Genetic heterogeneity and enrichment of variants in DNA-repair genes in ameloblastoma.

OBJECTIVE: Ameloblastomas are a group of relatively common odontogenic tumors that frequently originate from the dental epithelium. These tumors are aggressive in nature and present as slow-growing painless cortical expansion of the jaw. Histologically, the follicular and plexiform subtypes constitute two-thirds of solid/multicystic ameloblastomas. The objective of this study was to understand the genetic architecture of follicular and plexiform ameloblastomas using deep whole-exome sequencing. METHODS: Archived formalin-fixed paraffin-embedded tissue blocks of follicular (n = 4) and plexiform (n = 6) ameloblastomas were retrieved and genomic DNAs were isolated from the tumor tissue dissected from the formalin-fixed paraffin-embedded block. The exomes were enriched using the Integrated DNA Technologies Exome Research Panel (IDT, Coralville, IA) and paired-end sequencing was completed on an Illumina NovaSeq 6000 with an average output of 20 GB of data resulting in a mean coverage of 400×. Variant analysis was completed using custom-developed software: Rapid Understanding of Nucleotide variant Effect Software and variant integration and knowledge interpretation in genomes. RESULTS: Our analyses focused on examining somatic variants (gnomAD minor allele frequency ≤1%) in genes found on an Food and Drug Administration -approved clinical cancer sequencing panel (FoundationOne®CDx). In follicular tumors, variants (>20% of the reads) were identified in BRAF, KMT2D, and ABL1 genes. In plexiform tumors, variants (>20% of the reads) were identified in ALK, BRAF, KRAS, KMT2D, SMO, KMT2A, and BRCA2 genes. Enrichment analysis showed a significant role of DNA repair genes in the development of these tumors. CONCLUSION: The variants identified in follicular and plexiform ameloblastomas were enriched in DNA-repair genes. The observed genetic heterogeneity in these ameloblastomas may contribute to the aggressive nature and recurrence risk of these tumors.

Connecting the dots towards precision orthodontics.

Precision orthodontics entails the use of personalized clinical, biological, social and environmental knowledge of each patient for deep individualized clinical phenotyping and diagnosis combined with the delivery of care using advanced customized devices, technologies and biologics. From its historical origins as a mechanotherapy and materials driven profession, the most recent advances in orthodontics in the past three decades have been propelled by technological innovations including volumetric and surface 3D imaging and printing, advances in software that facilitate the derivation of diagnostic details, enhanced personalization of treatment plans and fabrication of custom appliances. Still, the use of these diagnostic and therapeutic technologies is largely phenotype driven, focusing mainly on facial/skeletal morphology and tooth positions. Future advances in orthodontics will involve comprehensive understanding of an individual's biology through omics, a field of biology that involves large-scale rapid analyses of DNA, mRNA, proteins and other biological regulators from a cell, tissue or organism. Such understanding will define individual biological attributes that will impact diagnosis, treatment decisions, risk assessment and prognostics of therapy. Equally important are the advances in artificial intelligence (AI) and machine learning, and its applications in orthodontics. AI is already being used to perform validation of approaches for diagnostic purposes such as landmark identification, cephalometric tracings, diagnosis of pathologies and facial phenotyping from radiographs and/or photographs. Other areas for future discoveries and utilization of AI will include clinical decision support, precision orthodontics, payer decisions and risk prediction. The synergies between deep 3D phenotyping and advances in materials, omics and AI will propel the technological and omics era towards achieving the goal of delivering optimized and predictable precision orthodontics.

Morphological integration in inferior alveolar canal and mandibular shapes.

