Genome-Wide Association Study (GWAS) of dental caries in diverse populations

BACKGROUND

Dental caries is one of the most common chronic diseases and is influenced by a complex interplay of genetic and environmental factors. Most previous genetic studies of caries have focused on identifying genes that contribute to dental caries in specific ethnic groups, usually of European descent.

METHODS

The aim of this study is to conduct a genome-wide association study (GWAS) to identify associations affecting susceptibility to caries in a large multiethnic population from Argentina, the Philippines, Guatemala, Hungary, and the USA, originally recruited for studies of orofacial clefts (POFC, N = 3686). Ages of the participants ranged from 2 to 12 years for analysis of the primary dentition, and 18-60 years for analysis of the permanent dentition. For each participant, dental caries was assessed by counts of decayed and filled teeth (dft/DFT) and genetic variants (single nucleotide polymorphisms, SNPs) were genotyped or imputed across the entire genome. Caries was analyzed separately for the primary and permanent dentitions, with age, gender, and presence/absence of any type of OFC treated as covariates. Efficient Mixed-Model Association eXpedited (EMMAX) was used to test genetic association, while simultaneously accounting for relatedness and stratification.

RESULTS

We identified several suggestive loci (5 × 10-8 < P < 5 × 10-6) within or near genes with plausible biological roles for dental caries, including a cluster of taste receptor genes (TAS2R38, TAS2R3, TAS2R4, TASR25) on chromosome 7 for the permanent dentition analysis, and DLX3 and DLX4 on chromosome 17 for the primary dentition analysis. Genome-wide significant results were seen with SNPs in the primary dentition only; however, none of the identified genes near these variants have known roles in cariogenesis.

CONCLUSION

The results of this study warrant further investigation and may lead to a better understanding of cariogenesis in diverse populations, and help to improve dental caries prediction, prevention, and/or treatment in future.

Soft tissue nasal asymmetry as an indicator of orofacial cleft predisposition

The biological relatives of offspring with nonsyndromic orofacial clefts have been shown to exhibit distinctive facial features, including excess asymmetry, which are hypothesized to indicate the presence of genetic risk factors. The significance of excess soft tissue nasal asymmetry in at-risk relatives is unclear and was examined in the present study. Our sample included 164 unaffected parents from families with a history of orofacial clefting and 243 adult controls. Geometric morphometric methods were used to analyze the coordinates of 15 nasal landmarks collected from three-dimensional facial surface images. Following generalized Procrustes analysis, Procrustes ANOVA and MANOVA tests were applied to determine the type and magnitude of nasal asymmetry present in each group. Group differences in mean nasal asymmetry were also assessed via permutation testing. We found that nasal asymmetry in both parents and controls was directional in nature, although the magnitude of the asymmetry was greater in parents. This was confirmed with permutation testing, where the mean nasal asymmetry was significantly different (p < .0001) between parents and controls. The asymmetry was greatest for midline structures and the nostrils. When subsets of parents were subsequently analyzed and compared (parents with bilateral vs. unilateral offspring; parents with left vs. right unilateral offspring), each group showed a similar pattern of asymmetry and could not be distinguished statistically. Thus, the side of the unilateral cleft (right vs. left) in offspring was not associated with the direction of the nasal asymmetry in parents.

Association studies of low-frequency coding variants in nonsyndromic cleft lip with or without cleft palate

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a group of common human birth defects with complex etiology. Although genome-wide association studies have successfully identified a number of risk loci, these loci only account for about 20% of the heritability of orofacial clefts. The "missing" heritability may be found in rare variants, copy number variants, or interactions. In this study, we investigated the role of low-frequency variants genotyped in 1995 cases and 1626 controls on the Illumina HumanCore + Exome chip. We performed two statistical tests, Sequence Kernel Association Test (SKAT) and Combined Multivariate and Collapsing (CMC) method using two minor allele frequency cutoffs (1% and 5%). We found that a burden of low-frequency coding variants in N4BP2, CDSN, PRTG, and AHRR were associated with increased risk of NSCL/P. Low-frequency variants in other genes were associated with decreased risk of NSCL/P. These results demonstrate that low-frequency variants contribute to the genetic etiology of NSCL/P.

