Identification of a new familial case of 3q29 deletion syndrome associated with cleft lip and palate via whole-exome sequencing.

Many unbalanced large copy number variants reviewed in the paper are associated with syndromic orofacial clefts, including a 1.6 Mb deletion on chromosome 3q29. The current report presents a new family with this recurrent deletion identified via whole-exome sequencing and confirmed by array comparative genomic hybridization. The proband exhibited a more severe clinical phenotype than his affected mother, comprising right-sided cleft lip/alveolus and cleft palate, advanced dental caries, heart defect, hypospadias, psychomotor, and speech delay, and an intellectual disability. Data analysis from the 3q29 registry revealed that the 3q29 deletion increases the risk of clefting by nearly 30-fold. No additional rare and pathogenic nucleotide variants were identified that could explain the clefting phenotype and observed intrafamilial phenotypic heterogeneity. These data suggest that the 3q29 deletion may be the primary risk factor for clefting, with additional genomic variants located outside the coding sequences, methylation changes, or environmental exposure serving as modifiers of this risk. Additional studies, including whole-genome sequencing or methylation analyses, should be performed to identify genetic factors underlying the phenotypic variation associated with the recurrent 3q29 deletion.

Identification of novel susceptibility genes for non-syndromic cleft lip with or without cleft palate using NGS-based multigene panel testing.

For non-syndromic cleft lip with or without cleft palate (ns-CL/P), the proportion of heritability explained by the known risk loci is estimated to be about 30% and is captured mainly by common variants identified in genome-wide association studies. To contribute to the explanation of the "missing heritability" problem for orofacial clefts, a candidate gene approach was taken to investigate the potential role of rare and private variants in the ns-CL/P risk. Using the next-generation sequencing technology, the coding sequence of a set of 423 candidate genes was analysed in 135 patients from the Polish population. After stringent multistage filtering, 37 rare coding and splicing variants of 28 genes were identified. 35% of these genetic alternations that may play a role of genetic modifiers influencing an individual's risk were detected in genes not previously associated with the ns-CL/P susceptibility, including COL11A1, COL17A1, DLX1, EFTUD2, FGF4, FGF8, FLNB, JAG1, NOTCH2, SHH, WNT5A and WNT9A. Significant enrichment of rare alleles in ns-CL/P patients compared with controls was also demonstrated for ARHGAP29, CHD7, COL17A1, FGF12, GAD1 and SATB2. In addition, analysis of panoramic radiographs of patients with identified predisposing variants may support the hypothesis of a common genetic link between orofacial clefts and dental abnormalities. In conclusion, our study has confirmed that rare coding variants might contribute to the genetic architecture of ns-CL/P. Since only single predisposing variants were identified in novel cleft susceptibility genes, future research will be required to confirm and fully understand their role in the aetiology of ns-CL/P.

Deep Learning Neural Modelling as a Precise Method in the Assessment of the Chronological Age of Children and Adolescents Using Tooth and Bone Parameters.

Dental age is one of the most reliable methods for determining a patient's age. The timing of teething, the period of tooth replacement, or the degree of tooth attrition is an important diagnostic factor in the assessment of an individual's developmental age. It is used in orthodontics, pediatric dentistry, endocrinology, forensic medicine, and pathomorphology, but also in scenarios regarding international adoptions and illegal immigrants. The methods used to date are time-consuming and not very precise. For this reason, artificial intelligence methods are increasingly used to estimate the age of a patient. The present work is a continuation of the work of Zaborowicz et al. In the presented research, a set of 21 original indicators was used to create deep neural network models. The aim of this study was to verify the ability to generate a more accurate deep neural network model compared to models produced previously. The quality parameters of the produced models were as follows. The MAE error of the produced models, depending on the learning set used, was between 2.34 and 4.61 months, while the RMSE error was between 5.58 and 7.49 months. The correlation coefficient R2 ranged from 0.92 to 0.96.

Tooth and Bone Parameters in the Assessment of the Chronological Age of Children and Adolescents Using Neural Modelling Methods.

