scholarly journals Identification of Wolf-Dog Hybrids in Europe – An Overview of Genetic Studies

2021 ◽  
Vol 9 ◽  
Author(s):  
Arkadiusz Dziech
Keyword(s):  
Bayesian Clustering ◽  
Nucleotide Polymorphisms ◽  
Ancestry Informative Markers ◽  
Single Nucleotide ◽  
Genetic Studies ◽  
Significant Development ◽  
Reliable Identification ◽  
Advantages And Disadvantages ◽  
Reliable Knowledge ◽  
Species Hybridization

Significant development of genetic tools during the last decades provided opportunities for more detailed analyses and deeper understanding of species hybridization. New genetic markers allowed for reliable identification of admixed individuals deriving from recent hybridization events (a few generations) and those originating from crossings up to 19 generations back. Implementation of microsatellites (STRs) together with Bayesian clustering provided abundant knowledge regarding presence of admixed individuals in numerous populations and helped understand the problematic nature of studying hybridization (i.a., defining a reliable thresholds for recognizing individuals as admixed or obtaining well-grounded results representing actual proportion of hybrids in a population). Nevertheless, their utilization is limited to recent crossbreeding events. Single Nucleotide Polymorphisms (SNPs) proved to be more sensible tools for admixture analyses furnishing more reliable knowledge, especially for older generation backcrosses. Small sets of Ancestry Informative Markers (AIMs) of both types of markers were effective enough to implement in monitoring programs, however, SNPs seem to be more appropriate because of their ability to identify admixed individuals up to 3rd generations. The main aim of this review is to summarize abundant knowledge regarding identification of wolf-dog hybrids in Europe and discuss the most relevant problems relating to the issue, together with advantages and disadvantages of implemented markers and approaches.

scholarly journals Detecting Genetic Associations betweenATG5and Lupus Nephritis bytrans-eQTL

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Yue-miao Zhang ◽  
Fa-juan Cheng ◽  
Xu-jie Zhou ◽  
Yuan-yuan Qi ◽  
Ping Hou ◽  
...  
Keyword(s):  
Lupus Nephritis ◽  
Lupus Erythematosus ◽  
Clinical Information ◽  
Nucleotide Polymorphisms ◽  
Genetic Associations ◽  
Single Nucleotide ◽  
Genetic Studies ◽  
Genome Wide ◽  
Custom Made ◽  
Regulatory Effects

Objectives. Numerous loci were identified to perturb gene expression intrans. As elevatedATG5expression was observed in systemic lupus erythematosus (SLE), the study was conducted to analyze the genome-wide genetic regulatory mechanisms associated withATG5expression in a Chinese population with lupus nephritis (LN).Methods. The online expression quantitative trait loci database was searched fortrans-expression single nucleotide polymorphisms (trans-eSNPs) ofATG5. Taggingtrans-eSNPs were genotyped by a custom-made genotyping chip in 280 patients and 199 controls. For positive findings, clinical information and bioinformation analyses were performed.Results. Fourtrans-eSNPs were observed to be associated with susceptibility to LN (P< 0.05), including ANKRD50 rs17008504, AGA rs2271100, PAK7 rs6056923, and TET2 rs1391441, while seven othertrans-eSNPs showed marginal significant associations (0.05 <P< 0.1). Correlations between thetrans-eSNPs andATG5expression and different expression levels ofATG5in SLE patients and controls were validated, and their regulatory effects were annotated. However, no significant associations were observed between different genotypes oftrans-eSNPs and severity or outcome of the patients.Conclusion. Using the new systemic genetics approach, we identified 10 loci associated with susceptibility to LN potentially, which may be complementary to future pathway based genetic studies.

scholarly journals Candidate single nucleotide polymorphisms of irritable bowel syndrome: a systemic review and meta-analysis

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Shiwei Zhu ◽  
Ben Wang ◽  
Qiong Jia ◽  
Liping Duan
Keyword(s):  
Irritable Bowel Syndrome ◽  
Single Nucleotide Polymorphisms ◽  
Meta Analysis ◽  
Systemic Review ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genetic Studies ◽  
Increased Risk ◽  
Rome Iii ◽  
Irritable Bowel