Neurosurgical sequelae of domestic dog attacks in children

OBJECTIVE The authors' goals in this study were to describe a series of dog attacks on children that required neurosurgical consultation and to better understand the pattern of injuries inflicted, the circumstances that place children at risk for attack, and the dog breeds involved. In addition, the authors review the surgical and medical management of these patients. METHODS The authors performed a retrospective review of all children requiring neurosurgical consultation for dog bite at a regional Level 1 pediatric trauma center over a 15-year period. RESULTS A total of 124 children with dog bites to the head, face, and neck were evaluated in the emergency department. Of these, 17 children (13.7%) incurred injuries requiring neurosurgical consultation. Fifty-three percent of victims were female. The mean age at the time of attack was 30 months. Twelve (71%) of the attacks were perpetrated by the family pet, and 13 (76%) occurred at the patient's home. Breeds involved in the attacks included German Shepherd, Pit Bull, American Bulldog, large mixed breed, Labrador Retriever, and Akita, with German Shepherds and Akitas being the most frequently involved. Neurosurgical injuries included nondepressed skull fracture in 5, depressed skull fracture in 10, intracranial hemorrhage in 5, cerebral contusions in 4, dural laceration in 4, pneumocephalus in 5, clinically evident CSF leak in 3, spinal fracture with complete spinal cord injury in 1, stroke in 2, vascular injury in 2, and cranial nerve injury (hypoglossal and facial nerve) in 1. Prophylactic antibiotics were administered in 16 patients (94%). Only 1 patient had a confirmed infection involving the site of injury. Neurosurgical intervention was required in 10 patients (59%) and ranged in severity from debridement and closure of a complex scalp wound to decompressive craniectomy. Neurological deficits, all of which were considered catastrophic, developed in 3 patients (18%). CONCLUSIONS Dog attacks on children requiring neurosurgical consultation commonly involve the family pet, which is usually a large-breed dog with no history of prior aggression. Neurosurgical injuries often involve the cranial vault, with depressed skull fractures being the most common injury pattern. Most patients do not suffer a neurological deficit, although catastrophic neurological injury may occur. Prophylactic antibiotics are commonly used and surgical intervention is required in the majority of cases.

Hypertelorism and Orofacial Clefting Revisited: An Anthropometric Investigation

OBJECTIVE

Since the 1960s, multiple studies have reported a tendency toward hypertelorism in individuals with nonsyndromic orofacial clefts (OFCs). However, the association between specific cleft types and increased interorbital distance has been inconsistent. Using three-dimensional (3D) surface imaging, we tested whether different forms of clefting showed evidence of increased interorbital distance.

METHODS

Intercanthal and outercanthal distances and intercanthal indices were calculated from 3D facial surface images of 287 individuals with repaired OFCs. Raw measurements were converted to sex and age-normalized Z-scores. Mean Z-scores for individuals with cleft lip (CL), cleft lip and palate (CLP), and cleft palate (CP) were compared with reference normative values (controls) and one another directly using t tests and analysis of variance.

RESULTS

The CLP group showed a significant increase in intercanthal width (P = .001) and intercanthal index (P < .001) compared with reference norms. The CP group showed a significant decrease (P < .001) in outercanthal width. The CL group showed no difference from reference norms. The proportion of clinically hyperteloric individuals was generally low but highest in the CLP group (7.4%). Cleft severity had little effect on interorbital spacing.

CONCLUSIONS

Individuals with CLP exhibited on average a tendency toward mild hypertelorism, driven primarily by an increase in intercanthal distance. This tendency was not seen in CL or CP.

Ear Infection in Isolated Cleft Lip: Etiological Implications

BACKGROUND AND HYPOTHESIS

Chronic ear infections are a common occurrence in children with orofacial clefts involving the secondary palate. Less is known about the middle ear status of individuals with isolated clefts of the lip, although several studies have reported elevated rates of ear infection in this group. The purpose of this retrospective study was to test the hypothesis that chronic ear infections occur more frequently in isolated cleft lip cases (n = 94) compared with controls (n = 183).

METHODS

A questionnaire was used to obtain information on history of chronic ear infection. The association between ear infection status (present/absent) and cleft lip status (cleft lip case/control) was tested using both chi-square and logistic regression.

RESULTS AND CONCLUSIONS

The reported occurrence of chronic ear infection was significantly greater in cleft lip cases (31%) compared with unaffected controls (11%). After adjusting for age and sex, having a cleft lip increased the odds of being positive for ear infection by a factor greater than 3 (odds ratio = 3.698; 95% confidence interval = 1.91 to 7.14). Within cleft lip cases, there was no difference in the occurrence of ear infection by defect laterality or by the type of clefting present in the family history. Although velopharyngeal insufficiency was present in 18.4% of our cleft lip sample, there was no statistical association between ear infection and abnormal speech patterns. These results may have potential implications both for the clinical management of isolated cleft lip cases and for understanding the etiology of orofacial clefting.