OBJECTIVE: During embryogenesis of mandible, the initial ossification centre begins at the bifurcation of the inferior alveolar (IA) and the mental nerves. Additionally, in congenital anomalies like craniofacial microsomia (CFM), the IA canal is completely absent on the microsomic side. These observations led us to hypothesise that there may be a morphological integration between these structures - the IA nerve and the mandibular shapes. Therefore, the primary objective of this study was to test for morphological integration between these structures and the secondary objective was to determine if there were shape variations in these structures among skeletal Classes I, II and III subjects. SETTING AND SAMPLE POPULATION: The sample size of the study is 80 full-head cone-beam computed tomography (CBCT) scans (age 16-56 years). METHODS: We retrieved CBCT scans from our archived database using specific inclusion/exclusion criteria. In the de-identified CBCT scans, traditional coordinate landmarks and sliding semi-landmarks were placed on the mandible and the IA canal (proxy for IA nerve). Using geometric morphometric analyses, we tested integration between the IA canal and the mandibular shapes. We used Procrustes ANOVA to test for overall shape variations among the three skeletal classes (Classes I, II and III). RESULTS: The IA canal and posterior/inferior border of mandible showed strong integration (r-PLS = .845, P = .001). Similar strong integration was also observed between the IA canal and the overall shape of the mandible (r-PLS = .866, P = .001). Additionally, there was a statistically significant variation in overall shape between skeletal Class I and Class II (P = .008) and Class II and Class III (P = .001). CONCLUSIONS: The strong integration between two structures suggests that the IA nerve may play a role in establishing mandibular shape early in development. We posit this may be important in driving mandibular defects seen in CFM, which warrants further investigation.

Transcriptome analyses of murine right and left maxilla-mandibular complex.

OBJECTIVE: The objective of the study was to investigate differential gene expression between murine right and left maxilla-mandibular (MxMn) complexes. SETTING AND SAMPLE POPULATION: Wild-type (WT) C57BL/6 embryonic (E) day 14.5 (n = 3) and 18.5 (n = 3) murine embryos. METHODS: The E14.5 and 18.5 embryos were harvested and hemi-sectioned the MxMn complexes into right and left halves in the mid-sagittal plane. We isolated total RNA using Trizol reagent and further purified using the RNA-easy kit (QIAGEN). We confirmed equal expression of house-keeping genes in right and left halves using RT-PCR and then performed paired-end whole mRNA sequencing in LC Sciences (Houston, TX) followed by differential transcript analyses (>1 or <-1 log fold change; p < .05; q < .05; and FPKM >0.5 in 2/3 samples). The Mouse Genome Informatics and Online Mendelian Inheritance in Man databases as well as gnomAD constraint scores were used to prioritize differentially expressed transcripts. RESULTS: There were 19 upregulated and 19 downregulated transcripts at E14.5 and 8 upregulated and 17 downregulated transcripts at E18.5 time-points. These differentially expressed transcripts were statistically significant and shown to be associated with craniofacial phenotypes in mouse models. These transcripts also have significant gnomAD constraint scores and are enriched in biological processes critical for embryogenesis. CONCLUSIONS: We identified significant differential expression of transcripts between E14.5 and 18.5 murine right and left MxMn complexes. These findings when extrapolated to humans, they may provide a biological basis for facial asymmetry. Further experiments are required to validate these findings in murine models with craniofacial asymmetry.

Examination of rare genetic variants in dental enamel genes: The potential role of next-generation sequencing in primary dental care.

OBJECTIVES: To examine the potential role of next-generation sequencing (NGS) and genetic testing to guide preventive care in dental enamel disorders using publicly available databases to access the frequency of deleterious alleles in AMTN, AMLEX and ENAM, associated with amelogenesis imperfecta (AI). SETTING AND SAMPLE POPULATION: Public resources, including gnomAD (The Broad Institute) and the Center for Pediatric Genomic Medicine's warehouse, which together contain variants from nearly 145 000 exomes and genomes. MATERIAL & METHODS: Public resources, including sequencing data from ~145 000 exomes and genomes were queried for predicted loss of function variants with a minor allele frequency <1% in AMTN, AMLEX and ENAM. RESULTS: A total of 95 variants were identified in the combined dataset. If confirmed, this could be diagnostic for autosomal dominant AI. CONCLUSIONS: The rapid integration of NGS into clinical care allows for the expansion of genetic testing for disorders that are not currently tested routinely, including non-syndromic dental enamel disorders. A genotypic-driven diagnosis of a disorder of enamel development could impact dental care, especially in young children, including early and more frequent monitoring to prevent complications. As new gene-disease associations continue to emerge, including those for common and non-syndromic craniofacial disorders, the possibility of genomic-guided precision medicine and dentistry and the development of targeted, individualized therapeutics into standard clinical care will increase substantially.