Abstract Background Genetic factors increase the risk of irritable bowel syndrome (IBS). Analysis of single nucleotide polymorphisms (SNPs) has been used in IBS patients, but the findings are inconsistent. The goal of this review was to synthesize all the published SNPs studies of IBS through meta-analysis to objectively evaluate the relevance of SNPs to IBS risks. Methods IBS - related polymorphisms studies from 2000 to 2018 were searched. Pooled odds ratios with a 95% confidence interval for each SNP were evaluated through five genetic models. Ethnicity, ROME criteria and IBS subtypes were defined for subgroup analyze. Results Ten relevant genes were evaluated. SNPs rs4263839 and rs6478108 of TNFSF15 associated with an increased risk of IBS; IL6 rs1800795 increased the risk for Caucasian IBS patients which diagnosed by Rome III criteria; and IL23R rs11465804 increased the risk for IBS-C patients. IL10 rs1800896 GG genotype associated with a decreased risk of IBS. No evidence supported the association of GNβ3 rs5443, TNFα rs1800629, and IL10 rs1800871 to IBS in this study. Conclusions This meta-analysis presents an in-depth overview for IBS SNPs analysis. It was confirmed that polymorphisms of TNFSF15 associated with increased IBS risk, while IL10 rs1800896 associated with decreased IBS risk. It might offer some insights into polymorphisms of inflammation factors which might affect IBS susceptibility. Moreover, the analysis also emphasizes the importance of diagnostic criteria and phenotype homogeneity in IBS genetic studies.

scholarly journals Genetic approaches to studying virulence and pathogenesis in Toxoplasma gondii

2002 ◽  
Vol 357 (1417) ◽  
pp. 81-88 ◽  
Author(s):  
L. David Sibley ◽  
Dana G. Mordue ◽  
Chunlei Su ◽  
Paul M. Robben ◽  
Dan K. Howe
Keyword(s):  
Toxoplasma Gondii ◽  
Linkage Mapping ◽  
Protozoan Parasite ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genetic Studies ◽  
Microarray Studies ◽  
Expressed Sequence ◽  
Surprising Finding ◽  
Host Genes

Toxoplasma gondii is a common protozoan parasite that causes disease in immunocompromised humans. Equipped with a wide array of experimental tools, T. gondii has rapidly developed as a model parasite for genetic studies. The population structure of T. gondii is highly clonal, consisting of three distinct lineages that differ dramatically in virulence. Acute virulence is probably mediated by the genetic differences that distinguish strain types. We have utilized a combination of genetic approaches to investigate the acute virulence of toxoplasmosis using the mouse model. These studies reveal the surprising finding that pathogenicity is due to the over–stimulation of normally protective immune responses. Classical genetic linkage mapping studies indicate that genes that mediate acute virulence are linked to chromosome VII in the parasite. To increase the resolution of genetic mapping studies, single–nucleotide polymorphisms are being developed based on an extensive database of expressed sequence tags (ESTs) from T. gondii . Separately, DNA microarray studies are being used to examine the expression of parasite and host genes during infection. Collectively, these approaches should improve current understanding of virulence and pathogenicity in toxoplasmosis.

scholarly journals Screening of single nucleotide polymorphisms among fuchs’ endothelial corneal dystrophy subjects in Malaysia

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ker Hsin Ng ◽  
Visvaraja Subrayan ◽  
Vasudevan Ramachandran ◽  
Fazliana Ismail
Keyword(s):  
Tertiary Care ◽  
Corneal Dystrophy ◽  
Nucleotide Polymorphisms ◽  
Older Individuals ◽  
Single Nucleotide ◽  
Genetic Studies ◽  
Novel Variant ◽  
Different Populations ◽  
Larger Sample ◽  
Control Study