Genome-wide association studies in dogs and humans identify ADAMTS20 as a risk variant for cleft lip and palate

Cleft lip with or without cleft palate (CL/P) is the most commonly occurring craniofacial birth defect. We provide insight into the genetic etiology of this birth defect by performing genome-wide association studies in two species: dogs and humans. In the dog, a genome-wide association study of 7 CL/P cases and 112 controls from the Nova Scotia Duck Tolling Retriever (NSDTR) breed identified a significantly associated region on canine chromosome 27 (unadjusted p=1.1 x 10^-13; adjusted p= 2.2 x 10^-3). Further analysis in NSDTR families and additional full sibling cases identified a 1.44 Mb homozygous haplotype (chromosome 27: 9.29 – 10.73 Mb) segregating with a more complex phenotype of cleft lip, cleft palate, and syndactyly (CLPS) in 13 cases. Whole-genome sequencing of 3 CLPS cases and 4 controls at 15X coverage led to the discovery of a frameshift mutation within ADAMTS20 (c.1360_1361delAA (p.Lys453Ilefs*3)), which segregated concordant with the phenotype. In a parallel study in humans, a family-based association analysis (DFAM) of 125 CL/P cases, 420 unaffected relatives, and 392 controls from a Guatemalan cohort, identified a suggestive association (rs10785430; p =2.67 x 10^-6) with the same gene, ADAMTS20. Sequencing of cases from the Guatemalan cohort was unable to identify a causative mutation within the coding region of ADAMTS20, but four coding variants were found in additional cases of CL/P. In summary, this study provides genetic evidence for a role of ADAMTS20 in CL/P development in dogs and as a candidate gene for CL/P development in humans.

Cleft lip with or without cleft palate (CL/P) is a commonly occurring birth defect that can lead to a lifetime of complications in affected children. To better understand the genetic cause of these disorders, we investigated CL/P in both dogs and humans. Genome-wide association studies in both species independently identify ADAMTS20 as a candidate gene for CL/P development. In dogs, a deletion within a functional domain of ADAMTS20 is responsible for CL/P in the Nova Scotia Duck Tolling Retriever dog breed. In humans, an associated region containing the same gene, ADAMTS20, was identified in a study population of native Guatemalans. Subsequent sequencing in humans was unable to identify a causative mutation within the coding region of ADAMTS20 in the Guatemalan cohort; however, sequencing of ADAMTS20 in additional cases with CL/P identified four novel coding variants. This work provides genetic evidence for a role for ADAMTS20 in CL/P development in both dogs and humans.

Association of AXIN2 with non-syndromic oral clefts in multiple populations

We have previously shown the association of AXIN2 with oral clefts in a US population. Here, we expanded our study to explore the association of 11 AXIN2 markers in 682 cleft families from multiple populations. Alleles for each AXIN2 marker were tested for transmission distortion with clefts by means of the Family-based Association Test. We observed an association with SNP rs7224837 and all clefts in the combined populations (p = 0.001), and with SNP rs3923086 and cleft lip and palate in Asian populations (p = 0.004). We confirmed our association findings in an additional 528 cleft families from the United States (p < 0.009). We tested for gene-gene interaction between AXIN2 and additional cleft susceptibility loci. We assessed and detected Axin2 mRNA and protein expression during murine palatogenesis. In addition, we also observed co-localization of Axin2 with Irf6 proteins, particularly in the epithelium. Our results continue to support a role for AXIN2 in the etiology of human clefting. Additional studies should be performed to improve our understanding of the biological mechanisms linking AXIN2 to oral clefts.

Subungual squamous cell carcinoma after organ transplantation

It is accepted that immunosuppressant therapy after organ transplantation is associated with an increase risk of neoplasm. Subungual squamous cell carcinoma of the toe is a rare condition and has not previously been reported, to our knowledge, in patients undergoing immunosuppressant therapy. The objective of this case study is to report the clinical and histopathologic findings and the multidisciplinary treatment approach for a case of subungual squamous cell carcinoma of the toe in an organ transplant recipient undergoing immunosuppressant drug therapy.

Anatomical Basis for Apparent Subepithelial Cleft Lip: A Histological and Ultrasonographic Survey of the Orbicularis Oris Muscle

Objective:

To determine if there is an anatomic basis for subepithelial orbicularis oris muscle defects by directly comparing ultrasonographic images of the upper lip with corresponding histological sections obtained from cadavers.

