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British Journal of Biomedical Science 2022The MIR137 gene acts as a tumor-suppressor gene in colon and gastric cancers. The aim of this study was to investigate the association of functional variable number...
The MIR137 gene acts as a tumor-suppressor gene in colon and gastric cancers. The aim of this study was to investigate the association of functional variable number tandem repeat (VNTR) polymorphism rs58335419 locating in the upstream of the MIR137 gene with the risk of colon and gastric cancers. Totally, 429 individuals were contributed in the study, including 154 colon and 120 gastric cancer patients and 155 healthy controls. The target VNTR was genotyped using PCR and electrophoresis for all samples. Statistical analysis was performed using SPSS 21.0 software and by T, χ2 and logistic regression tests. Excluding the rare genotypes, our results showed that genotype 3/5 (95% CI = 1.08-3.73, OR = 2.01, = 0.026) significantly increased the risk of colon cancer but not gastric cancer (95% CI = 0.88-3.30, OR = 1.70, = 0.114). Also, in the stratification analysis for VNTRs and sex, genotypes 3/4 (95% CI = 1.00-6.07, OR = 2.46, = 0.049) and 3/5 (95% CI = 1.25-7.18, OR = 2.99, = 0.014) significantly increased the risk of colon cancer in men but not in women. In addition, all genotypes including the rare genotypes as a group, significantly increase the risk of gastric (95% CI = 1.14-3.00, OR = 1.85, = 0.012) and colon (95% CI = 1.38-3.43, OR = 2.17, = 0.001) cancers compared to the genotype 3/3 as a reference. The results show that increasing the copy of VNTR in the MIR137 gene, increases the risk of colon and gastric cancers and can serve as a marker for susceptibility to colon and gastric cancers.
Topics: Case-Control Studies; Colonic Neoplasms; Female; Gene Frequency; Genetic Predisposition to Disease; Genotype; Humans; Male; MicroRNAs; Minisatellite Repeats; Polymorphism, Genetic; Stomach Neoplasms
PubMed: 35996520
DOI: 10.3389/bjbs.2021.10095 -
Croatian Medical Journal Oct 2018To analyze the distribution of SLC6A4 gene polymorphisms in Crohn's disease (CD) patients and their association with the disease.
AIM
To analyze the distribution of SLC6A4 gene polymorphisms in Crohn's disease (CD) patients and their association with the disease.
METHODS
We evaluated the presence/absence of promoter (5-HTTLPR, rs25531) and intron 2 (STin2 VNTR) polymorphic variants of SLC6A4 gene in a retrospective case-control study including 192 CD patients and 157 healthy controls (HC). Genotyping was performed by polymerase chain reaction. The association of polymorphisms with CD and its clinical subtypes was analyzed using χ2 and Fisher exact test, binary logistic regression, and haplotype analysis.
RESULTS
CD patients and healthy controls had similar sex (88 [45.8%] vs 84 [53.5%] women, respectively; P=0.154) and age (41.3±12.8 years vs 41.7±8.8 years, respectively, P=0.091) distribution. Significant differences were observed in the STin2 genotype and allele distribution between CD patients and healthy controls (P=0.003 and P=0.002, respectively) and between the corresponding female subgroups (P=0.004 and P=0.007, respectively), with a significant negative association of biallelic ss (STin2.9 and Stin2.10) STin2 genotype with CD (P=0.013, age- and sex-adjusted odds ratio [OR] 0.5, 95% confidence interval [CI] 0.29-0.86; women: P=0.006, age-adjusted OR 0.32, 95% CI 0.14-0.72) and a significantly higher S-STin2.12 (5-HTTLPR/rs25531: S-STin2: STin2.12) haplotype distribution in CD patients (P=0.004, OR 1.62, 95% CI 1.16-2.26). There was no significant association between 5-HTTLRP and rs25531 genotype or allele frequencies and CD and between any SLC6A4 polymorphic loci with clinical CD subtypes.
CONCLUSION
STin2 VNTR polymorphism of SLC6A4 gene may contribute to CD pathogenesis.