The analog methods used in the clinical assessment of the patient's chronological age are subjective and characterized by low accuracy. When using those methods, there is a noticeable discrepancy between the chronological age and the age estimated based on relevant scientific studies. Innovations in the field of information technology are increasingly used in medicine, with particular emphasis on artificial intelligence methods. The paper presents research aimed at developing a new, effective methodology for the assessment of the chronological age using modern IT methods. In this paper, a study was conducted to determine the features of pantomographic images that support the determination of metric age, and neural models were produced to support the process of identifying the age of children and adolescents. The whole conducted work was a new methodology of metric age assessment. The result of the conducted study is a set of 21 original indicators necessary for the assessment of the chronological age with the use of computer image analysis and neural modelling, as well as three non-linear models of radial basis function networks (RBF), whose accuracy ranges from 96 to 99%. The result of the research are three neural models that determine the chronological age.

PAX7 nucleotide variants and the risk of non-syndromic orofacial clefts in the Polish population.

OBJECTIVE: The etiology of non-syndromic cleft lip with or without cleft palate (nsCL/P) is multifactorial, heterogeneous, and still not completely understood. The aim of the present study was to examine the associations between common and rare PAX7 nucleotide variants and the risk of this common congenital anomaly in a Polish population. SUBJECTS AND METHODS: Eight top nsCL/P-associated PAX7 variants identified in our cleft genome-wide association study (GWAS) were selected for replication analysis in an independent group of patients and controls (n = 247 and n = 445, respectively). In addition, mutation screening of the PAX7 protein-coding region was conducted. RESULTS: Analysis of the pooled data from the GWAS and replication study confirmed that common PAX7 nucleotide variants are significantly associated with the increased risk of nsCL/P. The strongest individual variant was rs1339062 (c.586 + 15617T > C) with a p-value = 2.47E-05 (OR = 1.4, 95%CI: 1.20-1.64). Sequencing analysis identified a novel synonymous PAX7 substitution (c.87G > A, p.Val29Val) in a single patient with nsCLP. This transition located in the early exonic position was predicted to disrupt potential splice enhancer elements. CONCLUSION: Our study confirmed that PAX7 is a strong candidate gene for nsCL/P. Nucleotide variants of this gene contribute to the etiology of nsCL/P in the homogenous Polish population.

Association of CDKAL1 nucleotide variants with the risk of non-syndromic cleft lip with or without cleft palate.

Although the aetiology of non-syndromic cleft lip with or without cleft palate (nsCL/P) has been studied extensively, knowledge regarding the role of genetic factors in the pathogenesis of this common craniofacial anomaly is still limited. We conducted a follow-up association study to confirm that CDKAL1 nucleotide variants identified in our genome-wide association study (GWAS) for nsCL/P are associated with the risk of this anomaly. In addition, we performed a sequence analysis of the selected CDKAL1 exons. A mega-analysis of the pooled individual data from the GWAS and a replication study revealed that six out of thirteen CDKAL1 variants were positively replicated and reached the threshold of statistical significance (Ptrend < 3.85E-03). They represented a single association signal and were located within the fifth intron of CDKAL1. The strongest individual variant was rs9356746 with a Ptrend value = 5.71E-06 (odds ratio (OR) = 1.60, 95% confidence interval (CI): 1.30-1.97). Sequencing analysis did not reveal any pathogenic mutations of this gene. This study provides the first evidence that chromosomal region 6p22.3 is a novel susceptibility locus for nsCL/P. The location of the risk variants within the CDKAL1 intronic sequence containing enhancer elements predicted to regulate the SOX4 transcription may suggest that SOX4, rather than CDKAL1, is a potential candidate gene for this craniofacial anomaly.

WNT10A coding variants and maxillary lateral incisor agenesis with associated dental anomalies.

