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Kumar A, Skrahina V, Atta J, Boettcher V, Hanig N, Rolfs A, Oprea G, Ameziane N. Microbial contamination and composition of oral samples subjected to clinical whole genome sequencing. Front Genet 2023; 14:1081424. [PMID: 36824435 PMCID: PMC9941560 DOI: 10.3389/fgene.2023.1081424] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/24/2023] [Indexed: 02/10/2023] Open
Abstract
Biological material from the oral cavity is an excellent source of samples for genetic diagnostics. This is because collection is quick, easy-to-access, and non-invasive. We have set-up clinical whole genome sequence testing for patients with suspected hereditary disease. Beside the excellent quality of human DNA that can be isolated from such samples, we observed the presence of non-human DNA sequences at varying percentages. We investigated the proportion of non-human mapped reads (NHMR) sequenced from buccal swabs and saliva, the type of microbial genomes from which they were derived, and impact on molecular classification. Read sequences that did not map to the human reference genome were aligned to complete reference microbial reference sequences from the National Center for Biotechnology Information's (NCBI) RefSeq database using Kraken2. Out of 765 analyzed samples over 80% demonstrated more than 5% NHMRs. The majority of NHMRs were from bacterial genomes (average 69%, buccal swabs and 54% saliva), while the proportion of viruses was low, averaging 0.32% (buccal swabs) and 0.07% (saliva). We identified more than 30 different bacterial families of which Streptococcus mitis and Rothia mucilaginosa were the most common species. Importantly, the level of contamination did not impact the diagnostic yield.
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Affiliation(s)
| | | | | | | | | | - Arndt Rolfs
- Arcensus Diagnostics, Rostock, Germany,Medical Faculty University of Rostock, Rostock, Germany
| | | | - Najim Ameziane
- Arcensus Diagnostics, Rostock, Germany,*Correspondence: Najim Ameziane,
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Prediction of Early Childhood Caries Based on Single Nucleotide Polymorphisms Using Neural Networks. Genes (Basel) 2021; 12:genes12040462. [PMID: 33805090 PMCID: PMC8064067 DOI: 10.3390/genes12040462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/11/2021] [Accepted: 03/21/2021] [Indexed: 12/17/2022] Open
Abstract
Background: Several genes and single nucleotide polymorphisms (SNPs) have been associated with early childhood caries. However, they are highly age- and population-dependent and the majority of existing caries prediction models are based on environmental and behavioral factors only and are scarce in infants. Methods: We examined 6 novel and previously analyzed 22 SNPs in the cohort of 95 Polish children (48 caries, 47 caries-free) aged 2–3 years. All polymorphisms were genotyped from DNA extracted from oral epithelium samples. We used Fisher’s exact test, receiver operator characteristic (ROC) curve and uni-/multi-variable logistic regression to test the association of SNPs with the disease, followed by the neural network (NN) analysis. Results: The logistic regression (LogReg) model showed 90% sensitivity and 96% specificity, overall accuracy of 93% (p < 0.0001), and the area under the curve (AUC) was 0.970 (95% CI: 0.912–0.994; p < 0.0001). We found 90.9–98.4% and 73.6–87.2% prediction accuracy in the test and validation predictions, respectively. The strongest predictors were: AMELX_rs17878486 and TUFT1_rs2337360 (in both LogReg and NN), MMP16_rs1042937 (in NN) and ENAM_rs12640848 (in LogReg). Conclusions: Neural network prediction model might be a substantial tool for screening/early preventive treatment of patients at high risk of caries development in the early childhood. The knowledge of potential risk status could allow early targeted training in oral hygiene and modifications of eating habits.
