scholarly journals Genetic Aspects of Dental Erosive Wear and Dental Caries

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Amela Tulek ◽  
Aida Mulic ◽  
Maria Runningen ◽  
Jannike Lillemo ◽  
Tor Paaske Utheim ◽  
...  
Keyword(s):  
Dental Caries ◽  
Statistical Power ◽  
Erosive Wear ◽  
Dental Erosion ◽  
Present Review ◽  
Genome Wide ◽  
Study Selection ◽  
High Prevalence ◽  
Enamel Erosion ◽  
Candidate Gene Studies

Objectives. The present review aims to give an overview of the literature focusing on novel genetic aspects of dental erosion and dental caries. Once the tooth erupts into the oral cavity, the regenerative capability of enamel is fundamentally limited due to the loss of dental epithelium during eruption. The susceptibility or resistance to dental erosion and caries is presumably a result of environmental, phenotypic, and/or genetic influence. Even though it is evident that individuals frequently exposing their teeth to acid and sugar are at high risk of developing dental erosion and caries, the findings exclusively based on these factors are elusive. Data resources and study selection. The present review was based on data collected from the National Library of Medicine database with different combinations of the following terms: “tooth,” “dental,” “dentin,” “enamel,” “erosion,” “erosive wear,” “caries,” “decay,” “gene,” and “genetic.” A total of forty-six studies met the inclusion criteria. Data were extracted by one reviewer and verified by another. Conclusion. The high prevalence of erosion and caries among certain groups, and observations that not all individuals appearing to be at risk develop these lesions, has sparked research on identifying genetic effects to these conditions. A connection of genome-wide and candidate gene studies has increased considerably in the literature. This review reveals largely varying success among studies, demonstrating the difficulties of developing the study with adequate sample sizes and durable phenotype definitions that permit enough statistical power to identify genetic contributors.

scholarly journals Common genetic variants with fetal effects on birth weight are enriched for proximity to genes implicated in rare developmental disorders

2021 ◽  
Author(s):  
Robin N Beaumont ◽  
Isabelle K Mayne ◽  
Rachel M Freathy ◽  
Caroline F Wright
Keyword(s):  
Birth Weight ◽  
Statistical Power ◽  
Developmental Disorders ◽  
Association Studies ◽  
Later Life ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Common Genetic Variants ◽  
Causal Genes

Abstract Birth weight is an important factor in newborn survival; both low and high birth weights are associated with adverse later-life health outcomes. Genome-wide association studies (GWAS) have identified 190 loci associated with maternal or fetal effects on birth weight. Knowledge of the underlying causal genes is crucial to understand how these loci influence birth weight and the links between infant and adult morbidity. Numerous monogenic developmental syndromes are associated with birth weights at the extreme ends of the distribution. Genes implicated in those syndromes may provide valuable information to prioritize candidate genes at the GWAS loci. We examined the proximity of genes implicated in developmental disorders (DDs) to birth weight GWAS loci using simulations to test whether they fall disproportionately close to the GWAS loci. We found birth weight GWAS single nucleotide polymorphisms (SNPs) fall closer to such genes than expected both when the DD gene is the nearest gene to the birth weight SNP and also when examining all genes within 258 kb of the SNP. This enrichment was driven by genes causing monogenic DDs with dominant modes of inheritance. We found examples of SNPs in the intron of one gene marking plausible effects via different nearby genes, highlighting the closest gene to the SNP not necessarily being the functionally relevant gene. This is the first application of this approach to birth weight, which has helped identify GWAS loci likely to have direct fetal effects on birth weight, which could not previously be classified as fetal or maternal owing to insufficient statistical power.

scholarly journals A powerful and efficient two-stage method for detecting gene-to-gene interactions in GWAS

Biostatistics ◽  
2017 ◽  
Vol 18 (3) ◽  
pp. 477-494 ◽  
Author(s):  
Jakub Pecanka ◽  
Marianne A. Jonker ◽  
Zoltan Bochdanovits ◽  
Aad W. Van Der Vaart ◽  
Keyword(s):  
Complex Traits ◽  
Multiple Testing ◽  
Statistical Power ◽  
Genome Wide Association Study ◽  
Score Test ◽  
Interaction Model ◽  
Type I ◽  
Two Stage ◽  
Genome Wide ◽  
Strong Control