Topics: Adult; Alleles; Case-Control Studies; Crohn Disease; Female; Gene Frequency; Genotyping Techniques; Humans; Introns; Male; Middle Aged; Minisatellite Repeats; Odds Ratio; Polymerase Chain Reaction; Polymorphism, Single Nucleotide; Retrospective Studies; Serotonin Plasma Membrane Transport Proteins
PubMed: 30394015
DOI: 10.3325/cmj.2018.59.232 -
Translational Psychiatry Feb 2020The identification of biomarkers to support the diagnosis and prediction of treatment response for attention-deficit/hyperactivity disorder (ADHD) is still a challenge.... (Meta-Analysis)
Meta-Analysis
The identification of biomarkers to support the diagnosis and prediction of treatment response for attention-deficit/hyperactivity disorder (ADHD) is still a challenge. Our previous works highlighted the DRD4 (dopamine receptor D4) as the best potential genetic marker for childhood diagnosis and methylphenidate (MPH) response. Here, we aimed to provide additional evidence on biomarkers for ADHD diagnosis and treatment response, by using more specific approaches such as meta-analytic and bioinformatics tools. Via meta-analytic approaches including over 3000 cases and 16,000 controls, we demonstrated that, among the different variants studied in DRD4 gene, the 48-base pair, Variable Tandem Repeat Polymorphism, VNTR in exon 3 showed an age/population-specificity and an allelic heterogeneity. In particular, the 7R/"long" allele was identified as an ADHD risk factor in European-Caucasian populations (d = 1.31, 95%CI: 1.17-1.47, Z = 4.70/d = 1.36, 95%CI: 1.20-1.55, Z = 4.78, respectively), also, from the results of last meta-analysis, linked to the poor MPH efficacy. The 4R/"short" allele was a protective factor in European-Caucasian and South American populations (d = 0.83, 95%CI: 0.75-0.92, Z = 3.58), and was also associated to positive MPH response. These results refer to children with ADHD. No evidence of such associations was detected for adults with persistent ADHD (data from the last meta-analysis). Moreover, we found evidence that the 4R allele leads to higher receptor expression and increased sensitivity to dopamine, as compared with the 7R allele (d = 1.20, 95%CI: 0.71-1.69, Z = 4.81), and this is consistent with the ADHD protection/susceptibility effects of the respective alleles. Using bioinformatics tools, based on the latest genome-wide association (GWAS) meta-analysis of the Psychiatry Genomic Consortium (PGC), we demonstrated that the 48 bp VNTR is not in Linkage Disequilibrium with the DRD4 SNPs (Single Nucleotide Polymorphisms), which were not found to be associated with ADHD. Moreover, a DRD4 expression downregulation was found in ADHD specific brain regions (Putamen, Z score = -3.02, P = 0.00252). Overall, our results suggest that DRD4 48 bp VNTR variants should be considered as biomarkers to support the diagnosis of ADHD and to predict MPH response, although the accuracy of such a biomarker remains to be further elucidated.
Topics: Adult; Alleles; Attention Deficit Disorder with Hyperactivity; Biomarkers; Child; Genome-Wide Association Study; Genotype; Humans; Methylphenidate; Minisatellite Repeats; Receptors, Dopamine D4
PubMed: 32075956
DOI: 10.1038/s41398-020-0755-4 -
Scientific Reports Aug 2018Staphylococcus lugdunensis is an emergent virulent coagulase-negative Staphylococcus that is increasingly responsible for severe infections. In an attempt to generate...
Staphylococcus lugdunensis is an emergent virulent coagulase-negative Staphylococcus that is increasingly responsible for severe infections. In an attempt to generate informative sequence data for subtyping S. lugdunensis, we selected and sequenced seven polymorphic variable number of tandem repeats (VNTRs) to develop two new methods: a classic length-based multiple-locus VNTR analysis (MLVA) method and a tandem repeat sequence typing (TRST) method. We assessed their performances compared to two existing methods, multilocus sequence typing (MLST) and multivirulence-locus sequence typing (MVLST) for 128 isolates from diverse clinical settings and geographical origins. The clustering achieved by the four methods was highly congruent, with MLVA discriminating within clonal complexes as defined by MLST. Indeed, MLVA was highly discriminant compared to MLST and MVLST in terms of number of genotypes as well as diversity indexes. Sequencing of the seven VNTRs showed that they were stable, and analysis of sequence polymorphisms provided superior discriminatory power. The typeability, reproducibility, and epidemiological concordance of these new methods were excellent. Of note, no link between clustering and clinical settings was identified. This study demonstrates that MLVA and TRST provide valuable information for molecular epidemiological study of S. lugdunensis, and represent promising tools to distinguish between strains of homogenous lineages in this clonal species.
