VNTR (variable number of tandem repeats) markers show loss of chromosome 17p sequences in human colorectal carcinomas

1988 ◽  
Vol 48 (3) ◽  
pp. 167-169 ◽  
Author(s):  
R.A. Lothe ◽  
Y. Nakamura ◽  
S. Woodward ◽  
T.G. Gedde-Dahl, Jr ◽  
R. White
Keyword(s):  
Tandem Repeats ◽  
Variable Number ◽  
Colorectal Carcinomas

Quantitative evaluation of post-bone marrow transplant engraftment status using fluorescent-labeled variable number of tandem repeats

2000 ◽  
Vol 05 (2) ◽  
pp. 129-138
Author(s):  
Robert A. Luhm ◽  
Daniel B. Bellissimo ◽  
Arejas J. Uzgiris ◽  
William R. Drobyski ◽  
Martin J. Hessner
Keyword(s):  
Bone Marrow ◽  
Bone Marrow Transplant ◽  
Quantitative Evaluation ◽  
Tandem Repeats ◽  
Marrow Transplant ◽  
Variable Number

Dopaminergic Genes Polymorphisms and Prefrontal Cortex Efficiency Among Obese People - Whether Gender is a Differentiating Factor?

2019 ◽  
Vol 19 (6) ◽  
pp. 405-418
Author(s):  
Maciej Bieliński ◽  
Natalia Lesiewska ◽  
Roman Junik ◽  
Anna Kamińska ◽  
Andrzej Tretyn ◽  
...  
Keyword(s):  
Prefrontal Cortex ◽  
Executive Functions ◽  
Tandem Repeats ◽  
Wisconsin Card Sorting Test ◽  
Variable Number ◽  
Card Sorting ◽  
Obese People ◽  
Perseverative Errors ◽  
Wisconsin Card Sorting ◽  
Sorting Test

Background:Obesity is a chronic condition associated with poorer cognitive functioning. Wisconsin Card Sorting Test (WCST) is a useful tool for evaluating executive functions. In this study, we assessed the association between dopaminergic gene polymorphisms: DAT1 (SLC6A3), COMTVal158Met, DRD4 (48-bp variable number of tandem repeats - VNTR) and WCST parameters to investigate the functions of the frontal lobes in obese individuals.Objective:To find the significant correlations between polymorphisms of DAT1, COMTVal158Met, DRD4 and executive functions in obese subjects.Methods:The analysis of the frequency of individual alleles was performed in 248 obese patients (179 women, 69 men). Evaluation of the prefrontal cortex function (operating memory and executive functions) was measured with the Wisconsin Card Sorting Test (WCST). Separate analyzes were performed in age subgroups to determine different activities and regulation of genes in younger and older participants.Results:Scores of WCST parameters were different in the subgroups of women and men and in the age subgroups. Regarding the COMT gene, patients with A/A and G/A polymorphisms showed significantly better WCST results in WCST_P, WCST_CC and WCST_1st. Regarding DAT1 men with L/L and L/S made less non-perseverative errors, which was statistically significant. In DRD4, significantly better WCST_1st results were found only in older women with S allele.Conclusion:Obtained results indicate the involvement of dopaminergic transmission in the regulation of prefrontal cortex function. Data analysis indicates that prefrontal cortex function may ensue, from different elements such as genetic factors, metabolic aspects of obesity, and hormonal activity (estrogen).

scholarly journals Molecular characteristics of Brucella melitensis isolates from humans in Qinghai Province, China

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Zhi-Jun Zhao ◽  
Ji-Quan Li ◽  
Li Ma ◽  
Hong-Mei Xue ◽  
Xu-Xin Yang ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Brucella Melitensis ◽  
Draft Genome ◽  
Geographic Origin ◽  
Variable Number ◽  
Human Brucellosis ◽  
Molecular Characteristics ◽  
Whole Genome ◽  
Qinghai Province ◽  
Variable Number Tandem Repeats