Summary For over a decade functional gene-to-gene interaction (epistasis) has been suspected to be a determinant in the “missing heritability” of complex traits. However, searching for epistasis on the genome-wide scale has been challenging due to the prohibitively large number of tests which result in a serious loss of statistical power as well as computational challenges. In this article, we propose a two-stage method applicable to existing case-control data sets, which aims to lessen both of these problems by pre-assessing whether a candidate pair of genetic loci is involved in epistasis before it is actually tested for interaction with respect to a complex phenotype. The pre-assessment is based on a two-locus genotype independence test performed in the sample of cases. Only the pairs of loci that exhibit non-equilibrium frequencies are analyzed via a logistic regression score test, thereby reducing the multiple testing burden. Since only the computationally simple independence tests are performed for all pairs of loci while the more demanding score tests are restricted to the most promising pairs, genome-wide association study (GWAS) for epistasis becomes feasible. By design our method provides strong control of the type I error. Its favourable power properties especially under the practically relevant misspecification of the interaction model are illustrated. Ready-to-use software is available. Using the method we analyzed Parkinson’s disease in four cohorts and identified possible interactions within several SNP pairs in multiple cohorts.

Solutions and gels containing a sugarcane-derived cystatin (CaneCPI-5) reduce enamel and dentin erosion in vitro

2021 ◽  
Author(s):  
Lethycia Almeida Santos ◽  
Tatiana Martini ◽  
João Victor Frazão Câmara ◽  
Fabiana Navas Reis ◽  
Adriana de Cássia Ortiz ◽  
...  
Keyword(s):  
Artificial Saliva ◽  
Dental Erosion ◽  
Positive Control ◽  
New Approach ◽  
Enamel Erosion ◽  
Ph Cycling ◽  
Bovine Enamel ◽  
Dentin Erosion ◽  
Positive Controls

The effect of solutions and gels containing a sugarcane-derived cystatin (CaneCPI-5) on the protection against enamel and dentin erosion in vitro was evaluated. Bovine enamel and dentin specimens were divided into two groups (n=135 and 153/group for enamel and dentin, respectively) that were treated with solutions or chitosan gels containing 0.1 or 0.25 mg/ml CaneCPI-5. The positive controls for solutions and gels were Elmex Erosion Protection™ solution and NaF gel (12,300 ppm F), respectively. Deionized water and chitosan gel served as controls, respectively. The solutions were first applied on the specimens for 1 min and the gels for 4 min. Stimulated saliva was collected from 3 donors and used to form a 2 h acquired pellicle on the specimens. Then, the specimens were submitted to an erosive pH cycling protocol 4 times/day for 7 days (0.1% citric acid pH 2.5/90s, artificial saliva/2h, artificial saliva overnight). The solutions and gels were applied again during pH cycling, 2 times/day for 1 min and 4 min, respectively, after the first and last erosive challenges. Enamel and dentin losses (µm) were assessed by contact profilometry. Data were analyzed by 2-way ANOVA and Tukey´s test (p <0.05). All the treatments significantly reduced enamel and dentin loss in comparison with controls. Both CaneCPI-5 concentrations had a similar protective effect against enamel erosion, but only the higher concentration was as effective against dentin erosion as the positive control. Regarding the vehicles, only the 0.1 mg/ml gel performed worse than the positive control for dentin. CaneCPI-5 reduced enamel and dentin erosion to a similar extent as the fluoride-containing vehicles. However, dentin requires higher CaneCPI-5 concentrations, in the case of gels. Solutions or gels containing CaneCPI-5 might be a new approach to protect against dental erosion.

scholarly journals Coex-Rank: An approach incorporating co-expression information for combined analysis of microarray data

2012 ◽  
Vol 9 (1) ◽  
pp. 32-43 ◽  
Author(s):  
Jinlu Cai ◽  
Henry L. Keen ◽  
Curt D. Sigmund ◽  
Thomas L. Casavant
Keyword(s):  
Microarray Data ◽  
Statistical Power ◽  
Meta Analysis ◽  
Rank Aggregation ◽  
Microarray Data Analysis ◽  
Combined Approach ◽  
Linear Modeling ◽  
Modeling Process ◽  
Genome Wide ◽  
Gene Level