Methods:

Ultrasound was performed on the upper lips of previously frozen, unpreserved cadaver heads (n  =  32), followed by dissection and sectioning of the upper lips. The ultrasound sequences were scored by a panel of raters, classifying the orbicularis oris muscle as negative, positive, or unknown for the presence of an orbicularis oris discontinuity (subepithelial defect). Based on ultrasound, six lip specimens were chosen for histological sectioning, were stained with hematoxylin-eosin and Gomori trichrome stain, and were evaluated with light microscopy at low (8×) and intermediate (100×) magnification.

Results:

One cadaver was scored positive for an orbicularis oris muscle discontinuity based on ultrasound; whereas, the remaining cadavers were scored negative. Of the cadavers with negative ultrasound scores, two were noted to have orbicularis oris muscles with “irregular” features (e.g., excessive localized thinning or asymmetry). From histology, the area of discontinuity as visualized on the positively scored ultrasound was characterized by both disorganized orbicularis oris muscle fibers and excess connective tissue within the muscle belly. In contrast, the localized thinning observed on some of the negatively scored ultrasounds was not confirmed by histology.

Conclusions:

Abnormalities of the orbicularis oris muscle visualized by ultrasound have an anatomic basis as revealed through histology. Ultrasound is a useful tool for noninvasively identifying discontinuities of the orbicularis oris muscle.

Rethinking isolated cleft palate: evidence of occult lip defects in a subset of cases

Emerging research suggests that subepithelial defects of the upper lip musculature are part of the phenotypic spectrum of cleft lip and/or palate (CL/P) and may represent an occult, subclinical manifestation of the anomaly. The present study investigates whether similar occult lip defects are present in individuals affected with isolated cleft palate (CP). To this end, upper lip ultrasounds of 33 CP cases (12 males, 21 females) were evaluated retrospectively for the presence of discontinuities (i.e., breaks) within the orbicularis oris muscle (OOM). In four CP cases (2 males, 2 females), distinct discontinuities of the OOM were identified. Of the remaining CP individuals, 23 demonstrated normal lip morphology on ultrasound (7 males, 16 females), while, in 6 cases (3 males, 3 females), a definitive evaluation was not possible. As CP and CL/P are traditionally thought to be etiologically distinct, these findings raise the possibility that some CP cases may be misclassified. Such diagnostic errors could have important implications for recurrence risk estimation and studies aimed at discovering etiology. (c) 2008 Wiley-Liss, Inc.

The Pittsburgh Fistula Classification System: a standardized scheme for the description of palatal fistulas

OBJECTIVE

Vague terminology is a problem in cleft palate research. No classification scheme for palatal fistulas has been proposed to date. Although a well-healed velum is a significant outcome of palatoplasty, it is nearly impossible to compare fistula-related palatoplasty results in the literature or in medical records without a standardized vocabulary. We endeavor to devise a palatal fistula classification system that may have clinical and research applicability.

DESIGN

PubMed was searched for definitions and classifications of palatal fistula as well as incidence and recurrence rates of this outcome. Next, a 25-year retrospective review of our Cleft Center's records was performed, and fistulas were identified (n=641 charts reviewed). The fistula descriptions yielded by this chart review were evaluated in the context of anatomical descriptions in the literature, and a clinician-friendly classification scheme was designed.

RESULTS

A literature review failed to reveal a standardized fistula classification system. An anatomically based numerical fistula classification system was devised: type I, bifid uvula; type II, soft palate; type III, junction of the soft and hard palate; type IV, hard palate; type V, junction of the primary and secondary palates (for Veau IV clefts); type VI, lingual alveolar; and type VII, labial alveolar.

CONCLUSIONS

We propose a standardized numerical classification system for palatal fistulas. Its clinical adoption may prospectively clarify ambiguities in the literature and facilitate future cleft palate research and clinical practice.