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Khoramian Tusi S, Jafari A, Marashi SMA, Faramarzi Niknam S, Farid M, Ansari M. The effect of antimicrobial activity of Teucrium Polium on Oral Streptococcus Mutans: a randomized cross-over clinical trial study. BMC Oral Health 2020; 20:130. [PMID: 32357889 PMCID: PMC7195746 DOI: 10.1186/s12903-020-01116-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/19/2020] [Indexed: 01/05/2023] Open
Abstract
Background The purpose of this study is to determine the effect of a mouthwash containing Teucriumpolium herb on Streptococcus mutans in mouth. Methods This study was a randomized, crossover, double-blind clinical trial, where we selected 22 volunteers (dental students) randomly and we divided them into two groups. The study had two phases. In each phase, one group acted as the intervention group, while the other one was the control group. Both the intervention and control groups were given the mouthwash with and without Teucriumpolium, respectively. S. mutans of saliva were measured before and after each phase to compare the effects of the mouthwashes. A three-week washout period was considered between the two phases. An independent two-sample t-test was utilized to compare the mean of S. mutans colonies. Additionally, we used a standard AB/BA crossover model to find the results of the treatment and the impact of carryover on the residual’s biological effects. The significance level was considered 0.05 in this experiment. Results There is no significant difference observed between the two groups in the number of S. mutans before using the mouthwashes. When the mouthwash containing Teucriumpolium was used, there was a significant decrease in the number of S. mutans colonies in both phases’ extract (P = 0.002). Conclusion: The results of this study indicate the mouthwash containing aqueous extract of Teucrium polium can majorly reduce the colonization of S. mutans in human saliva. Trial registration Ethical issues approved by the Ethics Committee of the Rafsanjan University of Medical Sciences with the approval number of 937/9/31, IRCT code Number of IRCT2013121815842N1 and it was approved on 06/16/2014. The study was conducted in the period of September to November 2014.
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Affiliation(s)
- Somayeh Khoramian Tusi
- Department of Pediatric Dentistry, School of Dentistry, Alborz University of Medical Sciences, Alborz, Iran
| | - Ahmad Jafari
- Research Center for Caries Prevention, Dental Research Institute, Department of Community Oral Health, School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran. .,Department of Pediatric Dentistry, School of Dentistry, Al Hussain University, Karbala, Iraq.
| | | | - Salomeh Faramarzi Niknam
- Department of Pediatric Dentistry, School of Dentistry, Alborz University of Medical Sciences, Alborz, Iran
| | - Malihe Farid
- Department of Community Medicine, School of Medicine, Alborz University of Medical Sciences, Alborz, Iran
| | - Mehdi Ansari
- Department of Pharmaceutics, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
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Bayram M, Deeley K, Reis MF, Trombetta VM, Ruff TD, Sencak RC, Hummel M, Dizak PM, Washam K, Romanos HF, Lips A, Alves G, Costa MC, Granjeiro JM, Antunes LS, Küchler EC, Seymen F, Vieira AR. Genetic influences on dental enamel that impact caries differ between the primary and permanent dentitions. Eur J Oral Sci 2015; 123:327-334. [PMID: 26283008 DOI: 10.1111/eos.12204] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2015] [Indexed: 11/30/2022]
Abstract
Clinically, primary and permanent teeth are distinct anatomically and the presentation of caries lesions differs between the two dentitions. Hence, the possibility exists that genetic contributions to tooth formation of the two dentitions are different. The purpose of this study was to test the hypothesis that genetic associations with an artificial caries model will not be the same between primary and permanent dentitions. Enamel samples from primary and permanent teeth were tested for microhardness at baseline, after carious lesion creation, and after fluoride application to verify association with genetic variants of selected genes. Associations were found between genetic variants of ameloblastin, amelogenin, enamelin, tuftelin, tuftelin interactive protein 11, and matrix metallopeptidase 20 and enamel from permanent teeth but not with enamel from primary teeth. In conclusion, our data continue to support that genetic variation may impact enamel development and consequently individual caries susceptibility. These effects may be distinct between primary and permanent dentitions.
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Affiliation(s)
- Merve Bayram
- Department of Pedodontics, School of Dentistry, Istanbul Medipol University, Istanbul, Turkey
| | - Kathleen Deeley
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Maria F Reis
- Clinical Research Unit, Fluminense Federal University, Niterói, RJ, Brazil
| | - Vanessa M Trombetta
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Timothy D Ruff
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Regina C Sencak
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Hummel
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Piper M Dizak
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kelly Washam
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Helena F Romanos
- Department of Pediatric Dentistry and Orthodontics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Andrea Lips
- Clinical Research Unit, Fluminense Federal University, Niterói, RJ, Brazil
| | - Gutemberg Alves
- Clinical Research Unit, Fluminense Federal University, Niterói, RJ, Brazil
| | - Marcelo C Costa
- Department of Pediatric Dentistry and Orthodontics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - José M Granjeiro
- Directory of Programs, National Institute of Metrology, Quality and Technology (INMETRO), Duque de Caxias, RJ, Brazil