Abstract Background The prevalence of human brucellosis in Qinghai Province of China has been increasing rapidly, with confirmed cases distributed across 31 counties. However, the epidemiology of brucellosis transmission has not been fully elucidated. To characterize the infecting strains isolated from humans, multiple-locus variable-number tandem repeats analysis (MLVA) and whole-genome single-nucleotide polymorphism (SNP)-based approaches were employed. Methods Strains were isolated from two males blood cultures that were confirmed Brucella melitensis positive following biotyping and MLVA. Genomic DNA was extracted from these two strains, and whole-genome sequencing was performed. Next, SNP-based phylogenetic analysis was performed to compare the two strains to 94 B. melitensis strains (complete genome and draft genome) retrieved from online databases. Results The two Brucella isolates were identified as B. melitensis biovar 3 (QH2019001 and QH2019005) following conventional biotyping and were found to have differences in their variable number tandem repeats (VNTRs) using MLVA-16. Phylogenetic examination assigned the 96 strains to five genotype groups, with QH2019001 and QH2019005 assigned to the same group, but different subgroups. Moreover, the QH2019005 strain was assigned to a new subgenotype, IIj, within genotype II. These findings were then combined to determine the geographic origin of the two Brucella strains. Conclusions Utilizing a whole-genome SNP-based approach enabled differences between the two B. melitensis strains to be more clearly resolved, and facilitated the elucidation of their different evolutionary histories. This approach also revealed that QH2019005 is a member of a new subgenotype (IIj) with an ancient origin in the eastern Mediterranean Sea.

scholarly journals Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Tsung-Yu Lu ◽  
Katherine M. Munson ◽  
Alexandra P. Lewis ◽  
Qihui Zhu ◽  
Luke J. Tallon ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Traditional Approach ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Population Diversity ◽  
Protein Coding ◽  
Short Reads ◽  
Repeat Structure ◽  
Continental Population ◽  
Develop Software

AbstractVariable number tandem repeats (VNTRs) are composed of consecutive repetitive DNA with hypervariable repeat count and composition. They include protein coding sequences and associations with clinical disorders. It has been difficult to incorporate VNTR analysis in disease studies that use short-read sequencing because the traditional approach of mapping to the human reference is less effective for repetitive and divergent sequences. In this work, we solve VNTR mapping for short reads with a repeat-pangenome graph (RPGG), a data structure that encodes both the population diversity and repeat structure of VNTR loci from multiple haplotype-resolved assemblies. We develop software to build a RPGG, and use the RPGG to estimate VNTR composition with short reads. We use this to discover VNTRs with length stratified by continental population, and expression quantitative trait loci, indicating that RPGG analysis of VNTRs will be critical for future studies of diversity and disease.

scholarly journals Community-based geographical distribution of Mycobacterium ulcerans VNTR-genotypes from the environment and humans in the Nyong valley, Cameroon

2021 ◽  
Vol 49 (1) ◽  
Author(s):  
Francis Zeukeng ◽  
Anthony Ablordey ◽  
Solange E. Kakou-Ngazoa ◽  
Stephen Mbigha Ghogomu ◽  
David N’golo Coulibaly ◽  
...  
Keyword(s):  
Environmental Samples ◽  
Tandem Repeats ◽  
Buruli Ulcer ◽  
Variable Number ◽  
Mycobacterium Ulcerans ◽  
Community Based ◽  
Human Samples ◽  
Route Of Transmission ◽  
Mode Of Transmission ◽  
Animal Reservoirs

Abstract Background Genotyping is a powerful tool for investigating outbreaks of infectious diseases and it can provide useful information such as identifying the source and route of transmission, and circulating strains involved in the outbreak. Genotyping techniques based on variable number of tandem repeats (VNTR) are instrumental in detecting heterogeneity in Mycobacterium ulcerans (MU) and also for discriminating MU from other mycobacteria species. Here, we describe and map the distribution of MU genotypes in Buruli ulcer (BU) endemic communities of the Nyong valley in Cameroon. We also tested the hypothesis of whether the suspected animal reservoirs of BU that share the human microhabitat are shedding contaminated fecal matters and saliva into their surrounding environments. Methods Environmental samples from suspected MU-risk factors and lesion swabs from human patients were sampled in BU-endemic communities and tested for the presence of MU by qPCR targeting three independent sequences (IS2404, IS2606, KR-B). Positive samples to MU were further genotyped by VNTR with confirmation by sequencing of four loci (MIRU1, Locus 6, ST1, Locus 19). Results MU was detected in environmental samples including water bodies (23%), biofilms (14%), detritus (10%), and in human patients (73%). MU genotypes D, W, and C were found both in environmental and human samples. The micro geo-distribution of MU genotypes from communities showed that genotype D is found both in environmental and human samples, while genotypes W and C are specific to environmental samples and human lesions, respectively. No obvious focal grouping of MU genotypes was observed at the community scale. An additional survey in the human microhabitat suggests that domestic and wild animals do not shed MU in their saliva and feces in sampled communities. Conclusions VNTR typing uncovered different MU genotypes circulating in the endemic communities of the Akonolinga district. A MU environmental genotype was found in patients, yet the mechanism of contamination remains to be investigated; and recovering MU in culture from the environment remains key priority to enable a better understanding of the mode of transmission of BU. We also conclude that excretions from suspected animals are unlikely to be major sources of MU in the Nyong Valley in Cameroon.