Congenital maxillary lateral incisor agenesis (MLIA) is one of the most common subtypes of dental agenesis. Because little is known with regard to the aetiology of this anomaly, the aim of the study was to determine the contribution of nucleotide variants in wingless-type MMTV integration site family, member 10A (WNT10A), msh homeobox 1 (MSX1), and paired box 9 (PAX9) to the risk of MLIA in a Polish population. Coding regions of the selected genes were analysed by direct sequencing in a group of 20 individuals with unilateral and bilateral MLIA, associated or not with other dental anomalies. The frequencies of the identified nucleotide variants were assessed in an additional cohort of patients with isolated dental agenesis (n = 147) and in 178 controls. Mutation screening showed four non-synonymous substitutions located in the highly conserved coding sequence of WNT10A in five (25%) of the 20 patients. Analysis of genotyping results revealed that three of these variants--p.Arg113Cys, p.Phe228Ile, and the newly identified p.Arg171Leu--may represent aetiological mutations underlying MLIA with associated dental anomalies. No mutations that were potentially aetiologic were identified in MSX1 and PAX9. In conclusion, this is the first report implicating coding variants in the WNT10A gene in the aetiology of MLIA. These results will require further confirmation using larger-scale studies.

A Comparison of Teeth Measurements on Plaster and Digital Models.

(1) Background: Modern imaging methods and constantly developing technologies extend the range of diagnostic tools in medicine and in orthodontics. Thanks to them, scientists and doctors can use devices designed to diagnose 3D structures of the human body. The aim of the study was to assess the usefulness of digital orthodontic models as a diagnostic tool in the work of an orthodontist through a comparative analysis of the value of orthodontic measurements made on traditional plaster models and virtual models. (2) Methods: A total of 80 sets of models were made, including 40 sets of plaster models and 40 sets of digital models. A total of 48 diagnostic parameters were developed. They concerned dental parameters. (3) Results: Comparative analysis of crown height values on plaster and digital models showed statistically significant differences (p < 0.05) in 26 out of 48 dental parameters. (4) Conclusions: The differences between the measurements made with the software on the digital models and the measurements made with the traditional method of measurement using the digital caliper on the plaster models were small and clinically acceptable.

Identification of Novel Risk Variants of Non-Syndromic Cleft Palate by Targeted Gene Panel Sequencing.

Non-syndromic cleft palate (ns-CP) has a genetically heterogeneous aetiology. Numerous studies have suggested a crucial role of rare coding variants in characterizing the unrevealed component of genetic variation in ns-CP called the "missing heritability". Therefore, this study aimed to detect low-frequency variants that are implicated in ns-CP aetiology in the Polish population. For this purpose, coding regions of 423 genes associated with orofacial cleft anomalies and/or involved with facial development were screened in 38 ns-CP patients using the next-generation sequencing technology. After multistage selection and prioritisation, eight novel and four known rare variants that may influence an individual's risk of ns-CP were identified. Among detected alternations, seven were located in novel candidate genes for ns-CP, including COL17A1 (c.2435-1G>A), DLG1 (c.1586G>C, p.Glu562Asp), NHS (c.568G>C, p.Val190Leu-de novo variant), NOTCH2 (c.1997A>G, p.Tyr666Cys), TBX18 (c.647A>T, p.His225Leu), VAX1 (c.400G>A, p.Ala134Thr) and WNT5B (c.716G>T, p.Arg239Leu). The remaining risk variants were identified within genes previously linked to ns-CP, confirming their contribution to this anomaly. This list included ARHGAP29 (c.1706G>A, p.Arg569Gln), FLNB (c.3605A>G, Tyr1202Cys), IRF6 (224A>G, p.Asp75Gly-de novo variant), LRP6 (c.481C>A, p.Pro161Thr) and TP63 (c.353A>T, p.Asn118Ile). In summary, this study provides further insights into the genetic components contributing to ns-CP aetiology and identifies novel susceptibility genes for this craniofacial anomaly.

Tooth Migration in a Female Patient with Hyperdontia: 11-Year Follow-Up Case Report.

We described an 11-year follow-up of a patient with a non-syndrome multiple supernumerary teeth who had one extra tooth in the maxilla and four additional premolars in the mandible. Together with an additional distal migration of the second lower right premolar to the ramus of the mandible that also occurred, it comprises a unique combination of conditions that were not previously presented in the literature. We showed the significance of routine X-rays in cases of hyperdontia since the additional teeth may develop later than expected and the patient may not experience any symptoms.

Polymorphic variants at 10q25.3 and 17q22 loci and the risk of non-syndromic cleft lip and palate in the Polish population.