Topics: Biodiversity; Genetic Loci; Humans; Linkage Disequilibrium; Minisatellite Repeats; Phylogeny; Staphylococcus lugdunensis
PubMed: 30076395
DOI: 10.1038/s41598-018-30144-y -
Emerging Infectious Diseases Mar 2021Tuberculosis (TB) elimination requires interrupting transmission of Mycobacterium tuberculosis. We used a multidisciplinary approach to describe TB transmission in 2...
Tuberculosis (TB) elimination requires interrupting transmission of Mycobacterium tuberculosis. We used a multidisciplinary approach to describe TB transmission in 2 sociodemographically distinct districts in Botswana (Kopanyo Study). During August 2012-March 2016, all patients who had TB were enrolled, their sputum samples were cultured, and M. tuberculosis isolates were genotyped by using 24-locus mycobacterial interspersed repetitive units-variable number of tandem repeats. Of 5,515 TB patients, 4,331 (79%) were enrolled. Annualized TB incidence varied by geography (range 66-1,140 TB patients/100,000 persons). A total of 1,796 patient isolates had valid genotyping results and residential geocoordinates; 780 (41%) patients were involved in a localized TB transmission event. Residence in areas with a high burden of TB, age <24 years, being a current smoker, and unemployment were factors associated with localized transmission events. Patients with known HIV-positive status had lower odds of being involved in localized transmission.
Topics: Adult; Botswana; Epidemiologic Studies; Genotype; Humans; Minisatellite Repeats; Molecular Epidemiology; Mycobacterium tuberculosis; Tuberculosis; Young Adult
PubMed: 33622470
DOI: 10.3201/eid2703.203840 -
Ticks and Tick-borne Diseases Nov 2020The control of Theileria parva, a protozoan parasite that threatens almost 50% of the cattle population in Africa, is still a challenge in many affected countries....
Microsatellite and minisatellite genotyping of Theileria parva population from southern Africa reveals possible discriminatory allele profiles with parasites from eastern Africa.
The control of Theileria parva, a protozoan parasite that threatens almost 50% of the cattle population in Africa, is still a challenge in many affected countries. Theileria parva field parasites from eastern Africa, and parasites comprising the current live T. parva vaccine widely deployed in the same region have been reported to be genotypically diverse. However, similar reports on T. parva parasites from southern Africa are limited, especially in Corridor disease designated areas. Establishing the extent of genetic exchange in T. parva populations is necessary for effective control of the parasite infection. Twelve polymorphic microsatellite and minisatellite loci were targeted for genotypic and population genetics analysis of T. parva parasites from South Africa, Mozambique, Kenya and Uganda using genomic DNA prepared from cattle and buffalo blood samples. The results revealed genotypic similarities among parasites from the two regions of Africa, with possible distinguishing allelic profiles on three loci (MS8, MS19 and MS33) for parasites associated with Corridor disease in South Africa, and East Coast fever in eastern Africa. Individual populations were in linkage equilibrium (V
L) was observed. Genetic divergence was observed to be more within (AMOVA = 74%) than between (AMOVA = 26%) populations. Principal coordinate analysis showed clustering that separated buffalo-derived from cattle-derived T. parva parasites, although parasites from cattle showed a close genetic relationship. The results also demonstrated geographic sub-structuring of T. parva parasites based on the disease syndromes caused in cattle in the two regions of Africa. These findings provide additional information on the genotypic diversity of T. parva parasites from South Africa, and reveal possible differences based on three loci (MS8, MS19 and MS33) and similarities between buffalo-derived T. parva parasites from southern and eastern Africa. Topics: Africa, Eastern; Africa, Southern; Animals; Cattle; Cattle Diseases; Genotype; Genotyping Techniques; Microsatellite Repeats; Minisatellite Repeats; Theileria parva; Theileriasis
PubMed: 32993948
DOI: 10.1016/j.ttbdis.2020.101539 -
Turkiye Parazitolojii Dergisi Mar 2017Selecting polymorphic mini- and microsatellite markers to determine genetic diversity and chromosomal regions exhibiting elevated rates of recombination in Theileria...
