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International Journal of Surgery... Jun 2018Endothelial nitric oxide synthase (eNOS) polymorphisms have been implicated as risk factors for erectile dysfunction (ED), but the results of genetic association studies... (Meta-Analysis)
Meta-Analysis Review
PURPOSE
Endothelial nitric oxide synthase (eNOS) polymorphisms have been implicated as risk factors for erectile dysfunction (ED), but the results of genetic association studies are inconclusive. We performed a meta-analysis of published studies investigating the association between ED and three eNOS polymorphisms, intron 4 VNTR, G894T and T786C in humans.
METHODS
The PubMed, Web of Science, CNKI and Google Scholar databases were searched for relevant studies published up to November 2017. Association studies with case-control design were included. For each study with genotype information we calculated odds ratios (OR) and 95% confidence intervals (CI).
RESULTS
The search identified 13 eligible studies. The G894T and T786C polymorphisms showed a significant association with ED risk in Caucasians (GT + TT versus GG for G894T: OR = 2.13, 95% CI = 1.08-4.19; CC versus CT + TT for T786C: OR = 3.29, 95% CI = 2.30-4.72) and Asians (GT + TT versus GG for G894T: OR = 2.08, 95% CI = 1.53-2.84; CC + CT versus TT for T786C: OR = 3.13, 95% CI = 1.35-7.25). In addition, the intron 4 VNTR polymorphism was associated with ED risk only among Caucasian subjects (aa versus bb + ab: OR = 2.38, 95% CI = 1.15-4.93). We found no evidence of publication bias. The robustness of overall analyses was ensured in sensitivity analyses excluding studies deviating from Hardy-Weinberg equilibrium.
CONCLUSION
Our findings suggest that common genetic polymorphisms in the eNOS gene contribute to risk of ED, presumably by effects on eNOS activity and NO availability.
Topics: Case-Control Studies; Erectile Dysfunction; Genetic Association Studies; Genetic Predisposition to Disease; Genotype; Humans; Male; Minisatellite Repeats; Nitric Oxide Synthase Type III; Odds Ratio; Polymorphism, Genetic; Risk Factors; White People
PubMed: 29654965
DOI: 10.1016/j.ijsu.2018.04.012 -
Journal of Affective Disorders Dec 2020Evidences suggest that alterations in circadian rhythms trigger the development of mental disorders. Eveningness, sleep behavior, and circadian genes polymorphisms have...
BACKGROUND
Evidences suggest that alterations in circadian rhythms trigger the development of mental disorders. Eveningness, sleep behavior, and circadian genes polymorphisms have been associated with depression and anxiety symptomatology. However, the mechanism underlying these interactions is not well understood. We investigated the contribution of diurnal preference, sleep habits, and PER3 VNTR polymorphism (rs57875989) to depression and anxiety symptoms in a Northeast sample from the Brazilian population.
METHODS
Eight hundred and four young adults completed the Morningness-Eveningness (MEQ), Munich Chronotype (MCTQ), Center for Epidemiologic Studies - Depression (CES-D), and Beck Anxiety Inventory (BAI) questionnaires. All participants were genotyped and linear regression was performed to test the interactions between the genetic /behavioral variants and depression/ anxiety symptoms.
RESULTS
Eveningness and sleep behaviors (bedtime, wake-up time, sleep duration, and midpoint of sleep) were correlated with depression symptomatology, specifically in somatic factors of the CES-D questionnaire. No correlation was found between diurnal preference/sleep habits with anxiety symptoms for both BAI total score and its factors. However, women with PER3 genotype showed less interpesonal affect in depression symptomatology and more anxiety symptoms in four factors of the BAI questionnaire.
LIMITATIONS
Mainly because this study was based on self-report questionnaires and was limited to undergraduate students aging 18 to 30 years old.
CONCLUSION
These results reinforce a role for sleep and diurnal preference in depression, and PER3 VNTR polymorphism in anxiety symptomatology, particularly in women.
Topics: Adolescent; Adult; Anxiety; Brazil; Circadian Rhythm; Depression; Female; Humans; Minisatellite Repeats; Period Circadian Proteins; Polymorphism, Genetic; Sleep; Surveys and Questionnaires; Young Adult
PubMed: 32841827
DOI: 10.1016/j.jad.2020.07.138 -
DNA and Cell Biology Mar 2017The dopamine transporter SLC6A3 (DAT1) mediates uptake of dopamine into presynaptic terminals. In addition, in previous reports, hypertensive rats were associated with...