A novel nonsense substitution identified in the AMIGO2 gene in an Occulo-Auriculo-Vertebral spectrum patient.

OBJECTIVE: Craniofacial microsmia is the second most common congenital disorder with mostly unilateral defects of ear, temporomandibular joint, mandible, and muscles of facial expression and mastication. The objective of this study was to identify, if there were any, de novo germline or somatic variants in a patient with Occulo-Auriculo-Vertebral Spectrum (OAVS) using whole-exome sequencing. SETTINGS AND SAMPLE POPULATION: Trio/Family-based study of an OAVS proband. MATERIALS AND METHODS: Children's Mercy Hospital Institutional Review Board approved this study and a request-to-rely was procured from the University of Missouri Kansas City IRB. Informed assent/consent was obtained for all family members prior to any research activities. The peripheral blood/affected side tissues from corrective surgery of the proband and peripheral blood samples from unaffected parents were collected. The isolated genomic DNA were enriched for exomes and sequenced on an Illlumina HiSeq 2500 instrument yielding paired-end 125 nucleotide reads (84X coverage). Gapped alignment to reference sequences (GRCh37.p5) was performed with BWA and the GATK and analysis completed using custom-developed software. RESULTS: Analyses revealed that the proband carried a de novo germ line nonsense substitution (c.901C>T) in AMIGO2 gene, and missense substitutions in ZCCHC14 (c.1198C>T), and in SZT2 genes (c.2951C>T). CONCLUSIONS: The nonsense substitution in AMIGO2 gene introduces a premature stop codon possibly rendering the gene non-functional via nonsense-mediated pathway decay-therefore considered a stronger candidate. Further functional studies are required to confirm whether loss-of-function variants in AMIGO2 can cause OAVS.

Orthodontics in the era of big data analytics.

The objective of this report was to provide an overview of the current landscape of big data analytics in the healthcare sector, introduce various approaches of machine learning and discuss potential implications in the field of orthodontics. With the increasing availability of data from various sources, the traditional analytical methods may not be conducive anymore for examining clinical outcomes. Machine-learning approaches, which are algorithms trained to identify patterns in large data sets, are ideally suited to facilitate data-driven decision making. The field of orthodontics is particularly ripe for embracing the big data analytics platform to improve decision making in clinical practice. The availability of omics data, state-of-the-art imaging and potential for establishing large clinical data repositories have favourably positioned the specialty of orthodontics to deliver personalized and precision orthodontic care. Specifically, we discuss about next-generation sequencing, radiomics in the context of CBCT imaging, and how centralized data repositories can enable real-time data pooling from multiple sources.

Impact of Periapical Abscess on Infectious Complications in Patients Undergoing Extracorporeal Circulation Auxiliary to Open-Heart Surgical Procedures.

OBJECTIVE: Extracorporeal circulation auxiliary to open-heart surgeries (ECAOHS) may exert nonphysiological stresses on periapical abscessed tissues leading to hematogenous spread of microbes. The aim of this report was to estimate risk of postoperative infectious complications in patients with periapical abscesses and undergoing ECAOHS. METHODS: A retrospective analysis of Nationwide Inpatient Sample (years 2009 and 2010) was conducted. All patients (aged 19 to 65 years) who underwent ECAOHS were selected. International Classification of Diseases-9-Clinical Modification codes were used to identify the presence of periapical abscess and infectious complications. Multivariable logistic regression models were used to examine the associations between the presence of periapical abscess and occurrence of infectious complications. RESULTS: A total of 265,235 patients underwent an ECAOH procedure. Of these, 431 patients had a periapical abscess. Septicemia developed in 16% of those with periapical abscess (compared with 4.2% in those without periapical abscess). Those with periapical abscess had higher rates of any of the infectious complications when compared with those without periapical abscess (30.2% vs 11.6%, respectively). After adjustment for multiple confounders, those with periapical abscess were associated with higher odds for developing septicemia (odds ratio = 2.51, 95% confidence interval = 1.06-5.91, P = .04) and any of the infectious complications (odds ratio = 2.23, 95% confidence interval = 1.08-4.59, P = .03) when compared with those who did not have periapical abscess. CONCLUSIONS: Those with periapical abscess are associated with higher odds for infectious complications when compared with those without periapical abscess.

