[Show abstract][Hide abstract] ABSTRACT: With the current widespread use of three-dimensional (3D) facial surface imaging in clinical and research environments, there is a growing demand for high-quality craniofacial norms based on 3D imaging technology. The principal goal of the 3D Facial Norms (3DFN) project was to create an interactive, Web-based repository of 3D facial images and measurements. Unlike other repositories, users can gain access to both summary-level statistics and individual-level data, including 3D facial landmark coordinates, 3D-derived anthropometric measurements, 3D facial surface images, and genotypes from every individual in the dataset. The 3DFN database currently consists of 2454 male and female participants ranging in age from 3 to 40 years. The subjects were recruited at four US sites and screened for a history of craniofacial conditions. The goal of this article is to introduce readers to the 3DFN repository by providing a general overview of the project, explaining the rationale behind the creation of the database, and describing the methods used to collect the data. Sex- and age-specific summary statistics (means and standard deviations) and growth curves for every anthropometric measurement in the 3DFN dataset are provided as a supplement. These summary statistics and growth curves can aid clinicians in the assessment of craniofacial dysmorphology.
Full-text · Article · Oct 2015 · The Cleft Palate-Craniofacial Journal
[Show abstract][Hide abstract] ABSTRACT: Objectives: Occlusal discrepancies of the maxillary and mandibular arches can have serious impacts on dental health and quality of life by reducing masticatory, respiratory, and speech functionality in growing individuals. This study evaluates shape variation and patterns of integration or modularity in the dental arches of 4 cross-sectional snapshots of the Iowa Fluoride Study cohort to identify maxillary and mandibular arch discrepancies. Methods: Dental casts at ages 5 (n=305), 9 (n=272), 13 (n=151) and 17 (n=129) were scanned and digitized with 42–58 3D landmarks. After procrustes superimposition, the data were subjected to a Relative Warps Analysis to identify key components of dental arch variation. Two-Block Partial Least Squares analysis was employed to quantify levels of integration between the upper and lower arches using Escoufier’s RV coefficient. Results: The primary axis of arch shape variation across all time points (explaining 23.5%–28.5% of the variance) relates to the antero-posterior (AP) plane, with individuals ranging from an Angle Class II to a Class III malocclusion. Additional components of arch variation address vertical and transverse arch discrepancies. Maxillary and mandibular arch integration was high across all stages of dental development, with RV coefficients ranging from 0.74–0.79. However, testing for sets of landmarks with the least amount of integration resulted in the lowest levels of covariation (RV=0.45 at age 9) for the anterior vs. posterior regions of both dental arches. Conclusion: Results highlight that the greatest amount of occlusal discrepancy was in the AP dimension and such patterns were present as early as age 5. Also, the least amount of covariation was not between the maxillary and mandibular arches (as one might expect), but rather within the anterior vs. posterior portions of both arches. This modularity was found to be greatest at age 9, which is consistent with the mixed dentition stage.
[Show abstract][Hide abstract] ABSTRACT: Objectives: Dento-facial phenotypic variations resulting in moderate to severe dental and skeletal malocclusion are thought to be the result of susceptibility genes, environmental factors and/or their interactions. This study evaluates genetic associations between craniofacial genes and dento-facial phenotypes in patients with malocclusion.
Methods: Lateral cephalometric radiographs of 258 Euro-American untreated adults presenting with Class I (straight facial profiles), Class II (convex facial profiles mostly due to mandibular deficiencies) and Class III (concave profiles with maxillary deficiency, mandibular prognathism or both) malocclusion were digitized with 29 landmarks. 2D coordinates were submitted to a Procrustes fit prior to a principal component analysis (PCA). Individuals were genotyped with 198 single nucleotide polymorphisms (SNPs) located within 75 craniofacial genes and loci. Phenotype-genotype correlations for the first 4 components explaining 60% of the total variation were tested via multivariate regression.