| | - Leonardo S Antunes
- Clinical Research Unit, Fluminense Federal University, Niterói, RJ, Brazil
| | - Erika C Küchler
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA.,Clinical Research Unit, Fluminense Federal University, Niterói, RJ, Brazil
| | - Figen Seymen
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Istanbul, Turkey
| | - Alexandre R Vieira
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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Shimizu T, Ho B, Deeley K, Briseño-Ruiz J, Faraco IM, Schupack BI, Brancher JA, Pecharki GD, Küchler EC, Tannure PN, Lips A, Vieira TCS, Patir A, Yildirim M, Poletta FA, Mereb JC, Resick JM, Brandon CA, Orioli IM, Castilla EE, Marazita ML, Seymen F, Costa MC, Granjeiro JM, Trevilatto PC, Vieira AR. Enamel formation genes influence enamel microhardness before and after cariogenic challenge. PLoS One 2012; 7:e45022. [PMID: 23028741 PMCID: PMC3454391 DOI: 10.1371/journal.pone.0045022] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 08/11/2012] [Indexed: 11/19/2022] Open
Abstract
There is evidence for a genetic component in caries susceptibility, and studies in humans have suggested that variation in enamel formation genes may contribute to caries. For the present study, we used DNA samples collected from 1,831 individuals from various population data sets. Single nucleotide polymorphism markers were genotyped in selected genes (ameloblastin, amelogenin, enamelin, tuftelin, and tuftelin interacting protein 11) that influence enamel formation. Allele and genotype frequencies were compared between groups with distinct caries experience. Associations with caries experience can be detected but they are not necessarily replicated in all population groups and the most expressive results was for a marker in AMELX (p=0.0007). To help interpret these results, we evaluated if enamel microhardness changes under simulated cariogenic challenges are associated with genetic variations in these same genes. After creating an artificial caries lesion, associations could be seen between genetic variation in TUFT1 (p=0.006) and TUIP11 (p=0.0006) with enamel microhardness. Our results suggest that the influence of genetic variation of enamel formation genes may influence the dynamic interactions between the enamel surface and the oral cavity.
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Affiliation(s)
- Takehiko Shimizu
- Department of Pediatric Dentistry, Nihon University of Dentistry at Matsudo, Matsudo, Chiba, Japan
| | - Bao Ho
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kathleen Deeley
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jessica Briseño-Ruiz
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Italo M. Faraco
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Brett I. Schupack
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - João A. Brancher
- Center for Health and Biological Sciences, Pontifical Catholic University of Paraná (PUCPR), Curitiba, Brazil
| | - Giovana D. Pecharki
- Center for Health and Biological Sciences, Pontifical Catholic University of Paraná (PUCPR), Curitiba, Brazil
| | - Erika C. Küchler
- Clinical Research Unit, Biology Institute, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil
| | - Patricia N. Tannure
- Discipline of Pediatric Dentistry, Veiga de Almeida University, Rio de Janeiro, Brazil
| | - Andrea Lips
- Department of Pediatric Dentistry and Orthodontics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thays C. S. Vieira
- Clinical Research Unit, Biology Institute, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil
| | - Asli Patir
- Department of Pedodontics, Istanbul Medipol University, Istanbul, Turkey
| | - Mine Yildirim
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Istanbul, Turkey
| | - Fernando A. Poletta
- Latin American Collaborative Study of Congenital Malformations (ECLAMC), Center for Medical Education and Clinical Research (CEMIC), Buenos Aires, Argentina
| | - Juan C. Mereb
- Latin American Collaborative Study of Congenital Malformations (ECLAMC), Hospital de Area El Bolsón, Río Negro, Argentina
| | - Judith M. Resick
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Carla A. Brandon
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Iêda M. Orioli
- Latin American Collaborative Study of Congenital Malformations (ECLAMC), National Institute of Population Medical Genetics (INAGEMP-CNPq), Department of Genetics, Institute of Biology, Center of Health Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eduardo E. Castilla
- Latin American Collaborative Study of Congenital Malformations (ECLAMC), Center for Medical Education and Clinical Research (CEMIC), Buenos Aires, Argentina
- Latin American Collaborative Study of Congenital Malformations (ECLAMC), National Institute of Population Medical Genetics (INAGEMP-CNPq), Department of Genetics, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Mary L. Marazita
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Craniofacial and Dental Genetics, Department of Human Genetics, and Clinical and Translational Science, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Figen Seymen
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Istanbul, Turkey
| | - Marcelo C. Costa
- Department of Pediatric Dentistry and Orthodontics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - José M. Granjeiro
- Clinical Research Unit, Biology Institute, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil
| | - Paula C. Trevilatto
- Center for Health and Biological Sciences, Pontifical Catholic University of Paraná (PUCPR), Curitiba, Brazil
| | - Alexandre R. Vieira
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Craniofacial and Dental Genetics, Department of Pediatric Dentistry, School of Dental Medicine, and Clinical and Translational Science, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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