Interdisciplinary Role of Orthodontist in Screening and Managing Obstructive Sleep Apnea in Children and Adults.

Obstructive sleep apnea (OSA) can affect children and adults, and, if left untreated, could have a major impact on the general and overall well-being of the patient. Dental health care providers and orthodontists have an interdisciplinary role in screening patients at risk for OSA and make a referral to establish a definitive diagnosis by a sleep physician. The gold standard of diagnostic testing is polysomnography. The adeno-tonsillar hypertrophy is the primary cause of sleep apnea in children; therefore, adeno-tonsillectomy must be the first line of treatment. Post adeno-tonsillectomy, if there is residual OSA due to underlying skeletal discrepancy, the patient may be referred to an orthodontist for appropriate management. Currently the evidence in the literature for prophylactic growth modification in children to prevent OSA is weak. In adults, the gold standard for managing OSA is Positive Airway Pressure (PAP) therapy; however, adherence to this treatment is rather low. The oral appliance (OA) therapy is an alternate for PAP intolerant patients and for mild to moderate OSA patients. The OA therapy has to be administered by a qualified dentist or orthodontist after careful examination of dental and periodontal health as well as any pre-existing joint conditions. The OA therapy could cause OA-associated malocclusion and patients have to be made aware of prior to initiating treatment. In patients with severe OSA, surgical maxilla-mandibular advancement (MMA) is highly effective.

A cone beam computed tomographic analysis of cervical vertebral nonsegmentation.

OBJECTIVE: Using cone beam computed tomography (CBCT), this study aimed to investigate the radiologic features of cervical vertebral nonsegmentation (CVN) in patients with no known syndromes or pathoses. STUDY DESIGN: In this retrospective study, we examined CBCT scans of patients with CVN for the following parameters: type of nonsegmentation (partial or complete); laterality of partial nonsegmentation; level of vertebrae affected in nonsegmentation; anatomic parts of the vertebrae involved; and the presence or absence of degenerative joint disease (DJD). RESULTS: From the structured reports of 13,458 CBCT scans, we found 110 CBCT scans (0.82%) with CVN. Of this total, 77.3% were partial and 22.7% were complete. Most were located at the level of the C2 and C3 vertebrae. The transverse process alone and the transverse process and body were most frequently involved in partial CVN, whereas most complete types occurred in the transverse process and body. Degenerative joint disease was present in 45.9% of partial CVN (clearly distinguishable from nonsegmentation in 36.5%) and 20% of complete CVN, with all cases clearly distinguishable. CONCLUSIONS: Cervical vertebral nonsegmentation has a low prevalence. It is mostly partial, occurs most commonly in C2-C3, and usually involves the transverse process and body. Identification of CVN on CBCT images is important because this condition can lead to DJD in older age and may increase the risk for muscle weakness, head and neck pain, limited movement, and neurologic complications.

The Skull's Girder: A Brief Review of the Cranial Base.

The cranial base is a multifunctional bony platform within the core of the cranium, spanning rostral to caudal ends. This structure provides support for the brain and skull vault above, serves as a link between the head and the vertebral column below, and seamlessly integrates with the facial skeleton at its rostral end. Unique from the majority of the cranial skeleton, the cranial base develops from a cartilage intermediate-the chondrocranium-through the process of endochondral ossification. Owing to the intimate association of the cranial base with nearly all aspects of the head, congenital birth defects impacting these structures often coincide with anomalies of the cranial base. Despite this critical importance, studies investigating the genetic control of cranial base development and associated disorders lags in comparison to other craniofacial structures. Here, we highlight and review developmental and genetic aspects of the cranial base, including its transition from cartilage to bone, dual embryological origins, and vignettes of transcription factors controlling its formation.