Results: PC1 explains 25 % and is related to vertical discrepancies ranging from skeletal deep to skeletal open bites and is correlated (p<0.01) with a SNP in the PAX5 gene. PC2 explains 21.5% of the variation and depicts horizontal maxillary discrepancies ranging from maxillary retrusion to protrusion and it is correlated with SNPs in MYO1H and SNAI3. PC3 explains 7.7% of the variation and shows variation ranging from bimaxillary retrusion and a steep cranial base to bimaxillary protrusion and a flat cranial base. PC3 is correlated with SNPs in RUNX2, PAX5, NRIP2 and loci 12q13.13. Finally, PC4 explains 6% of the variance and shows variation ranging from a large to a small mandibular body and is correlated with SNPs in IRX1 and TWIST1.
Conclusion: Our findings indicate top priority candidate genes for future analyses related to vertical and horizontal facial variation. Also, our results replicated those of previous studies since both SNPs in 12q13.13 and MYOH1 were previously associated with maxillary retrusion and mandibular prognathism.
[Show abstract][Hide abstract] ABSTRACT: Previous evidence from tooth agenesis studies suggested IRF6 and TGFA interact. Since tooth agenesis is commonly found in individuals with cleft lip/palate (CL/P), we used four large cohorts to evaluate if IRF6 and TGFA interaction contributes to CL/P. Markers within and flanking IRF6 and TGFA genes were tested using Taqman or SYBR green chemistries for case-control analyses in 1,000 Brazilian individuals. We looked for evidence of gene-gene interaction between IRF6 and TGFA by testing if markers associated with CL/P were overtransmitted together in the case-control Brazilian dataset and in the additional family datasets. Genotypes for an additional 142 case-parent trios from South America drawn from the Latin American Collaborative Study of Congenital Malformations (ECLAMC), 154 cases from Latvia, and 8,717 individuals from several cohorts were available for replication of tests for interaction. Tgfa and Irf6 expression at critical stages during palatogenesis was analyzed in wild type and Irf6 knockout mice. Markers in and near IRF6 and TGFA were associated with CL/P in the Brazilian cohort (p<10(-6)). IRF6 was also associated with cleft palate (CP) with impaction of permanent teeth (p<10(-6)). Statistical evidence of interaction between IRF6 and TGFA was found in all data sets (p = 0.013 for Brazilians; p = 0.046 for ECLAMC; p = 10(-6) for Latvians, and p = 0.003 for the 8,717 individuals). Tgfa was not expressed in the palatal tissues of Irf6 knockout mice. IRF6 and TGFA contribute to subsets of CL/P with specific dental anomalies. Moreover, this potential IRF6-TGFA interaction may account for as much as 1% to 10% of CL/P cases. The Irf6-knockout model further supports the evidence of IRF6-TGFA interaction found in humans.
[Show abstract][Hide abstract] ABSTRACT: We have applied a GWAS to 40 consanguineous families segregating cases of non-syndromic cleft lip with or without cleft palate (NS CL/P) (a total of 160 affected and unaffected individuals) in order to trace potential recessive loci that confer susceptibility to this common facial malformation. Pedigree-based association test (PBAT) analyses reported nominal evidence of association and linkage over SNP markers located at 11q25 (rs4937877, P = 2.7 × 10(-6)), 19p12 (rs4324267, P = 1.6 × 10(-5)), 5q14.1 (rs4588572, P-value = 3.36 × 10(-5)), and 15q21.1 (rs4774497, P = 1.08 × 10(-4)). Using the Versatile Gene-Based Association Study to complement the PBAT results, we found clusters of markers located at chromosomes 19p12, 11q25, and 8p23.2 overcome the threshold for GWAS significance (P < 1 × 10(-7)). From this study, new recessive loci implicated in NS CL/P include: B3GAT1, GLB1L2, ZNF431, ZNF714, and CSMD1, even though the functional association with the genesis of NS CL/P remains to be elucidated. These results emphasize the importance of using homogeneous populations, phenotypes, and family structures for GWAS combined with gene-based association analyses, and should encourage. other researchers to evaluate these genes on independent patient samples affected by NS CL/P.
Full-text · Article · Jun 2012 · European journal of medical genetics
[Show abstract][Hide abstract] ABSTRACT: Objective: : Inherent to the study of landmark-based facial asymmetry are the determination of a midline and a method of superimposition to align the reference and opposing portions of the face. Choice of the method of standardization can have a substantial impact on the results of facial asymmetry studies. The goals of this study were to develop a methodology for superimposition using translation and rotational standardization and to determine the impact of rotational standardization on landmark-based measures of asymmetry.