The dopamine transporter SLC6A3 (DAT1) mediates uptake of dopamine into presynaptic terminals. In addition, in previous reports, hypertensive rats were associated with DAT gene, but the genetic association with SLC6A3 and hypertension is still unknown. We examined the distribution of variable number of tandem repeats (VNTRs) and conducted polymorphic analysis of the entire region of SLC6A3. Ten VNTR regions (MS1-10) were revealed throughout the intronic and UTRs; seven VNTR regions were newly isolated and three VNTRs were previously reported. Four VNTR regions (SLC6A3-MS1, -MS4, -MS8 [rs3836790], and -MS9 [rs28363170]) showed polymorphism and these loci were found to be transmitted through meiosis following Mendelian inheritance. These VNTR polymorphisms may be useful markers for paternity mapping and DNA fingerprinting. Furthermore, we also conducted a case-control study between the controls and essential hypertensive cases. Analysis of the genotypes of SLC6A3-MS8 (rs3836790) revealed that having an 8/6-repeat allele, which was only detected in hypertensive cases, was associated with hypertension (p < 0.05). Additional significant association was identified between the short 7-repeat allele of SLC6A3-MS9 (rs28363170) and the occurrence of hypertension (odds ratio 2.02; p < 0.05). These results revealed the genetic association between SLC6A3 and hypertension, and the specific VNTR alleles of SLC6A3 may be a risk factor for hypertension.
Topics: Adult; Aged; Aged, 80 and over; Alleles; Case-Control Studies; Dopamine Plasma Membrane Transport Proteins; Family Health; Female; Gene Frequency; Genetic Predisposition to Disease; Genotype; Humans; Hypertension; Male; Middle Aged; Minisatellite Repeats; Odds Ratio; Pedigree; Polymorphism, Genetic; Risk Factors
PubMed: 28055236
DOI: 10.1089/dna.2016.3448 -
The SLC6A3 gene polymorphism is related to the development of attentional functions but not to ADHD.Scientific Reports Apr 2020Neuropharmacological and human clinical studies have suggested that the brain dopaminergic system is substantively involved in normal and pathological phenotypes of... (Observational Study)
Observational Study
Neuropharmacological and human clinical studies have suggested that the brain dopaminergic system is substantively involved in normal and pathological phenotypes of attention. Dopamine transporter gene (SLC6A3) was proposed as a candidate gene for Attention-Deficit/Hyperactivity Disorder (ADHD). We investigated the effect of the SLC6A3 variants on cognitive performance in ADHD and healthy children and teenagers. Participants completed cognitive tasks measuring attentional switching, selective and sustained attention, and effectiveness of alerting, orienting and executive attention. We estimated the effects of 40 bp variable number of tandem repeat (VNTR) polymorphism located in the 3' untranslated region (3' UTR) (9-repeat vs 10-repeat allele) of the SLC6A3 gene, ADHD diagnosis, age, and their interactions as predictors of cognitive performance. ADHD children demonstrated deficits in most of the examined attention processes, persistent within the examined age range (9-16 years). No significant effects were observed for the interaction of ADHD and the SLC6A3 polymorphism, but the results revealed a significant main effect of SLC6A3 genotype in the entire research sample. Subjects carrying 9R allele performed the switching task significantly worse in comparison to children with 10R/10R or 10R/11R genotype. SLC6A3 polymorphism moderated age-related improvements in orienting and attentional switching. Results suggest that SLC6A3 genotype influence these attentional/cognitive functions which deficits are not the key symptoms in ADHD.