scholarly journals Multi-country outbreak of Salmonella enteritidis infection linked to the international ice hockey tournament

2017 ◽  
Vol 145 (11) ◽  
pp. 2221-2230 ◽  
Author(s):  
T. PÄRN ◽  
V. DAHL ◽  
T. LIENEMANN ◽  
J. PEREVOSČIKOVS ◽  
B. DE JONG
Keyword(s):  
Information Exchange ◽  
Salmonella Enteritidis ◽  
Tandem Repeats ◽  
Relevant Information ◽  
Variable Number ◽  
Ice Hockey ◽  
Waterborne Diseases ◽  
Trace Back ◽  
Epidemic Intelligence ◽  
Public Health Authorities

SUMMARYIn April 2015, Finnish public health authorities alerted European Union member states of a possible multi-country Salmonella enteritidis outbreak linked to an international youth ice-hockey tournament in Latvia. The European Centre for Disease Prevention and Control (ECDC), Finnish and Latvian authorities initiated an outbreak investigation to identify the source. The investigation included a description of the outbreak, retrospective cohort study, microbiological investigation and trace-back. We identified 154 suspected and 96 confirmed cases from seven countries. Consuming Bolognese sauce and salad at a specific event arena significantly increased the risk of illness. Isolates from Finnish, Swedish and Norwegian cases had an identical multiple-locus variable-number of tandem repeats analysis-profile (3-10-6-4-1). Breaches in hygiene and food storing practices in the specific arena's kitchen allowing for cross-contamination were identified. Riga Cup participants were recommended to follow good hand hygiene and consume only freshly cooked foods. This investigation demonstrated that the use of ECDC's Epidemic Intelligence Information System for Food- and Waterborne Diseases and Zoonoses platform was essential to progress the investigation by facilitating information exchange between countries. Cross-border data sharing to perform whole genome sequencing gave relevant information regarding the source of the outbreak.

scholarly journals DRD4 Gene Polymorphisms as a Risk Factor for Children with Attention Deficit Hyperactivity Disorder in Iranian Population

2017 ◽  
Vol 2017 ◽  
pp. 1-5
Author(s):  
Seyed Mahmoud Tabatabaei ◽  
Shahrokh Amiri ◽  
Sara Faghfouri ◽  
Seyed Gholamreza Noorazar ◽  
Shahin AbdollahiFakhim ◽  
...  
Keyword(s):  
Attention Deficit Hyperactivity Disorder ◽  
Attention Deficit ◽  
Tandem Repeats ◽  
Receptor Gene ◽  
Variable Number ◽  
Healthy Children ◽  
Drd4 Gene ◽  
Hyperactivity Disorder ◽  
Significant Difference ◽  
Northwest Of Iran

Background and Objective. Dopamine dysfunction is known to be associated with attention deficit hyperactivity disorder (ADHD). Dopamine D4 receptor gene (DRD4) is one of the important genes in this pathway. This study intended to investigate the variable number of tandem repeats (VNTR) in exon 3 of the DRD4 gene in Iranian children and adolescents. Materials and Methods. In this study, 130 children with ADHD, aged 6–14 years, and 130 healthy children, within the same age range, were enrolled. All children were selected from northwest of Iran which have Caucasian ethnic background and are of a Turkic ethnic group. VNTR polymorphisms of the DRD4 gene were evaluated by PCR using exon 3-specific primers followed by agarose gel electrophoresis. Findings. The Hardy-Weinberg principle and Chi-square test showed a significant difference in 4-repetition (4R) alleles between the ADHD (76.2%) and control (53.8%) groups (p=0.004; X2=17.39; df=5). The least percentage of repetition alleles in both groups was 2R. Conclusion. There is a significant correlation between the 4R alleles of DRD4 and ADHD in the northwest of Iran.

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