Method: Three-dimensional stereophotogrammetric images of 182 unrelated adults (118F/64M) were soft-tissue landmarked using 3dMD Software and configurations were translated to the origin via the landmark subnasale. The left configuration was reflected over the X-Y plane and the Euclidean distance between each pair of 9 bilateral landmarks was calculated to measure landmark asymmetry without rotational standardization. To compute the standardized asymmetry scores, the landmarks nasion, subnasale, and sublabiale were chosen to define the mid facial plane of the translated configurations. Standardization of the configurations to the X-Y plane at Z=0 and the X-Z plane at Y=0 utilized iterative methods of rotation to determine optimal vertical position of the mid-facial plane. Similar reflections and calculations of the Euclidean distance were performed for the standardized data. Standardized and non-standardized landmark asymmetry scores were examined for differences using the Wilcoxon Signed Rank test to determine the impact of standardization on the estimate of asymmetry.
Result: Significant differences existed between the unstandardized and the standardized asymmetry scores for endocanthion (Wilcoxon p<0.0001), exocanthion (p=0.0286), subalare (p=0.0383), crista philtri (p<0.0001), and chelion (p=0.0407). For these landmarks, the estimate of asymmetry was significantly larger in the unstandardized data compared to the standardized data.
Conclusion: Insufficient rotational standardization of facial landmark data may result in an inaccurate estimate of bilateral landmark asymmetry, particularly in landmarks close to the mid-facial plane.
[Show abstract][Hide abstract] ABSTRACT: Objective: Nonsyndromic cleft lip and palate (NSCL/P) is a complex trait caused by genetic and environmental factors that interact producing a wide spectrum of orofacial malformations including dental anomalies. The underlying genetic etiology that accounts for the phenotypic variation in affected families is still poorly understood. This study utilized a microesthetic analysis to characterize the maxillary anterior dental morphology in unaffected parents of children with NSCL/P (cases) compared to control adults with no CL/P history to identify dental morphology features that are part of the NSCL/P phenotypic spectrum and can therefore be used in refining NSCL/P phenotypes and identifying genetic risk factors.
Method: Digital photographs for 139 females (68 cases, 71 controls) and 59 males (31 cases, 28 controls) were analyzed using both linear metrics and 2D-coordinate landmark-based geometric morphometrics (GM) to compare dental esthetics and deviations from “golden proportions” between cases and controls. Differences in central incisor and anterior connector height proportions were evaluated using paired T-tests. Anterior tooth shapes, angulations, and gingival margin heights were examined using GM techniques.
Result: Female cases had significantly (p<0.05) wider central incisors, more square anterior tooth shapes, increased inward (towards the upper midline) dental angulations, and more unaesthetic gingival margin height configurations compared to female controls. Male cases also displayed increased inward dental angulations and a tendency for unaesthetic gingival margin height configurations.
Conclusion: Significant differences in anterior dental morphology were found between cases and controls, with controls displaying a more ideal dental morphology than the cases for most evaluated measures. The identification of these distinct dental features in carriers of NSCL/P genetic risk factors further characterizes the phenotypic spectrum of NSCL/P which can enhance the power of genetic studies.
[Show abstract][Hide abstract] ABSTRACT: Objectives: To compare patterns of three-dimensional facial asymmetry in unaffected siblings of individuals with nonsyndromic cleft lip with or without palate (NSCL/P) to those of controls, including assessment of feasibility, standardization procedures, reliability, and the effects of age and gender as a first step toward the long-term goal of developing a diagnostic system for craniofacial phenotyping.
Methods: Existing 3D facial scans of 51 unaffected siblings (30M/21F) and 29 controls (15M/14F) with no family history of clefting were landmarked by a calibrated rater using 3dMD software (Atlanta, GA) for 8 midline and 8 pairs of bilateral sites, for a total of 24 standard anthropometric soft tissue landmarks . Subject ages ranged from 5 to 16 years (median 10 years). 3D landmark coordinates were extracted and standardized through translation and rotation. Reflection of the left landmark configuration over the right yielded bilateral Euclidean distances which were used as measures of facial asymmetry. Differences in asymmetry between NSCL/P siblings vs. controls were assessed using the Wilcoxon Rank Sum test, and via multivariate logistic regression to adjust for age and gender. Analyses were carried out with and without centroid scaling to adjust for facial size.