Topics: Adolescent; Adolescent Development; Age Factors; Alleles; Attention; Attention Deficit Disorder with Hyperactivity; Case-Control Studies; Child; Child Development; Cognition; Dopamine Plasma Membrane Transport Proteins; Female; Healthy Volunteers; Humans; Male; Minisatellite Repeats; Polymorphism, Genetic
PubMed: 32277231
DOI: 10.1038/s41598-020-63296-x -
Journal of Radiological Protection :... Mar 2015
Topics: Female; Germ-Line Mutation; Humans; Male; Maternal Exposure; Minisatellite Repeats; Paternal Exposure; Pregnancy; Prenatal Exposure Delayed Effects; Radiation Exposure; Risk Assessment; Risk Factors
PubMed: 25485602
DOI: 10.1088/0952-4746/35/1/E1 -
Tropical Animal Health and Production Sep 2021This study aimed to systematically collect and appraise the scientific evidence to answer the research question: What MAP genotypes have been isolated from cattle,... (Review)
Review
This study aimed to systematically collect and appraise the scientific evidence to answer the research question: What MAP genotypes have been isolated from cattle, sheep, and goats in Latin America and the Caribbean? An electronic search was conducted on three platforms (i.e., OVID®, Web of Science®, SciELO) as well as on the proceedings of the International Colloquium on Paratuberculosis. Inclusion and exclusion criteria were defined a priori and conserved through the systematic process and only articles published in peer-reviewed journals were considered. A total of 26 articles met the definitive inclusion criteria. All were published in English, in 15 different journals, and between 1989 and 2020. The relevant articles reported the use of six different genotyping techniques (i.e., polymerase chain reaction-restriction endonuclease analysis, restriction fragment length polymorphism, type-specific-PCR, mycobacterial interspersed repetitive units-variable number of tandem repeats, multi-locus short sequence repeat, single nucleotide polymorphism) in isolates from seven countries. Genotypes found so far in the region using typing techniques were mainly C type. MIRU-VNTR mostly reported INMV 1, INMV 2, and INMV 11 subtypes, among others. MLSSR reported genotypes from four different countries, reporting nine different subtypes of which 7g-10g-4ggt was the most common for loci 1, 2, and 8, respectively. Regardless the high diversity of techniques used so far to genotype Latin American and Caribbean MAP isolates, the original question of this systematic review has been answered. In addition, a relative genetic similarity between MAP strains recovered from cattle, goats, and sheep unrelatedly of the matrix and geographic origin was identified.
Topics: Animals; Cattle; Genotype; Goat Diseases; Goats; Latin America; Minisatellite Repeats; Mycobacterium avium subsp. paratuberculosis; Paratuberculosis; Sheep; Sheep Diseases
PubMed: 34546430
DOI: 10.1007/s11250-021-02923-9 -
Journal of Clinical Immunology Apr 2018In the current study, we aimed to accurately evaluate donor/recipient or male/female chimerism in samples from patients who underwent hematopoietic stem cell...
OBJECTIVE
In the current study, we aimed to accurately evaluate donor/recipient or male/female chimerism in samples from patients who underwent hematopoietic stem cell transplantation (HSCT).
METHODS
We designed the droplet digital polymerase chain reaction (ddPCR) for SRY and RPP30 to detect the male/female chimerism. We also developed mutation-specific ddPCR for four primary immunodeficiency diseases.
RESULTS
The accuracy of the male/female chimerism analysis using ddPCR was confirmed by comparing the results with those of conventional methods (fluorescence in situ hybridization and short tandem repeat-PCR) and evaluating dilution assays. In particular, we found that this method was useful for analyzing small samples. Thus, this method could be used with patient samples, especially to sorted leukocyte subpopulations, during the early post-transplant period. Four mutation-specific ddPCR accurately detected post-transplant chimerism.
CONCLUSION
ddPCR-based male/female chimerism analysis and mutation-specific ddPCR were useful for all HSCT, and these simple methods contribute to following the post-transplant chimerism, especially in disease-specific small leukocyte fractions.
Topics: Alleles; Chimerism; Female; Hematopoietic Stem Cell Transplantation; Humans; Immunologic Deficiency Syndromes; In Situ Hybridization, Fluorescence; Male; Minisatellite Repeats; Mutation; Real-Time Polymerase Chain Reaction; Transplantation Chimera; Transplantation, Homologous
PubMed: 29671114
DOI: 10.1007/s10875-018-0497-8 -
Acta Diabetologica Dec 2015A variable number of tandem repeat (VNTRs) region in the insulin gene (INS) possibly influences the progression of type 1 diabetes (T1D) and latent autoimmune diabetes... (Meta-Analysis)
Meta-Analysis Review
AIMS
A variable number of tandem repeat (VNTRs) region in the insulin gene (INS) possibly influences the progression of type 1 diabetes (T1D) and latent autoimmune diabetes in adults (LADA). However, effects of INS VNTR polymorphisms in these contexts remain inconclusive.