BACKGROUND: Non-syndromic cleft lip and palate (CLP) is one of the most common birth defects. Recent genome-wide association studies (GWAS) have identified several novel risk loci associated with this craniofacial anomaly. Therefore, the objective of this report was to investigate the contribution of the top seven polymorphisms reaching genome-wide statistical significance in GWAS analyses in the Polish population. METHODS AND RESULTS: Nucleotide variants located at chromosomal regions 1p22.1, 10q25.3, 17q22, and 20q12 were tested in a group of 206 patients with nonsyndromic CLP and a properly matched control group. Significant results, which persisted even after Bonferroni correction (p < 0.0071), were observed for polymorphisms located at 10q25.3 (rs7078160 and rs4752028) and 17q22 (rs227731). Under a recessive model, both rs7078160 and rs4752028 were associated with a greater than fourfold increase in the risk of CLP (odds ratio [OR] = 4.536; 95% confidence interval [CI], 1.678-12.265; p = 0.0012 and OR = 4.573; 95% CI, 1.817-11.512; p = 0.0004, respectively). Polymorphism rs227731 increased the risk of CLP when analyzed under a dominant model (OR = 1.732; 95% CI, 0.184-2.253; p = 0.0044). Borderline association was alsoidentified for the 1p22.1 locus (rs481931). Moreover, 10q25.3 haplotypes were significantly associated with a susceptibility to CLP. CONCLUSION: Our evaluation study confirmed a substantial association of polymorphisms located at chromosomal regions 10q25.3 and 17q22 with nonsyndromic CLP in the Polish population.

Genotype and haplotype analysis of WNT genes in non-syndromic cleft lip with or without cleft palate.

The wingless-type MMTV integration site family (Wnt) signalling pathway plays a crucial role in craniofacial development. Recently, nucleotide variants in WNT genes have been shown to be associated with oral congenital anomalies, including facial clefts. Therefore, in the current study we decided to assay the association of nucleotide variants in selected WNT genes with the risk of non-syndromic cleft lip with or without cleft palate (NCL/P) in the Polish population. Fourteen polymorphisms in WNT3, WNT3A, WNT5A, WNT8A, WNT9B, and WNT11 were tested in a group of 210 patients with NCL/P and in a properly matched control group. The most significant results were found for the WNT3 rs3809857 variant, which, under the assumption of a recessive model, was associated with a two-fold decrease in the risk of NCL/P (OR(TT vs. GT + GG) = 0.492, 95% CI: 0.276-0.879, P = 0.015). Moreover, haplotype analysis revealed that WNT3 is significantly correlated with NCL/P. The global P-values for haplotypes of rs12452064_rs7207916 and rs3809857_rs12452064_rs7207916 were 0.0034 and 0.0014, respectively, and these results were statistically significant, even after the permutation test correction. In conclusion, our study confirmed the involvement of polymorphisms in the WNT3 gene in NCL/P aetiology in the tested population.

Evaluation of the Second Premolar's Bud Position Using Computer Image Analysis and Neural Modelling Methods.

Panoramic radiograph is a universally used diagnostic method in dentistry for identifying various dental anomalies and assessing developmental stages of the dentition. The second premolar is the tooth with the highest number of developmental abnormalities. The purpose of this study was to generate neural models for assessing the position of the bud of the second premolar tooth based on analysis of tooth-bone indicators of other teeth. The study material consisted of 300 digital pantomographic radiographs of children in their developmental period. The study group consisted of 165 boys and 135 girls. The study included radiographs of patients of Polish nationality, aged 6-10 years, without diagnosed systemic diseases and local disorders. The study resulted in a set of original indicators to accurately assess the development of the second premolar tooth using computer image analysis and neural modelling. Five neural networks were generated, whose test quality was between 68-91%. The network dedicated to all quadrants of the dentition showed the highest test quality at 91%. The training, validation and test subsets were divided in a standard 2:1;1 ratio into 150 training cases, 75 test cases and 75 validation cases.

Eruption Pattern of Permanent Canines and Premolars in Polish Children.