Summary Microarrays have been widely used to study differential gene expression at the genomic level. They can also provide genome-wide co-expression information. Biologically related datasets from independent studies are publicly available, which requires robust combined approaches for integration and validation. Previously, meta-analysis has been adopted to solve this problem.As an alternative to meta-analysis, for microarray data with high similarity in biological experimental design, a more direct combined approach is possible. Gene-level normalization across datasets is motivated by the different scale and distribution of data due to separate origins. However, there has been limited discussion about this point in the past. Here we describe a combined approach for microarray analysis, including gene-level normalization and Coex-Rank approach. After normalization, a linear modeling process is used to identify lists of differentially expressed genes. The Coex-Rank approach incorporates co-expression information into a rank-aggregation procedure. We applied this computational approach to our data, which illustrated an improvement in statistical power and a complementary advantage of the Coex-Rank approach from a biological perspective.Our combined approach for microarray data analysis (Coex-rank) is based on normalization, which is naturally driven. The Coex-rank process not only takes advantage of merging the power of multiple methods regarding normalization but also assists in the discovery of functional clusters of genes.

scholarly journals Assessment of oxidative stress in saliva of children with dental erosion

2018 ◽  
Vol 16 (2) ◽  
Author(s):  
Caleb Shitsuka ◽  
Flávia Kazue Ibuki ◽  
Fernando Neves Nogueira ◽  
Fausto Medeiros Mendes ◽  
Marcelo Bönecker
Keyword(s):  
Oxidative Stress ◽  
Erosive Wear ◽  
Total Antioxidant Status ◽  
Pediatric Dentistry ◽  
Dental Erosion ◽  
Dental Biofilm ◽  
Total Antioxidant ◽  
Unstimulated Saliva ◽  
Biochemical Analyses ◽  
Saliva Flow

ABSTRACT Objective To evaluate oxidative stress in saliva of children with dental erosion as compared to children with no erosion. Methods One single examiner, trained and prepared to make diagnosis of dental erosion according to the Basic Erosive Wear Examination index, selected 40 children aged 4 to 6 years, who attended a pediatric dentistry prevention clinic. Two groups were formed - one comprising children with dental erosion (n=22), and another with no dental erosion (n=18). The quantity of dental biofilm was verified using the Simplified Index of Oral Hygiene, and unstimulated saliva was collected for biochemical analyses. The following were assessed in saliva: flow rate, buffering capacity, pH, and total protein concentration. Malondialdehyde levels were also verified to determine oxidative stress and total antioxidant status. Results The quantity of biofilm was smaller in children with mean dental erosion±standard deviation (0.76±0.25), as compared to those with no dental erosion (1.18±0.28). There was no statistical difference in saliva parameters of oxidative stress in children with dental erosion. Conclusion The activity of oxidative stress in saliva did not influence dental erosion process when in its early stages.

scholarly journals Characterizing the mechanism behind the progression of NAFLD to hepatocellular carcinoma

2020 ◽  
pp. HEP36
Author(s):  
Pierre Nahon ◽  
Manon Allaire ◽  
Jean-Charles Nault ◽  
Valérie Paradis
Keyword(s):  
Hepatocellular Carcinoma ◽  
Fatty Liver Disease ◽  
Association Studies ◽  
Cost Effective ◽  
Genome Wide Association Studies ◽  
Alcoholic Fatty Liver ◽  
Genome Wide ◽  
High Prevalence ◽  
Prevalence Of Obesity ◽  
Alcoholic Fatty Liver Disease

Hepatocellular carcinoma (HCC) developed in non-alcoholic fatty liver disease (NAFLD) individuals presents substantial clinical and biological characteristics, which remain to be elucidated. Its occurrence in noncirrhotic patients raises issues regarding surveillance strategies, which cannot be considered as cost-effective given the high prevalence of obesity and metabolic syndrome, and furthermore delineates specific oncogenic process that could be targeted in the setting of primary or secondary prevention. In this context, the identification of a genetic heterogeneity modulating HCC risk as well as specific biological pathways have been made possible through genome-wide association studies, development of animal models and in-depth analyses of human samples at the pathological and genomic levels. These advances must be confirmed and pursued to pave the way for personalized management of NAFLD-related HCC.

scholarly journals A Tool to Build Up-To-Date Gene Annotations for Affymetrix Microarrays

2017 ◽  
Vol 3 (2) ◽  
pp. 38 ◽  
Author(s):  
Vladislava Milchevskaya ◽  
Grischa Tödt ◽  
Toby James Gibson
Keyword(s):  
Statistical Power ◽  
Gene Annotation ◽  
Clinical Diagnostics ◽  
Specific Gene ◽  
Microarray Probe ◽  
New Genes ◽  
Affymetrix Microarrays ◽  
Genome Wide ◽  
Definition Of ◽  
Genome Annotations

