthy controls. INF-γ+874 A/T (rs2430561), TNF-α-308 G/A (rs1800629), and IL-10-1082 G/A (rs1800896) were genotyped.ResultsThere were no differences in genotypes or allele frequencies between the patient and control groups, regardless of accompanying agoraphobia. However, for female patients, the G allele frequency in IL-10 SNP was higher in the control group than in the patient group. Additionally, the female control group had a higher frequency of the A/G and G/G genotype in the IL-10 SNP than the female patient group.ConclusionWe suggest that the G allele in IL-10-1082 G/A might have a role in reducing the manifestations of PD in female patients. Further studies are needed to extend and confirm our findings.

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Association Analysis of Single Nucleotide Polymorphisms in the 5′ Regulatory Region of the IL-6 Gene with Eimeria tenella Resistance in Jinghai Yellow Chickens

Genes ◽

10.3390/genes10110890 ◽

2019 ◽

Vol 10 (11) ◽

pp. 890 ◽

Cited By ~ 1

Author(s):

Hailiang Yu ◽

Wenbin Zou ◽

Shijie Xin ◽

Xiaohui Wang ◽

Changhao Mi ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Association Analysis ◽

Direct Sequencing ◽

Regulatory Region ◽

Eimeria Tenella ◽

Least Square ◽

Bursa Of Fabricius ◽

Control Group ◽

Nucleotide Polymorphisms ◽

Single Nucleotide

Interleukin 6 (IL-6) is an immunoregulatory cytokine involved in various inflammatory and immune responses. To investigate the effects of single nucleotide polymorphisms (SNPs) and haplotypes of IL-6 on resistance to Eimeria tenella (E. tenella), SNPs in the 5′ regulatory region of IL-6 were detected with direct sequencing, and the effects of SNPs and haplotypes on resistance to E. tenella were analyzed by the least square model in Jinghai yellow chickens. Nineteen SNPs were identified in the 5′ regulation region of IL-6, among which three SNPs were newly discovered. The SNP association analysis results showed that nine of the SNPs were significantly associated with E. tenella resistance indexes; the A-483G locus was significantly associated with the GSH-Px, IL-2, and IL-17 indexes (p < 0.05); the C-447G locus was significantly associated with the SOD, GSH-Px, IL-17, and IL-2 indexes (p < 0.05); and the G-357A locus had significant effects on the CAT and IL-16 indexes (p < 0.05). Haplotype analysis showed that H2H3 and H2H5 were favorable haplotype combinations with good coccidium resistance. Furthermore, we used qRT-PCR and observed that the expression of IL-6 in the infection group was higher than that in the control group in the liver, proventriculus, small intestine, thymus, kidney, and bursa of Fabricius and extremely significantly different than that in the cecum especially (p < 0.01). In summary, SNPs and haplotypes in the 5′ regulatory region of IL-6 have important effects on E. tenella resistance, and the results will provide a reference for molecular marker selection of E. tenella resistance in Jinghai yellow chickens.

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The German Shorthair Pointer Dog Breed (Canis lupus familiaris): Genomic Inbreeding and Variability

Animals ◽

10.3390/ani10030498 ◽

2020 ◽

Vol 10 (3) ◽

pp. 498 ◽

Cited By ~ 1

Author(s):

Antonio Boccardo ◽

Stefano Paolo Marelli ◽

Davide Pravettoni ◽

Alessandro Bagnato ◽

Giuseppe Achille Busca ◽

...

Keyword(s):

Canis Lupus ◽

Inbreeding Coefficient ◽

Nucleotide Polymorphisms ◽

Canis Lupus Familiaris ◽

Runs Of Homozygosity ◽

Single Nucleotide ◽

The Mean ◽

Dog Breed ◽

Genomic Inbreeding ◽

Genealogical Information

The German Shorthaired Pointer (GSHP) is a breed worldwide known for its hunting versatility. Dogs of this breed are appreciated as valuable companions, effective trackers, field trailers and obedience athletes. The aim of the present work is to describe the genomic architecture of the GSHP breed and to analyze inbreeding levels under a genomic and a genealogic perspective. A total of 34 samples were collected (24 Italian, 10 USA), and the genomic and pedigree coefficients of inbreeding have been calculated. A total of 3183 runs of homozygosity (ROH) across all 34 dogs have been identified. The minimum and maximum number of Single Nucleotide Polymorphisms (SNPs) defining all ROH are 40 and 3060. The mean number of ROH for the sample was 93.6. ROH were found on all chromosomes. A total of 854 SNPs (TOP_SNPs) defined 11 ROH island regions (TOP_ROH), in which some gene already associated with behavioral and morphological canine traits was annotated. The proportion of averaged observed homozygotes estimated on total number of SNPs was 0.70. The genomic inbreeding coefficient based on ROH was 0.17. The mean inbreeding based on genealogical information resulted 0.023. The results describe a low inbred population with quite a good level of genetic variability.

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