Abstract Background The pathophysiology underlying Fuchs' Endothelial Corneal Dystrophy (FECD), especially in older individuals, remains unclear, with a genetic predisposition being reported as the single best predictor of the disease. Genetic studies have shown that several genes in various loci such as COL8A2, SLC4A11, TCF8/ZEB1 and TCF4 are associated with FECD in different populations and ethnicities. A case–control study was conducted to determine the association between genetic variants and FECD in a tertiary care setting in Malaysia. A total number of 12 patients with clinically diagnosed FECD and 12 age, gender and race matched control subjects were recruited. Extracted genomic DNA were genotyped using Infinium Global Screening Array (GSA)-24 version 1.0 BeadChip with iScan high-throughput system. Illumina GenomeStudio 2.0 Data Analysis and PLINK version 1.9 software were used to perform association tests and determine the distribution of obtained variants among the cases and controls. Results A significant novel genetic variant, rs11626651, a variant of the LOC105370676 gene or known as the LINC02320 gene, located at chromosome 14, has been identified as a suggestive association with FECD (p < 5 × 10−6). Further analysis in this study suggested that candidate genes such as COL8A2, ZEB1/TCF8, TCF4 and SLC4A11 had no significant associations with FECD. Conclusions The discovery of a novel variant may influence the underlying pathogenic basis of FECD in Malaysia. The current study is the first genetic study on FECD to use Infinium GSA. It is the first comprehensive report in Malaysia to provide genetic information of potential relevance to FECD, which may pave the way for new therapeutic strategies in the future. A detailed analysis with a larger sample size is recommended for further evaluation.

Association of PPARG Gene Polymorphisms Pro12Ala with Type 2 Diabetes Mellitus: A Meta-analysis

2019 ◽  
Vol 15 (4) ◽  
pp. 277-283 ◽  
Author(s):  
Junyan Li ◽  
Xiaohong Niu ◽  
JianBo Li ◽  
Qingzhong Wang
Keyword(s):  
Publication Bias ◽  
Chinese Population ◽  
Meta Analysis ◽  
Genetic Data ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genetic Studies ◽  
Combined Analysis ◽  
Pparg Gene

Background:Previous studies suggested that the single nucleotide polymorphisms of Pro12Ala located within the PPARG gene were significantly associated with the T2DM. Recently, the genetic studies on Pro12Ala were conducted in the different ethnic groups and the results of each study were shown to be inconsistent. Moreover, the systematic review has not been updated since 2000.Objective:To further validate the risk of Pro12Ala for T2DM disease based on the genetic data.Methods:The genetic studies on the Pro12Ala in the T2DM were searched in the PubMed and PMC database from January 2000 to October 2017. The meta-analysis was conducted with the CMA software.Results:The meta-analysis collected 14 studies including 20702 cases and 36227 controls. The combined analysis of all studies found that Pro12Ala was shown to be significantly associated with T2DM and the Ala allele played the increasing risks for the disease. Nevertheless, publication bias was detected in the combined analysis. The subgroup analysis indicated that Pro12Ala was found to be significant in the Caucasian and Chinese population. There was no heterogeneity and publication bias in these two groups.Conclusion:The meta-analysis confirmed the evidence that the Pro12Ala was the susceptible variant for the decreasing risks for the T2DM

scholarly journals Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland

2019 ◽  
Author(s):  
S. Eryn McFarlane ◽  
Darren C. Hunter ◽  
Helen V. Senn ◽  
Stephanie L. Smith ◽  
Rebecca Holland ◽  
...  
Keyword(s):  
Cervus Elaphus ◽  
Native Species ◽  
Red Deer ◽  
Cervus Nippon ◽  
Natural Process ◽  
Nucleotide Polymorphisms ◽  
Ancestry Informative Markers ◽  
Pure Species ◽  
Single Nucleotide ◽  
Better Than

AbstractHybridization is a natural process at species range boundaries, but increasing numbers of species are hybridizing due to direct or indirect human activities. In such cases of anthropogenic hybridization, subsequent introgression can threaten the survival of native species. To date many such systems have been studied with too few genetic markers to assess the level of threat resulting from advanced backcrossing. Here we use 44,999 single nucleotide polymorphisms and the ADMIXTURE program to study two areas of Scotland where a panel of 22 diagnostic microsatellites previously identified introgression between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon). In Kintyre we reclassify 26% of deer from the pure species categories to the hybrid category whereas in the NW Highlands we only reclassify 2%. As expected, the reclassified individuals are mostly advanced backcrosses. We also investigate the ability of marker panels selected on different posterior allele frequency criteria to find hybrids assigned by the full marker set, and show that in our data, ancestry informative markers (i.e. those that are highly differentiated between the species, but not fixed) are better than diagnostic markers (those markers that are fixed between the species) because they are more evenly distributed in the genome. Diagnostic loci are concentrated on the X chromosome to the detriment of autosomal coverage.