Results: Feasibility of the method was established, with excellent intra-rater reliability (ICCs of 0.83 – 0.99 in all three coordinates of 24 landmarks). Evidence was found for an effect of age (p=0.037) on crista philtri asymmetry which strengthened (p=0.0085) after facial size adjustment via centroid scaling; a gender effect was also suggested (p=0.06); other suggestive results were noted. No significant results were found for comparisons of asymmetry measures in relatives of NSCL/P cases vs. controls.
Conclusion: Soft tissue asymmetry studies are feasible and results from this pilot study will provide useful information for future well-powered studies, which should consider adjustment for the effects of age, facial size, and gender.
[Show abstract][Hide abstract] ABSTRACT: This study uses instrumental variable (IV) models with genetic instruments to assess the effects of maternal smoking on the child's risk of orofacial clefts (OFC), a common birth defect. The study uses genotypic variants in neurotransmitter and detoxification genes relateded to smoking as instruments for cigarette smoking before and during pregnancy. Conditional maximum likelihood and two-stage IV probit models are used to estimate the IV model. The data are from a population-level sample of affected and unaffected children in Norway. The selected genetic instruments generally fit the IV assumptions but may be considered "weak" in predicting cigarette smoking. We find that smoking before and during pregnancy increases OFC risk substantially under the IV model (by about 4-5 times at the sample average smoking rate). This effect is greater than that found with classical analytic models. This may be because the usual models are not able to consider self-selection into smoking based on unobserved confounders, or it may to some degree reflect limitations of the instruments. Inference based on weak-instrument robust confidence bounds is consistent with standard inference. Genetic instruments may provide a valuable approach to estimate the "causal" effects of risk behaviors with genetic-predisposing factors (such as smoking) on health and socioeconomic outcomes.
Preview · Article · Jul 2011 · Health Services and Outcomes Research Methodology
[Show abstract][Hide abstract] ABSTRACT: There is a large literature showing the detrimental effects of prenatal smoking on birth and childhood health outcomes. It is somewhat unclear though, whether these effects are causal or reflect other characteristics and choices by mothers who choose to smoke that may also affect child health outcomes or biased reporting of smoking. In this paper we use genetic markers that predict smoking behaviors as instruments to address the endogeneity of smoking choices in the production of birth and childhood health outcomes. Our results indicate that prenatal smoking produces more dramatic declines in birth weight than estimates that ignore the endogeneity of prenatal smoking, which is consistent with previous studies with non-genetic instruments. We use data from two distinct samples from Norway and the United States with different measured instruments and find nearly identical results. The study provides a novel application that can be extended to study several behavioral impacts on health and social and economic outcomes.
Full-text · Article · Jan 2011 · Biodemography and Social Biology
[Show abstract][Hide abstract] ABSTRACT: Case-parent trios were used in a genome-wide association study of cleft lip with and without cleft palate. SNPs near two genes not previously associated with cleft lip with and without cleft palate (MAFB, most significant SNP rs13041247, with odds ratio (OR) per minor allele = 0.704, 95% CI 0.635-0.778, P = 1.44 x 10(-11); and ABCA4, most significant SNP rs560426, with OR = 1.432, 95% CI 1.292-1.587, P = 5.01 x 10(-12)) and two previously identified regions (at chromosome 8q24 and IRF6) attained genome-wide significance. Stratifying trios into European and Asian ancestry groups revealed differences in statistical significance, although estimated effect sizes remained similar. Replication studies from several populations showed confirming evidence, with families of European ancestry giving stronger evidence for markers in 8q24, whereas Asian families showed stronger evidence for association with MAFB and ABCA4. Expression studies support a role for MAFB in palatal development.
[Show abstract][Hide abstract] ABSTRACT: Nonsyndromic orofacial clefts are a common complex birth defect caused by genetic and environmental factors and/or their interactions.
A previous genome-wide linkage scan discovered a novel locus for cleft lip with or without cleft palate (CL/P) at 9q22–q33.
