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 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 Mining for Single Nucleotide Polymorphisms and Insertions/Deletions in Maize Expressed Sequence Tag Data

2003 ◽  
Vol 132 (1) ◽  
pp. 84-91 ◽  
Author(s):  
Jacqueline Batley ◽  
Gary Barker ◽  
Helen O'Sullivan ◽  
Keith J. Edwards ◽  
David Edwards
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Expressed Sequence Tag ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Expressed Sequence

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.

Population structure of pigs determined by single nucleotide polymorphisms observed in assembled expressed sequence tags

2011 ◽  
Vol 83 (1) ◽  
pp. 14-22 ◽  
Author(s):  
Toshimi MATSUMOTO ◽  
Naohiko OKUMURA ◽  
Hirohide UENISHI ◽  
Takeshi HAYASHI ◽  
Noriyuki HAMASIMA ◽  
...  
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Expressed Sequence Tags ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Expressed Sequence

scholarly journals Confirming Single Nucleotide Polymorphisms from Expressed Sequence Tag Datasets Derived from Three Cattle cDNA Libraries

BMB Reports ◽  
2006 ◽  
Vol 39 (2) ◽  
pp. 183-188 ◽  
Author(s):  
Seung-Hwan Lee ◽  
Eung-Woo Park ◽  
Yong-Min Cho ◽  
Ji-Woong Lee ◽  
Hyoung-Yong Kim ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Expressed Sequence Tag ◽  
Cdna Libraries ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Expressed Sequence

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 Genome-wide Linkage Analysis with Clustered SNP Markers

2008 ◽  
Vol 14 (1) ◽  
pp. 92-96 ◽  
Author(s):  
Kaja K. Selmer ◽  
Kristin Brandal ◽  
Ole K. Olstad ◽  
Bård Birkenes ◽  
Dag E. Undlien ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Linkage Mapping ◽  
Snp Markers ◽  
Monogenic Disease ◽  
Comparison Of Methods ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome ◽  
Large Families

Single nucleotide polymorphisms (SNPs) have recently replaced microsatellites as the genetic markers of choice in linkage analysis, primarily because they are more abundant and the genotypes more amenable for automatic calling. One of the most recently launched linkage mapping sets (LMS) is the Applied Biosystems Human LMS 4K, which is a genome-wide linkage set based on the SNPlex™ technology and the use of clustered SNPs. In this article the authors report on their experience with this set and the associated genotyping software GeneMapper® version 4.0, which they have used for linkage analyses in 17 moderate to large families with assumed monogenic disease. For comparison of methods, they also performed a genome-wide linkage analysis in 1 of the 17 families using the Affymetrix GeneChip® Human Mapping 10K 2.0 array. The conclusion is that both methods performed technically well, with high call rates and comparable and low rates of Mendelian inconsistencies. However, genotyping is less automated in GeneMapper® version 4.0 than in the Affymetrix software and thus more time consuming. ( Journal of Biomolecular Screening 2009:92-96)

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