scholarly journals In silico analysis of single nucleotide polymorphisms (SNPs) in human FOXC2 gene

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 243
Author(s):  
Mohammed Nimir ◽  
Mohanad Abdelrahim ◽  
Mohamed Abdelrahim ◽  
Mahil Abdalla ◽  
Wala eldin Ahmed ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Conservation Score ◽  
Interaction Network ◽  
In Silico Analysis ◽  
Gene Interaction ◽  
Nucleotide Polymorphisms ◽  
Gene Interaction Network ◽  
Single Nucleotide ◽  
Functional Studies ◽  
Advantages And Disadvantages

Introduction: Lymphedema is an abnormal accumulation of interstitial fluid, due to inefficient uptake and reduced flow, leading to swelling and disability, mostly in the extremities. Hereditary lymphedema usually occurs as an autosomal dominant trait with allelic heterogeneity. Methods: We identified single nucleotide polymorphisms (SNPs) in the FOXC2 gene using dbSNP, analyzed their effect on the resulting protein using VEP and Biomart, modelled the resulting protein using Project HOPE, identified gene – gene interactions using GeneMANIA and predicted miRNAs affected and the resulting effects of SNPs in the 5’ and 3’ regions using PolymiRTS. Results: We identified 473 SNPs - 429 were nsSNPs and 44 SNPs were in the 5’ and 3’ UTRs. In total, 2 SNPs - rs121909106 and rs121909107 - have deleterious effects on the resulting protein, and a 3D model confirmed those effects. The gene – gene interaction network showed the involvement of FOXC2 protein in the development of the lymphatic system. hsa-miR-6886-5p, hsa-miRS-6886-5p, hsa-miR-6720-3p, which were affected by the SNPs rs201118690, rs6413505, rs201914560, respectively, were the most important miRNAs affected, due to their high conservation score. Conclusions: rs121909106 and rs121909107 were predicted to have the most harmful effects, while hsa-miR-6886-5p, hsa-miR-6886-5p and hsa-miR-6720-3p were predicted to be the most important miRNAs affected. Computational biology tools have advantages and disadvantages, and the results they provide are predictions that require confirmation using methods such as functional studies.

The Influence of Single Nucleotide Polymorphisms of NOD2 or CD14 on Susceptibility to Tuberculosis: A Systematic Review

2020 ◽  
Author(s):  
Juan M Cubillos-Angulo ◽  
Catarina D Fernandes ◽  
Davi N Araújo ◽  
Cristinna A Carmo ◽  
María B Arriaga ◽  
...  
Keyword(s):  
Systematic Review ◽  
Single Nucleotide Polymorphisms ◽  
Causes Of Death ◽  
Nucleotide Polymorphisms ◽  
Chinese Han ◽  
Single Nucleotide ◽  
Genetic Studies ◽  
Quality Scale ◽  
Reported Data ◽  
The Relationship

Abstract Background: Tuberculosis (TB) is still one of the leading causes of death worldwide. Genetic studies have pointed to the relevance of the NOD2 and CD14 polymorphic alleles in association with susceptibility or resistance to TB. Methods: A systematic review was performed on search platforms to examine the association between single nucleotide polymorphisms (SNP) and TB risk. Study quality was evaluated using the Newcastle-Ottawa Quality Scale (NOQS) Results: Thirteen studies matched the selection criteria. Of those, 9 investigated CD14 SNPs, and 6 reported a significant association between the T allele and TT genotypes of the rs2569190 SNP and increased TB risk. In contrast, the genotype CC was found to be protective against the disease. Furthermore, in two studies, rs2569191 SNP of the CD14, G allele was described to be significantly associated with increased TB risk. Four studies reported data uncovering the relationship between NOD2 SNPs and TB risk, with two of them reporting significant associations of rs1861759 and rs7194886 and higher TB risk in a Chinese Han population. Paradoxically, minor allele carriers (CG or GG) of rs2066842 and rs2066844 NOD2 SNPs were associated with lower TB risk in African Americans. Conclusions: The CD14 rs2569190 and rs2569191 polymorphisms influence TB risk depending on the allele. Furthermore, there is significant association between NOD2 SNPs rs1861759 and rs7194886 and augmented risk of TB, especially in persons with Chinese ethnicity. The referred polymorphisms of CD14 and NOD2 genes likely play an important role in TB susceptibility and physiopathology; such effect may be affected by ethnicity.Systematic review registration: CRD42020186523