To identify the etiologic gene, we undertook an iterative and complementary fine mapping strategy using family-based CL/P
samples from Colombia, USA and the Philippines. Candidate genes within 9q22–q33 were sequenced, revealing 32 new variants.
Concurrently, 397 SNPs spanning the 9q22–q33 2-LOD-unit interval were tested for association. Significant SNP and haplotype
association signals (P = 1.45E − 08) narrowed the interval to a 200 kb region containing: FOXE1, C9ORF156 and HEMGN. Association results were replicated in CL/P families of European descent and when all populations were combined the two
most associated SNPs, rs3758249 (P = 5.01E − 13) and rs4460498 (P = 6.51E − 12), were located inside a 70 kb high linkage disequilibrium block containing FOXE1. Association signals for Caucasians and Asians clustered 5′ and 3′ of FOXE1, respectively. Isolated cleft palate (CP) was also associated, indicating that FOXE1 plays a role in two phenotypes thought
to be genetically distinct. Foxe1 expression was found in the epithelium undergoing fusion between the medial nasal and maxillary processes. Mutation screens
of FOXE1 identified two family-specific missense mutations at highly conserved amino acids. These data indicate that FOXE1 is a major gene for CL/P and provides new insights for improved counseling and genetic interaction studies.
Full-text · Article · Sep 2009 · Human Molecular Genetics
[Show abstract][Hide abstract] ABSTRACT: Visceral leishmaniasis (VL) in northeast Brazil is a disease caused by infection with the protozoan Leishmania chagasi. Infection leads to variable clinical outcomes ranging from asymptomatic infection to potentially fatal disease. Prior studies suggest the genetic background of the host contributes to the development of different outcomes after infection, although it is not known if ancestral background itself influences outcomes. VL is endemic in peri-urban areas around the city of Natal in northeast Brazil. The population of northeast Brazil is a mixture of distinct racial and ethnic groups. We hypothesized that some sub-populations may be more susceptible than others to develop different clinical outcomes after L. chagasi infection. Using microsatellite markers, we examined whether admixture of the population as a whole, or markers likely inherited from a distinct ethnic background, differed between individuals with VL, individuals with an asymptomatic infection, or individuals with no infection. There was no apparent significant difference in overall population admixture proportions among the three clinical phenotype groups. However, one marker on Chr. 22 displayed evidence of excess ancestry from putative ancestral populations among different clinical phenotypes, suggesting this region may contain genes determining the course of L. chagasi infection.
Full-text · Article · Apr 2009 · Annals of Human Genetics
[Show abstract][Hide abstract] ABSTRACT: Cleft lip with or without cleft palate is the most common facial birth defect and it is caused by a complex interaction between genetic and environmental factors. The purpose of this review is to provide an overview of the spectrum of the genetic causes for cleft lip and cleft palate using both syndromic and nonsyndromic forms of clefting as examples. Although the gene identification process for orofacial clefting in humans is in the early stages, the pace is rapidly accelerating. Recently, several genes have been identified that have a combined role in up to 20% of all clefts. While this is a significant step forward, it is apparent that additional cleft causing genes have yet to be identified. Ongoing human genome-wide linkage studies have identified regions in the genome that likely contain genes that when mutated cause orofacial clefting, including a major gene on chromosome 9 that is positive in multiple racial groups. Currently, efforts are focused to identify which genes are mutated in these regions. In addition, parallel studies are also evaluating genes involved in environmental pathways. Furthermore, statistical geneticists are developing new methods to characterize both gene-gene and gene-environment interactions to build better models for pathogenesis of this common birth defect. The ultimate goal of these studies is to provide knowledge for more accurate risk counseling and the development of preventive therapies.