OBJECTIVE
Selecting polymorphic mini- and microsatellite markers to determine genetic diversity and chromosomal regions exhibiting elevated rates of recombination in Theileria annulata populations after recombination.
METHODS
The Unipro UGENE software was used to select markers. A score at which 10 times more tandem repeats (TRs) were identified in the real DNA sequence than those in the scrambled sequences of T. annulata was used as the cutoff. TRs containing minimum three nucleotides in length for microsatellite and six nucleotides for minisatellite regions and having a repeat motif identity between 96%-100% with the unit size repeated minimum three times were screened through the whole genome using the suffix array algorithm.
RESULTS
A total of 359 minisatellites and 8973 microsatellites were identified. TRs were screened one by one through the whole genome; mini- and microsatellites representing a single region and having suitable regions for primer design were selected based on their localization on T. annulata chromosomes, their repeat motif identity (>96%), and their repeat length (<1500 bp). The primers used to amplify selected candidates were designed, and each primer was used to check 27 different isolates of T. annulata.
CONCLUSION
In the present study, a total of 13 polymorphic mini- and microsatellite markers located on the different chromosomes were selected to determine the population diversity of T. annulata.
Topics: DNA Primers; Genetic Markers; Genetic Variation; Microsatellite Repeats; Minisatellite Repeats; Polymorphism, Genetic; Recombination, Genetic; Software; Theileria annulata
PubMed: 28483728
DOI: 10.5152/tpd.2017.4970 -
Medicine and Science in Sports and... Apr 2018Most candidate gene studies on the neurobiology of voluntary exercise behavior have focused on the dopaminergic signaling pathway and its role in the mesolimbic reward...
PURPOSE
Most candidate gene studies on the neurobiology of voluntary exercise behavior have focused on the dopaminergic signaling pathway and its role in the mesolimbic reward system. We hypothesized that dopaminergic candidate genes may influence exercise behavior through additional effects on executive functioning and that these effects are only detected when the types of exercise activity are taken into account.
METHODS
Data on voluntary exercise behavior and at least one single-nucleotide polymorphism/variable number of tandem repeat (VNTR) were available for 12,929 participants of the Netherlands Twin Registry. Exercise activity was classified as externally paced if a high level of executive function skill was required. The total volume of voluntary exercise (minutes per week) as well as the volume specifically spent on externally paced activities were tested for association with nine functional dopaminergic polymorphisms (DRD1: rs265981, DRD2/ANKK1: rs1800497, DRD3: rs6280, DRD4: VNTR 48 bp, DRD5: VNTR 130-166 bp, DBH: rs2519152, DAT1: VNTR 40 bp, COMT: rs4680, MAOA: VNTR 30 bp), a polygenic score (PGS) based on nine alleles leading to lower dopamine responsiveness, and a PGS based on three alleles associated with both higher reward sensitivity and better executive functioning (DRD2/ANKK1: "G" allele, COMT: Met allele, DAT1: 440-bp allele).
RESULTS
No association with total exercise volume or externally paced exercise volume was found for individual alleles or the nine-allele PGS. The volume of externally paced exercise behavior was significantly associated with the reward and executive function congruent PGS. This association was driven by the DAT1 440-bp and COMT Met allele, which acted as increaser alleles for externally paced exercise behavior.
CONCLUSIONS
Taking into account the types of exercise activity may increase the success of identifying genetic variants and unraveling the neurobiology of voluntary exercise behavior.
Topics: Adolescent; Adult; Aged; Aged, 80 and over; Alleles; Child; Dopamine; Dopamine Plasma Membrane Transport Proteins; Exercise; Female; Genotype; Humans; Male; Middle Aged; Minisatellite Repeats; Multifactorial Inheritance; Netherlands; Phenotype; Polymorphism, Single Nucleotide; Receptors, Dopamine; Reward; Young Adult
PubMed: 29135816
DOI: 10.1249/MSS.0000000000001479 -
PloS One 2023Cassava Bacterial Blight (CBB) is a destructive disease widely distributed in the different areas where this crop is grown. Populations studies have been performed at...