Eruption is a complex and dynamic process determined by both genetic and epigenetic factors. This process involves a number of changes in the tissues surrounding the tooth and in tooth morphology. The aim of this study was to analyze the eruption sequence of permanent canines and premolars on the basis of pantomographic images. The study material consisted of 300 digital pantomographic images of children in the developmental period. The study group consisted of 165 boys and 135 girls. Images of patients of Polish nationality, aged 6-10 years, without diagnosed systemic diseases and local disorders were used in the study. Results: The study has shown that the most common pattern of tooth eruption in the lateral zones is type A positioning of the lateral teeth, which is 4-5-3. This pattern is characteristic of both girls and boys. This pattern also occurs most frequently in the maxilla in both boys and girls. In the mandible, on the contrary, two patterns of lateral tooth eruption were predominant. In girls, types A and E/4-5-3 and 3-4-5/occurred in the mandible, while in boys, types A and C/4-5-3 and 5-4-3/were observed in the mandible. The process of tooth eruption is a recognized measure of a child's physical development, and pantomographic images are an effective and common diagnostic tool.

Robust Estimation of the Chronological Age of Children and Adolescents Using Tooth Geometry Indicators and POD-GP.

Determining the chronological age of children or adolescents is becoming an extremely necessary and important issue. Correct age-assessment methods are especially important in the process of international adoption and in the case of immigrants without valid documents confirming their identity. It is well known that traditional, analog methods widely used in clinical evaluation are burdened with a high error rate and are characterized by low accuracy. On the other hand, new digital approaches appear in medicine more and more often, which allow the increase of the accuracy of these estimates, and thus equip doctors with a tool for reliable estimation of the chronological age of children and adolescents. In this study, the work on a fast and effective metamodel is continued. Metamodels have one great advantage over all other analog and quasidigital methods-if they are well trained, a priori, on a representative set of samples, then in the age-assessment phase, results are obtained in a fraction of a second and with little error (reduced to ±7.5 months). In the here-proposed method, the standard deviation for each estimate is additionally obtained, which allows the assessment of the certainty of each result. In this study, 619 pantomographic photos of 619 patients (296 girls and 323 boys) of different ages were used. In the numerical procedure, on the other hand, a metamodel based on the Proper Orthogonal Decomposition (POD) and Gaussian processes (GP) were utilized. The accuracy of the trained model was up to 95%.

Novel Candidate Genes for Non-Syndromic Tooth Agenesis Identified Using Targeted Next-Generation Sequencing.

Non-syndromic tooth agenesis (ns-TA) is one of the most common dental anomalies characterized by the congenital absence of at least one permanent tooth (excluding third molars). Regarding the essential role of genetic factors in ns-TA aetiology, the present study aimed to identify novel pathogenic variants underlying hypodontia and oligodontia. In a group of 65 ns-TA patients and 127 healthy individuals from the genetically homogenous Polish population, the coding sequences of 423 candidate genes were screened using targeted next-generation sequencing. Pathogenic and likely pathogenic variants were identified in 37 (56.92%) patients, including eight nucleotide alternations of genes not previously implicated in ns-TA (CHD7, CREBBP, EVC, LEF1, ROR2, TBX22 and TP63). However, since only single variants were detected, future research is required to confirm and fully understand their role in the aetiology of ns-TA. Additionally, our results support the importance of already known ns-TA candidate genes (AXIN2, EDA, EDAR, IRF6, LAMA3, LRP6, MSX1, PAX9 and WNT10A) and provide additional evidence that ns-TA might be an oligogenic condition involving the cumulative effect of rare variants in two or more distinct genes.

Mechanical Properties of 3D Printed Orthodontic Retainers.