METHODS
We performed a systematic review of work on the INS VNTR -2221MspI and -23HphI polymorphisms to estimate the overall effects thereof on disease susceptibility; we included 17,498 T1D patients and 24,437 controls, and 1960 LADA patients and 5583 controls.
RESULTS
For T1D, the C allele at -2221MspI and the A allele at -23HphI were associated with estimated relative risks of 2.13 (95 % CI 1.94, 2.35) and 0.46 (95 % CI 0.44, 0.48), which contributed to absolute increases of 46.76 and 46.98 % in the risk of all T1D, respectively. The estimated lambda values were 0.44 and 0.42, respectively, suggesting that a co-dominant model most likely explained the effects of -2221MspI and -23HphI on T1D. For -23HphI, the A allele carried an estimated relative risk of 0.55 (95 % CI 0.50, 0.61) for LADA and increased the risk of all LADA by 36.94 %. The λ value was 0.43, suggesting that a co-dominant model most likely explained the effect of -23HphI on LADA.
CONCLUSIONS
Our results support the existence of associations of INS with T1D and LADA.
Topics: Adult; Autoimmune Diseases; Diabetes Mellitus, Type 1; Gene Frequency; Genetic Predisposition to Disease; Humans; Minisatellite Repeats; Polymorphism, Genetic
PubMed: 26362169
DOI: 10.1007/s00592-015-0805-1 -
Bioinformatics (Oxford, England) Mar 2020Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing is widely used to genotype Mycobacterium tuberculosis complex in...
SUMMARY
Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing is widely used to genotype Mycobacterium tuberculosis complex in epidemiological studies for tracking tuberculosis transmission. Recent long-read sequencing technologies from Pacific Biosciences and Oxford Nanopore Technologies can produce reads that are long enough to cover the entire repeat regions in each MIRU-VNTR locus which was previously not possible using the short reads from Illumina high-throughput sequencing technologies. We thus developed MIRUReader for MIRU-VNTR typing directly from long sequence reads.
AVAILABILITY AND IMPLEMENTATION
Source code and documentation for MIRUReader program is freely available at https://github.com/phglab/MIRUReader.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Bacterial Typing Techniques; Genotype; Interspersed Repetitive Sequences; Minisatellite Repeats; Mycobacterium tuberculosis; Polymorphism, Restriction Fragment Length
PubMed: 31603462
DOI: 10.1093/bioinformatics/btz771 -
PloS One 2022Nigeria ranks 1st in Africa and 6th globally with the highest burden of tuberculosis (TB). However, only a relatively few studies have addressed the molecular...
Nigeria ranks 1st in Africa and 6th globally with the highest burden of tuberculosis (TB). However, only a relatively few studies have addressed the molecular epidemiology of Mycobacterium tuberculosis in this country. The aim of this work was to analyze the genetic structure of drug-resistant (DR) M. tuberculosis population in the Plateau State (central Nigeria), with the results placed in the broader context of West Africa. The study sample included 67 DR M. tuberculosis isolates, recovered from as many TB patients between November 2015 and January 2016, in the Plateau State. The isolates were subjected to spoligotyping and MIRU-VNTR typing. A total of 20 distinct spoligotypes were obtained, split into 3 clusters (n = 50, 74.6%, 2-33 isolates per cluster) and 17 (25.4%) unique patterns. The Cameroon clade was the largest lineage (62.7%) followed by T (28.3%), LAM (3%), and Haarlem (3%) clades. Upon MIRU-VNTR typing, the isolates produced 31 profiles, i.e. 7 clusters (n = 43, 64.2%, 2-17 isolates per cluster) and 24 singletons. A combined spoligotyping and MIRU-VNTR typing analysis showed 20.9% of the cases clustered and estimated the recent transmission rate at 11.9%. In conclusion, two lineages, namely Cameroon, and T accounted for the majority (91%) of cases. No association was observed between the most prevalent Cameroon lineage and drug resistance, including multidrug resistant (MDR) phenotype, or any of the patient demographic characteristics.
Topics: Genotype; Humans; Minisatellite Repeats; Mycobacterium tuberculosis; Nigeria; Tuberculosis; Tuberculosis, Multidrug-Resistant
PubMed: 35609028
DOI: 10.1371/journal.pone.0266837