Orbicularis oris muscle defects as an expanded phenotypic feature in nonsyndromic cleft lip with or without cleft palate

Nonsyndromic cleft lip+/-cleft palate is a complex disease with a wide phenotypic spectrum; occult defects of the superior orbicularis oris muscle may represent the mildest subclinical form of the lip portion of the phenotype. This study used high-resolution ultrasonography to compare the frequency of discontinuities in the OO muscle in 525 unaffected relatives of individuals with nonsyndromic cleft lip+/-cleft palate versus 257 unaffected controls. OO muscle discontinuities were observed in 54 (10.3%) of the non-cleft relatives, compared to 15 (5.8%) of the controls-a statistically significant increase (P=0.04). Male relatives had a significantly higher rate of discontinuities than male controls (12.0% vs. 3.2%; P=0.01); female relatives also had a higher rate of discontinuities than female controls, but the increase was not statistically significant (8.9% vs. 7.4%; P=0.56). These data confirm the hypothesis that subepithelial OO muscle defects are a mild manifestation of the cleft lip phenotype. Identification of subepithelial OO muscle defects may be important in a clinical setting, as a means of providing more accurate recurrence risk estimates to relatives in cleft families. Furthermore, the expansion of the cleft lip+/-cleft palate phenotypic spectrum should improve the power of genetic studies.

Diagnosis and Treatment of Velopharyngeal Insufficiency

INTRODUCTION

The workup of velopharyngeal insufficiency (VPI) includes speech pathology evaluation and examination of velopharyngeal anatomy and physiology. This study sought to determine whether perceptual speech symptoms were predictive of velopharyngeal closure.

PATIENTS AND METHODS

A retrospective chart review of patients with VPI following primary palatoplasty was performed. All patients underwent perceptual speech evaluation using the Pittsburgh Weighted Speech Scale (PWSS) and examination of velopharyngeal anatomy by videofluoroscopy. PWSS scores were correlated to velopharyngeal closure.

RESULTS

All patients exhibited clinical VPI (PWSS = 5-27). No patient demonstrated complete velopharyngeal closure on videofluoroscopy. Velopharyngeal closure on the lateral view showed a statistically significant, moderate correlation with both the PWSS total score (rs = -0.424; P = 0.03) and the phonation subscore (rs = -0.405; P = 0.04).

CONCLUSIONS

Although certain aspects of speech are related to velopharyngeal anatomy, speech and videofluoroscopic studies each provide unique information in the workup of VPI. Selection of surgical approach often depends on anatomic factors, and improvement in speech postoperatively indicates successful treatment.

Candidate Genes for Oral-Facial Clefts in Guatemalan Families

Nonsyndromic cleft lip +/- cleft palate (CL/P) is a complex trait of unknown etiology. Most genetic studies of CL/P define affection status in a way that ignores subtle subclinical manifestations, resulting in a potential loss of statistical power. This study investigated 10 candidate genes in 155 individuals from 25 Guatemalan CL/P families. High-resolution ultrasound images of the orbicularis oris (OO) muscle were obtained. CL/P was present in 28 family members; an additional 10 had subcutaneous OO muscle defects. Family-based association studies were performed for both narrow (CL/P only) and broad (CL/P plus OO muscle defects) definitions of affection status. PVRL1 was significantly associated under both definitions (P = 0.04, narrow; P = 0.02, broad). Association with JAG2 improved from P = 0.09 under the narrow definition to P = 0.04 under the broad definition. Broadening the oral-facial cleft phenotype to include subclinical variants may improve power in genetic studies.

One-Stage Reanimation of the Paralyzed Face Using the Rectus Abdominis Neurovascular Free Flap

BACKGROUND

Functional free muscle transfer for the surgical correction of long-standing facial paralysis has gained validity over the past three decades. These traditionally multistep reconstructions often achieve clinical success, but at the cost of significant morbidity and lengthy recovery periods. To address this dilemma, the authors propose reconstruction using the rectus abdominis and accompanying intercostal nerve in a one-stage neurovascular free flap reanimation procedure.

METHODS

Between 1998 and 2001, five patients with long-standing unilateral facial paralysis at the University of Pittsburgh Facial Nerve Center underwent reanimation using the authors' protocol. Preoperative and postoperative assessments included clinical evaluation using the Facial Grading System and electromyography. The patients were followed for a mean of 16 months.

RESULTS

At the final postoperative visit, all five patients demonstrated improved levator electromyographic potential, with a median 67 percent improvement. All five patients further demonstrated an increase in zygomaticus electromyographic potential, with a median 225 percent improvement. All five patients demonstrated increased Facial Grading System score at most recent follow-up.

CONCLUSIONS

The one-step reanimation using free rectus abdominis neurovascular free flap demonstrated a consistent positive outcome in electromyographic and clinical assessments. The additional benefits of reduced recovery time and anatomical reliability of the flap render the authors' method preferable to other traditional methods of surgical reanimation of the paralyzed face.