Orthodontic retention is the final important stage of orthodontic treatment, the aim of which is to consolidate the functional and aesthetic position of teeth. Among adults, fixed retainers made of different types of wires are the most common. The aim of this study was to analyse the mechanical properties of a new generation of fixed orthodontic retainers-printed by 3D printers. MATERIALS AND METHODS: The study was conducted using samples made of Nextdent MFH C&B N1 resin in the form of cuboid bars with nominal dimensions of width b = 3 mm, thickness d = 0.8 mm; 1 mm; 1.2 mm, length l = 30 mm for each type. The influence of the thickness of the retainers on their strength under loaded conditions was evaluated. Flexural strength, elastic properties, deflection, and creep were compared. The samples were aged in an artificial saliva bath at 37 ± 1 °C during the strength tests. RESULTS: It was shown that differences in the thickness of the samples affected their elastic and strength properties. The highest average flexural modulus, the highest deflection, creep, and strength was characteristic of the samples with the highest thickness (1.2 mm). Samples with an average thickness of 1 mm had the lowest modulus of elasticity. CONCLUSIONS: The mechanical properties of 3D printed retainers show that they can be an alternative to metal retainers and the procedure of making new retainers, especially when patients have aesthetic requirements or allergies to metals.

Polymorphisms in CHDH gene and the risk of tooth agenesis.

BACKGROUND: Tooth agenesis is one of the most common anomalies of human dentition and is due to a complex and not fully elucidated etiology. The purpose of this study was to evaluate the possibility that polymorphic variants of genes encoding the main folate and choline metabolism enzymes might be associated with the risk of hypodontia in the Polish population. METHODS AND RESULTS: We analyzed 21 polymorphisms of 13 candidate genes and found that single nucleotide polymorphisms (SNPs) in the CHDH gene are significantly correlated with the risk of dental agenesis. The strongest association was found for the SNP located in the intronic sequence of CHDH. Individuals carrying one copy of the rs6445606 C allele had an over two-fold decreased risk of having hypodontia (odds ratio [OR]CTvsTT=0.434; 95% confidence interval [CI], 0.2724-0.6915; p=0.0004; pcorr=0.0084). A reduced risk of tooth agenesis was also observed in individuals with one or two copies of the rs6445606 C allele compared to T allele carriers (ORCT+CCvsTT=0.524; 95% CI, 0.3386-0.8097; p=0.0035; pcorr=0.0735). Moreover, the gene-gene interaction analysis revealed a significant epistatic interaction between CHDH (rs6445606) and PLD2 (rs3764897) in the susceptibility to hypodontia (p=0.004). CONCLUSION: Our study identified CHDH and PLD2 as novel candidate genes, the nucleotide variants of which could be associated with the risk of tooth agenesis.

The Primary Outbreaks of Burkitt Lymphoma in the Oral Cavity. A Report of Two Cases, Review of the Literature and Dental Implications.

Two cases of Sporadic Burkitt's lymphoma in children aged 11 and 8 years with primary symptoms in the oral cavity are reported. The first symptoms of the disease appeared in the oral cavity and were initially misdiagnosed as an inflammatory condition in one case and incidental findings not associated with the primary reason for visiting the dentist's office in the second case. Biopsies of the lesions revealed the actual cause of the observed changes and contributed to the prompt initiation of polychemotherapy treatment. A review of current literature presents the known symptoms of Burkitt's Lymphoma in the oral cavity and the available diagnostic methods. The role of the primary care physicians-the pedodontist and paediatrician-in the diagnostic and therapeutic process is discussed.

Analysis of the Statistical Comparability of the Hardness and Wear of Polymeric Materials for Orthodontic Applications.

BACKGROUND: Clinical success depends on the contact strength and wear resistance of medical devices made of polymer materials. The scientific goal resulted from the problem of using different methods of surface evaluation of materials used in the production of orthodontic appliances. The purpose of the work was an experimental comparative assessment of indentation hardness and scratch hardness and the sliding wear of four selected polymeric materials used in the manufacture of orthodontic appliances. METHODS: Four commercial materials were compared. Shore hardness tests and a scratch test with a Rockwell indenter were performed. A sliding wear test was performed using the ball-on-disc method. Statistical PCA and correlation analyses were performed. RESULTS: The results of scratch hardness measurements using a contact profilometer correlated with the Shore hardness to a greater extent than measurements made using an optical microscope. PCA showed that Shore hardness explains 45% of the total variance in all the results across the materials. CONCLUSIONS: The scratch hardness method allows for a more explicit ranking of orthodontic polymeric materials when measurements are made with a profilometer. The ranking of sliding wear resistance should be made separately.