Cassava Bacterial Blight (CBB) is a destructive disease widely distributed in the different areas where this crop is grown. Populations studies have been performed at local and national scales revealing a geographical genetic structure with temporal variations. A global epidemiology analysis of its causal agent Xanthomonas phaseoli pv. manihotis (Xpm) is needed to better understand the expansion of the disease for improving the monitoring of CBB. We targeted new tandem repeat (TR) loci with large repeat units, i.e. minisatellites, that we multiplexed in a scheme of Multi-Locus Variable number of TR Analysis (MLVA-8). This genotyping scheme separated 31 multilocus haplotypes in three clusters of single-locus variants and a singleton within a worldwide collection of 93 Xpm strains isolated over a period of fifty years. The major MLVA-8 cluster 1 grouped strains originating from all countries, except the unique Chinese strain. On the contrary, all the Xpm strains genotyped using the previously developed MLVA-14 microsatellite scheme were separated as unique haplotypes. We further propose an MLVA-12 scheme which takes advantage of combining TR loci with different mutation rates: the eight minisatellites and four faster evolving microsatellite markers, for global epidemiological surveillance. This MLVA-12 scheme identified 78 haplotypes and separated most of the strains in groups of double-locus variants (DLV) supporting some phylogenetic relationships. DLV groups were subdivided into closely related clusters of strains most often sharing the same geographical origin and isolated over a short period, supporting epidemiological relationships. The main MLVA-12 DLV group#1 was composed by strains from South America and all the African strains. The MLVA-12 scheme combining both minisatellite and microsatellite loci with different discriminatory power is expected to increase the accuracy of the phylogenetic signal and to minimize the homoplasy effects. Further investigation of the global epidemiology of Xpm will be helpful for a better control of CBB worldwide.
Topics: Minisatellite Repeats; Manihot; Phylogeny; Genotype; Microsatellite Repeats; Bacterial Typing Techniques
PubMed: 37167330
DOI: 10.1371/journal.pone.0285491 -
Annali Di Igiene : Medicina Preventiva... 2019As a great opportunistic pathogen, Staphylococcus epidermidis participates in a wide spectrum of infections by residing in the medical devices. Regardless of the...
BACKGROUND
As a great opportunistic pathogen, Staphylococcus epidermidis participates in a wide spectrum of infections by residing in the medical devices. Regardless of the clinical importance of S. epidermidis, there are a few data about typing of clinical and non-clinical isolates at the subspecies level in Iran. We used the technique of "Multiple-Locus Variable number tandem repeat Analysis" for genetic differentiation of 107 clinical and non-clinical S. epidermidis isolates.
METHODS
Five appropriate Tandem Repeats were selected using bioinformatics programs and PCR-amplified using specific primers. Clustering of the "Multiple-Locus Variable number tandem repeat Analysis" profile was performed using BioNumerics. All isolates yielded a PCR product for all Variable Number Tandem Repeat loci.
RESULTS
Approximately 28% of the isolates were Methicillin Resistant S. epidermidis. High level of genetic diversity between isolates was observed. Overly, the S. epidermidis isolates were discriminated into 43 various "Multiple-Locus Variable number tandem repeat Analysis" types. Twenty-seven isolates obtained from blood showed in 21 "Multiple-Locus Variable number tandem repeat Analysis" types, and 10 samples collected from the environment were distributed in three Multiple-Locus Variable number tandem repeat Analysis" types. There was a significant relationship between the Multiple-Locus Variable number tandem repeat Analysis types and isolated strains of blood and the environment indicating the successful colonization of environmental clones in the hospitalized patients in the surgical ward.
CONCLUSIONS
The Multiple-Locus Variable number tandem repeat Analysis technique showed information about the transmission of this bacterium among patients, staff and the hospital environment.
Topics: Bacterial Typing Techniques; Hospitals; Humans; Iran; Italy; Minisatellite Repeats; Polymerase Chain Reaction; Staphylococcal Infections; Staphylococcus epidermidis
PubMed: 30554239
DOI: 10.7416/ai.2019.2258