Full-text · Article · Jul 2008 · Seminars in Orthodontics
[Show abstract][Hide abstract] ABSTRACT: Non-syndromic cleft lip with or without cleft palate (NSCLP) results from the complex interaction between genes and environmental factors. Candidate gene analysis and genome scans have been employed to identify the genes contributing to NSCLP. In this study, we evaluated the 16q24.1 chromosomal region, which has been identified by multiple genome scans as an NSCLP region of interest. Two candidate genes were found in the region: interferon regulatory factor 8 (IRF8) and cysteine-rich secretory protein LCCL domain containing 2 (CRISPLD2). Initially, Caucasian and Hispanic NSCLP multiplex families and simplex parent-child trios were genotyped for single nucleotide polymorphisms (SNPs) in both IRF8 and CRISPLD2. CRISPLD2 was subsequently genotyped in a data set comprised of NSCLP families from Colombia, South America. Linkage disequilibrium analysis identified a significant association between CRISPLD2 and NSCLP in both our Caucasian and Hispanic NSCLP cohorts. SNP rs1546124 and haplotypes between rs1546124 and either rs4783099 or rs16974880 were significant in the Caucasian multiplex population (P=0.01, P=0.002 and P=0.001, respectively). An altered transmission of CRISPLD2 SNPs rs8061351 (P=0.02) and rs2326398 (P=0.06) was detected in the Hispanic population. No association was found between CRISPLD2 and our Colombian population or IRF8 and NSCLP. In situ hybridization showed that CRISPLD2 is expressed in the mandible, palate and nasopharynx regions during craniofacial development at E13.5-E17.5, respectively. Altogether, these data suggest that genetic variation in CRISPLD2 has a role in the etiology of NSCLP.
Full-text · Article · Oct 2007 · Human Molecular Genetics
[Show abstract][Hide abstract] ABSTRACT: MSX1 has been considered a strong candidate for orofacial clefting, based on mouse expression studies and knockout models, as well as association and linkage studies in humans. MSX1 mutations are also causal for hereditary tooth agenesis. We tested the hypothesis that individuals with orofacial clefting with or without tooth agenesis have MSX1 coding mutations by screening 33 individuals with cleft lip with or without cleft palate (CL/P) and 19 individuals with both orofacial clefting and tooth agenesis. Although no MSX1 coding mutations were identified, the known 101C > G variant occurred more often in subjects with both CL/P and tooth agenesis (p = 0.0008), while the *6C-T variant was found more often in CL/P subjects (p = 0.001). Coding mutations in MSX1 are not the cause of orofacial clefting with or without tooth agenesis in this study population. However, the significant association of MSX1 with both phenotypes implies that MSX1 regulatory elements may be mutated.
Preview · Article · Jun 2006 · Journal of Dental Research
[Show abstract][Hide abstract] ABSTRACT: Orofacial clefts are common birth defects with a known genetic component to their etiology. Most orofacial clefts are nonsyndromic, isolated defects, which can be separated into two different phenotypes: (1) cleft lip with or without cleft palate and (2) cleft palate only. Both are genetically complex traits, which has limited the ability to identify disease loci or genes. The purpose of this review is to summarize recent progress of human genetic studies in identifying causal genes for isolated or nonsyndromic cleft lip with or without cleft palate.
The results of multiple genome scans and a subsequent meta-analysis have significantly advanced our knowledge by revealing novel loci. Furthermore, candidate gene approaches have identified important roles for IRF6 and MSX1. To date, causal mutations with a known functional effect have not yet been described.
With the implementation of genome-wide association studies and inexpensive sequencing, future studies will identify disease genes and characterize both gene-environment and gene-gene interactions to provide knowledge for risk counseling and the development of preventive therapies.
Preview · Article · Jan 2006 · Current Opinion in Pediatrics
[Show abstract][Hide abstract] ABSTRACT: Isolated or nonsyndromic cleft lip with or without cleft palate (CL/P) is a common birth defect with a complex etiology. A 10-cM genome scan of 388 extended multiplex families with CL/P from seven diverse populations (2,551 genotyped individuals) revealed CL/P genes in six chromosomal regions, including a novel region at 9q21 (heterogeneity LOD score [HLOD]=6.6). In addition, meta-analyses with the addition of results from 186 more families (six populations; 1,033 genotyped individuals) showed genomewide significance for 10 more regions, including another novel region at 2q32-35 (P=.0004). These are the first genomewide significant linkage results ever reported for CL/P, and they represent an unprecedented demonstration of the power of linkage analysis to detect multiple genes simultaneously for a complex disorder.
Full-text · Article · Sep 2004 · The American Journal of Human Genetics