Genome-wide expression profiling and genotyping is widely applied in functional genomics research, ranging from stem cell studies to cancer, in drug response studies, and in clinical diagnostics. The Affymetrix GeneChip microarrays represent the most popular platform for such assays. Nevertheless, due to rapid and continuous improvement of the knowledge about the genome, the definition of many of the genes and transcripts change, and new genes are discovered. Thus the original probe information is out-dated for a number of Affymetrix platforms, and needs to be re-defined. It has been demonstrated, that accurate probe set definition improves both coverage of the gene expression analysis and its statistical power. Therefore we developed a method that incorporates the most recent genome annotations into the annotation of the microarray probe sets, using tools from the next generation sequencing. Additionally our method allows to quickly build project specific gene annotation models, as well as for comparison of microarray to RNAseq data.

scholarly journals Status Karies Gigi pada Pengidap HIV/AIDS

e-GIGI ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 261
Author(s):  
Michael J. Sundah ◽  
Christy N. Mintjelungan ◽  
Damajanty H. C. Pangemanan
Keyword(s):  
Dental Caries ◽  
Immune Deficiency Syndrome ◽  
Salivary Flow ◽  
Deficiency Syndrome ◽  
People Living With Hiv ◽  
Human Immune System ◽  
Immunodeficiency Virus ◽  
High Prevalence ◽  
Living With Hiv ◽  
Hiv Aids

Abstract: Human immunodeficiency virus (HIV) is a virus that attacks the human immune system, especially white blood cells called CD4 cells. Meanwhile, acquired immune deficiency syndrome (AIDS) is a syndrome that arises due to the decline in the human immune system caused by HIV infection. Several studies showed that people living with HIV/AIDS had a higher risk of developing dental caries compared to those without HIV/AIDS. Maintenance of oral hygiene, consumption of antiretroviral (ARV) drugs, and low salivary flow play a role in increasing the risk of caries in people living with HIV/AIDS. This study was aimed to determine the status of dental caries in people living with HIV/AIDS. This was a literature review using the databases of Google Scholar, PubMed, and Clinical Key. The results obtained five journals that were relevant to the topic of discussion. There was a high prevalence of caries in people with HIV/AIDS (56.78%-78.7%) and a higher average caries status (12.83±9.6, 15.14±6.09, and 11.87±8.08) compared to those without HIV/AIDS. The high prevalence of caries in people with HIV/AIDS was influenced by decreased salivary flow, use of ARVs, consumption of sweet foods, and lack of oral hygiene. In conclusion, the prevalence of caries in people living with HIV/AIDS was high.Keywords: dental caries, HIV/AIDS  Abstrak: Human immunodeficiency virus (HIV) adalah virus yang menyerang sistem kekebalan tubuh manusia kususnya sel darah putih yang disebut sel CD4 sedangkan acquired immune deficiency syndrome (AIDS) merupakan sindrom yang muncul akibat menurunnya sistem kekebalan tubuh manusia yang diakibatkan infeksi HIV. Beberapa penelitian menunjukkan bahwa pengidap HIV/AIDS berisiko lebih tinggi mengalami karies gigi dibandingkan dengan orang tanpa HIV/AIDS. Pemeliharaan kebersihan gigi mulut, konsumsi obat antiretroviral (ARV), dan aliran saliva yang rendah berperan dalam peningkatan risiko karies gigi pada pengidap HIV/AIDS. Penelitian ini bertujuan untuk mengetahui status karies gigi pada pengidap HIV/AIDS. Jenis penelitian ialah suatu literature review. Database yang digunakan untuk pencarian literatur ialah Google Scholar, PubMed, dan Clinical Key. Hasil penelitian mendapatkan prevalensi karies yang tinggi pada pengidap HIV/AIDS (56,78%-78,7%) dan rerata status karies lebih tinggi (12,83±9,6, 15,14±6,09, dan 11,87±8,08) dibandingkan dengan yang tanpa HIV/AIDS. Tingginya prevalensi karies pada pengidap HIV/AIDS dipengaruhi oleh penurunan laju aliran saliva, penggunaan ARV, konsumsi makanan manis, dan kurangnya menjaga kebersihan gigi mulut. Simpulan penelitian ini ialah prevalensi karies pada pengidap HIV/AIDS tergolong tinggi.Kata kunci: karies gigi, HIV/AIDS

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