Hsa-miR-196a2 Rs 11614913 C>T polymorphism and CRC susceptibility: A case-control study.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e16066-e16066
Author(s):  
Li-zhu Chen ◽  
Yu Chen ◽  
Wei-feng Tang ◽  
Lin Chen ◽  
Jin Lin ◽  
...  
Keyword(s):  
Alcohol Use ◽  
Smoking Status ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genetic Studies ◽  
Incidence And Mortality ◽  
Genes Encoding ◽  
Pcr Method ◽  
Relationship Of ◽  
The Relationship

e16066 Background: The incidence and mortality rate of Colorectal cancer (CRC) is high worldwide. Many genetic studies have suggested that single nucleotide polymorphisms (SNPS) in genes encoding small molecule RNAs were associated with CRC risk, but the results were different in different studies. In our study, we investigated the general demographic characteristics and the relationship of hsa-mir-196a2 rs11614913 C > T polymorphism and CRC susceptibility in Chinese CRC. Methods: Our study included 1,003 CRC patients and 1,303 controls. Restriction fragment length polymorphism (RFLP-PCR) method was used for genotyping and SAS version 9.4 software for statistical analysis. Results: The incidence of smoking status,alcohol use and BMI in the CRC group (25.82%,17.35%,66.80%) were much higher than that in the control subjects (20.34%,10.44%,52.80%) respectively(P < 0.05). After adjusting age and other factors, hsa-mir-196a2 rs11614913 C > T genotypes were not statistically correlated with CRC risk and tumor location.But the TT genotype in the hsa-mir-196a2 rs11614913 C > T polymorphism reduced the risk of CRC in women (OR = 0.64, 95 CI: 0.42-0.97, P = 0.036). Conclusions: Smoking status,alcohol use and BMI may be main risk factors for CRC development in our study population.The polymorphism of hsa-mir-196a2 rs11614913 C > T gene may affect the risk of CRC in women, which requires further investigation in a larger cohort in the future.

Replication of European Rheumatoid Arthritis Loci in a Pakistani Population

2013 ◽  
Vol 40 (4) ◽  
pp. 401-407 ◽  
Author(s):  
Syed Fazal Jalil ◽  
Attya Bhatti ◽  
F. Yesim Demirci ◽  
Xingbin Wang ◽  
Iltaf Ahmed ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Nucleotide Polymorphisms ◽  
Susceptibility Loci ◽  
Control Software ◽  
Single Nucleotide ◽  
Genetic Studies ◽  
P Values ◽  
Pakistani Population ◽  
Family Case ◽  
Different Populations

Objective.Genetic studies have identified several rheumatoid arthritis (RA) susceptibility loci in European-derived populations. The same biological pathways may be involved in determining the RA risk in different population groups. We sought to replicate the association of 33 single-nucleotide polymorphisms (SNP) from 31 RA susceptibility loci confirmed among Europeans in a unique Pakistani population.Methods.We genotyped 33 SNP in a sample of 366 Pakistanis that comprised related and unrelated cases and controls. Genotyping was performed using TaqMan assays and the results were analyzed with family case-control software.Results.Twelve of the 33 SNP were replicated in this sample with significant p values ranging from 7.05E-06 to 3.72E-02, the most significant being the KIF5A-PIP4K2C/rs1678542 SNP.Conclusion.Our observations suggest that a number of RA susceptibility loci and related pathways are shared across different populations.

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